diff --git a/doc/create_plugin_doc.py b/doc/create_plugin_doc.py index 049e14419..3044b54e6 100644 --- a/doc/create_plugin_doc.py +++ b/doc/create_plugin_doc.py @@ -63,8 +63,12 @@ def add_package_entry(f, files_present, output, module_name): for fi in files_present: # TODO At the moment if a directory contains files, and none of # their classes load correctly, the content will be blank - file_path = module_name + '.' + fi.split('.py')[0] - py_module_name = 'savu.' + str(file_path) + mod_path = module_name + '.' + fi.split('.py')[0] + # Use the module path '.' file name for api documentation + # Use the file path '/' file name for plugin documentation + file_path = mod_path.replace('.', '/') \ + if output == 'plugin_documentation' else mod_path + py_module_name = 'savu.' + str(mod_path) try: # If the plugin class exists, put it's name into the contents plugin_class = pu.load_class(py_module_name) @@ -76,28 +80,25 @@ def add_package_entry(f, files_present, output, module_name): def create_plugin_documentation(files, output, module_name, savu_base_path): - # Create template download page - create_plugin_template_downloads(savu_base_path) - - # Only document the plugin python files - if not os.path.exists(savu_base_path + 'doc/source/' + output): - # Create the directory if it does not exist - os.makedirs(savu_base_path + 'doc/source/' + output) - for fi in files: - file_path = module_name + '.' + fi.split('.py')[0] - py_module_name = 'savu.' + str(file_path) + mod_path = module_name + '.' + fi.split('.py')[0] + file_path = mod_path.replace('.', '/') + py_module_name = 'savu.' + str(mod_path) try: # Load the associated class plugin_class = pu.load_class(py_module_name)() plugin_class._populate_default_parameters() plugin_tools = plugin_class.tools.tools_list if plugin_tools: + # Create rst additional documentation directory + # and file and image directory + create_documentation_directory(savu_base_path, fi) # Create an empty rst file inside this directory where # the plugin tools documentation will be stored - new_rst_file = open(savu_base_path + 'doc/source/' - + output + '/' + file_path - + '.rst', 'w+') + full_file_path = savu_base_path + 'doc/source/' + output \ + + '/' + file_path + '.rst' + pu.create_dir(full_file_path) + new_rst_file = open(full_file_path, 'w+') # Populate this file populate_plugin_doc_files(new_rst_file, plugin_tools, file_path, plugin_class, @@ -124,7 +125,7 @@ def populate_plugin_doc_files(new_rst_file, tool_class_list, file_path, :param savu_base_path: Savu file path """ - title = file_path.split('.') + title = file_path.split('/') # Depending on the number of nested directories, determine which section # heading and title to apply plugin_type = title[-1] @@ -146,9 +147,8 @@ def populate_plugin_doc_files(new_rst_file, tool_class_list, file_path, # Locate documentation file doc_folder = savu_base_path + 'doc/source/documentation/' - plugin_file_path = file_path.replace('.','/') - file_str = doc_folder + plugin_file_path + '_doc.rst' - inner_file_str = '/../documentation/' + plugin_file_path + '_doc.rst' + file_str = doc_folder + file_path + '_doc.rst' + inner_file_str = '/../documentation/' + file_path + '_doc.rst' if os.path.isfile(file_str): # If there is a documentation file @@ -322,37 +322,35 @@ def create_plugin_template_downloads(savu_base_path): + 'doc/source/dev_guides/dev_plugin_templates.rst' # Populate dictionary with template class and template class docstring docstring_text = create_template_class_dict(savu_base_path) - - doc_f = open(doc_template_file, 'w') - # Create a 'ref' for linking to other rst files - doc_f.write('.. _plugin_templates:\n') - doc_f.write('\n') - - doc_f.write('Plugin templates \n=======================\n') - doc_f.write('\n') - - doc_name = 'plugin_template1_with_detailed_notes' - detailed_template = docstring_text[doc_name] - docstring_text.pop(doc_name) - title = convert_title(doc_name) - title, number = filter_template_numbers(title) - inner_file_str = '../../../' + 'plugin_examples/plugin_templates/general' - doc_text = detailed_template['docstring'].split(':param')[0] - doc_text = " ".join(doc_text.splitlines()) - doc_f.write(title - + '\n--------------------------------' - '----------------------------------\n') - doc_f.write(doc_text) - doc_f.write('\n') - doc_f.write('\n') - doc_f.write(':download:`' + title + ' <' + inner_file_str - + '/' + doc_name + '.py>`\n\n') - - doc_f.write('Further Examples' - + '\n--------------------------------' - '----------------------------------\n') - # Begin the table layout - doc_f.write(''' + if docstring_text: + doc_template = open(doc_template_file, 'w') + doc_template.write('.. _plugin_templates:\n') + doc_template.write('\n') + doc_template.write('Plugin templates \n=======================\n') + doc_template.write('\n') + + doc_name = 'plugin_template1_with_detailed_notes' + detailed_template = docstring_text.get(doc_name) + if detailed_template: + docstring_text.pop(doc_name) + title = convert_title(doc_name) + title, number = filter_template_numbers(title) + inner_file_str = '../../../' + 'plugin_examples/plugin_templates/general' + doc_text = detailed_template['docstring'].split(':param')[0] + doc_text = " ".join(doc_text.splitlines()) + doc_template.write(title + + '\n--------------------------------' + '----------------------------------\n') + doc_template.write(doc_text) + doc_template.write('\n') + doc_template.write('\n') + doc_template.write(':download:`' + title + ' <' + inner_file_str + + '/' + doc_name + '.py>`\n\n') + doc_template.write('Further Examples' + + '\n--------------------------------' + '----------------------------------\n') + # Begin the table layout + doc_template.write(''' .. list-table:: :widths: 10 90 :header-rows: 1 @@ -360,24 +358,24 @@ def create_plugin_template_downloads(savu_base_path): * - Link - Description''') - for doc_name, doc_str in docstring_text.items(): - title = convert_title(doc_name) - title, number = filter_template_numbers(title) - # Remove the parameter information from the docstring - doc_text = doc_str['docstring'].split(':param')[0] - doc_text = " ".join(doc_text.splitlines()) - # Create a link to the restructured text page view of the python - # code for the template - doc_f.write('\n * - :ref:`'+doc_name+'`') - # The template description from the docstring - doc_f.write('\n - '+doc_text) - doc_f.write('\n') - # Create the restructured text page for the plugin template - # python code - generate_template_files(doc_name, title) - - doc_f.write('\n') - doc_f.close() + for doc_name, doc_str in docstring_text.items(): + title = convert_title(doc_name) + title, number = filter_template_numbers(title) + # Remove the parameter information from the docstring + doc_text = doc_str['docstring'].split(':param')[0] + doc_text = " ".join(doc_text.splitlines()) + # Create a link to the restructured text page view of the python + # code for the template + doc_template.write('\n * - :ref:`'+doc_name+'`') + # The template description from the docstring + doc_template.write('\n - '+doc_text) + doc_template.write('\n') + # Create the restructured text page for the plugin template + # python code + generate_template_files(doc_name, title) + + doc_template.write('\n') + doc_template.close() def generate_template_files(doc_name, title): @@ -396,7 +394,7 @@ def generate_template_files(doc_name, title): # Add the orphan instruction as this file is not inside a toctree template_file.write(':orphan:\n') template_file.write('\n') - template_file.write('.. _' + doc_name + ':\n') + template_file.write('\n.. _' + doc_name + ':\n') template_file.write('\n') template_file.write(title+'\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n') template_file.write('\n') @@ -461,6 +459,23 @@ def create_template_class_dict(savu_base_path): return docstring_text + +def create_documentation_directory(savu_base_path, plugin_file): + """ Create plugin directory inside documentation and + documentation file and image folders + """ + # Create directory inside + doc_path = savu_base_path + 'doc/source/documentation/plugins/' + doc_image_path = savu_base_path \ + + 'doc/source/files_and_images/documentation/plugins/' + + # find the directories to create + doc_dir = doc_path + plugin_file + image_dir = doc_image_path + plugin_file + pu.create_dir(doc_dir) + pu.create_dir(image_dir) + + if __name__ == "__main__": out_folder, rst_file, api_type = sys.argv[1:] @@ -486,6 +501,13 @@ def create_template_class_dict(savu_base_path): 'hdf5_utils.py'] exclude_dir = ['driver'] + # Create template download page + create_plugin_template_downloads(savu_base_path) + + # Only document the plugin python files + # Create the directory if it does not exist + pu.create_dir(savu_base_path + 'doc/source/' + out_folder) + for root, dirs, files in os.walk(base_path, topdown=True): tools_files = [fi for fi in files if 'tools' in fi] base_files = [fi for fi in files if fi.startswith('base')] @@ -505,4 +527,4 @@ def create_template_class_dict(savu_base_path): add_package_entry(f, files, out_folder, module_name) if out_folder == 'plugin_documentation': create_plugin_documentation(files, out_folder, - module_name, savu_base_path) \ No newline at end of file + module_name, savu_base_path) \ No newline at end of file diff --git a/doc/source/_static/css/plugin_template.css b/doc/source/_static/css/plugin_template.css new file mode 100644 index 000000000..3244cadf5 --- /dev/null +++ b/doc/source/_static/css/plugin_template.css @@ -0,0 +1,17 @@ +td a:link, td a:visited { + line-height: 2em; + border-radius: .25rem; + display: inline; + padding: .25rem .5rem; + color: white; + background-color: #2c7aa3; +} + +td a:hover, td a:active { + line-height: 2em; + border-radius: .25rem; + display: inline; + padding: .25rem .5rem; + color: white; + background-color: #609ebf; +} diff --git a/doc/source/_static/css/plugin_template_download.css b/doc/source/_static/css/plugin_template_download.css new file mode 100644 index 000000000..1dc5d40c8 --- /dev/null +++ b/doc/source/_static/css/plugin_template_download.css @@ -0,0 +1,17 @@ +a:link .download, a:visited .download { + line-height: 2em; + border-radius: .25rem; + display: inline; + padding: .25rem .5rem; + color: white; + background-color: #2c7aa3; +} + +a:hover .download, a:active .download { + line-height: 2em; + border-radius: .25rem; + display: inline; + padding: .25rem .5rem; + color: white; + background-color: #609ebf; +} \ No newline at end of file diff --git a/doc/source/conf.py b/doc/source/conf.py index 20b303940..79558356f 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -168,7 +168,7 @@ # The name of an image file (relative to this directory) to place at the top # of the sidebar. #html_logo = 'files_and_images/Savu_black_square_downsample2.png' -file_path = savu.__path__[0] + '/../' +file_path = os.path.dirname(os.path.realpath(__file__)).split('doc')[0] html_logo = file_path + 'doc/source/files_and_images/logo_downsample.png' # The name of an image file (within the static path) to use as favicon of the @@ -179,7 +179,7 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -#html_static_path = ['_static'] +html_static_path = ['_static'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. @@ -304,3 +304,7 @@ # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'http://docs.python.org/': None} + +def setup(app): + app.add_stylesheet( "css/plugin_template.css" ) + app.add_stylesheet( "css/plugin_template_download.css" ) \ No newline at end of file diff --git a/doc/source/dev_guides/dev_plugin.rst b/doc/source/dev_guides/dev_plugin.rst index c7e13ef6d..362b25985 100644 --- a/doc/source/dev_guides/dev_plugin.rst +++ b/doc/source/dev_guides/dev_plugin.rst @@ -1,8 +1,8 @@ .. raw:: html - + -.. role:: red +.. role:: blue Developing a Savu plugin @@ -11,11 +11,13 @@ Developing a Savu plugin A module is a file containing python definitions and statements. To \ create a plugin for Savu you will need to create two modules: -1. A plugin module, named :red:`plugin_name`.py containing a class :red:`PluginName` -2. A plugin tools module named :red:`plugin_name_tools`.py, containing a class :red:`PluginNameTools` +1. A plugin module, named :blue:`plugin_name`.py containing a class :blue:`PluginName` +2. A plugin tools module named :blue:`plugin_name_tools`.py, containing a class :blue:`PluginNameTools` -:red:`PluginName` should be replaced by the name of your plugin without \ -any spaces. The words should be capitalised. +.. note:: + + :blue:`PluginName` should be replaced by the name of your plugin without \ + any spaces. The words should be capitalised. Examples are: @@ -462,7 +464,7 @@ precede the docstring with the letter 'u'. Below is a longer example of the yaml text. -.. code-block:: yaml +.. code-block:: none The CCPi-Regularisation toolkit provides a set of variational regularisers (denoisers) which can be embedded in @@ -470,7 +472,6 @@ Below is a longer example of the yaml text. image reconstruction. CCPi-RGL comes with algorithms that can satisfy various prior expectations of the reconstructed object, for example being piecewise-constant or piecewise-smooth nature. - short_name_article: ccpi regularisation toolkit for CT bibtex: @article{kazantsev2019ccpi, title={Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms}, @@ -494,6 +495,7 @@ Below is a longer example of the yaml text. %@ 2352-7110 %D 2019 %I Elsevier + short_name_article: ccpi regularisation toolkit for CT doi: "10.1016/j.softx.2019.04.003" @@ -513,7 +515,7 @@ Bibtex The bibtex text. -.. code-block:: yaml +.. code-block:: none bibtex: @article{kazantsev2019ccpi, @@ -531,7 +533,7 @@ Endnote The endnote text. -.. code-block:: yaml +.. code-block:: none endnote: @article{kazantsev2019ccpi, diff --git a/doc/source/documentation/plugins/centering/vo_centering_doc.rst b/doc/source/documentation/plugins/centering/vo_centering_doc.rst new file mode 100644 index 000000000..64ffe896d --- /dev/null +++ b/doc/source/documentation/plugins/centering/vo_centering_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Vo Centering Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/centering/vo_centering.png" diff --git a/doc/source/documentation/plugins/corrections/convert_360_180_sinogram_doc.rst b/doc/source/documentation/plugins/corrections/convert_360_180_sinogram_doc.rst new file mode 100644 index 000000000..f1ff4bfa5 --- /dev/null +++ b/doc/source/documentation/plugins/corrections/convert_360_180_sinogram_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Convert 360 180 Sinogram Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/corrections/convert_360_180_sinogram.png" diff --git a/doc/source/documentation/plugins/corrections/distortion_correction_doc.rst b/doc/source/documentation/plugins/corrections/distortion_correction_doc.rst new file mode 100644 index 000000000..00a00973a --- /dev/null +++ b/doc/source/documentation/plugins/corrections/distortion_correction_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Distortion Correction Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/corrections/distortion_correction.png" diff --git a/doc/source/documentation/plugins/corrections/mtf_deconvolution_doc.rst b/doc/source/documentation/plugins/corrections/mtf_deconvolution_doc.rst new file mode 100644 index 000000000..cf11098d2 --- /dev/null +++ b/doc/source/documentation/plugins/corrections/mtf_deconvolution_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Mtf Deconvolution Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/corrections/mtf_deconvolution.png" diff --git a/doc/source/documentation/plugins/filters/dezinger_sinogram_doc.rst b/doc/source/documentation/plugins/filters/dezinger_sinogram_doc.rst new file mode 100644 index 000000000..138cb2570 --- /dev/null +++ b/doc/source/documentation/plugins/filters/dezinger_sinogram_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Dezinger Sinogram Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/filters/dezinger_sinogram.png" diff --git a/doc/source/documentation/plugins/filters/fresnel_filter_doc.rst b/doc/source/documentation/plugins/filters/fresnel_filter_doc.rst new file mode 100644 index 000000000..83a44f1e5 --- /dev/null +++ b/doc/source/documentation/plugins/filters/fresnel_filter_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Fresnel Filter Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/filters/fresnel_filter.png" diff --git a/doc/source/documentation/plugins/filters/paganin_filter_doc.rst b/doc/source/documentation/plugins/filters/paganin_filter_doc.rst new file mode 100644 index 000000000..4cea72263 --- /dev/null +++ b/doc/source/documentation/plugins/filters/paganin_filter_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Paganin Filter Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/filters/paganin_filter.png" diff --git a/doc/source/documentation/plugins/ring_removal/remove_large_rings_doc.rst b/doc/source/documentation/plugins/ring_removal/remove_large_rings_doc.rst new file mode 100644 index 000000000..20066f867 --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/remove_large_rings_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Remove Large Rings Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/remove_large_rings.png" diff --git a/doc/source/documentation/plugins/ring_removal/remove_unresponsive_and_fluctuating_rings_doc.rst b/doc/source/documentation/plugins/ring_removal/remove_unresponsive_and_fluctuating_rings_doc.rst new file mode 100644 index 000000000..18588e307 --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/remove_unresponsive_and_fluctuating_rings_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Remove Unresponsive And Fluctuating Rings Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/remove_unresponsive_and_fluctuating_rings.png" diff --git a/doc/source/documentation/plugins/ring_removal/ring_removal_filtering_doc.rst b/doc/source/documentation/plugins/ring_removal/ring_removal_filtering_doc.rst new file mode 100644 index 000000000..edfd39fc5 --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/ring_removal_filtering_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Ring Removal Filtering Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/ring_removal_filtering.png" diff --git a/doc/source/documentation/plugins/ring_removal/ring_removal_fitting_doc.rst b/doc/source/documentation/plugins/ring_removal/ring_removal_fitting_doc.rst new file mode 100644 index 000000000..c77ab8ee1 --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/ring_removal_fitting_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Ring Removal Fitting Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/ring_removal_fitting.png" diff --git a/doc/source/documentation/plugins/ring_removal/ring_removal_normalization_doc.rst b/doc/source/documentation/plugins/ring_removal/ring_removal_normalization_doc.rst new file mode 100644 index 000000000..26fdf26b9 --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/ring_removal_normalization_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Ring Removal Normalization Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/ring_removal_normalization.png" diff --git a/doc/source/documentation/plugins/ring_removal/ring_removal_regularization_doc.rst b/doc/source/documentation/plugins/ring_removal/ring_removal_regularization_doc.rst new file mode 100644 index 000000000..98dab4b9d --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/ring_removal_regularization_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Ring Removal Regularization Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/ring_removal_regularization.png" diff --git a/doc/source/documentation/plugins/ring_removal/ring_removal_sorting_doc.rst b/doc/source/documentation/plugins/ring_removal/ring_removal_sorting_doc.rst new file mode 100644 index 000000000..e8c2941e4 --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/ring_removal_sorting_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Ring Removal Sorting Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/ring_removal_sorting.png" diff --git a/doc/source/documentation/plugins/ring_removal/ring_removal_waveletfft_doc.rst b/doc/source/documentation/plugins/ring_removal/ring_removal_waveletfft_doc.rst new file mode 100644 index 000000000..5c048a14d --- /dev/null +++ b/doc/source/documentation/plugins/ring_removal/ring_removal_waveletfft_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Ring Removal Waveletfft Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/ring_removal/ring_removal_waveletfft.png" diff --git a/doc/source/documentation/plugins/savers/image_saver_doc.rst b/doc/source/documentation/plugins/savers/image_saver_doc.rst new file mode 100644 index 000000000..ed6b6a6f2 --- /dev/null +++ b/doc/source/documentation/plugins/savers/image_saver_doc.rst @@ -0,0 +1,9 @@ +:orphan: + +Image Saver Documentation +################################################################# + +(Change this) Include your plugin documentation here. Use a restructured text format. + +.. + This is a comment. Include an image or file by using the following text ".. figure:: ../files_and_images/documentation/plugins/savers/image_saver.png" diff --git a/doc/source/plugin_documentation/plugins.absorption_corrections.mc_near_absorption_correction.rst b/doc/source/plugin_documentation/plugins.absorption_corrections.mc_near_absorption_correction.rst deleted file mode 100644 index dada96d7c..000000000 --- a/doc/source/plugin_documentation/plugins.absorption_corrections.mc_near_absorption_correction.rst +++ /dev/null @@ -1,49 +0,0 @@ -Mc Near Absorption Correction -################################################################# - -Description --------------------------- - -McNears absorption correction, takes in a normalised absorption sinogram -and xrf sinogram stack. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: A list of the dataset(s) to process. - default: ['xrf', 'stxm'] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - azimuthal_offset: - visibility: basic - dtype: float - description: Angle between detectors. - default: -90.0 - - density: - visibility: intermediate - dtype: float - description: The density - default: 3.5377 - - compound: - visibility: intermediate - dtype: str - description: The compound - default: Co0.1Re0.01Ti0.05(SiO2)0.84 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.alignment.projection_shift.rst b/doc/source/plugin_documentation/plugins.alignment.projection_shift.rst deleted file mode 100644 index cf5e68b69..000000000 --- a/doc/source/plugin_documentation/plugins.alignment.projection_shift.rst +++ /dev/null @@ -1,66 +0,0 @@ -Projection Shift -################################################################# - -Description --------------------------- - -Horizontal and vertical shift are calculated using a chosen method and -added to the metadata. The vertical and horizontal shifts can be corrected -using the ProjectionVerticalAlignment and SinogramAlignment (in 'shift' mode) -plugins respectively. - -Method: Uses either skimage template_matching or orb feature tracking plus -robust ransac matching to calculate the translation between different -combinations of 10 consecutive projection images. A least squares solution to -the shift values between images is calculated and returned for the middle 8 images. - -.. toctree:: - Plugin documention and guidelines on use - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Set the output dataset name - default: ['proj_shift'] - - method: - visibility: basic - dtype: str - description: "Method used to calculate the shift between images. Choose from 'template_matching' and 'orb_ransac'." - default: orb_ransac - options: ['template_matching', 'orb_ransac'] - - template: - visibility: basic - dtype: list - description: "Position of the template to match (required) e.g. [300:500, 300:500]." - default: None - - threshold: - visibility: intermediate - dtype: list - description: "e.g. [a, b] will set all values above a to b." - default: None - - n_keypoints: - visibility: intermediate - dtype: int - description: Number of keypoints to use in ORB feature detector. - default: 20 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.alignment.projection_vertical_alignment.rst b/doc/source/plugin_documentation/plugins.alignment.projection_vertical_alignment.rst deleted file mode 100644 index 635e95451..000000000 --- a/doc/source/plugin_documentation/plugins.alignment.projection_vertical_alignment.rst +++ /dev/null @@ -1,8 +0,0 @@ -Projection Vertical Alignment -################################################################# - -Description --------------------------- - -Correct for vertical shift over projection images. - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.alignment.sinogram_alignment.rst b/doc/source/plugin_documentation/plugins.alignment.sinogram_alignment.rst deleted file mode 100644 index c85eb593d..000000000 --- a/doc/source/plugin_documentation/plugins.alignment.sinogram_alignment.rst +++ /dev/null @@ -1,96 +0,0 @@ -Sinogram Alignment -################################################################# - -Description --------------------------- - -The centre of mass of each row is determined and then a sine function fit -through these to determine the centre of rotation. The residual between -each centre of mass and the sine function is then used to align each row. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - threshold: - visibility: basic - dtype: str - description: e.g. a.b will set all values above a to b. - default: None - - p0: - visibility: basic - dtype: tuple - description: Initial guess for the parameters of scipy.optimize.curve_fit. - default: (1, 1, 1) - - type: - visibility: intermediate - dtype: list - description: Either centre_of_mass or shift, with the latter requiring ProjectionVerticalAlignment prior to this plugin. - default: centre_of_mass - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Chemical imaging of single catalyst particles with scanning μ-XANES-CT and μ-XRF-CT by Price, SWT et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{price2015chemical, - title={Chemical imaging of single catalyst particles with scanning $\mu$-XANES-CT and $\mu$-XRF-CT}, - author={Price, SWT and Ignatyev, K and Geraki, K and Basham, M and Filik, J and Vo, NT and Witte, PT and Beale, AM and Mosselmans, JFW}, - journal={Physical Chemistry Chemical Physics}, - volume={17}, - number={1}, - pages={521--529}, - year={2015}, - publisher={Royal Society of Chemistry}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Chemical imaging of single catalyst particles with scanning μ-XANES-CT and μ-XRF-CT - %A Price, SWT - %A Ignatyev, K - %A Geraki, K - %A Basham, M - %A Filik, J - %A Vo, NT - %A Witte, PT - %A Beale, AM - %A Mosselmans, JFW - %J Physical Chemistry Chemical Physics - %V 17 - %N 1 - %P 521-529 - %D 2015 - %I Royal Society of Chemistry - - diff --git a/doc/source/plugin_documentation/plugins.alignment.sinogram_clean.rst b/doc/source/plugin_documentation/plugins.alignment.sinogram_clean.rst deleted file mode 100644 index b50535b43..000000000 --- a/doc/source/plugin_documentation/plugins.alignment.sinogram_clean.rst +++ /dev/null @@ -1,42 +0,0 @@ -Sinogram Clean -################################################################# - -Description --------------------------- - -A plugin to calculate the centre of rotation using the Vo Method - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: The default names. - default: [] - - ratio: - visibility: basic - dtype: float - description: The ratio between the size of object and FOV of the camera. - default: 2.0 - - row_drop: - visibility: basic - dtype: int - description: Drop lines around vertical center of the mask scipy.optimize.curve_fit. - default: 20 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.analysis.histogram.rst b/doc/source/plugin_documentation/plugins.analysis.histogram.rst deleted file mode 100644 index 8d28807a4..000000000 --- a/doc/source/plugin_documentation/plugins.analysis.histogram.rst +++ /dev/null @@ -1,8 +0,0 @@ -Histogram -################################################################# - -Description --------------------------- - -This plugin uses peakutils to find peaks in spectra. This is then metadata. - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.analysis.stats.rst b/doc/source/plugin_documentation/plugins.analysis.stats.rst deleted file mode 100644 index 217bb750a..000000000 --- a/doc/source/plugin_documentation/plugins.analysis.stats.rst +++ /dev/null @@ -1,37 +0,0 @@ -Stats -################################################################# - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: the output dataset. - default: ['stats'] - - required_stats: - visibility: intermediate - dtype: list - description: Create a list of required stats calcs. - default: ['max'] - - direction: - visibility: intermediate - dtype: str - description: Which direction to perform this. - default: PROJECTION - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.analysis.stxm_analysis.rst b/doc/source/plugin_documentation/plugins.analysis.stxm_analysis.rst deleted file mode 100644 index 6b03043dc..000000000 --- a/doc/source/plugin_documentation/plugins.analysis.stxm_analysis.rst +++ /dev/null @@ -1,48 +0,0 @@ -Stxm Analysis -################################################################# - -Description --------------------------- - -This plugin performs basic STXM analysis of diffraction patterns. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: - default: ['bf', 'df', 'dpc_x', 'dpc_y', 'combined_dpc'] - - mask_file: - visibility: basic - dtype: list - description: Takes in a mask currently in hdf format. - default: None - - mask_path: - visibility: intermediate - dtype: int_path - description: Path to the mask inside the file. - default: /mask - - threshold: - visibility: intermediate - dtype: float - description: Intensity threshold for the dark field. - default: 0.05 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator.rst b/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator.rst deleted file mode 100644 index 3a61b2487..000000000 --- a/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator.rst +++ /dev/null @@ -1,42 +0,0 @@ -Pyfai Azimuthal Integrator -################################################################# - -Description --------------------------- - -1D azimuthal integrator by pyFAI - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - use_mask: - visibility: basic - dtype: bool - description: Should we mask. - default: False - - num_bins: - visibility: basic - dtype: int - description: Number of bins. - default: 1005 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator_separate.rst b/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator_separate.rst deleted file mode 100644 index f921daa36..000000000 --- a/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator_separate.rst +++ /dev/null @@ -1,54 +0,0 @@ -Pyfai Azimuthal Integrator Separate -################################################################# - -Description --------------------------- - -1D azimuthal integrator by pyFAI - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: A - default: ['powder', 'spots'] - - use_mask: - visibility: basic - dtype: bool - description: Should we mask. - default: False - - num_bins: - visibility: basic - dtype: int - description: Number of bins. - default: 1005 - - percentile: - visibility: intermediate - dtype: int - description: Percentile to threshold - default: 50 - - num_bins_azim: - visibility: basic - dtype: int - description: Number of azimuthal bins. - default: 20 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator_with_bragg_filter.rst b/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator_with_bragg_filter.rst deleted file mode 100644 index 6588480e4..000000000 --- a/doc/source/plugin_documentation/plugins.azimuthal_integrators.pyfai_azimuthal_integrator_with_bragg_filter.rst +++ /dev/null @@ -1,54 +0,0 @@ -Pyfai Azimuthal Integrator With Bragg Filter -################################################################# - -Description --------------------------- - -Uses pyfai to remap the data. We then remap, percentile file and integrate. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - use_mask: - visibility: basic - dtype: bool - description: Should we mask. - default: False - - num_bins: - visibility: basic - dtype: int - description: Number of bins. - default: 1005 - - num_bins_azim: - visibility: intermediate - dtype: int - description: Number of azimuthal bins. - default: 200 - - thresh: - visibility: intermediate - dtype: list - description: Threshold of the percentile filter - default: "[5,95]" - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.arithmetic_operations.rst b/doc/source/plugin_documentation/plugins.basic_operations.arithmetic_operations.rst deleted file mode 100644 index a66140d78..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.arithmetic_operations.rst +++ /dev/null @@ -1,53 +0,0 @@ -Arithmetic Operations -################################################################# - -Description --------------------------- - -Basic arithmetic operations on data: addition, subtraction, -multiplication and division. Operations can be performed by extracting -scalars from METADATA (min, max, mean) OR providing a scalar value. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - scalar_value: - visibility: basic - dtype: int - description: A scalar value value for arithmetic operation (it not in metadata). - default: None - - operation: - visibility: intermediate - dtype: str - description: Arithmetic operation to apply to data, choose from addition, subtraction, multiplication and division. - options: ['addition', 'subtraction', 'multiplication', 'division'] - default: division - - metadata_value: - visibility: intermediate - dtype: str - description: A type of scalar extracted from metadata (min, max, mean). - default: max - options: ['min', 'max', 'mean'] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.basic_operations.rst b/doc/source/plugin_documentation/plugins.basic_operations.basic_operations.rst deleted file mode 100644 index 5a04f716a..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.basic_operations.rst +++ /dev/null @@ -1,43 +0,0 @@ -Basic Operations -################################################################# - -Description --------------------------- - -A class that performs basic mathematical operations on datasets. -How should the information be passed to the plugin? - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - operations: - visibility: basic - dtype: list - description: Operations to perform. - default: [] - - pattern: - visibility: intermediate - dtype: str - description: Pattern associated with the datasets - default: PROJECTION - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.data_rescale.rst b/doc/source/plugin_documentation/plugins.basic_operations.data_rescale.rst deleted file mode 100644 index 6925dd8f4..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.data_rescale.rst +++ /dev/null @@ -1,45 +0,0 @@ -Data Rescale -################################################################# - -Description --------------------------- - -The plugin performs stretching or shrinking the data intensity levels -based on skimage rescale_intensity module. Min-max scalars for rescaling can -be passed from METADATA OR by providing as an input. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - min_value: - visibility: basic - dtype: int - description: the global minimum data value. - default: None - - max_value: - visibility: basic - dtype: int - description: the global maximum data value. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.data_threshold.rst b/doc/source/plugin_documentation/plugins.basic_operations.data_threshold.rst deleted file mode 100644 index 54c98dd71..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.data_threshold.rst +++ /dev/null @@ -1,52 +0,0 @@ -Data Threshold -################################################################# - -Description --------------------------- - -The module to threshold the data (less, lessequal, equal, greater, -greaterequal) than the given value, based on the condition the data values -will be replaced by the provided new value - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - inequality_condition: - visibility: basic - dtype: str - description: Set to less, lessequal, equal, greater, greaterequal - options: ['less', 'lessequal', 'equal', 'greater', 'greaterequal'] - default: greater - - given_value: - visibility: basic - dtype: int - description: The value to be replaced with by inequality_condition. - default: 1 - - new_value: - visibility: basic - dtype: int - description: The new value. - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.elementwise_arrays_arithmetics.rst b/doc/source/plugin_documentation/plugins.basic_operations.elementwise_arrays_arithmetics.rst deleted file mode 100644 index 57666795d..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.elementwise_arrays_arithmetics.rst +++ /dev/null @@ -1,39 +0,0 @@ -Elementwise Arrays Arithmetics -################################################################# - -Description --------------------------- - -Basic arithmetic operations on two input datasets: -addition, subtraction, multiplication and division. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - operation: - visibility: basic - dtype: str - description: Arithmetic operation to apply to data, choose from addition, subtraction, multiplication and division. - options: ['addition', 'subtraction', 'multiplication', 'division'] - default: multiplication - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.get_data_statistics.rst b/doc/source/plugin_documentation/plugins.basic_operations.get_data_statistics.rst deleted file mode 100644 index 1f8fc60a1..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.get_data_statistics.rst +++ /dev/null @@ -1,30 +0,0 @@ -Get Data Statistics -################################################################# - -Description --------------------------- - -Collect input data global statistcs. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: The default names - default: ['data', 'data_statistics'] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.no_process.rst b/doc/source/plugin_documentation/plugins.basic_operations.no_process.rst deleted file mode 100644 index 43880ad5b..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.no_process.rst +++ /dev/null @@ -1,162 +0,0 @@ -No Process -################################################################# - -Description --------------------------- - -The base class from which all plugins should inherit. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: list - description: - default: [] - - pattern: - visibility: advanced - dtype: str - description: Explicitly state the slicing pattern. - default: None - - other: - visibility: advanced - dtype: int - description: Temporary parameter for testing. - default: 10 - - yaml_file: - visibility: advanced - dtype: yaml_file - description: Yaml file path. - default: savu/plugins/loaders/full_field_loaders/nxtomo_loader.yaml - - vocentering_search_area: - visibility: basic - dtype: tuple - description: Search area around the estimated centre of rotation - default: (-50, 50) - - ica_w_init: - visibility: intermediate - dtype: list - description: The initial mixing matrix - default: None - - distcorr_polynomial_coeffs: - visibility: basic - dtype: tuple - description: Parameters of the radial distortion function. - default: (1.0, 0.0e-1, 0.0e-2, 0.0e-3, 0.0e-4) - - pymca_config: - visibility: intermediate - dtype: str - description: Pattern used to create and store the hdf5 dataset default is the first pattern in the pattern dictionary. - default: Savu/test_data/data/test_config.cfg - - medianfilt_kernel_size: - visibility: basic - dtype: tuple - description: Kernel size for filter - default: (1, 3, 3) - - yamlconverter_yaml_file: - visibility: basic - dtype: yaml_file - description: Path to file containing data descriptions - default: None - - savunexusloader_datasets: - visibility: basic - dtype: list - description: Override the default by choosing specific dataset(s) to load, by stating the NXdata name - default: [] - - savunexusloader_names: - visibility: basic - dtype: list - description: Override the dataset names associated with the datasets parameter above - default: [] - - randomhdf5loader_axis_labels: - visibility: basic - dtype: list - description: "A list of the axis labels to be associated with each dimension, of the form ['name1.unit1', 'name2. unit2',...]." - default: [] - - randomhdf5loader_patterns: - visibility: basic - dtype: list - description: "A list of data access patterns e.g. [SINOGRAM.0c.1s.2c, PROJECTION.0s.1c.2s], where 'c' and 's' represent core and slice dimensions respectively and every dimension must be specified." - default: [] - - randomhdf5loader_dtype: - visibility: basic - dtype: nptype - description: A numpy array data type - default: int16 - - randomhdf5loader_angles: - visibility: basic - dtype: list - description: A python statement to be evaluated or a file - default: None - - multisavuloader_filename: - visibility: basic - dtype: filename - description: The shared part of the name of each file (not including .nxs) - default: None - - multisavuloader_stack_or_cat_dim: - visibility: basic - dtype: int - description: Dimension to stack or concatenate - default: 3 - - multisavuloader_axis_label: - visibility: basic - dtype: str - description: "New axis label if required, in form 'name.units'." - default: scan.number - - random3Dtomoloader_image_key: - visibility: basic - dtype: list - description: Specify position of darks and flats (in that order) in the data - default: "[[0, 1], [2, 3]]" - - dxchangeloader_dark: - visibility: basic - dtype: int_path_int - description: dark data path and scale value - default: "['exchange/data_dark', 1]" - - dxchangeloader_flat: - visibility: basic - dtype: int_path_int - description: flat data path and scale value - default: "['exchange/data_white', 1]" - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.no_process_plugin.rst b/doc/source/plugin_documentation/plugins.basic_operations.no_process_plugin.rst deleted file mode 100644 index c40e15c92..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.no_process_plugin.rst +++ /dev/null @@ -1,42 +0,0 @@ -No Process Plugin -################################################################# - -Description --------------------------- - -The base class from which all plugins should inherit. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - pattern: - visibility: intermediate - dtype: list - description: Explicitly state the slicing pattern. - default: None - - dummy: - visibility: basic - dtype: int - description: Dummy parameter for testing. - default: 10 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.basic_operations.value_mask_replacement.rst b/doc/source/plugin_documentation/plugins.basic_operations.value_mask_replacement.rst deleted file mode 100644 index 2c1404ed9..000000000 --- a/doc/source/plugin_documentation/plugins.basic_operations.value_mask_replacement.rst +++ /dev/null @@ -1,43 +0,0 @@ -Value Mask Replacement -################################################################# - -Description --------------------------- - -The function looks for a specific value in the provided second array -(e.g. a mask) and substitutes the value in the first array with a given value. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - seek_value: - visibility: basic - dtype: int - description: The value to be located in the provided second array. - default: 0 - - new_value: - visibility: basic - dtype: int - description: The value to be replaced with in the first array. - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.centering.vo_centering.rst b/doc/source/plugin_documentation/plugins.centering.vo_centering.rst deleted file mode 100644 index fbee7ba9d..000000000 --- a/doc/source/plugin_documentation/plugins.centering.vo_centering.rst +++ /dev/null @@ -1,141 +0,0 @@ -Vo Centering -################################################################# - -Description --------------------------- - -A plugin to calculate the centre of rotation using the Vo Method - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: The default names - default: "['cor_preview', 'cor_broadcast']" - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames (sinograms) to use in the calculation of the centre of rotation (this will not reduce the data size for subsequent plugins). - default: "[]" - example: "The typical three dimensional data structure is [angles, detY, detZ], e.g. for sinogram choose [:,sliceNo,:] [angles, detZ, detY]. If the data is four dimensional, include a time parameter." - - start_pixel: - visibility: intermediate - dtype: int - description: The estimated centre of rotation. If value is None, use the horizontal centre of the image. - default: None - - search_area: - visibility: intermediate - dtype: tuple - description: Search area around the estimated centre of rotation - default: (-50, 50) - - ratio: - visibility: intermediate - dtype: float - description: The ratio between the size of object and FOV of the camera - default: 0.5 - - search_radius: - visibility: intermediate - dtype: int - description: Use for fine searching - default: 6 - - step: - visibility: intermediate - dtype: float - description: Step of fine searching - default: 0.5 - - datasets_to_populate: - visibility: advanced - dtype: range - description: A list of datasets which require this information - default: "[]" - - broadcast_method: - visibility: advanced - dtype: str - options: ['median', 'mean', 'nearest', 'linear_fit'] - description: - summary: Method of broadcasting centre values calculated from preview slices to full dataset. - options: - median: - mean: - nearest: - linear_fit: - default: median - - row_drop: - visibility: advanced - dtype: int - description: Drop lines around vertical center of the mask - default: 20 - - average_radius: - visibility: advanced - dtype: int - description: Averaging sinograms around a required sinogram to improve signal-to-noise ratio - default: 5 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Reliable method for calculating the center of rotation in parallel-beam tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2014reliable, - title={Reliable method for calculating the center of rotation in parallel-beam tomography}, - author={Vo, Nghia T and Drakopoulos, Michael and Atwood, Robert C and Reinhard, Christina}, - journal={Optics express}, - volume={22}, - number={16}, - pages={19078--19086}, - year={2014}, - publisher={Optical Society of America} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Reliable method for calculating the center of rotation in parallel-beam tomography - %A Vo, Nghia T - %A Drakopoulos, Michael - %A Atwood, Robert C - %A Reinhard, Christina - %J Optics express - %V 22 - %N 16 - %P 19078-19086 - %@ 1094-4087 - %D 2014 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.centering.vo_centering_iterative.rst b/doc/source/plugin_documentation/plugins.centering.vo_centering_iterative.rst deleted file mode 100644 index afd41288c..000000000 --- a/doc/source/plugin_documentation/plugins.centering.vo_centering_iterative.rst +++ /dev/null @@ -1,126 +0,0 @@ -Vo Centering Iterative -################################################################# - -Description --------------------------- - -A plugin to calculate the centre of rotation using the Vo Method - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: The default names - default: "['cor_raw','cor_fit', 'reliability']" - - ratio: - visibility: intermediate - dtype: float - description: The ratio between the size of object and FOV of the camera - default: 0.5 - - row_drop: - visibility: intermediate - dtype: int - description: Drop lines around vertical center of the mask. - default: 20 - - search_radius: - visibility: intermediate - dtype: int - description: Use for fine searching - default: 6 - - step: - visibility: intermediate - dtype: float - description: Step of fine searching - default: 0.5 - - expand_by: - visibility: advanced - dtype: int - description: The number of pixels to expand the search region by on each iteration - default: 5 - - boundary_distance: - visibility: advanced - dtype: int - description: Accepted distance of minima from the boundary of the listshift in the coarse search. - default: 3 - - preview: - visibility: intermediate - dtype: int_list - description: A slice list of required frames (sinograms) to use in the calculation of the centre of rotation (this will not reduce the data size for subsequent plugins). - default: "[]" - - datasets_to_populate: - visibility: advanced - dtype: list - description: A list of datasets which require this information - default: "[]" - - start_pixel: - visibility: advanced - dtype: int - description: The approximate centre. If value is None, take the value from .nxs file else set to image centre. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Reliable method for calculating the center of rotation in parallel-beam tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2014reliable, - title={Reliable method for calculating the center of rotation in parallel-beam tomography}, - author={Vo, Nghia T and Drakopoulos, Michael and Atwood, Robert C and Reinhard, Christina}, - journal={Optics express}, - volume={22}, - number={16}, - pages={19078--19086}, - year={2014}, - publisher={Optical Society of America}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Reliable method for calculating the center of rotation in parallel-beam tomography - %A Vo, Nghia T - %A Drakopoulos, Michael - %A Atwood, Robert C - %A Reinhard, Christina - %J Optics express - %V 22 - %N 16 - %P 19078-19086 - %@ 1094-4087 - %D 2014 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.component_analysis.ica.rst b/doc/source/plugin_documentation/plugins.component_analysis.ica.rst deleted file mode 100644 index af6bf1b40..000000000 --- a/doc/source/plugin_documentation/plugins.component_analysis.ica.rst +++ /dev/null @@ -1,60 +0,0 @@ -Ica -################################################################# - -Description --------------------------- - -This plugin performs independent component analysis on XRD/XRF spectra. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: A list of the dataset(s) to process. - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: A list of the dataset(s) to process. - default: "['scores', 'eigenvectors']" - - number_of_components: - visibility: basic - dtype: int - description: The number of expected components. - default: 3 - - chunk: - visibility: intermediate - dtype: str - description: The chunk to work on - default: SINOGRAM - - whiten: - visibility: intermediate - dtype: int - description: To subtract the mean or not. - default: 1 - - w_init: - visibility: basic - dtype: list - description: The initial mixing matrix. - default: None - - random_state: - visibility: intermediate - dtype: int - description: The state - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.component_analysis.pca.rst b/doc/source/plugin_documentation/plugins.component_analysis.pca.rst deleted file mode 100644 index 99e88f61d..000000000 --- a/doc/source/plugin_documentation/plugins.component_analysis.pca.rst +++ /dev/null @@ -1,8 +0,0 @@ -Pca -################################################################# - -Description --------------------------- - -This plugin performs independent component analysis on XRD/XRF spectra. - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.corrections.camera_rot_correction.rst b/doc/source/plugin_documentation/plugins.corrections.camera_rot_correction.rst deleted file mode 100644 index 10b439500..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.camera_rot_correction.rst +++ /dev/null @@ -1,67 +0,0 @@ -Camera Rot Correction -################################################################# - -Description --------------------------- - -A plugin to apply a rotation to projection images, for example to correct -for missing camera alignment. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - angle: - visibility: intermediate - dtype: float - description: The rotation angle for the output image in degrees. - default: 0.0 - - crop_edges: - visibility: intermediate - dtype: int - description: When a rotation is applied to any image, the result will contain zeros around the edges, which can be removed by cropping the edges by a specified number of pixels. - default: 0 - - auto_crop: - visibility: intermediate - dtype: bool - description: If activated, this feature will automatically crop the image to eliminate any regions without data (because of the rotation). - default: False - - use_auto_centre: - visibility: intermediate - dtype: bool - description: This parameter automatically sets the centre of rotation to the centre of the image. If set to False, the values from centre_x and centre_y are used. Note - The centre needs to be within the image dimensions. - default: True - - center_x: - visibility: intermediate - dtype: float - description: If not use_auto_centre, this value determines the detector x coordinate for the centre of rotation. - default: 1279.5 - - centre_y: - visibility: intermediate - dtype: float - description: If not use_auto_centre, this value determines the detector x coordinate for the centre of rotation. - default: 1079.5 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.corrections.convert_360_180_sinogram.rst b/doc/source/plugin_documentation/plugins.corrections.convert_360_180_sinogram.rst deleted file mode 100644 index b0704dea3..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.convert_360_180_sinogram.rst +++ /dev/null @@ -1,36 +0,0 @@ -Convert 360 180 Sinogram -################################################################# - -Description --------------------------- - -Method to convert the 0-360 degree sinogram to 0-180 sinogram. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the output datatsets to create. - default: ['in_datasets[0]', 'cor'] - - center: - visibility: intermediate - dtype: float - description: Center of rotation. - default: 0.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.corrections.dark_flat_field_correction.rst b/doc/source/plugin_documentation/plugins.corrections.dark_flat_field_correction.rst deleted file mode 100644 index 2e6f2d8dc..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.dark_flat_field_correction.rst +++ /dev/null @@ -1,57 +0,0 @@ -Dark Flat Field Correction -################################################################# - -Description --------------------------- - -A Plugin to apply a simple dark and flat field correction to data. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - pattern: - visibility: advanced - dtype: str - options: ['SINOGRAM', 'PROJECTION'] - description: Data processing pattern - default: PROJECTION - - lower_bound: - visibility: advanced - dtype: float - description: Set all values below the lower_bound to this value. - default: None - - upper_bound: - visibility: advanced - dtype: float - description: Set all values above the upper bound to this value. - default: None - - warn_proportion: - visibility: advanced - dtype: float - description: - summary: Output a warning if this proportion of values, or greater, are below and/or above the lower/upper bounds - verbose: Enter 0.05 for 5% - default: 0.05 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.corrections.distortion_correction.rst b/doc/source/plugin_documentation/plugins.corrections.distortion_correction.rst deleted file mode 100644 index d0dd7dbac..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.distortion_correction.rst +++ /dev/null @@ -1,102 +0,0 @@ -Distortion Correction -################################################################# - -Description --------------------------- - -A plugin to apply radial distortion correction. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - polynomial_coeffs: - visibility: basic - dtype: tuple - description: Parameters of the radial distortion - default: (1.00015076, 1.9289e-6, -2.4325e-8, 1.00439e-11, -3.99352e-15) - - center_from_top: - visibility: intermediate - dtype: float - description: The centre of distortion in pixels from the top of the image. - default: 995.24 - - center_from_left: - visibility: intermediate - dtype: float - description: The centre of distortion in pixels from the left of the image. - default: 1283.25 - - file_path: - visibility: intermediate - dtype: filepath - description: Path to the text file having distortion coefficients . Set to None for manually inputing. - default: None - - crop_edges: - visibility: intermediate - dtype: int - description: When applied to previewed/cropped data, the result may contain zeros around the edges, which can be removed by cropping the edges by a specified number of pixels - default: 0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2015radial, - title={Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={23}, - number={25}, - pages={32859--32868}, - year={2015}, - publisher={Optical Society of America} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 23 - %N 25 - %P 32859-32868 - %@ 1094-4087 - %D 2015 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.corrections.distortion_correction_deprecated.rst b/doc/source/plugin_documentation/plugins.corrections.distortion_correction_deprecated.rst deleted file mode 100644 index f2561dac2..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.distortion_correction_deprecated.rst +++ /dev/null @@ -1,96 +0,0 @@ -Distortion Correction Deprecated -################################################################# - -Description --------------------------- - -A plugin to apply radial distortion correction. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - polynomial_coeffs: - visibility: intermediate - dtype: tuple - description: Parameters of the radial distortion - default: (1.00015076, 1.9289e-6, -2.4325e-8, 1.00439e-11, -3.99352e-15) - - centre_from_top: - visibility: intermediate - dtype: float - description: The centre of distortion in pixels from the top of the image. - default: 995.24 - - centre_from_left: - visibility: intermediate - dtype: float - description: The centre of distortion in pixels from the left of the image. - default: 1283.25 - - crop_edges: - visibility: intermediate - dtype: int - description: When applied to previewed/cropped data, the result may contain zeros around the edges, which can be removed by cropping the edges by a specified number of pixels - default: 0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2015radial, - title={Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={23}, - number={25}, - pages={32859--32868}, - year={2015}, - publisher={Optical Society of America} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 23 - %N 25 - %P 32859-32868 - %@ 1094-4087 - %D 2015 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.corrections.monitor_correction.rst b/doc/source/plugin_documentation/plugins.corrections.monitor_correction.rst deleted file mode 100644 index 095c5de8a..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.monitor_correction.rst +++ /dev/null @@ -1,62 +0,0 @@ -Monitor Correction -################################################################# - -Description --------------------------- - -Corrects the data to the monitor counts. -This plugin corrects data[0] from data[1] by dividing. We allow a scale -and offset due to I18's uncalibrated ic - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: A list of the dataset(s) to process. - default: ['to_be_corrected', 'monitor'] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - nominator_scale: - visibility: intermediate - dtype: float - description: a - default: 1.0 - - nominator_offset: - visibility: intermediate - dtype: float - description: b - default: 0.0 - - denominator_scale: - visibility: intermediate - dtype: float - description: c - default: 1.0 - - denominator_offset: - visibility: intermediate - dtype: float - description: d - default: 0.0 - - pattern: - visibility: intermediate - dtype: str - description: The pattern to apply to it. - default: PROJECTION - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.corrections.monitor_correction_nd.rst b/doc/source/plugin_documentation/plugins.corrections.monitor_correction_nd.rst deleted file mode 100644 index 09c46882d..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.monitor_correction_nd.rst +++ /dev/null @@ -1,66 +0,0 @@ -Monitor Correction Nd -################################################################# - -Description --------------------------- - -Corrects the data to the monitor counts. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: A list of the dataset(s) to process. - default: "['to_be_corrected', 'monitor']" - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - nominator_scale: - visibility: intermediate - dtype: float - description: a - default: 1.0 - - nominator_offset: - visibility: intermediate - dtype: float - description: b - default: 0.0 - - denominator_scale: - visibility: intermediate - dtype: float - description: c - default: 1.0 - - denominator_offset: - visibility: intermediate - dtype: float - description: d - default: 0.0 - - pattern: - visibility: intermediate - dtype: str - description: The pattern to apply to it. - default: SPECTRUM - - monitor_pattern: - visibility: intermediate - dtype: str - description: The pattern to apply to it. - default: CHANNEL - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.corrections.mtf_deconvolution.rst b/doc/source/plugin_documentation/plugins.corrections.mtf_deconvolution.rst deleted file mode 100644 index 0b63c1bb7..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.mtf_deconvolution.rst +++ /dev/null @@ -1,87 +0,0 @@ -Mtf Deconvolution -################################################################# - -Description --------------------------- - -Method to correct the point-spread-function effect. -Working on raw projections and flats. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - file_path: - visibility: intermediate - dtype: filepath - description: "Path to file containing a 2D array of a MTF function. File formats are 'npy', or 'tif'." - default: None - - pad_width: - visibility: intermediate - dtype: int - description: Pad the image before the deconvolution. - default: 128 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Preprocessing techniques for removing artifacts in synchrotron-based tomographic images by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @inproceedings{vo2019preprocessing, - title={Preprocessing techniques for removing artifacts in synchrotron-based tomographic images}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - booktitle={Developments in X-Ray Tomography XII}, - volume={11113}, - pages={111131I}, - year={2019}, - organization={International Society for Optics and Photonics} - publisher = {SPIE}, - pages = {309 -- 328}, - year = {2019}, - doi = {10.1117/12.2530324}, - URL = {https://doi.org/10.1117/12.2530324} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Conference Proceedings - %T Preprocessing techniques for removing artifacts in synchrotron-based tomographic images - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %B Developments in X-Ray Tomography XII - %V 11113 - %P 111131I - %D 2019 - %I International Society for Optics and Photonics - - diff --git a/doc/source/plugin_documentation/plugins.corrections.subpixel_shift.rst b/doc/source/plugin_documentation/plugins.corrections.subpixel_shift.rst deleted file mode 100644 index a8d452425..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.subpixel_shift.rst +++ /dev/null @@ -1,44 +0,0 @@ -Subpixel Shift -################################################################# - -Description --------------------------- - -A plugin to apply a sub-pixel correction to images, for example to allow -subpixel alignment for the AstraGpu plugin. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - x_shift: - visibility: intermediate - dtype: float - description: The shift in x for the output image in pixels. Positive values correspond to data being shifted towards larger indices. - default: 0.0 - - transform_module: - visibility: intermediate - dtype: str - description: The module (skimage|scipy) to be used for image translation. skimage corresponds to skimage.transform.SimilarityTransform while scipy corresponds to scipy.ndimage.interpolation. - default: skimage - options: ['skimage', 'scipy'] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.corrections.time_based_correction.rst b/doc/source/plugin_documentation/plugins.corrections.time_based_correction.rst deleted file mode 100644 index 66dd1335b..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.time_based_correction.rst +++ /dev/null @@ -1,36 +0,0 @@ -Time Based Correction -################################################################# - -Description --------------------------- - -Apply a time-based dark and flat field correction to data. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - in_range: - visibility: basic - dtype: ['range', 'bool'] - description: "Set to True if you require values in the range [0, 1]." - default: False - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.corrections.time_based_plus_drift_correction.rst b/doc/source/plugin_documentation/plugins.corrections.time_based_plus_drift_correction.rst deleted file mode 100644 index 59290e326..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.time_based_plus_drift_correction.rst +++ /dev/null @@ -1,9 +0,0 @@ -Time Based Plus Drift Correction -################################################################# - -Description --------------------------- - -Apply a time-based dark and flat field correction on data with an -image drift using linear interpolation and template matching. - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.corrections.timeseries_field_corrections.rst b/doc/source/plugin_documentation/plugins.corrections.timeseries_field_corrections.rst deleted file mode 100644 index 5bdf62c26..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.timeseries_field_corrections.rst +++ /dev/null @@ -1,9 +0,0 @@ -Timeseries Field Corrections -################################################################# - -Description --------------------------- - -A Plugin to apply a simple dark and flatfield correction to some -raw timeseries data - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.corrections.xrd_absorption_approximation.rst b/doc/source/plugin_documentation/plugins.corrections.xrd_absorption_approximation.rst deleted file mode 100644 index 14acb2253..000000000 --- a/doc/source/plugin_documentation/plugins.corrections.xrd_absorption_approximation.rst +++ /dev/null @@ -1,55 +0,0 @@ -Xrd Absorption Approximation -################################################################# - -Description --------------------------- - -McNears absorption correction, takes in a normalised absorption sinogram -and xrd sinogram stack. A base absorption correction for stxm and xrd - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - azimuthal_offset: - visibility: intermediate - dtype: int - description: angle between detectors. - default: 0 - - density: - visibility: intermediate - dtype: float - description: The density - default: 3.5377 - - compound: - visibility: intermediate - dtype: str - description: The compound - default: Co0.2(Al2O3)0.8 - - log_me: - visibility: intermediate - dtype: int - description: should we log the transmission. - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.developing.testing_sino_align.rst b/doc/source/plugin_documentation/plugins.developing.testing_sino_align.rst deleted file mode 100644 index 25636a096..000000000 --- a/doc/source/plugin_documentation/plugins.developing.testing_sino_align.rst +++ /dev/null @@ -1,91 +0,0 @@ -Testing Sino Align -################################################################# - -Description --------------------------- - -The centre of mass of each row is determined and then a sine function fit -through these to determine the centre of rotation. The residual between -each centre of mass and the sine function is then used to align each row. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - threshold: - visibility: intermediate - dtype: list - description: "e.g. [a, b] will set all values above a to b." - default: None - - p0: - visibility: basic - dtype: tuple - description: Initial guess for the parameters of scipy.optimize.curve_fit. - default: (1,1,1) - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Chemical imaging of single catalyst particles with scanning μ-XANES-CT and μ-XRF-CT by Price, SWT et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{price2015chemical, - title={Chemical imaging of single catalyst particles with scanning $\mu$-XANES-CT and $\mu$-XRF-CT}, - author={Price, SWT and Ignatyev, K and Geraki, K and Basham, M and Filik, J and Vo, NT and Witte, PT and Beale, AM and Mosselmans, JFW}, - journal={Physical Chemistry Chemical Physics}, - volume={17}, - number={1}, - pages={521--529}, - year={2015}, - publisher={Royal Society of Chemistry} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Chemical imaging of single catalyst particles with scanning μ-XANES-CT and μ-XRF-CT - %A Price, SWT - %A Ignatyev, K - %A Geraki, K - %A Basham, M - %A Filik, J - %A Vo, NT - %A Witte, PT - %A Beale, AM - %A Mosselmans, JFW - %J Physical Chemistry Chemical Physics - %V 17 - %N 1 - %P 521-529 - %D 2015 - %I Royal Society of Chemistry - - diff --git a/doc/source/plugin_documentation/plugins.filters.band_pass.rst b/doc/source/plugin_documentation/plugins.filters.band_pass.rst deleted file mode 100644 index dfd6b3423..000000000 --- a/doc/source/plugin_documentation/plugins.filters.band_pass.rst +++ /dev/null @@ -1,44 +0,0 @@ -Band Pass -################################################################# - -Description --------------------------- - -A plugin to filter each frame with a BandPass T - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - blur_width: - visibility: basic - dtype: tuple - description: Kernel size - default: (0, 3, 3) - - type: - visibility: basic - dtype: str - description: Filter type (High|Low). - options: ['High', 'Low'] - default: High - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_cpu.rst b/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_cpu.rst deleted file mode 100644 index b764d160f..000000000 --- a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_cpu.rst +++ /dev/null @@ -1,517 +0,0 @@ -Ccpi Denoising Cpu -################################################################# - -Description --------------------------- - -Wrapper for CCPi-Regularisation Toolkit (CPU) for efficient 2D/3D denoising - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'SB_TV', 'NLTV', 'TGV', 'LLT_ROF', 'NDF', 'Diff4th'] - description: - summary: The denoising method - verbose: Iterative methods can help to solve ill-posed inverse problems by choosing a suitable noise model for the measurement - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model. It is a good model for piecewise-constant images with sharp abrupt boundaries. - FGP_TV: Fast Gradient Projection Total Variation model - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - reg_parameter: - visibility: basic - dtype: ['float', 'int'] - description: - summary: Regularisation parameter could control the level of smoothing or denoising. - verbose: Higher regularisation values lead to stronger smoothing effect. If the value is too high, you will obtain a very blurry reconstructed image. - range: Recommended between 0.0001 and 0.1 - example: A good value to start with is {default}, {range} - default: 0.0001 - - max_iterations: - visibility: basic - dtype: int - description: - summary: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - range: The recommended value with the chosen method would be 500 - default: - method: - ROF_TV: 2000 - FGP_TV: 500 - PD_TV: 500 - SB_TV: 100 - LLT_ROF: 2000 - NDF: 2000 - Diff4th: 1000 - TGV: 500 - NLTV: 5 - - time_step: - visibility: advanced - dtype: float - dependency: - regularisation_method: - ROF_TV - LLT_ROF - NDF - Diff4th - description: - summary: Time marching parameter for convergence of explicit schemes - verbose: the time step constant defines the speed of convergence, the larger values can lead to divergence - range: Recommended between 0.0001 and 0.003 - default: 0.003 - - lipshitz_constant: - visibility: advanced - dtype: float - description: TGV method, Lipshitz constant. - default: 12 - dependency: - method: TGV - - alpha1: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 1st-order term. - default: 1.0 - dependency: - method: TGV - - alpha0: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 2nd-order term. - default: 2.0 - dependency: - method: TGV - - reg_parLLT: - visibility: advanced - dtype: float - dependency: - method: LLT_ROF - description: LLT-ROF method, parameter to control the 2nd-order term. - default: 0.05 - - penalty_type: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey', 'Constr', 'Constrhuber'] - description: - summary: Penalty type - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey - dependency: - method: NDF - default: Huber - - edge_par: - visibility: advanced - dtype: float - dependency: - method: - NDF - Diff4th - description: NDF and Diff4th methods, noise magnitude parameter. - default: 0.01 - - tolerance_constant: - visibility: advanced - dtype: float - description: Tolerance constant to stop iterations earlier. - default: 0.0 - - pattern: - visibility: advanced - dtype: str - description: Pattern to apply this to. - default: VOLUME_XZ - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2019ccpi, - title={Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms}, - author={Kazantsev, Daniil and Pasca, Edoardo and Turner, Martin J and Withers, Philip J}, - journal={SoftwareX}, - volume={9}, - pages={317--323}, - year={2019}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms - %A Kazantsev, Daniil - %A Pasca, Edoardo - %A Turner, Martin J - %A Withers, Philip J - %J SoftwareX - %V 9 - %P 317-323 - %@ 2352-7110 - %D 2019 - %I Elsevier - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D: nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D: nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_cpu_3D.rst b/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_cpu_3D.rst deleted file mode 100644 index 6e9141cb0..000000000 --- a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_cpu_3D.rst +++ /dev/null @@ -1,495 +0,0 @@ -Ccpi Denoising Cpu 3D -################################################################# - -Description --------------------------- - -Wrapper for CCPi-Regularisation Toolkit (GPU) for -efficient 2D/3D denoising. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'SB_TV', 'NLTV', 'TGV', 'LLT_ROF', 'NDF', 'Diff4th'] - description: - summary: The denoising method - verbose: Iterative methods can help to solve ill-posed inverse problems by choosing a suitable noise model for the measurement - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model - FGP_TV: Fast Gradient Projection Total Variation model - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - reg_parameter: - visibility: basic - dtype: float - description: - summary: Regularisation (smoothing) parameter. The higher the value, the stronger the smoothing effect - range: Recommended between 0 and 1 - default: 0.01 - - max_iterations: - visibility: basic - dtype: int - description: Total number of regularisation iterations. - default: 300 - - time_step: - visibility: advanced - dtype: int - description: Time marching step, relevant for ROF_TV, LLT_ROF, NDF, Diff4th methods. - default: 0.001 - dependency: - method: - ROF_TV - LLT_ROF - NDF - Diff4th - - lipshitz_constant: - visibility: advanced - dtype: int - description: TGV method, Lipshitz constant. - default: 12 - dependency: - method: TGV - - alpha1: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 1st-order term. - default: 1.0 - dependency: - method: TGV - - alpha0: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 2nd-order term. - default: 2.0 - dependency: - method: TGV - - reg_parLLT: - visibility: advanced - dtype: float - dependency: - method: LLT_ROF - description: LLT-ROF method, parameter to control the 2nd-order term. - default: 0.05 - - penalty_type: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey', 'Constr', 'Constrhuber'] - description: - summary: Penalty type - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey - dependency: - method: NDF - default: Huber - - edge_par: - visibility: advanced - dtype: float - dependency: - method: - NDF - Diff4th - description: NDF and Diff4th methods, noise magnitude parameter. - default: 0.01 - - tolerance_constant: - visibility: advanced - dtype: float - description: Tolerance constant to stop iterations earlier. - default: 0.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2019ccpi, - title={Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms}, - author={Kazantsev, Daniil and Pasca, Edoardo and Turner, Martin J and Withers, Philip J}, - journal={SoftwareX}, - volume={9}, - pages={317--323}, - year={2019}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms - %A Kazantsev, Daniil - %A Pasca, Edoardo - %A Turner, Martin J - %A Withers, Philip J - %J SoftwareX - %V 9 - %P 317-323 - %@ 2352-7110 - %D 2019 - %I Elsevier - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D: nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D: nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_gpu.rst b/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_gpu.rst deleted file mode 100644 index f3c340162..000000000 --- a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_gpu.rst +++ /dev/null @@ -1,501 +0,0 @@ -Ccpi Denoising Gpu -################################################################# - -Description --------------------------- - -Wrapper for CCPi-Regularisation Toolkit (GPU) for -efficient 2D/3D denoising. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'SB_TV', 'NLTV', 'TGV', 'LLT_ROF', 'NDF', 'Diff4th'] - description: - summary: The denoising method - verbose: Iterative methods can help to solve ill-posed inverse problems by choosing a suitable noise model for the measurement - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model - FGP_TV: Fast Gradient Projection Total Variation model - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - reg_parameter: - visibility: basic - dtype: float - description: - summary: Regularisation (smoothing) parameter. The higher the value, the stronger the smoothing effect - range: Recommended between 0 and 1 - default: 0.01 - - max_iterations: - visibility: basic - dtype: int - description: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - default: 300 - - time_step: - visibility: advanced - dtype: int - description: Time marching step, relevant for ROF_TV, LLT_ROF, NDF, Diff4th methods. - default: 0.001 - dependency: - method: - ROF_TV - LLT_ROF - NDF - Diff4th - - lipshitz_constant: - visibility: advanced - dtype: int - description: TGV method, Lipshitz constant. - default: 12 - dependency: - method: TGV - - alpha1: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 1st-order term. - default: 1.0 - dependency: - method: TGV - - alpha0: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 2nd-order term. - default: 2.0 - dependency: - method: TGV - - reg_parLLT: - visibility: advanced - dtype: float - dependency: - method: LLT_ROF - description: LLT-ROF method, parameter to control the 2nd-order term. - default: 0.05 - - penalty_type: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey', 'Constr', 'Constrhuber'] - description: - summary: Penalty type - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey - dependency: - method: NDF - default: Huber - - edge_par: - visibility: advanced - dtype: float - dependency: - method: - NDF - Diff4th - description: NDF and Diff4th methods, noise magnitude parameter. - default: 0.01 - - tolerance_constant: - visibility: advanced - dtype: float - description: Tolerance constant to stop iterations earlier. - default: 0.0 - - pattern: - visibility: advanced - dtype: str - description: Pattern to apply this to. - default: VOLUME_XZ - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2019ccpi, - title={Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms}, - author={Kazantsev, Daniil and Pasca, Edoardo and Turner, Martin J and Withers, Philip J}, - journal={SoftwareX}, - volume={9}, - pages={317--323}, - year={2019}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms - %A Kazantsev, Daniil - %A Pasca, Edoardo - %A Turner, Martin J - %A Withers, Philip J - %J SoftwareX - %V 9 - %P 317-323 - %@ 2352-7110 - %D 2019 - %I Elsevier - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_gpu_3D.rst b/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_gpu_3D.rst deleted file mode 100644 index 755ebd713..000000000 --- a/doc/source/plugin_documentation/plugins.filters.denoising.ccpi_denoising_gpu_3D.rst +++ /dev/null @@ -1,495 +0,0 @@ -Ccpi Denoising Gpu 3D -################################################################# - -Description --------------------------- - -Wrapper for CCPi-Regularisation Toolkit (GPU) for -efficient 2D/3D denoising - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'SB_TV', 'NLTV', 'TGV', 'LLT_ROF', 'NDF', 'Diff4th'] - description: - summary: The denoising method - verbose: Iterative methods can help to solve ill-posed inverse problems by choosing a suitable noise model for the measurement - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model - FGP_TV: Fast Gradient Projection Total Variation model - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - reg_parameter: - visibility: basic - dtype: float - description: - summary: Regularisation (smoothing) parameter. The higher the value, the stronger the smoothing effect - range: Recommended between 0 and 1 - default: 0.01 - - max_iterations: - visibility: basic - dtype: int - description: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - default: 300 - - time_step: - visibility: advanced - dtype: int - description: Time marching step, relevant for ROF_TV, LLT_ROF, NDF, Diff4th methods. - default: 0.001 - dependency: - method: - ROF_TV - LLT_ROF - NDF - Diff4th - - lipshitz_constant: - visibility: advanced - dtype: int - description: TGV method, Lipshitz constant. - default: 12 - dependency: - method: TGV - - alpha1: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 1st-order term. - default: 1.0 - dependency: - method: TGV - - alpha0: - visibility: advanced - dtype: float - description: TGV method, parameter to control the 2nd-order term. - default: 2.0 - dependency: - method: TGV - - reg_parLLT: - visibility: advanced - dtype: float - dependency: - method: LLT_ROF - description: LLT-ROF method, parameter to control the 2nd-order term. - default: 0.05 - - penalty_type: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey', 'Constr', 'Constrhuber'] - description: - summary: Penalty type - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey - dependency: - method: NDF - default: Huber - - edge_par: - visibility: advanced - dtype: float - dependency: - method: - NDF - Diff4th - description: NDF and Diff4th methods, noise magnitude parameter. - default: 0.01 - - tolerance_constant: - visibility: advanced - dtype: float - description: Tolerance constant to stop iterations earlier. - default: 0.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2019ccpi, - title={Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms}, - author={Kazantsev, Daniil and Pasca, Edoardo and Turner, Martin J and Withers, Philip J}, - journal={SoftwareX}, - volume={9}, - pages={317--323}, - year={2019}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Ccpi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms - %A Kazantsev, Daniil - %A Pasca, Edoardo - %A Turner, Martin J - %A Withers, Philip J - %J SoftwareX - %V 9 - %P 317-323 - %@ 2352-7110 - %D 2019 - %I Elsevier - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D: nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D: nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.filters.denoising.denoise_bregman_filter.rst b/doc/source/plugin_documentation/plugins.filters.denoising.denoise_bregman_filter.rst deleted file mode 100644 index 6fea2a6fb..000000000 --- a/doc/source/plugin_documentation/plugins.filters.denoising.denoise_bregman_filter.rst +++ /dev/null @@ -1,55 +0,0 @@ -Denoise Bregman Filter -################################################################# - -Description --------------------------- - -Split Bregman method for solving the denoising Total Variation ROF model. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - weight: - visibility: basic - dtype: float - description: Denoising factor. - default: 2.0 - - max_iterations: - visibility: basic - dtype: int - description: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - default: 30 - - error_threshold: - visibility: advanced - dtype: float - description: Convergence threshold. - default: 0.001 - - isotropic: - visibility: advanced - dtype: ['bool', 'str'] - description: Isotropic or Anisotropic filtering. - options: ['Isotropic', 'Anisotropic'] - default: False - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.denoising.median_filter.rst b/doc/source/plugin_documentation/plugins.filters.denoising.median_filter.rst deleted file mode 100644 index 5ec5115c2..000000000 --- a/doc/source/plugin_documentation/plugins.filters.denoising.median_filter.rst +++ /dev/null @@ -1,42 +0,0 @@ -Median Filter -################################################################# - -Description --------------------------- - -A plugin to filter each frame with a 3x3 median filter. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - kernel_size: - visibility: basic - dtype: tuple - description: Kernel size for the filter. - default: (1, 3, 3) - - pattern: - visibility: advanced - dtype: str - description: Pattern to apply this to. - default: PROJECTION - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.dezinger.rst b/doc/source/plugin_documentation/plugins.filters.dezinger.rst deleted file mode 100644 index 747bdf5de..000000000 --- a/doc/source/plugin_documentation/plugins.filters.dezinger.rst +++ /dev/null @@ -1,49 +0,0 @@ -Dezinger -################################################################# - -Description --------------------------- - -A plugin for cleaning x-ray strikes based on statistical evaluation of -the near neighbourhood - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - outlier_mu: - visibility: basic - dtype: float - description: Threshold for defecting outliers, greater is less sensitive. - default: 10.0 - - kernel_size: - visibility: basic - dtype: int - description: Number of frames included in average. - default: 5 - - mode: - visibility: basic - dtype: int - description: output mode, 0=normal 5=zinger strength 6=zinger yes/no. - default: 0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.dezinger_simple.rst b/doc/source/plugin_documentation/plugins.filters.dezinger_simple.rst deleted file mode 100644 index cfd0ce618..000000000 --- a/doc/source/plugin_documentation/plugins.filters.dezinger_simple.rst +++ /dev/null @@ -1,43 +0,0 @@ -Dezinger Simple -################################################################# - -Description --------------------------- - -A plugin for cleaning x-ray strikes based on statistical evaluation of -the near neighbourhood - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - outlier_mu: - visibility: basic - dtype: float - description: Threshold for defecting outliers, greater is less sensitive. - default: 1000.0 - - kernel_size: - visibility: basic - dtype: int - description: Number of frames included in average. If the number is not odd, use kernel_size + 1 - default: 5 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.dezinger_sinogram.rst b/doc/source/plugin_documentation/plugins.filters.dezinger_sinogram.rst deleted file mode 100644 index b0f6d411e..000000000 --- a/doc/source/plugin_documentation/plugins.filters.dezinger_sinogram.rst +++ /dev/null @@ -1,38 +0,0 @@ -Dezinger Sinogram -################################################################# - -Description --------------------------- - -Method to remove scratches in the reconstructed image caused by -zingers. Remove zingers (caused by scattered X-rays hitting the CCD chip -directly) - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - tolerance: - visibility: basic - dtype: float - description: Threshold for detecting zingers, greater is less sensitive. - default: 0.08 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.find_peaks.rst b/doc/source/plugin_documentation/plugins.filters.find_peaks.rst deleted file mode 100644 index e7fe351a6..000000000 --- a/doc/source/plugin_documentation/plugins.filters.find_peaks.rst +++ /dev/null @@ -1,43 +0,0 @@ -Find Peaks -################################################################# - -Description --------------------------- - -This plugin uses peakutils to find peaks in spectra. This is then metadata. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s). - default: ['Peaks'] - - thresh: - visibility: basic - dtype: float - description: Threshold for peak detection - default: 0.03 - - min_distance: - visibility: basic - dtype: int - description: Minimum distance for peak detection. - default: 15 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.fresnel_filter.rst b/doc/source/plugin_documentation/plugins.filters.fresnel_filter.rst deleted file mode 100644 index f8eb8eb6b..000000000 --- a/doc/source/plugin_documentation/plugins.filters.fresnel_filter.rst +++ /dev/null @@ -1,51 +0,0 @@ -Fresnel Filter -################################################################# - -Description --------------------------- - -Method similar to the Paganin filter working both on sinograms and -projections. Used to improve the contrast of the reconstruction image. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - ratio: - visibility: datasets - dtype: float - description: Control the strength of the filter. Greater is stronger - default: 100.0 - - pattern: - visibility: basic - dtype: str - description: Data processing pattern - options: ['PROJECTION', 'SINOGRAM'] - default: SINOGRAM - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -The filter built is based on the Fresnel propagator -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/source/plugin_documentation/plugins.filters.hilbert_filter.rst b/doc/source/plugin_documentation/plugins.filters.hilbert_filter.rst deleted file mode 100644 index e57da829e..000000000 --- a/doc/source/plugin_documentation/plugins.filters.hilbert_filter.rst +++ /dev/null @@ -1,9 +0,0 @@ -Hilbert Filter -################################################################# - -Description --------------------------- - -A plugin to apply Hilbert filter (for phase gradient image) on projections. - - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.filters.image_interpolation.rst b/doc/source/plugin_documentation/plugins.filters.image_interpolation.rst deleted file mode 100644 index 285d39008..000000000 --- a/doc/source/plugin_documentation/plugins.filters.image_interpolation.rst +++ /dev/null @@ -1,43 +0,0 @@ -Image Interpolation -################################################################# - -Description --------------------------- - -A plugin to interpolate an image by a factor - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - size: - visibility: basic - dtype: ['int', 'float', 'tuple'] - description: int, float or tuple. - default: 2.0 - - interp: - visibility: basic - dtype: str - description: nearest lanczos bilinear bicubic cubic. - options: ['nearest', 'lanczos', 'bilinear', 'bicubic', 'cubic'] - default: bicubic - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.list_to_projections.rst b/doc/source/plugin_documentation/plugins.filters.list_to_projections.rst deleted file mode 100644 index 2ec75ed1e..000000000 --- a/doc/source/plugin_documentation/plugins.filters.list_to_projections.rst +++ /dev/null @@ -1,48 +0,0 @@ -List To Projections -################################################################# - -Description --------------------------- - -Converts a list of points into a 2D projection - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - step_size_x: - visibility: basic - dtype: int - description: step size in the interp, None if minimum chosen. - default: None - - step_size_y: - visibility: basic - dtype: int - description: step size in the interp, None if minimum chosen. - default: None - - fill_value: - visibility: basic - dtype: ['int', 'str', 'float'] - description: The value to fill with, takes an average if nothing else chosen. - default: mean - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.paganin_filter.rst b/doc/source/plugin_documentation/plugins.filters.paganin_filter.rst deleted file mode 100644 index 41f2759f9..000000000 --- a/doc/source/plugin_documentation/plugins.filters.paganin_filter.rst +++ /dev/null @@ -1,122 +0,0 @@ -Paganin Filter -################################################################# - -Description --------------------------- - -A plugin to apply Paganin filter (contrast enhancement) on projections. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - Energy: - visibility: basic - dtype: float - description: Given X-ray energy in keV. - default: 53.0 - - Distance: - visibility: basic - dtype: float - description: Distance from sample to detection - Unit is metre. - default: 1.0 - - Resolution: - visibility: intermediate - dtype: float - description: Pixel size - Unit is micron. - default: 1.28 - - Ratio: - visibility: intermediate - dtype: float - description: Ratio of delta/beta. - default: 250.0 - - Padtopbottom: - visibility: intermediate - dtype: float - description: Pad to the top and bottom of projection. - default: 10 - - Padleftright: - visibility: intermediate - dtype: float - description: Pad to the left and right of projection. - default: 10 - - Padmethod: - visibility: intermediate - dtype: str - description: Numpy pad method. - default: edge - - increment: - visibility: intermediate - dtype: float - description: Increment all values by this amount before taking the log. - default: 0.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object by Paganin, David et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{paganin2002simultaneous, - title={Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object}, - author={Paganin, David and Mayo, Sheridan C and Gureyev, Tim E and Miller, Peter R and Wilkins, Steve W}, - journal={Journal of microscopy}, - volume={206}, - number={1}, - pages={33--40}, - year={2002}, - publisher={Wiley Online Library} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object - %A Paganin, David - %A Mayo, Sheridan C - %A Gureyev, Tim E - %A Miller, Peter R - %A Wilkins, Steve W - %J Journal of microscopy - %V 206 - %N 1 - %P 33-40 - %@ 0022-2720 - %D 2002 - %I Wiley Online Library - - diff --git a/doc/source/plugin_documentation/plugins.filters.poly_background_estimator.rst b/doc/source/plugin_documentation/plugins.filters.poly_background_estimator.rst deleted file mode 100644 index 2744a7327..000000000 --- a/doc/source/plugin_documentation/plugins.filters.poly_background_estimator.rst +++ /dev/null @@ -1,54 +0,0 @@ -Poly Background Estimator -################################################################# - -Description --------------------------- - -This plugin uses peakutils to find peaks in spectra. This is then metadata. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s). - default: ['Peaks'] - - n: - visibility: basic - dtype: int - description: max number of polys. - default: 2 - - MaxIterations: - visibility: intermediate - dtype: int - description: max number of iterations. - default: 12 - - weights: - visibility: intermediate - dtype: ['int', 'str', 'float', 'list'] - description: weightings to apply. - default: 1/data - - pvalue: - visibility: intermediate - dtype: float - description: Ratio of variance between successive poly iterations. - default: 0.9 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.pymca.rst b/doc/source/plugin_documentation/plugins.filters.pymca.rst deleted file mode 100644 index ac426d185..000000000 --- a/doc/source/plugin_documentation/plugins.filters.pymca.rst +++ /dev/null @@ -1,36 +0,0 @@ -Pymca -################################################################# - -Description --------------------------- - -Uses pymca to fit spectral data - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - config: - visibility: intermediate - dtype: config_file - description: Path to the config file - default: Savu/test_data/data/test_config.cfg - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.quantisation_filter.rst b/doc/source/plugin_documentation/plugins.filters.quantisation_filter.rst deleted file mode 100644 index 6afe28c4e..000000000 --- a/doc/source/plugin_documentation/plugins.filters.quantisation_filter.rst +++ /dev/null @@ -1,54 +0,0 @@ -Quantisation Filter -################################################################# - -Description --------------------------- - -A plugin to quantise an image into discrete levels. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - explicit_min_max: - visibility: intermediate - dtype: bool - description: "False if min/max intensity comes from the metadata, True if it's user-defined. " - default: False - - min_intensity: - visibility: intermediate - dtype: int - description: Global minimum intensity. - default: 0 - - max_intensity: - visibility: intermediate - dtype: int - description: Global maximum intensity. - default: 65535 - - levels: - visibility: intermediate - dtype: int - description: Number of levels. - default: 5 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.spectrum_crop.rst b/doc/source/plugin_documentation/plugins.filters.spectrum_crop.rst deleted file mode 100644 index 99fa05b12..000000000 --- a/doc/source/plugin_documentation/plugins.filters.spectrum_crop.rst +++ /dev/null @@ -1,42 +0,0 @@ -Spectrum Crop -################################################################# - -Description --------------------------- - -Crops a spectrum to a range - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - crop_range: - visibility: intermediate - dtype: list - description: Range to crop to. - default: [2.0, 18.0] - - axis: - visibility: intermediate - dtype: str - description: Axis. - default: energy - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.strip_background.rst b/doc/source/plugin_documentation/plugins.filters.strip_background.rst deleted file mode 100644 index e3fa4d357..000000000 --- a/doc/source/plugin_documentation/plugins.filters.strip_background.rst +++ /dev/null @@ -1,61 +0,0 @@ -Strip Background -################################################################# - -Description --------------------------- - -1D background removal. PyMca magic function - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: A list of the dataset(s) to process. - default: ['in_datasets[0]', 'background'] - - iterations: - visibility: intermediate - dtype: int - description: Number of iterations. - default: 100 - - window: - visibility: intermediate - dtype: int - description: Half width of the rolling window. - default: 10 - - SG_filter_iterations: - visibility: intermediate - dtype: int - description: How many iterations until smoothing occurs. - default: 5 - - SG_width: - visibility: intermediate - dtype: int - description: Whats the savitzgy golay window. - default: 35 - - SG_polyorder: - visibility: intermediate - dtype: int - description: Whats the savitzgy-golay poly order. - default: 5 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.filters.threshold_filter.rst b/doc/source/plugin_documentation/plugins.filters.threshold_filter.rst deleted file mode 100644 index babde69b9..000000000 --- a/doc/source/plugin_documentation/plugins.filters.threshold_filter.rst +++ /dev/null @@ -1,43 +0,0 @@ -Threshold Filter -################################################################# - -Description --------------------------- - -A plugin to quantise an image into discrete levels. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - explicit_threshold: - visibility: basic - dtype: bool - description: "False if plugin calculates black/white threshold, True if it's user-defined." - default: True - - intensity_threshold: - visibility: basic - dtype: int - description: Threshold for black/white quantisation. - default: 32768 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.fitters.reproduce_fit.rst b/doc/source/plugin_documentation/plugins.fitters.reproduce_fit.rst deleted file mode 100644 index f925c57a6..000000000 --- a/doc/source/plugin_documentation/plugins.fitters.reproduce_fit.rst +++ /dev/null @@ -1,48 +0,0 @@ -Reproduce Fit -################################################################# - -Description --------------------------- - -This plugin reproduces the fitted curves. Its for diagnostics. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the input dataset(s) - default: ['FitWeights', 'FitWidths', 'FitAreas', 'Backgrounds'] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the output dataset(s) - default: ['Sum', 'Individual_curves'] - - width_guess: - visibility: intermediate - dtype: float - description: An initial guess at the width. - default: 0.02 - - peak_shape: - visibility: intermediate - dtype: str - description: Which shape do you want. - default: gaussian - - PeakIndex: - visibility: intermediate - dtype: list - description: The peak index. - default: [] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.fitters.simple_fit.rst b/doc/source/plugin_documentation/plugins.fitters.simple_fit.rst deleted file mode 100644 index c53bceffc..000000000 --- a/doc/source/plugin_documentation/plugins.fitters.simple_fit.rst +++ /dev/null @@ -1,48 +0,0 @@ -Simple Fit -################################################################# - -Description --------------------------- - -This plugin fits peaks. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) - default: ['FitWeights', 'FitWidths', 'FitAreas', 'residuals'] - - width_guess: - visibility: basic - dtype: float - description: An initial guess at the width. - default: 0.02 - - peak_shape: - visibility: intermediate - dtype: str - description: Which shape do you want. - default: gaussian - - PeakIndex: - visibility: basic - dtype: list - description: The peak index - default: [] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.fluo_fitters.fastxrf_fitting.rst b/doc/source/plugin_documentation/plugins.fluo_fitters.fastxrf_fitting.rst deleted file mode 100644 index e46c9cc99..000000000 --- a/doc/source/plugin_documentation/plugins.fluo_fitters.fastxrf_fitting.rst +++ /dev/null @@ -1,126 +0,0 @@ -Fastxrf Fitting -################################################################# - -Description --------------------------- - -Fast fluorescence fitting with FastXRF. Needs to be on the path. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: A - default: ['FitWeights', 'FitWidths', 'FitAreas', 'residuals'] - - width_guess: - visibility: intermediate - dtype: float - description: An initial guess at the width - default: 0.02 - - mono_energy: - visibility: intermediate - dtype: float - description: The mono energy - default: 18.0 - - peak_shape: - visibility: intermediate - dtype: str - description: "What shape do you want?" - default: gaussian - - pileup_cutoff_keV: - visibility: intermediate - dtype: float - description: The cut off - default: 5.5 - - include_pileup: - visibility: intermediate - dtype: str - description: Include pileup - default: 1 - - include_escape: - visibility: intermediate - dtype: int - description: Include escape - default: 1 - - fitted_energy_range_keV: - visibility: intermediate - dtype: list - description: The fitted energy range. - default: [2.0, 18.0] - - elements: - visibility: intermediate - dtype: list - description: The fitted elements, - default: ['Zn', 'Cu', 'Ar'] - - detector_type: - visibility: basic - dtype: str - description: The type of detector - default: Vortex_SDD_Xspress - - sample_attenuators: - visibility: intermediate - dtype: list - description: Attentuators used and thickness. - default: ['FitWeights', 'FitWidths', 'FitAreas', 'residuals'] - - detector_distance: - visibility: intermediate - dtype: int - description: sample to the detector in mm. - default: 70 - - exit_angle: - visibility: intermediate - dtype: float - description: In degrees - default: 90.0 - - incident_angle: - visibility: intermediate - dtype: float - description: In degrees - default: 0.0 - - flux: - visibility: intermediate - dtype: float - description: Flux in - default: 649055.0 - - background: - visibility: intermediate - dtype: str - description: Type of background subtraction. - default: strip - - average_spectrum: - visibility: intermediate - dtype: int - description: pass an average to do the strip. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.fluo_fitters.simple_fit_xrf.rst b/doc/source/plugin_documentation/plugins.fluo_fitters.simple_fit_xrf.rst deleted file mode 100644 index 8b7f577b9..000000000 --- a/doc/source/plugin_documentation/plugins.fluo_fitters.simple_fit_xrf.rst +++ /dev/null @@ -1,78 +0,0 @@ -Simple Fit Xrf -################################################################# - -Description --------------------------- - -This plugin fits XRF peaks. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: A - default: ['FitWeights', 'FitWidths', 'FitAreas', 'residuals'] - - width_guess: - visibility: intermediate - dtype: float - description: An initial guess at the width. - default: 0.02 - - mono_energy: - visibility: intermediate - dtype: float - description: The mono energy - default: 18.0 - - peak_shape: - visibility: intermediate - dtype: str - description: "What shape do you want?" - default: gaussian - - pileup_cutoff_keV: - visibility: intermediate - dtype: float - description: The cut off - default: 5.5 - - include_pileup: - visibility: intermediate - dtype: str - description: Include pileup - default: 1 - - include_escape: - visibility: intermediate - dtype: int - description: Include escape - default: 1 - - fitted_energy_range_keV: - visibility: intermediate - dtype: list - description: The fitted energy range. - default: [2.0, 18.0] - - elements: - visibility: intermediate - dtype: list - description: The fitted elements, - default: ['Zn', 'Cu', 'Ar'] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.kinematics.stage_motion.rst b/doc/source/plugin_documentation/plugins.kinematics.stage_motion.rst deleted file mode 100644 index 74edd6bd8..000000000 --- a/doc/source/plugin_documentation/plugins.kinematics.stage_motion.rst +++ /dev/null @@ -1,48 +0,0 @@ -Stage Motion -################################################################# - -Description --------------------------- - -A Plugin to calculate stage motion from motion positions. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) - default: ['pmean'] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) - default: ['qmean'] - - use_min_max: - visibility: intermediate - dtype: bool - description: Also use the min and max datasets including all combinations of min, mean and max. - default: False - - extra_in_datasets: - visibility: intermediate - dtype: list - description: The extra datasets to use as input for min and max. - default: ['pmin', 'pmax'] - - extra_out_datasets: - visibility: intermediate - dtype: list - description: The extra datasets to use as output for min and max. - default: ['qmin', 'qmax'] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.dxchange_loader.rst b/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.dxchange_loader.rst deleted file mode 100644 index 17d80e95e..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.dxchange_loader.rst +++ /dev/null @@ -1,96 +0,0 @@ -Dxchange Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from a hdf5 file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - name: - visibility: basic - dtype: str - description: A name assigned to the dataset. - default: tomo - - data_path: - visibility: basic - dtype: int_path - description: Path to the data. - default: exchange/data - - image_key_path: - visibility: advanced - dtype: int_path - description: Not required. - default: None - - dark: - visibility: intermediate - dtype: int_path_int - description: Dark data path and scale - default: "['exchange/data_dark', 1]" - - flat: - visibility: intermediate - dtype: int_path_int - description: Flat data path and scale value. - default: "['exchange/data_white', 1]" - - angles: - visibility: hidden - dtype: list - description: Angles list - default: "[1,2,3]" - - 3d_to_4d: - visibility: intermediate - dtype: bool - description: Many tomography datasets can be loaded. Value of True indicates the data must be reshaped. - default: False - - ignore_flats: - visibility: intermediate - dtype: list - description: List of batch numbers of flats to ignore (starting at 1). Useful for excluding comprimised flats in combined data sets containing multiple batches of interspaced flats. The batch indexing begins at 1. - default: None - - logfile: - visibility: intermediate - dtype: filepath - description: Path to the log file. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.image_loader.rst b/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.image_loader.rst deleted file mode 100644 index 9f4dfd878..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.image_loader.rst +++ /dev/null @@ -1,78 +0,0 @@ -Image Loader -################################################################# - -Description --------------------------- - -Load any FabIO compatible formats (e.g. tiffs) - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - dataset_name: - visibility: basic - dtype: str - description: The name assigned to the dataset. - default: tomo - - angles: - visibility: intermediate - dtype: str - description: A python statement to be evaluated (e.g np.linspace(0, 180, nAngles)) or a file. - default: None - - frame_dim: - visibility: intermediate - dtype: int - description: "Which dimension requires stitching?" - default: None - - data_prefix: - visibility: intermediate - dtype: str - description: A file prefix for the data file. - default: None - - dark_prefix: - visibility: intermediate - dtype: str - description: A file prefix for the dark field files, including the folder path if different from the data. - default: None - - flat_prefix: - visibility: intermediate - dtype: str - description: A file prefix for the flat field files, including the folder path if different from the data. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.mrc_loader.rst b/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.mrc_loader.rst deleted file mode 100644 index 695df819d..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.mrc_loader.rst +++ /dev/null @@ -1,54 +0,0 @@ -Mrc Loader -################################################################# - -Description --------------------------- - -Load Medical Research Council (MRC) formatted image data. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - angles: - visibility: basic - dtype: str - description: A python statement to be evaluated (e.g np.linspace(0, 180, nAngles)) or a file. - default: None - - name: - visibility: basic - dtype: str - description: The name assigned to the dataset - default: tomo - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.multi_nxtomo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.multi_nxtomo_loader.rst deleted file mode 100644 index d5d21cbef..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.multi_nxtomo_loader.rst +++ /dev/null @@ -1,84 +0,0 @@ -Multi Nxtomo Loader -################################################################# - -Description --------------------------- - -A class to load multiple scans in Nexus format into one dataset. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - name: - visibility: basic - dtype: str - description: The name assigned to the dataset. - default: tomo - - file_name: - visibility: intermediate - dtype: filename - description: The shared part of the name of each file (not including .nxs). - default: None - - data_path: - visibility: intermediate - dtype: int_path - description: Path to the data inside the file. - default: entry1/tomo_entry/data/data - - stack_or_cat: - visibility: intermediate - dtype: str - description: Stack or concatenate the data (4D and 3D respectively) - default: stack - - stack_or_cat_dim: - visibility: intermediate - dtype: int - description: Dimension to stack or concatenate. - default: 3 - - axis_label: - visibility: intermediate - dtype: str - description: "New axis label, if required, in the form 'name.units'" - default: scan.number - - range: - visibility: intermediate - dtype: range - description: The start and end of file numbers - default: [0, 10] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.nxtomo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.nxtomo_loader.rst deleted file mode 100644 index 60d2e2952..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.nxtomo_loader.rst +++ /dev/null @@ -1,90 +0,0 @@ -Nxtomo Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from a hdf5 file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - name: - visibility: basic - dtype: str - description: A name assigned to the dataset. - default: tomo - - data_path: - visibility: intermediate - dtype: str - description: Path to the data inside the file. - default: entry1/tomo_entry/data/data - - image_key_path: - visibility: intermediate - dtype: int_path - description: Path to the image key entry inside the nxs file. Set this parameter to None if use this loader for radiography. - default: entry1/tomo_entry/instrument/detector/image_key - - dark: - visibility: intermediate - dtype: file_int_path_int - description: Specify the nexus file location where the dark field images are stored. Then specify the path within this nexus file, at which the dark images are located. The last value will be a scale value. - default: "[None, None, 1]" - - flat: - visibility: intermediate - dtype: file_int_path_int - description: This parameter needs to be specified only if flats not stored in the same dataset as sample projections. Optional Path to the flat field data file, nxs path and scale value. - default: "[None, None, 1]" - - angles: - visibility: intermediate - dtype: list - description: If this if 4D data stored in 3D then pass an integer value equivalent to the number of projections per 180 degree scan. If the angles parameter is set to None, then values from default dataset used. - default: None - - 3d_to_4d: - visibility: intermediate - dtype: bool - description: Many tomography datasets can be loaded. Value of True indicates the data must be reshaped. - default: False - - ignore_flats: - visibility: intermediate - dtype: list - description: List of batch numbers of flats to ignore (starting at 1). Useful for excluding comprimised flats in combined data sets containing multiple batches of interspaced flats. The batch indexing begins at 1. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.random_3d_tomo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.random_3d_tomo_loader.rst deleted file mode 100644 index 5fb8a63ad..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.full_field_loaders.random_3d_tomo_loader.rst +++ /dev/null @@ -1,108 +0,0 @@ -Random 3D Tomo Loader -################################################################# - -Description --------------------------- - -A hdf5 dataset of a specified size is created at runtime using numpy -random sampling (numpy.random), saved with relevant meta_data to a NeXus -file, and used as input. It recreates the behaviour of the nxtomo loader -but with random data. The input file path passed to Savu will be ignored -(use a dummy). -Note: Further extensions planned to allow the generated data to be -re-loaded with the nxtomo_loader. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - size: - visibility: basic - dtype: list - description: A list specifiying the required data size. - default: [] - - axis_labels: - visibility: basic - dtype: list - description: A list of axis labels. - default: "['rotation_angle.degrees', 'detector_y.angles', 'detector_x.angles']" - - patterns: - visibility: hidden - dtype: list - description: Patterns. - default: "['SINOGRAM.0c.1s.2c', 'PROJECTION.0s.1c.2c']" - - file_name: - visibility: intermediate - dtype: filename - description: Assign a name to the created h5 file. - default: input_array - - dtype: - visibility: intermediate - dtype: nptype - description: A numpy array data type - default: int16 - - dataset_name: - visibility: hidden - dtype: str - description: The name assigned to the dataset. - default: tomo - - angles: - visibility: intermediate - dtype: str - description: "A python statement to be evaluated or a file - if the value is None, values will be in the interval [0, 180]" - default: None - - pattern: - visibility: intermediate - dtype: str - description: Pattern used to create and store the hdf5 dataset default is the first pattern in the pattern dictionary. - default: None - - range: - visibility: intermediate - dtype: range - description: Set the distribution interval. - default: [1, 10] - - image_key: - visibility: intermediate - dtype: list - description: Specify position of darks and flats (in that order) in the data. - default: [[0, 1], [2, 3]] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.hdf5_template_loader.rst b/doc/source/plugin_documentation/plugins.loaders.hdf5_template_loader.rst deleted file mode 100644 index e65c1ac93..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.hdf5_template_loader.rst +++ /dev/null @@ -1,55 +0,0 @@ -Hdf5 Template Loader -################################################################# - -Description --------------------------- - -A class to load data from a non-standard nexus/hdf5 file using -descriptions loaded from a yaml file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - yaml_file: - visibility: basic - dtype: filepath - description: Path to the file containing the data descriptions. - default: None - - template_param: - visibility: hidden - dtype: str - description: A hidden parameter to hold parameters passed in via a savu template file. - default: - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.image_template_loader.rst b/doc/source/plugin_documentation/plugins.loaders.image_template_loader.rst deleted file mode 100644 index 4d483c693..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.image_template_loader.rst +++ /dev/null @@ -1,55 +0,0 @@ -Image Template Loader -################################################################# - -Description --------------------------- - -A class to load data from a folder of FabIO compatible images using data -descriptions loaded from a yaml file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - yaml_file: - visibility: basic - dtype: filepath - description: Path to the file containing the data descriptions. - default: None - - template_param: - visibility: hidden - dtype: str - description: A hidden parameter to hold parameters passed in via a savu template file. - default: - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i08_loaders.i08_fluo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i08_loaders.i08_fluo_loader.rst deleted file mode 100644 index 59760b98e..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i08_loaders.i08_fluo_loader.rst +++ /dev/null @@ -1,48 +0,0 @@ -I08 Fluo Loader -################################################################# - -Description --------------------------- - -A class to load i08s xrf data - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - mono_path: - visibility: basic - dtype: int_path - description: The mono energy. - default: /entry/instrument/PlaneGratingMonochromator/pgm_energy - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_fluo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_fluo_loader.rst deleted file mode 100644 index 2a628efa2..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_fluo_loader.rst +++ /dev/null @@ -1,84 +0,0 @@ -I13 Fluo Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXstxm file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - fluo_offset: - visibility: basic - dtype: float - description: fluo scale offset. - default: 0.0 - - fluo_gain: - visibility: intermediate - dtype: float - description: fluo gain - default: 0.01 - - is_tomo: - visibility: intermediate - dtype: bool - description: Is tomo - default: True - - theta_step: - visibility: intermediate - dtype: float - description: The theta step. - default: 1.0 - - theta_start: - visibility: intermediate - dtype: float - description: The theta start. - default: -90.0 - - theta_end: - visibility: intermediate - dtype: float - description: The theta end. - default: 90.0 - - mono_energy: - visibility: intermediate - dtype: float - description: The mono energy. - default: 11.8 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_ptycho_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_ptycho_loader.rst deleted file mode 100644 index 1adf0b710..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_ptycho_loader.rst +++ /dev/null @@ -1,72 +0,0 @@ -I13 Ptycho Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXstxm file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - mono_energy: - visibility: basic - dtype: float - description: The mono energy. - default: 9.1 - - is_tomo: - visibility: intermediate - dtype: bool - description: Is tomo - default: True - - theta_step: - visibility: intermediate - dtype: float - description: The theta step. - default: 1.0 - - theta_start: - visibility: intermediate - dtype: float - description: The theta start. - default: -90.0 - - theta_end: - visibility: intermediate - dtype: float - description: The theta end. - default: 90.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_speckle_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_speckle_loader.rst deleted file mode 100644 index 65a6a1fc6..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_speckle_loader.rst +++ /dev/null @@ -1,66 +0,0 @@ -I13 Speckle Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXstxm file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - signal_key: - visibility: basic - dtype: float - description: Path to the signals - default: 9.1 - - reference_key: - visibility: intermediate - dtype: int_path - description: Path to the reference - default: /entry/reference - - angle_key: - visibility: intermediate - dtype: int_path - description: Path to the reference - default: /entry/theta - - dataset_names: - visibility: intermediate - dtype: list - description: The output sets. - default: ['signal', 'reference'] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_loader.rst deleted file mode 100644 index c72b6ca11..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_loader.rst +++ /dev/null @@ -1,8 +0,0 @@ -I13 Stxm Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from the txm - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_monitor_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_monitor_loader.rst deleted file mode 100644 index 35cbbb2e1..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_monitor_loader.rst +++ /dev/null @@ -1,9 +0,0 @@ -I13 Stxm Monitor Loader -################################################################# - -Description --------------------------- - - - A class to load tomography data from the txm - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_xrf_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_xrf_loader.rst deleted file mode 100644 index 167871b64..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i13_loaders.i13_stxm_xrf_loader.rst +++ /dev/null @@ -1,43 +0,0 @@ -I13 Stxm Xrf Loader -################################################################# - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - is_map: - visibility: basic - dtype: bool - description: Is it a map. - default: True - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i14_loaders.i14_fluo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i14_loaders.i14_fluo_loader.rst deleted file mode 100644 index 21e1b89ce..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i14_loaders.i14_fluo_loader.rst +++ /dev/null @@ -1,48 +0,0 @@ -I14 Fluo Loader -################################################################# - -Description --------------------------- - -A class to load i14s xrf data - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - mono_path: - visibility: basic - dtype: int_path - description: The mono energy. - default: /entry/instrument/beamline/DCM/dcm_energy - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_fluo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_fluo_loader.rst deleted file mode 100644 index 877386dfc..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_fluo_loader.rst +++ /dev/null @@ -1,90 +0,0 @@ -I18 Fluo Loader -################################################################# - -Description --------------------------- - -A class to load I18's data from an NXstxm file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - fast_axis: - visibility: basic - dtype: str - description: What is the fast axis called. - default: x - - scan_pattern: - visibility: intermediate - dtype: list - description: What was the scan. - default: ['rotation', 'x'] - - x: - visibility: intermediate - dtype: int_path - description: Where is x in the file. - default: entry1/raster_counterTimer01/traj1ContiniousX - - y: - visibility: intermediate - dtype: int_path - description: Where is y in the file - default: None - - rotation: - visibility: intermediate - dtype: int_path - description: Where is rotation in the file - default: entry1/raster_counterTimer01/sc_sample_thetafine - - monochromator: - visibility: intermediate - dtype: int_path - description: Where is the monochromator - default: entry1/instrument/DCM/energy - - fluo_detector: - visibility: basic - dtype: str - description: Path to fluo. - default: entry1/xspress3/AllElementSum - - name: - visibility: basic - dtype: str - description: The new name assigned to the dataset. - default: fluo - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_mm_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_mm_loader.rst deleted file mode 100644 index d8531c331..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_mm_loader.rst +++ /dev/null @@ -1,8 +0,0 @@ -I18 Mm Loader -################################################################# - -Description --------------------------- - -A class to load data - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_monitor_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_monitor_loader.rst deleted file mode 100644 index fa89a1815..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_monitor_loader.rst +++ /dev/null @@ -1,90 +0,0 @@ -I18 Monitor Loader -################################################################# - -Description --------------------------- - -A class to load I18's data from a monitor file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - fast_axis: - visibility: basic - dtype: str - description: What is the fast axis called. - default: x - - scan_pattern: - visibility: intermediate - dtype: list - description: What was the scan. - default: ['rotation', 'x'] - - x: - visibility: intermediate - dtype: int_path - description: Where is x in the file. - default: entry1/raster_counterTimer01/traj1ContiniousX - - y: - visibility: intermediate - dtype: int_path - description: Where is y in the file - default: None - - rotation: - visibility: intermediate - dtype: int_path - description: Where is rotation in the file - default: entry1/raster_counterTimer01/sc_sample_thetafine - - monochromator: - visibility: intermediate - dtype: int_path - description: Where is the monochromator - default: entry1/instrument/DCM/energy - - monitor_detector: - visibility: basic - dtype: str - description: Path to monitor. - default: entry1/raster_counterTimer01/I0 - - name: - visibility: basic - dtype: str - description: The new name assigned to the dataset. - default: monitor - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_stxm_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_stxm_loader.rst deleted file mode 100644 index d755eccbe..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_stxm_loader.rst +++ /dev/null @@ -1,90 +0,0 @@ -I18 Stxm Loader -################################################################# - -Description --------------------------- - -A class to load I18's data from a Nxstxm file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - fast_axis: - visibility: basic - dtype: str - description: What is the fast axis called. - default: x - - scan_pattern: - visibility: intermediate - dtype: list - description: What was the scan. - default: ['rotation', 'x'] - - x: - visibility: intermediate - dtype: int_path - description: Where is x in the file. - default: entry1/raster_counterTimer01/traj1ContiniousX - - y: - visibility: intermediate - dtype: int_path - description: Where is y in the file - default: None - - rotation: - visibility: intermediate - dtype: int_path - description: Where is rotation in the file - default: entry1/raster_counterTimer01/sc_sample_thetafine - - monochromator: - visibility: intermediate - dtype: int_path - description: Where is the monochromator - default: entry1/instrument/DCM/energy - - monitor_detector: - visibility: basic - dtype: str - description: Path to stxm. - default: entry1/raster_counterTimer01/It - - name: - visibility: basic - dtype: str - description: The new name assigned to the dataset. - default: stxm - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_xrd_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_xrd_loader.rst deleted file mode 100644 index f9a8fe758..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i18_loaders.i18_xrd_loader.rst +++ /dev/null @@ -1,96 +0,0 @@ -I18 Xrd Loader -################################################################# - -Description --------------------------- - -A class to load I18's data from an xrd file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - fast_axis: - visibility: basic - dtype: str - description: What is the fast axis called. - default: x - - scan_pattern: - visibility: intermediate - dtype: list - description: What was the scan. - default: ['rotation', 'x'] - - x: - visibility: intermediate - dtype: int_path - description: Where is x in the file. - default: entry1/raster_counterTimer01/traj1ContiniousX - - y: - visibility: intermediate - dtype: int_path - description: Where is y in the file - default: None - - rotation: - visibility: intermediate - dtype: int_path - description: Where is rotation in the file - default: entry1/raster_counterTimer01/sc_sample_thetafine - - monochromator: - visibility: intermediate - dtype: int_path - description: Where is the monochromator - default: entry1/instrument/DCM/energy - - monitor_detector: - visibility: basic - dtype: str - description: Path to the folder containing the data. - default: None - - calibration_path: - visibility: basic - dtype: int_path - description: path to the calibration file. - default: None - - name: - visibility: basic - dtype: str - description: The new name assigned to the dataset. - default: xrd - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i22_loaders.i22_tomo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i22_loaders.i22_tomo_loader.rst deleted file mode 100644 index 57fff3e55..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.i22_loaders.i22_tomo_loader.rst +++ /dev/null @@ -1,9 +0,0 @@ -I22 Tomo Loader -################################################################# - -Description --------------------------- - -A class to load tomography data for I22 that has been previously -processed using dawn - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.mm_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.mm_loader.rst deleted file mode 100644 index e16771d6f..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.mm_loader.rst +++ /dev/null @@ -1,8 +0,0 @@ -Mm Loader -################################################################# - -Description --------------------------- - -A class to load tomography data - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxfluo_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxfluo_loader.rst deleted file mode 100644 index 770cebc6b..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxfluo_loader.rst +++ /dev/null @@ -1,60 +0,0 @@ -Nxfluo Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXFluo file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - fluo_offset: - visibility: basic - dtype: float - description: fluo scale offset. - default: 0.0 - - fluo_gain: - visibility: intermediate - dtype: float - description: fluo gain - default: 0.01 - - name: - visibility: basic - dtype: str - description: The name assigned to the dataset. - default: fluo - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxmonitor_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxmonitor_loader.rst deleted file mode 100644 index be6d2b14d..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxmonitor_loader.rst +++ /dev/null @@ -1,48 +0,0 @@ -Nxmonitor Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXmonitor file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - name: - visibility: basic - dtype: str - description: The name assigned to the dataset. - default: monitor - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxptycho_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxptycho_loader.rst deleted file mode 100644 index ac3ad0d8e..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxptycho_loader.rst +++ /dev/null @@ -1,48 +0,0 @@ -Nxptycho Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXstxm file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - name: - visibility: basic - dtype: str - description: The name assigned to the dataset. - default: ptycho - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxstxm_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxstxm_loader.rst deleted file mode 100644 index f526e583c..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxstxm_loader.rst +++ /dev/null @@ -1,48 +0,0 @@ -Nxstxm Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXstxm file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - name: - visibility: basic - dtype: str - description: The name assigned to the dataset. - default: stxm - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxxrd_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxxrd_loader.rst deleted file mode 100644 index dffa03b68..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.nxxrd_loader.rst +++ /dev/null @@ -1,54 +0,0 @@ -Nxxrd Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from an NXxrd file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - name: - visibility: basic - dtype: str - description: The name assigned to the dataset. - default: xrd - - calibration_path: - visibility: basic - dtype: str - description: Path to the calibration file - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.p2r_fly_scan_detector_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.p2r_fly_scan_detector_loader.rst deleted file mode 100644 index 5a28224a3..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.p2r_fly_scan_detector_loader.rst +++ /dev/null @@ -1,84 +0,0 @@ -P2R Fly Scan Detector Loader -################################################################# - -Description --------------------------- - -A class to load p2r fly scan detector data from a Nexus file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - data_path: - visibility: intermediate - dtype: str - description: Path to the data inside the file - default: entry1/tomo_entry/data/data - - image_key_path: - visibility: intermediate - dtype: int_path - description: Path to the image key entry inside the nxs file. - default: entry1/tomo_entry/instrument/detector/image_key - - dark: - visibility: intermediate - dtype: file_int_path_int - description: Optional path to the dark field data file, nxs path and scale value. - default: "[None, None, 1]" - - flat: - visibility: intermediate - dtype: file_int_path_int - description: Optional path to the flat field data file, nxs path and scale value. - default: "[None, None, 1]" - - angles: - visibility: intermediate - dtype: str - description: A python statement to be evaluated or a file. - default: None - - 3d_to_4d: - visibility: intermediate - dtype: bool - description: Set to true if this reshape is required. - default: False - - ignore_flats: - visibility: intermediate - dtype: list - description: List of batch numbers of flats (start at 1) to ignore. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.txm_loader.rst b/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.txm_loader.rst deleted file mode 100644 index 081640241..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.mapping_loaders.txm_loader.rst +++ /dev/null @@ -1,8 +0,0 @@ -Txm Loader -################################################################# - -Description --------------------------- - -A class to load tomography data from the txm - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.loaders.random_hdf5_loader.rst b/doc/source/plugin_documentation/plugins.loaders.random_hdf5_loader.rst deleted file mode 100644 index a2d5964c0..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.random_hdf5_loader.rst +++ /dev/null @@ -1,99 +0,0 @@ -Random Hdf5 Loader -################################################################# - -Description --------------------------- - -A hdf5 dataset of a specified size is created at runtime using numpy -random sampling (numpy.random) and saved to file. This created dataset -will be used as the input file, and the input file path passed to Savu -will be ignored (use a dummy). - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - size: - visibility: basic - dtype: list - description: A list specifiying the required data size. - default: [] - - axis_labels: - visibility: basic - dtype: list - description: "A list of the axis labels to be associated with each dimension, of the form ['name1.unit1', 'name2.unit2',...]" - default: [] - - patterns: - visibility: intermediate - dtype: list - description: "A list of data access patterns e.g. [SINOGRAM.0c.1s.2c, PROJECTION.0s.1c.2s], where 'c' and 's' represent core and slice dimensions respectively and every dimension must be specified." - default: [] - - file_name: - visibility: intermediate - dtype: filename - description: Assign a name to the created h5 file. - default: input_array - - dtype: - visibility: intermediate - dtype: nptype - description: A numpy array data type - default: int16 - - dataset_name: - visibility: intermediate - dtype: str - description: The name assigned to the dataset - default: tomo - - angles: - visibility: intermediate - dtype: str - description: "A python statement to be evaluated or a file - if the value is None, values will be in the interval [0, 180]" - default: None - - pattern: - visibility: intermediate - dtype: str - description: Pattern used to create and store the hdf5 dataset default is the first pattern in the pattern dictionary. - default: None - - range: - visibility: intermediate - dtype: range - description: Set the distribution interval. - default: [1, 10] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.savu_nexus_loader.rst b/doc/source/plugin_documentation/plugins.loaders.savu_nexus_loader.rst deleted file mode 100644 index 02a163d81..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.savu_nexus_loader.rst +++ /dev/null @@ -1,60 +0,0 @@ -Savu Nexus Loader -################################################################# - -Description --------------------------- - -A class to load datasets, and associated metadata, from a Savu output -nexus file. - -By default, the last instance of each unique dataset name will be loaded. -Opt instead to load a subset of these datasets, or individual datasets by -populating the parameters. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: list - description: A slice list of required frames to apply to ALL datasets, else a dictionary of slice lists where the key is the dataset name. - default: - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - datasets: - visibility: basic - dtype: list - description: Override the default by choosing specific dataset(s) to load, by stating the NXdata name. - default: [] - - names: - visibility: basic - dtype: list - description: Override the dataset names associated with the datasets parameter above. - default: [] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.loaders.yaml_converter.rst b/doc/source/plugin_documentation/plugins.loaders.yaml_converter.rst deleted file mode 100644 index 968ad31e1..000000000 --- a/doc/source/plugin_documentation/plugins.loaders.yaml_converter.rst +++ /dev/null @@ -1,55 +0,0 @@ -Yaml Converter -################################################################# - -Description --------------------------- - -A class to load data from a non-standard nexus/hdf5 file using -descriptions loaded from a yaml file. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - preview: - visibility: basic - dtype: int_list - description: A slice list of required frames. - default: [] - - data_file: - visibility: hidden - dtype: str - description: hidden parameter for savu template - default: <> - - yaml_file: - visibility: basic - dtype: filepath - description: Path to the file containing the data descriptions. - default: None - - template_param: - visibility: hidden - dtype: str - description: A hidden parameter to hold parameters passed in via a savu template file. - default: - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.ptychography.dummy_ptycho.rst b/doc/source/plugin_documentation/plugins.ptychography.dummy_ptycho.rst deleted file mode 100644 index c476fe7f1..000000000 --- a/doc/source/plugin_documentation/plugins.ptychography.dummy_ptycho.rst +++ /dev/null @@ -1,8 +0,0 @@ -Dummy Ptycho -################################################################# - -Description --------------------------- - -This plugin performs ptychography using the ptypy package - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.reconstructions.astra_recons.astra_recon_cpu.rst b/doc/source/plugin_documentation/plugins.reconstructions.astra_recons.astra_recon_cpu.rst deleted file mode 100644 index 2364dbe3a..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.astra_recons.astra_recon_cpu.rst +++ /dev/null @@ -1,267 +0,0 @@ -Astra Recon Cpu -################################################################# - -Description --------------------------- - -A Plugin to run the astra reconstruction - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram to centre it in order to fill the reconstructed volume ROI for asthetic purposes. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - example: "Is it a scalar or a list?" - - outer_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - n_iterations: - visibility: basic - dtype: int - description: Number of Iterations is only valid for iterative algorithms - default: 1 - - algorithm: - visibility: basic - dtype: str - options: ['FBP', 'SIRT', 'SART', 'ART', 'CGLS', 'FP', 'BP'] - description: - summary: Reconstruction type - options: - FBP: Filtered Backprojection Method - SIRT: Simultaneous Iterative Reconstruction Technique - SART: Simultaneous Algebraic Reconstruction Technique - ART: Iterative Reconstruction Technique - CGLS: Conjugate Gradient Least Squares - FP: Forward Projection - BP: Back Projection - default: FBP - - FBP_filter: - visibility: basic - dtype: str - options: ['none', 'ram-lak', 'shepp-logan', 'cosine', 'hamming', 'hann', 'tukey', 'lanczos', 'triangular', 'gaussian', 'barlett-hann', 'blackman', 'nuttall', 'blackman-harris', 'blackman-nuttall', 'flat-top', 'kaiser', 'parzen'] - description: - summary: The FBP reconstruction filter type - options: - none: No filtering - ram-lak: Ram-Lak or ramp filter - shepp-logan: Multiplies the Ram-Lak filter by a sinc function - cosine: Multiplies the Ram-Lak filter by a cosine function - hamming: Multiplies the Ram-Lak filter by a hamming window - hann: Multiplies the Ram-Lak filter by a hann window - tukey: - lanczos: - triangular: - gaussian: - barlett-hann: - blackman: - nuttall: - blackman-harris: - blackman-nuttall: - flat-top: - kaiser: - parzen: - default: ram-lak - - projector: - visibility: advanced - dtype: str - options: ['line', 'strip', 'linear'] - description: - summary: Set astra projector - options: - line: The weight of a ray/pixel pair is given by the length of the intersection of the pixel and the ray, considered as a zero-thickness line. - strip: The weight of a ray/pixel pair is given by the area of the intersection of the pixel and the ray, considered as a strip with the same width as a detector pixel. - linear: Linear interpolation between the two nearest volume pixels of the intersection of the ray and the column/row. - default: line - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Fast and flexible X-ray tomography using the ASTRA toolbox by Van Aarle, Wim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{van2016fast, - title={Fast and flexible X-ray tomography using the ASTRA toolbox}, - author={Van Aarle, Wim and Palenstijn, Willem Jan and Cant, Jeroen and Janssens, Eline and Bleichrodt, Folkert and Dabravolski, Andrei and De Beenhouwer, Jan and Batenburg, K Joost and Sijbers, Jan}, - journal={Optics express}, - volume={24}, - number={22}, - pages={25129--25147}, - year={2016}, - publisher={Optical Society of America} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast and flexible X-ray tomography using the ASTRA toolbox - %A Van Aarle, Wim - %A Palenstijn, Willem Jan - %A Cant, Jeroen - %A Janssens, Eline - %A Bleichrodt, Folkert - %A Dabravolski, Andrei - %A De Beenhouwer, Jan - %A Batenburg, K Joost - %A Sijbers, Jan - %J Optics express - %V 24 - %N 22 - %P 25129-25147 - %@ 1094-4087 - %D 2016 - %I Optical Society of America - - -The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography by Van Aarle, Wim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{van2015astra, - title={The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography}, - author={Van Aarle, Wim and Palenstijn, Willem Jan and De Beenhouwer, Jan and Altantzis, Thomas and Bals, Sara and Batenburg, K Joost and Sijbers, Jan}, - journal={Ultramicroscopy}, - volume={157}, - pages={35--47}, - year={2015}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography - %A Van Aarle, Wim - %A Palenstijn, Willem Jan - %A De Beenhouwer, Jan - %A Altantzis, Thomas - %A Bals, Sara - %A Batenburg, K Joost - %A Sijbers, Jan - %J Ultramicroscopy - %V 157 - %P 35-47 - %@ 0304-3991 - %D 2015 - %I Elsevier - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.astra_recons.astra_recon_gpu.rst b/doc/source/plugin_documentation/plugins.reconstructions.astra_recons.astra_recon_gpu.rst deleted file mode 100644 index 8dee7e3b9..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.astra_recons.astra_recon_gpu.rst +++ /dev/null @@ -1,305 +0,0 @@ -Astra Recon Gpu -################################################################# - -Description --------------------------- - -A Plugin to run the astra reconstruction - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram to centre it in order to fill the reconstructed volume ROI for asthetic purposes. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - example: "Is it a scalar or a list?" - - outer_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - n_iterations: - visibility: basic - dtype: int - description: Number of Iterations is only valid for iterative algorithms - default: 1 - - res_norm: - visibility: basic - dtype: int - description: Output the residual norm at each iteration (Error in the solution - iterative solvers only) - default: False - dependency: - algorithm: - SIRT_CUDA - SART_CUDA - CGLS_CUDA - - algorithm: - visibility: basic - dtype: str - options: ['FBP_CUDA', 'SIRT_CUDA', 'SART_CUDA', 'CGLS_CUDA', 'FP_CUDA', 'BP_CUDA', 'SIRT3D_CUDA', 'CGLS3D_CUDA'] - description: - summary: Reconstruction type - options: - FBP_CUDA: Filtered Backprojection Method - SIRT_CUDA: Simultaneous Iterative Reconstruction Technique - SART_CUDA: Simultaneous Algebraic Reconstruction Technique - CGLS_CUDA: Conjugate Gradient Least Squares - FP_CUDA: Forward Projection - BP_CUDA: Backward Projection - SIRT3D_CUDA: Simultaneous Iterative Reconstruction Technique 3D - CGLS3D_CUDA: Conjugate Gradient Least Squares 3D - default: FBP_CUDA - - FBP_filter: - visibility: basic - dtype: str - options: ['none', 'ram-lak', 'shepp-logan', 'cosine', 'hamming', 'hann', 'tukey', 'lanczos', 'triangular', 'gaussian', 'barlett-hann', 'blackman', 'nuttall', 'blackman-harris', 'blackman-nuttall', 'flat-top', 'kaiser', 'parzen'] - description: - summary: The FBP reconstruction filter type - options: - none: No filtering - ram-lak: Ram-Lak or ramp filter - shepp-logan: Multiplies the Ram-Lak filter by a sinc function - cosine: Multiplies the Ram-Lak filter by a cosine function - hamming: Multiplies the Ram-Lak filter by a hamming window - hann: Multiplies the Ram-Lak filter by a hann window - tukey: - lanczos: - triangular: - gaussian: - barlett-hann: - blackman: - nuttall: - blackman-harris: - blackman-nuttall: - flat-top: - kaiser: - parzen: - default: ram-lak - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Fast and flexible X-ray tomography using the ASTRA toolbox by Van Aarle, Wim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{van2016fast, - title={Fast and flexible X-ray tomography using the ASTRA toolbox}, - author={Van Aarle, Wim and Palenstijn, Willem Jan and Cant, Jeroen and Janssens, Eline and Bleichrodt, Folkert and Dabravolski, Andrei and De Beenhouwer, Jan and Batenburg, K Joost and Sijbers, Jan}, - journal={Optics express}, - volume={24}, - number={22}, - pages={25129--25147}, - year={2016}, - publisher={Optical Society of America} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast and flexible X-ray tomography using the ASTRA toolbox - %A Van Aarle, Wim - %A Palenstijn, Willem Jan - %A Cant, Jeroen - %A Janssens, Eline - %A Bleichrodt, Folkert - %A Dabravolski, Andrei - %A De Beenhouwer, Jan - %A Batenburg, K Joost - %A Sijbers, Jan - %J Optics express - %V 24 - %N 22 - %P 25129-25147 - %@ 1094-4087 - %D 2016 - %I Optical Society of America - - -The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography by Van Aarle, Wim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{van2015astra, - title={The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography}, - author={Van Aarle, Wim and Palenstijn, Willem Jan and De Beenhouwer, Jan and Altantzis, Thomas and Bals, Sara and Batenburg, K Joost and Sijbers, Jan}, - journal={Ultramicroscopy}, - volume={157}, - pages={35--47}, - year={2015}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography - %A Van Aarle, Wim - %A Palenstijn, Willem Jan - %A De Beenhouwer, Jan - %A Altantzis, Thomas - %A Bals, Sara - %A Batenburg, K Joost - %A Sijbers, Jan - %J Ultramicroscopy - %V 157 - %P 35-47 - %@ 0304-3991 - %D 2015 - %I Elsevier - - -Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs) by Palenstijn, WJ et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{palenstijn2011performance, - title={Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)}, - author={Palenstijn, WJ and Batenburg, KJ and Sijbers, J}, - journal={Journal of structural biology}, - volume={176}, - number={2}, - pages={250--253}, - year={2011}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs) - %A Palenstijn, WJ - %A Batenburg, KJ - %A Sijbers, J - %J Journal of structural biology - %V 176 - %N 2 - %P 250-253 - %@ 1047-8477 - %D 2011 - %I Elsevier - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.ccpi_cgls_recon.rst b/doc/source/plugin_documentation/plugins.reconstructions.ccpi_cgls_recon.rst deleted file mode 100644 index c367007ca..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.ccpi_cgls_recon.rst +++ /dev/null @@ -1,126 +0,0 @@ -Ccpi Cgls Recon -################################################################# - -Description --------------------------- - -A Plugin to run the CCPi implementation of the CGLS reconstruction -algorithm. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Not an option. - default: None - - centre_pad: - visibility: hidden - dtype: int - description: Not an option. - default: False - - outer_pad: - visibility: advanced - dtype: str - description: Not an option. - default: False - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - n_iterations: - visibility: basic - dtype: tuple - description: Number of rows and columns in the reconstruction. - default: 5 - - resolution: - visibility: basic - dtype: str - description: Number of output voxels (res = n_pixels/n_voxels), set res > 1 for reduced resolution. - default: 1 - - n_frames: - visibility: basic - dtype: int - description: This algorithm requires a multiple of 8 frames for processing and this number may affect performance depending on your data size (choose from 8, 16, 24, 32) - options: [8, 16, 24, 32] - default: 16 - - enforce_position: - visibility: advanced - dtype: int - description: Not an option. - default: False - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.reconstructions.scikitimage_filter_back_projection.rst b/doc/source/plugin_documentation/plugins.reconstructions.scikitimage_filter_back_projection.rst deleted file mode 100644 index 891166053..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.scikitimage_filter_back_projection.rst +++ /dev/null @@ -1,170 +0,0 @@ -Scikitimage Filter Back Projection -################################################################# - -Description --------------------------- - -A Plugin to reconstruct an image by filter back projection using the -inverse radon transform from scikit-image. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: hidden - dtype: int - description: Not required. - default: False - - outer_pad: - visibility: hidden - dtype: str - description: Not required. - default: False - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - output_size: - visibility: basic - dtype: tuple - description: Number of rows and columns in the reconstruction. - default: auto - - filter: - visibility: intermediate - dtype: str - description: Filter used in frequency domain filtering. Ramp filter used by default. Assign None to use no filter. - options: ['ramp', 'shepp-logan', 'cosine', 'hamming', 'hann', 'None'] - default: ramp - - interpolation: - visibility: advanced - dtype: int - description: "Interpolation method used in reconstruction. Methods available: 'linear', 'nearest', and 'cubic' ('cubic' is slow)." - options: ['linear', 'nearest', 'cubic'] - default: linear - - circle: - visibility: advanced - dtype: bool - description: Assume the reconstructed image is zero outside the inscribed circle. Also changes the default output_size to match the behaviour of radon called with circle=True. - default: False - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Principles Of Ct Imaging by Kak, Avinash C et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kak2002principles, - title={Principles of computerized tomographic imaging}, - author={Kak, Avinash C and Slaney, Malcolm and Wang, Ge}, - journal={Medical Physics}, - volume={29}, - number={1}, - pages={107--107}, - year={2002}, - publisher={Wiley Online Library} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Principles of computerized tomographic imaging - %A Kak, Avinash C - %A Slaney, Malcolm - %A Wang, Ge - %J Medical Physics - %V 29 - %N 1 - %P 107-107 - %@ 0094-2405 - %D 2002 - %I Wiley Online Library - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.scikitimage_sart.rst b/doc/source/plugin_documentation/plugins.reconstructions.scikitimage_sart.rst deleted file mode 100644 index 00ddcb86a..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.scikitimage_sart.rst +++ /dev/null @@ -1,200 +0,0 @@ -Scikitimage Sart -################################################################# - -Description --------------------------- - -A Plugin to reconstruct an image by filter back projection using the -inverse radon transform from scikit-image. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: hidden - dtype: int - description: Not required. - default: False - - outer_pad: - visibility: hidden - dtype: int - description: Not required. - default: False - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - iterations: - visibility: basic - dtype: int - description: Number of iterations in the reconstruction. - default: 1 - - output_size: - visibility: basic - dtype: tuple - description: Number of rows and columns in the reconstruction. - default: None - - filter: - visibility: intermediate - dtype: str - description: Filter used in frequency domain filtering. Ramp filter used by default. Assign None to use no filter. - options: ['ramp', 'shepp-logan', 'cosine', 'hamming', 'hann', 'None'] - default: ramp - - interpolation: - visibility: advanced - dtype: int - description: "Interpolation method used in reconstruction. Methods available: 'linear', 'nearest', and 'cubic' ('cubic' is slow)." - options: ['linear', 'nearest', 'cubic'] - default: linear - - circle: - visibility: advanced - dtype: bool - description: Assume the reconstructed image is zero outside the inscribed circle. Also changes the default output_size to match the behaviour of radon called with circle=True. - default: False - - image: - visibility: advanced - dtype: list - description: "2D array, dtype=float, optional. Image containing an initial reconstruction estimate. Shape of this array should be (radon_image.shape[0], radon_image.shape[0]). The default is a filter backprojection using scikit.image.iradon as 'result'." - default: None - - projection_shifts: - visibility: advanced - dtype: list - description: "1D array dtype = float Shift the projections contained in radon_image (the sinogram) by this many pixels before reconstructing the image. The i'th value defines the shift of the i'th column of radon_image." - default: None - - clip: - visibility: advanced - dtype: list - description: "length-2 sequence of floats. Force all values in the reconstructed tomogram to lie in the range [clip[0], clip[1]]." - default: None - - relaxation: - visibility: advanced - dtype: float - description: Float. Relaxation parameter for the update step. A higher value can improve the convergence rate, but one runs the risk of instabilities. Values close to or higher than 1 are not recommended. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Principles of computerized tomographic imaging by Kak, Avinash C et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kak2002principles, - title={Principles of computerized tomographic imaging}, - author={Kak, Avinash C and Slaney, Malcolm and Wang, Ge}, - journal={Medical Physics}, - volume={29}, - number={1}, - pages={107--107}, - year={2002}, - publisher={Wiley Online Library} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Principles of computerized tomographic imaging - %A Kak, Avinash C - %A Slaney, Malcolm - %A Wang, Ge - %J Medical Physics - %V 29 - %N 1 - %P 107-107 - %@ 0094-2405 - %D 2002 - %I Wiley Online Library - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.simple_recon.rst b/doc/source/plugin_documentation/plugins.reconstructions.simple_recon.rst deleted file mode 100644 index 17536bb23..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.simple_recon.rst +++ /dev/null @@ -1,48 +0,0 @@ -Simple Recon -################################################################# - -Description --------------------------- - -A Plugin to apply a simple reconstruction with no dependancies - -Citations --------------------------- - -Principles of computerized tomographic imaging by Kak, Avinash C et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kak2002principles, - title={Principles of computerized tomographic imaging}, - author={Kak, Avinash C and Slaney, Malcolm and Wang, Ge}, - journal={Medical Physics}, - volume={29}, - number={1}, - pages={107--107}, - year={2002}, - publisher={Wiley Online Library}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Principles of computerized tomographic imaging - %A Kak, Avinash C - %A Slaney, Malcolm - %A Wang, Ge - %J Medical Physics - %V 29 - %N 1 - %P 107-107 - %@ 0094-2405 - %D 2002 - %I Wiley Online Library - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon.rst b/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon.rst deleted file mode 100644 index 6fd91ca50..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon.rst +++ /dev/null @@ -1,696 +0,0 @@ -Tomobar Recon -################################################################# - -Description --------------------------- - -A plugin to reconstruct full-field tomographic projection data using -state-of-the-art regularised iterative algorithms from the ToMoBAR package. -ToMoBAR includes FISTA and ADMM iterative methods and depends on the ASTRA -toolbox and the CCPi RGL toolkit - -.. toctree:: - Plugin documention and guidelines on use - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram to centre it in order to fill the reconstructed volume ROI for asthetic purposes. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - example: "Is it a scalar or a list?" - - outer_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - data_fidelity: - visibility: advanced - dtype: str - description: Least Squares only at the moment. - default: LS - - data_Huber_thresh: - visibility: advanced - dtype: int - description: - summary: Threshold parameter for __Huber__ data fidelity. - verbose: Parameter which controls the level of suppression of outliers in the data - default: None - - data_any_rings: - visibility: hidden - dtype: int - description: a parameter to suppress various artifacts including rings and streaks - default: None - - data_any_rings_winsizes: - visibility: hidden - dtype: tuple - description: "half window sizes to collect background information [detector, angles, num of projections]" - default: (9,7,9) - dependency: data_any_rings - - data_any_rings_power: - visibility: hidden - dtype: float - description: a power parameter for Huber model. - default: 1.5 - dependency: data_any_rings - - data_full_ring_GH: - visibility: advanced - dtype: float - description: - summary: Regularisation variable of Group-Huber method to suppress constant intensity stripes in the data to minimise ring artefacts. - verbose: Group-Huber ring removal method by Paleo and Mirone - default: None - - data_full_ring_accelerator_GH: - visibility: advanced - dtype: float - description: - summary: Acceleration constant for Group-Huber ring removal method - verbose: A large value can lead to divergence of the method - default: 10.0 - dependency: data_full_ring_GH - - algorithm_iterations: - visibility: basic - dtype: int - description: - summary: Number of outer iterations for FISTA (default) or ADMM methods. - verbose: Less than 10 iterations for the ordered-subsets iterative method (FISTA) can deliver a blurry reconstruction. The suggested value is 15 iterations, however the algorithm can stop prematurely based on the tolerance value. - default: 20 - - algorithm_verbose: - visibility: advanced - dtype: bool - description: Print iterations number and other messages (off by default). - default: off - - algorithm_ordersubsets: - visibility: advanced - dtype: int - description: - summary: The number of ordered-subsets to accelerate image reconstruction algorithm. - verbose: Ordered subsets number is the number of smaller sets of projection data - default: 6 - - algorithm_nonnegativity: - visibility: advanced - dtype: str - options: ['ENABLE', 'DISABLE'] - description: - summary: ENABLE or DISABLE nonnegativity constraint for reconstructed image. - options: - ENABLE: This enables nonnegativity constraint (meaning no negative values in the reconstruction) - DISABLE: Reconstructed image can include negative values - default: ENABLE - - regularisation_method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'PD_TV', 'SB_TV', 'LLT_ROF', 'NDF', 'TGV', 'NLTV', 'Diff4th', 'None'] - description: - summary: The regularisation (denoising) method to stabilise the iterative method - verbose: The regularised iterative methods can help to reduce noise and artefacts in undersampled and noisy data conditions - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model (piecewise-constant recovery) - FGP_TV: Fast Gradient Projection Total Variation model - PD_TV: Primal-Dual Total Variation - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - regularisation_parameter: - visibility: basic - dtype: ['float', 'int'] - description: - summary: Regularisation parameter could control the level of smoothing or denoising. - verbose: Higher regularisation values lead to stronger smoothing effect. If the value is too high, you will obtain a very blurry reconstructed image. - range: Recommended between 0.0001 and 0.1 - example: A good value to start with is {default}, {range} - default: 0.0001 - dependency: - regularisation_method: not None - - regularisation_iterations: - visibility: basic - dtype: int - description: - summary: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - range: The recommended value with the chosen regularisation_method would be 500 - default: - regularisation_method: - ROF_TV: 1000 - FGP_TV: 500 - PD_TV: 100 - SB_TV: 100 - LLT_ROF: 1000 - NDF: 1000 - Diff4th: 1000 - TGV: 80 - NLTV: 80 - dependency: - regularisation_method: not None - - regularisation_device: - visibility: advanced - dtype: str - description: The device for regularisation - default: gpu - dependency: - regularisation_method: not None - - regularisation_PD_lip: - visibility: advanced - dtype: int - description: Primal-dual TV method convergence parameter. - default: 8 - dependency: - regularisation_method: PD_TV - - regularisation_methodTV: - visibility: advanced - dtype: str - description: 0/1 - TV specific isotropic/anisotropic choice. - default: 0 - dependency: - regularisation_method: - ROF_TV - FGP_TV - PD_TV - SB_TV - NLTV - - regularisation_timestep: - visibility: advanced - dtype: float - description: - summary: Time marching parameter for convergence of explicit schemes - verbose: the time step constant defines the speed of convergence, the larger values can lead to divergence - range: Recommended between 0.0001 and 0.003 - default: 0.003 - dependency: - regularisation_method: - ROF_TV - LLT_ROF - NDF - Diff4th - - regularisation_edge_thresh: - visibility: advanced - dtype: float - description: - summary: Edge (noise) related threshold for diffusion methods - default: 0.01 - dependency: - regularisation_method: - NDF - Diff4th - - regularisation_parameter2: - visibility: advanced - dtype: float - description: - summary: Regularisation (smoothing) value for LLT_ROF method - verbose: The higher the value stronger the smoothing effect - default: 0.005 - dependency: - regularisation_method: LLT_ROF - - regularisation_NDF_penalty: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey'] - description: - summary: Penalty dtype - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey Biweight - dependency: - regularisation_method: NDF - default: Huber - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -A fast iterative shrinkage-thresholding algorithm for linear inverse problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={A fast iterative shrinkage-thresholding algorithm for linear inverse problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={1}, - pages={183--202}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T A fast iterative shrinkage-thresholding algorithm for linear inverse problems - %A Beck, Amir - %A Teboulle, Marc - %J SIAM journal on imaging sciences - %V 2 - %N 1 - %P 183-202 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D: nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D: nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_3D.rst b/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_3D.rst deleted file mode 100644 index 5de856894..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_3D.rst +++ /dev/null @@ -1,670 +0,0 @@ -Tomobar Recon 3D -################################################################# - -Description --------------------------- - -A Plugin to reconstruct full-field tomographic projection data using -state-of-the-art regularised iterative algorithms from the ToMoBAR package. -ToMoBAR includes FISTA and ADMM iterative methods and depends on the ASTRA -toolbox and the CCPi RGL toolkit: https://github.com/vais-ral/CCPi-Regularisation-Toolkit. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram to centre it in order to fill the reconstructed volume ROI for asthetic purposes. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - example: "Is it a scalar or a list?" - - outer_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - output_size: - visibility: advanced - dtype: tuple - description: The dimension of the reconstructed volume (only X-Y dimension). - default: auto - - param_padding: - visibility: advanced - dtype: int - description: The amount of pixels to pad each slab of the cropped projection data. - default: 17 - - data_fidelity: - visibility: advanced - dtype: str - description: Least Squares only at the moment. - default: LS - - data_Huber_thresh: - visibility: advanced - dtype: int - description: Threshold parameter for __Huber__ data fidelity. - default: None - - data_any_rings: - visibility: hidden - dtype: int - description: A parameter to suppress various artifacts including rings and streaks - default: None - - data_any_rings_winsizes: - visibility: hidden - dtype: tuple - description: "half window sizes to collect background information [detector, angles, num of projections]" - default: (9,7,9) - - data_any_rings_power: - visibility: hidden - dtype: float - description: A power parameter for Huber model. - default: 1.5 - - data_full_ring_GH: - visibility: advanced - dtype: str - description: Regularisation variable for full constant ring removal (GH model). - default: None - - data_full_ring_accelerator_GH: - visibility: advanced - dtype: float - description: Acceleration constant for GH ring removal. (use with care) - default: 10.0 - - algorithm_iterations: - visibility: basic - dtype: int - description: - summary: Number of outer iterations for FISTA (default)or ADMM methods. - verbose: Less than 10 iterations for the iterative method (FISTA) can deliver a blurry reconstruction. The suggested value is 15 iterations, however the algorithm can stop prematurely based on the tolerance value. - default: 20 - - algorithm_verbose: - visibility: advanced - dtype: bool - description: Print iterations number and other messages (off by default). - default: off - - algorithm_ordersubsets: - visibility: advanced - dtype: int - description: The number of ordered-subsets to accelerate reconstruction. - default: 6 - - algorithm_nonnegativity: - visibility: advanced - dtype: str - options: ['ENABLE', 'DISABLE'] - description: - summary: ENABLE or DISABLE nonnegativity constraint. - default: ENABLE - - regularisation_method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'PD_TV', 'SB_TV', 'LLT_ROF', 'NDF', 'TGV', 'NLTV', 'Diff4th'] - description: - summary: The denoising method - verbose: Iterative methods can help to solve ill-posed inverse problems by choosing a suitable noise model for the measurement - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model - FGP_TV: Fast Gradient Projection Total Variation model - PD_TV: Primal-Dual Total Variation - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - regularisation_parameter: - visibility: basic - dtype: float - description: - summary: Regularisation parameter. The higher the value, the stronger the smoothing effect - range: Recommended between 0 and 1 - default: 0.0001 - - regularisation_iterations: - visibility: basic - dtype: int - description: - summary: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - default: 80 - - regularisation_device: - visibility: advanced - dtype: str - description: The device for regularisation - default: gpu - - regularisation_PD_lip: - visibility: advanced - dtype: int - description: Primal-dual parameter for convergence. - default: 8 - dependency: - regularisation_method: PD_TV - - regularisation_methodTV: - visibility: advanced - dtype: str - description: 0/1 - TV specific isotropic/anisotropic choice. - default: 0 - dependency: - regularisation_method: - ROF_TV - FGP_TV - SB_TV - NLTV - - regularisation_timestep: - visibility: advanced - dtype: float - dependency: - regularisation_method: - ROF_TV - LLT_ROF - NDF - Diff4th - description: - summary: Time marching parameter - range: Recommended between 0.0001 and 0.003 - default: 0.003 - - regularisation_edge_thresh: - visibility: advanced - dtype: float - dependency: - regularisation_method: - NDF - Diff4th - description: - summary: Edge (noise) related parameter - default: 0.01 - - regularisation_parameter2: - visibility: advanced - dtype: float - dependency: - regularisation_method: LLT_ROF - description: - summary: Regularisation (smoothing) value - verbose: The higher the value stronger the smoothing effect - default: 0.005 - - regularisation_NDF_penalty: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey'] - description: - summary: Penalty dtype - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey - dependency: - regularisation_method: NDF - default: Huber - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -A fast iterative shrinkage-thresholding algorithm for linear inverse problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={A fast iterative shrinkage-thresholding algorithm for linear inverse problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={1}, - pages={183--202}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T A fast iterative shrinkage-thresholding algorithm for linear inverse problems - %A Beck, Amir - %A Teboulle, Marc - %J SIAM journal on imaging sciences - %V 2 - %N 1 - %P 183-202 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D: nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D: nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_cpu.rst b/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_cpu.rst deleted file mode 100644 index 9288ab72d..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_cpu.rst +++ /dev/null @@ -1,665 +0,0 @@ -Tomobar Recon Cpu -################################################################# - -Description --------------------------- - -A Plugin to reconstruct full-field tomographic projection data using -state-of-the-art regularised iterative algorithms from the ToMoBAR package. -ToMoBAR includes FISTA and ADMM iterative methods and depends on the ASTRA -toolbox and the CCPi RGL toolkit: -https://github.com/vais-ral/CCPi-Regularisation-Toolkit. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram to centre it in order to fill the reconstructed volume ROI for asthetic purposes. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - example: "Is it a scalar or a list?" - - outer_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - output_size: - visibility: advanced - dtype: tuple - description: The dimension of the reconstructed volume (only X-Y dimension). - default: auto - - data_fidelity: - visibility: advanced - dtype: str - description: Least Squares only at the moment. - default: LS - - data_Huber_thresh: - visibility: advanced - dtype: int - description: Threshold parameter for __Huber__ data fidelity. - default: None - - data_any_rings: - visibility: hidden - dtype: int - description: a parameter to suppress various artifacts including rings and streaks - default: None - - data_any_rings_winsizes: - visibility: hidden - dtype: tuple - description: "half window sizes to collect background information [detector, angles, num of projections]" - default: (9,7,9) - - data_any_rings_power: - visibility: hidden - dtype: float - description: a power parameter for Huber model. - default: 1.5 - - data_full_ring_GH: - visibility: advanced - dtype: str - description: Regularisation variable for full constant ring removal (GH model). - default: None - - data_full_ring_accelerator_GH: - visibility: advanced - dtype: float - description: Acceleration constant for GH ring removal. (use with care) - default: 10.0 - - algorithm_iterations: - visibility: basic - dtype: int - description: - summary: Number of outer iterations for FISTA (default)or ADMM methods. - verbose: Less than 10 iterations for the iterative method (FISTA) can deliver a blurry reconstruction. The suggested value is 15 iterations, however the algorithm can stop prematurely based on the tolerance value. - default: 20 - - algorithm_verbose: - visibility: advanced - dtype: bool - description: Print iterations number and other messages (off by default). - default: off - - algorithm_ordersubsets: - visibility: advanced - dtype: int - description: The number of ordered-subsets to accelerate reconstruction. - default: 6 - - algorithm_nonnegativity: - visibility: advanced - dtype: str - options: ['ENABLE', 'DISABLE'] - description: - summary: ENABLE or DISABLE nonnegativity constraint. - default: ENABLE - - regularisation_method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'PD_TV', 'SB_TV', 'LLT_ROF', 'NDF', 'TGV', 'NLTV', 'Diff4th'] - description: - summary: The denoising method - verbose: Iterative methods can help to solve ill-posed inverse problems by choosing a suitable noise model for the measurement - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model - FGP_TV: Fast Gradient Projection Total Variation model - PD_TV: Primal-Dual Total Variation - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - regularisation_parameter: - visibility: basic - dtype: float - description: - summary: Regularisation parameter. The higher the value, the stronger the smoothing effect - range: Recommended between 0 and 1 - default: 0.0001 - - regularisation_iterations: - visibility: basic - dtype: int - description: - summary: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - default: 80 - - regularisation_device: - visibility: advanced - dtype: str - description: The device for regularisation - default: cpu - - regularisation_PD_lip: - visibility: advanced - dtype: int - description: Primal-dual parameter for convergence. - default: 8 - dependency: - regularisation_method: PD_TV - - regularisation_methodTV: - visibility: advanced - dtype: str - description: 0/1 - TV specific isotropic/anisotropic choice. - default: 0 - dependency: - regularisation_method: - ROF_TV - FGP_TV - SB_TV - NLTV - - regularisation_timestep: - visibility: advanced - dtype: float - dependency: - regularisation_method: - ROF_TV - LLT_ROF - NDF - Diff4th - description: - summary: Time marching parameter - range: Recommended between 0.0001 and 0.003 - default: 0.003 - - regularisation_edge_thresh: - visibility: advanced - dtype: float - dependency: - regularisation_method: - NDF - Diff4th - description: - summary: Edge (noise) related parameter - default: 0.01 - - regularisation_parameter2: - visibility: advanced - dtype: float - dependency: - regularisation_method: LLT_ROF - description: - summary: Regularisation (smoothing) value - verbose: The higher the value stronger the smoothing effect - default: 0.005 - - regularisation_NDF_penalty: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey'] - description: - summary: Penalty dtype - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey - dependency: - regularisation_method: NDF - default: Huber - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -A fast iterative shrinkage-thresholding algorithm for linear inverse problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={A fast iterative shrinkage-thresholding algorithm for linear inverse problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={1}, - pages={183--202}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T A fast iterative shrinkage-thresholding algorithm for linear inverse problems - %A Beck, Amir - %A Teboulle, Marc - %J SIAM journal on imaging sciences - %V 2 - %N 1 - %P 183-202 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D: nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D: nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_fully_3D.rst b/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_fully_3D.rst deleted file mode 100644 index 31380fa07..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.tomobar.tomobar_recon_fully_3D.rst +++ /dev/null @@ -1,664 +0,0 @@ -Tomobar Recon Fully 3D -################################################################# - -Description --------------------------- - -A Plugin to reconstruct full-field tomographic projection data -using state-of-the-art regularised iterative algorithms from -the ToMoBAR package. ToMoBAR includes FISTA and ADMM iterative -methods and depends on the ASTRA toolbox and the CCPi RGL toolkit: -https://github.com/vais-ral/CCPi-Regularisation-Toolkit. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram to centre it in order to fill the reconstructed volume ROI for asthetic purposes. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - example: "Is it a scalar or a list?" - - outer_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - output_size: - visibility: advanced - dtype: tuple - description: The dimension of the reconstructed volume (only X-Y dimension). - default: auto - - data_fidelity: - visibility: advanced - dtype: str - description: Least Squares only at the moment. - default: LS - - data_Huber_thresh: - visibility: advanced - dtype: int - description: Threshold parameter for __Huber__ data fidelity. - default: None - - data_any_rings: - visibility: hidden - dtype: int - description: A parameter to suppress various artifacts including rings and streaks - default: None - - data_any_rings_winsizes: - visibility: hidden - dtype: tuple - description: "Half window sizes to collect background information [detector, angles, num of projections]" - default: (9,7,9) - - data_any_rings_power: - visibility: hidden - dtype: float - description: A power parameter for Huber model. - default: 1.5 - - data_full_ring_GH: - visibility: advanced - dtype: str - description: Regularisation variable for full constant ring removal (GH model). - default: None - - data_full_ring_accelerator_GH: - visibility: advanced - dtype: float - description: Acceleration constant for GH ring removal. (use with care) - default: 10.0 - - algorithm_iterations: - visibility: basic - dtype: int - description: - summary: Number of outer iterations for FISTA (default)or ADMM methods. - verbose: Less than 10 iterations for the iterative method (FISTA) can deliver a blurry reconstruction. The suggested value is 15 iterations, however the algorithm can stop prematurely based on the tolerance value. - default: 20 - - algorithm_verbose: - visibility: advanced - dtype: bool - description: Print iterations number and other messages (off by default). - default: off - - algorithm_ordersubsets: - visibility: advanced - dtype: int - description: The number of ordered-subsets to accelerate reconstruction. - default: 6 - - algorithm_nonnegativity: - visibility: advanced - dtype: str - options: ['ENABLE', 'DISABLE'] - description: - summary: ENABLE or DISABLE nonnegativity constraint. - default: ENABLE - - regularisation_method: - visibility: advanced - dtype: str - options: ['ROF_TV', 'FGP_TV', 'PD_TV', 'SB_TV', 'LLT_ROF', 'NDF', 'TGV', 'NLTV', 'Diff4th'] - description: - summary: The denoising method - verbose: Iterative methods can help to solve ill-posed inverse problems by choosing a suitable noise model for the measurement - options: - ROF_TV: Rudin-Osher-Fatemi Total Variation model - FGP_TV: Fast Gradient Projection Total Variation model - PD_TV: Primal-Dual Total Variation - SB_TV: Split Bregman Total Variation model - LLT_ROF: Lysaker, Lundervold and Tai model combined with Rudin-Osher-Fatemi - NDF: Nonlinear/Linear Diffusion model (Perona-Malik, Huber or Tukey) - TGV: Total Generalised Variation - NLTV: Non Local Total Variation - Diff4th: Fourth-order nonlinear diffusion model - default: FGP_TV - - regularisation_parameter: - visibility: basic - dtype: float - description: - summary: Regularisation parameter. The higher the value, the stronger the smoothing effect - range: Recommended between 0 and 1 - default: 0.0001 - - regularisation_iterations: - visibility: basic - dtype: int - description: Total number of regularisation iterations. The smaller the number of iterations, the smaller the effect of the filtering is. A larger number will affect the speed of the algorithm. - default: 80 - - regularisation_device: - visibility: advanced - dtype: str - description: The device for regularisation - default: gpu - - regularisation_PD_lip: - visibility: advanced - dtype: int - description: Primal-dual parameter for convergence. - default: 8 - dependency: - regularisation_method: PD_TV - - regularisation_methodTV: - visibility: advanced - dtype: str - description: 0/1 - TV specific isotropic/anisotropic choice. - default: 0 - dependency: - regularisation_method: - ROF_TV - FGP_TV - SB_TV - NLTV - - regularisation_timestep: - visibility: advanced - dtype: float - dependency: - regularisation_method: - ROF_TV - LLT_ROF - NDF - Diff4th - description: - summary: Time marching parameter - range: Recommended between 0.0001 and 0.003 - default: 0.003 - - regularisation_edge_thresh: - visibility: advanced - dtype: float - dependency: - regularisation_method: - NDF - Diff4th - description: - summary: Edge (noise) related parameter - default: 0.01 - - regularisation_parameter2: - visibility: advanced - dtype: float - dependency: - regularisation_method: LLT_ROF - description: - summary: Regularisation (smoothing) value - verbose: The higher the value stronger the smoothing effect - default: 0.005 - - regularisation_NDF_penalty: - visibility: advanced - dtype: str - options: ['Huber', 'Perona', 'Tukey'] - description: - summary: Penalty dtype - verbose: Nonlinear/Linear Diffusion model (NDF) specific penalty type. - options: - Huber: Huber - Perona: Perona-Malik model - Tukey: Tukey - dependency: - regularisation_method: NDF - default: Huber - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -A fast iterative shrinkage-thresholding algorithm for linear inverse problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={A fast iterative shrinkage-thresholding algorithm for linear inverse problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={1}, - pages={183--202}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T A fast iterative shrinkage-thresholding algorithm for linear inverse problems - %A Beck, Amir - %A Teboulle, Marc - %J SIAM journal on imaging sciences - %V 2 - %N 1 - %P 183-202 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Nonlinear total variation based noise removal algorithms by Rudin, Leonid I et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the ROF_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{rudin1992nonlinear, - title={Nonlinear total variation based noise removal algorithms}, - author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad}, - journal={Physica D: nonlinear phenomena}, - volume={60}, - number={1-4}, - pages={259--268}, - year={1992}, - publisher={North-Holland} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlinear total variation based noise removal algorithms - %A Rudin, Leonid I - %A Osher, Stanley - %A Fatemi, Emad - %J Physica D: nonlinear phenomena - %V 60 - %N 1-4 - %P 259-268 - %@ 0167-2789 - %D 1992 - %I North-Holland - - -Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems by Beck, Amir et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the FGP_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{beck2009fast, - title={Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems}, - author={Beck, Amir and Teboulle, Marc}, - journal={IEEE transactions on image processing}, - volume={18}, - number={11}, - pages={2419--2434}, - year={2009}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Fast gradient-based algorithms for constrained total variation image denoising and deblurring problems - %A Beck, Amir - %A Teboulle, Marc - %J IEEE transactions on image processing - %V 18 - %N 11 - %P 2419-2434 - %@ 1057-7149 - %D 2009 - %I IEEE - - -The split Bregman method for L1-regularized problems by Goldstein, Tom et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the SB_TV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{goldstein2009split, - title={The split Bregman method for L1-regularized problems}, - author={Goldstein, Tom and Osher, Stanley}, - journal={SIAM journal on imaging sciences}, - volume={2}, - number={2}, - pages={323--343}, - year={2009}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The split Bregman method for L1-regularized problems - %A Goldstein, Tom - %A Osher, Stanley - %J SIAM journal on imaging sciences - %V 2 - %N 2 - %P 323-343 - %@ 1936-4954 - %D 2009 - %I SIAM - - -Total generalized variation by Bredies, Kristian et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the TGV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{bredies2010total, - title={Total generalized variation}, - author={Bredies, Kristian and Kunisch, Karl and Pock, Thomas}, - journal={SIAM Journal on Imaging Sciences}, - volume={3}, - number={3}, - pages={492--526}, - year={2010}, - publisher={SIAM} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Total generalized variation - %A Bredies, Kristian - %A Kunisch, Karl - %A Pock, Thomas - %J SIAM Journal on Imaging Sciences - %V 3 - %N 3 - %P 492-526 - %@ 1936-4954 - %D 2010 - %I SIAM - - -Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the LLT_ROF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2017model, - title={Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data}, - author={Kazantsev, Daniil and Guo, Enyu and Phillion, AB and Withers, Philip J and Lee, Peter D}, - journal={Measurement Science and Technology}, - volume={28}, - number={9}, - pages={094004}, - year={2017}, - publisher={IOP Publishing} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Model-based iterative reconstruction using higher-order regularization of dynamic synchrotron data - %A Kazantsev, Daniil - %A Guo, Enyu - %A Phillion, AB - %A Withers, Philip J - %A Lee, Peter D - %J Measurement Science and Technology - %V 28 - %N 9 - %P 094004 - %@ 0957-0233 - %D 2017 - %I IOP Publishing - - -Scale-space and edge detection using anisotropic diffusion by Perona, Pietro et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NDF regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{perona1990scale, - title={Scale-space and edge detection using anisotropic diffusion}, - author={Perona, Pietro and Malik, Jitendra}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={12}, - number={7}, - pages={629--639}, - year={1990}, - publisher={IEEE}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Scale-space and edge detection using anisotropic diffusion - %A Perona, Pietro - %A Malik, Jitendra - %J IEEE Transactions on pattern analysis and machine intelligence - %V 12 - %N 7 - %P 629-639 - %@ 0162-8828 - %D 1990 - %I IEEE - - -An anisotropic fourth-order diffusion filter for image noise removal by Hajiaboli, Mohammad Reza et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the Diff4th regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{hajiaboli2011anisotropic, - title={An anisotropic fourth-order diffusion filter for image noise removal}, - author={Hajiaboli, Mohammad Reza}, - journal={International Journal of Computer Vision}, - volume={92}, - number={2}, - pages={177--191}, - year={2011}, - publisher={Springer} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An anisotropic fourth-order diffusion filter for image noise removal - %A Hajiaboli, Mohammad Reza - %J International Journal of Computer Vision - %V 92 - %N 2 - %P 177-191 - %@ 0920-5691 - %D 2011 - %I Springer - - -Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing by Elmoataz, Abderrahim et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -(Please use this citation if you are using the NLTV regularisation_method) - -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{elmoataz2008nonlocal, - title={Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing}, - author={Elmoataz, Abderrahim and Lezoray, Olivier and Bougleux, S{'e}bastien}, - journal={IEEE transactions on Image Processing}, - volume={17}, - number={7}, - pages={1047--1060}, - year={2008}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Nonlocal discrete regularization on weighted graphs, a framework for image and manifold processing - %A Elmoataz, Abderrahim - %A Lezoray, Olivier - %A Bougleux, Sebastien - %J IEEE transactions on Image Processing - %V 17 - %N 7 - %P 1047-1060 - %@ 1057-7149 - %D 2008 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.tomopy_recon.rst b/doc/source/plugin_documentation/plugins.reconstructions.tomopy_recon.rst deleted file mode 100644 index 375674388..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.tomopy_recon.rst +++ /dev/null @@ -1,177 +0,0 @@ -Tomopy Recon -################################################################# - -Description --------------------------- - -A wrapper to the tomopy reconstruction library. Extra keywords not -required for the chosen algorithm will be ignored. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: hidden - dtype: int - description: Not an option. - default: None - - centre_pad: - visibility: hidden - dtype: int - description: Not an option. - default: None - - outer_pad: - visibility: intermediate - dtype: float - description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1. - default: False - dependency: - algorithm: - FP_CUDA - FBP_CUDA - BP_CUDA - FP - FBP - BP - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - algorithm: - visibility: intermediate - dtype: tuple - description: The reconstruction algorithm (art|bart|fbp|gridrec| mlem|osem|ospml_hybrid|ospml_quad|pml_hybrid|pml_quad|sirt). - default: gridrec - - filter_name: - visibility: intermediate - dtype: str - description: Valid for fbp|gridrec, options - none|shepp|cosine| hann|hamming|ramlak|parzen|butterworth). - default: ramlak - options: ['none', 'shepp', 'cosine', 'hann', 'hamming', 'ramlak', 'parzen', 'butterworth'] - - reg_par: - visibility: intermediate - dtype: float - description: Regularization parameter for smoothing, valid for ospml_hybrid|ospml_quad|pml_hybrid|pml_quad. - default: 0.0 - - n_iterations: - visibility: intermediate - dtype: int - description: Number of iterations - only valid for iterative algorithms. - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -TomoPy: a framework for the analysis of synchrotron tomographic data by Gu'ü'rsoy, Doga et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{gursoy2014tomopy, - title={TomoPy: a framework for the analysis of synchrotron tomographic data}, - author={G{"u}rsoy, Doga and De Carlo, Francesco and Xiao, Xianghui and Jacobsen, Chris}, - journal={Journal of synchrotron radiation}, - volume={21}, - number={5}, - pages={1188--1193}, - year={2014}, - publisher={International Union of Crystallography} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T TomoPy: a framework for the analysis of synchrotron tomographic data - %A Gu'ü'rsoy, Doga - %A De Carlo, Francesco - %A Xiao, Xianghui - %A Jacobsen, Chris - %J Journal of synchrotron radiation - %V 21 - %N 5 - %P 1188-1193 - %@ 1600-5775 - %D 2014 - %I International Union of Crystallography - - diff --git a/doc/source/plugin_documentation/plugins.reconstructions.visual_hulls_recon.rst b/doc/source/plugin_documentation/plugins.reconstructions.visual_hulls_recon.rst deleted file mode 100644 index d7cd4f8b0..000000000 --- a/doc/source/plugin_documentation/plugins.reconstructions.visual_hulls_recon.rst +++ /dev/null @@ -1,148 +0,0 @@ -Visual Hulls Recon -################################################################# - -Description --------------------------- - -A Plugin to reconstruct an image by filter back projection -using the inverse radon transform from scikit-image. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - centre_of_rotation: - visibility: basic - dtype: ['float', 'int'] - description: Centre of rotation to use for the reconstruction. - default: 0.0 - example: It could be scalar or list of centre of rotation - - init_vol: - visibility: advanced - dtype: str - description: Dataset to use as volume initialiser (does not currently work with preview) - default: None - example: "Type the name of the initialised dataset e.g. ['tomo']" - - centre_pad: - visibility: hidden - dtype: int - description: Not required. - default: False - - outer_pad: - visibility: hidden - dtype: str - description: Not required. - default: False - - log: - visibility: advanced - dtype: bool - description: - summary: Take the log of the data before reconstruction (true or false). - verbose: Should be set to false if PaganinFilter is set beforehand - default: True - example: Set to True to take the log of the data before reconstruction - - preview: - visibility: advanced - dtype: list - description: A slice list of required frames. - default: "[]" - example: "[angle, detectorZ, detectorY], where detectorZ is the vertical coordinate, detectorY is the horizontal coordinate." - - force_zero: - visibility: intermediate - dtype: range - description: Set any values in the reconstructed image outside of this range to zero. - default: "[None, None]" - example: "[0,1]" - - ratio: - visibility: intermediate - dtype: float - description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. - default: 0.95 - example: "Is this a proper name for this parameter? Would mask_diameter or mask_circle be more accurate?" - - log_func: - visibility: advanced - dtype: str - description: Override the default log function - default: np.nan_to_num(-np.log(sino)) - example: You write a function as default - - vol_shape: - visibility: basic - dtype: ['str', 'int'] - description: - summary: Override the size of the reconstuction volume with an integer value. - verbose: When fixed, you get the dimension of the horizontal detector Or you can specify any reconstruction size you like with an integer. - default: fixed - - threshold: - visibility: advanced - dtype: float - description: Threshold to binarize the input sinogram. - default: 0.5 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -The visual hull concept for silhouette-based image understanding by Laurentini, Aldo et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{laurentini1994visual, - title={The visual hull concept for silhouette-based image understanding}, - author={Laurentini, Aldo}, - journal={IEEE Transactions on pattern analysis and machine intelligence}, - volume={16}, - number={2}, - pages={150--162}, - year={1994}, - publisher={IEEE} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T The visual hull concept for silhouette-based image understanding - %A Laurentini, Aldo - %J IEEE Transactions on pattern analysis and machine intelligence - %V 16 - %N 2 - %P 150-162 - %@ 0162-8828 - %D 1994 - %I IEEE - - diff --git a/doc/source/plugin_documentation/plugins.reshape.data_removal.rst b/doc/source/plugin_documentation/plugins.reshape.data_removal.rst deleted file mode 100644 index 815962cdf..000000000 --- a/doc/source/plugin_documentation/plugins.reshape.data_removal.rst +++ /dev/null @@ -1,48 +0,0 @@ -Data Removal -################################################################# - -Description --------------------------- - -A class to remove any unwanted data from the specified pattern frame. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - indices: - visibility: intermediate - dtype: list - description: "A list or range of values to remove, e.g. [0, 1, 2] , 0:2 (start:stop) or 0:2:1 (start:stop:step)." - default: None - - pattern: - visibility: intermediate - dtype: int - description: Explicitly state the slicing pattern. - default: SINOGRAM - - dim: - visibility: intermediate - dtype: int - description: Data dimension to reduce. - default: 0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.reshape.downsample_filter.rst b/doc/source/plugin_documentation/plugins.reshape.downsample_filter.rst deleted file mode 100644 index a30477301..000000000 --- a/doc/source/plugin_documentation/plugins.reshape.downsample_filter.rst +++ /dev/null @@ -1,48 +0,0 @@ -Downsample Filter -################################################################# - -Description --------------------------- - -A plugin to reduce the data in the selected dimension by a proportion. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - bin_size: - visibility: basic - dtype: list - description: Bin Size for the downsample. - default: 2 - - mode: - visibility: basic - dtype: int - description: "One of 'mean', 'median', 'min', 'max'." - default: mean - - pattern: - visibility: basic - dtype: int - description: "One of 'PROJECTION' or 'SINOGRAM'." - default: PROJECTION - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.reshape.mipmap.rst b/doc/source/plugin_documentation/plugins.reshape.mipmap.rst deleted file mode 100644 index 7ce9ea2fb..000000000 --- a/doc/source/plugin_documentation/plugins.reshape.mipmap.rst +++ /dev/null @@ -1,51 +0,0 @@ -Mipmap -################################################################# - -Description --------------------------- - -A plugin to downsample multidimensional data successively by powers of 2. -The output is multiple 'mipmapped' datasets, each a power of 2 smaller in -each dimension than the previous dataset. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Hidden out_datasets list as this is created dynamically. - default: [] - - mode: - visibility: basic - dtype: str - description: One of mean, median, min, max. - default: mean - options: ['mean', 'median', 'min', 'max'] - - n_mipmaps: - visibility: basic - dtype: int - description: The number of successive downsamples of powers of 2 (e.g. n_mipmaps=3 implies downsamples (of the original data) of binsize 1, 2 and 4 in each dimension). - default: 3 - - out_dataset_prefix: - visibility: intermediate - dtype: str - description: The name of the dataset, to which the binsize will be appended for each instance. - default: Mipmap - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.ring_removal.ccpi_ring_artefact_filter.rst b/doc/source/plugin_documentation/plugins.ring_removal.ccpi_ring_artefact_filter.rst deleted file mode 100644 index ee51206d1..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.ccpi_ring_artefact_filter.rst +++ /dev/null @@ -1,91 +0,0 @@ -Ccpi Ring Artefact Filter -################################################################# - -Description --------------------------- - -This plugin applies the same ring removal method as the DLS -tomo_recon reconstruction software. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - param_r: - visibility: basic - dtype: float - description: The correction strength - decrease (typically in order of magnitude steps) to increase ring supression, or increase to reduce ring supression. - default: 0.005 - - param_n: - visibility: intermediate - dtype: int - description: Unknown description (for plate-like objects only). - default: 0 - - num_series: - visibility: basic - dtype: int - description: High aspect ration compensation (for plate-like objects only) - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Regularization methods for inverse problems in x-ray tomography by Titarenko, Valeriy et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @inproceedings{ - titarenko2010regularization, - title={Regularization methods for inverse problems in x-ray tomography}, - author={Titarenko, Valeriy and Bradley, Robert and Martin, Christopher and Withers, Philip J and Titarenko, Sofya}, - booktitle={Developments in X-Ray Tomography VII}, - volume={7804}, - pages={78040Z}, - year={2010}, - organization={International Society for Optics and Photonics} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Conference Proceedings - %T Regularization methods for inverse problems in x-ray tomography - %A Titarenko, Valeriy - %A Bradley, Robert - %A Martin, Christopher - %A Withers, Philip J - %A Titarenko, Sofya - %B Developments in X-Ray Tomography VII - %V 7804 - %P 78040Z - %D 2010 - %I International Society for Optics and Photonics - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.raven_filter.rst b/doc/source/plugin_documentation/plugins.ring_removal.raven_filter.rst deleted file mode 100644 index 2c2d7a055..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.raven_filter.rst +++ /dev/null @@ -1,94 +0,0 @@ -Raven Filter -################################################################# - -Description --------------------------- - -Ring artefact removal method - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - uvalue: - visibility: basic - dtype: int - description: To define the shape of filter, e.g. bad=10, moderate=20, minor=50. - default: 20 - - vvalue: - visibility: intermediate - dtype: int - description: How many rows to be applied the filter. - default: 2 - - nvalue: - visibility: intermediate - dtype: int - description: To define the shape of filter - default: 4 - - padFT: - visibility: intermediate - dtype: int - description: Padding for Fourier transform. - default: 20 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Numerical removal of ring artifacts in microtomography by Raven, Carsten et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{raven1998numerical, - title={Numerical removal of ring artifacts in microtomography}, - author={Raven, Carsten}, - journal={Review of scientific instruments}, - volume={69}, - number={8}, - pages={2978--2980}, - year={1998}, - publisher={American Institute of Physics} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Numerical removal of ring artifacts in microtomography - %A Raven, Carsten - %J Review of scientific instruments - %V 69 - %N 8 - %P 2978-2980 - %@ 0034-6748 - %D 1998 - %I American Institute of Physics - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.remove_all_rings.rst b/doc/source/plugin_documentation/plugins.ring_removal.remove_all_rings.rst deleted file mode 100644 index 4fb94f505..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.remove_all_rings.rst +++ /dev/null @@ -1,90 +0,0 @@ -Remove All Rings -################################################################# - -Description --------------------------- - -Method to remove all types of stripe artifacts in a sinogram (<-> -ring artefacts in a reconstructed image). - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - la_size: - visibility: intermediate - dtype: int - description: Size of the median filter window to remove large stripes. - default: 71 - - sm_size: - visibility: intermediate - dtype: int - description: Size of the median filter window to remove small-to-medium stripes. - default: 31 - - snr: - visibility: intermediate - dtype: float - description: Ratio used to detect locations of stripes. Greater is less sensitive. - default: 3.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Superior techniques for eliminating ring artifacts in X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2018superior, - title = {Superior techniques for eliminating ring artifacts in X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={26}, - number={22}, - pages={28396--28412}, - year={2018}, - publisher={Optical Society of America}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Superior techniques for eliminating ring artifacts in X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 26 - %N 22 - %P 28396-28412 - %@ 1094-4087 - %D 2018 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.remove_large_rings.rst b/doc/source/plugin_documentation/plugins.ring_removal.remove_large_rings.rst deleted file mode 100644 index 4767d1249..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.remove_large_rings.rst +++ /dev/null @@ -1,84 +0,0 @@ -Remove Large Rings -################################################################# - -Description --------------------------- - -Method to remove large stripe artefacts in a sinogram (<-> ring -artefacts in a reconstructed image). - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - size: - visibility: intermediate - dtype: int - description: Size of the median filter window. Greater is stronger - default: 71 - - snr: - visibility: intermediate - dtype: int - description: Ratio used to detect locations of large stripes. Greater is less sensitive. - default: 3.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Superior techniques for eliminating ring artifacts in X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2018superior, - title = {Superior techniques for eliminating ring artifacts in X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={26}, - number={22}, - pages={28396--28412}, - year={2018}, - publisher={Optical Society of America}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Superior techniques for eliminating ring artifacts in X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 26 - %N 22 - %P 28396-28412 - %@ 1094-4087 - %D 2018 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.remove_unresponsive_and_fluctuating_rings.rst b/doc/source/plugin_documentation/plugins.ring_removal.remove_unresponsive_and_fluctuating_rings.rst deleted file mode 100644 index 8e5d87f16..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.remove_unresponsive_and_fluctuating_rings.rst +++ /dev/null @@ -1,84 +0,0 @@ -Remove Unresponsive And Fluctuating Rings -################################################################# - -Description --------------------------- - -Method to remove large stripe artefacts in a sinogram (<-> ring -artefacts in a reconstructed image). - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - size: - visibility: intermediate - dtype: int - description: Size of the median filter window. Greater is stronger - default: 71 - - snr: - visibility: intermediate - dtype: int - description: Ratio used to detect locations of large stripes. Greater is less sensitive. - default: 3.0 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Superior techniques for eliminating ring artifacts in X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2018superior, - title = {Superior techniques for eliminating ring artifacts in X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={26}, - number={22}, - pages={28396--28412}, - year={2018}, - publisher={Optical Society of America}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Superior techniques for eliminating ring artifacts in X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 26 - %N 22 - %P 28396-28412 - %@ 1094-4087 - %D 2018 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_filtering.rst b/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_filtering.rst deleted file mode 100644 index b238b553a..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_filtering.rst +++ /dev/null @@ -1,87 +0,0 @@ -Ring Removal Filtering -################################################################# - -Description --------------------------- - -Method to remove stripe artefacts in a sinogram (<-> ring -artefacts in a reconstructed image) using a filtering-based -method in the combination with a sorting-based method. -Note that it's different to a FFT-based or wavelet-FFT-based -method. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - sigma: - visibility: intermediate - dtype: int - description: Sigma of the Gaussian window. Used to separate the low-pass and high-pass components of each sinogram column. - default: 3 - - size: - visibility: intermediate - dtype: int - description: Size of the median filter window. Used to clean stripes. - default: 31 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Superior techniques for eliminating ring artifacts in X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2018superior, - title = {Superior techniques for eliminating ring artifacts in X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={26}, - number={22}, - pages={28396--28412}, - year={2018}, - publisher={Optical Society of America}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Superior techniques for eliminating ring artifacts in X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 26 - %N 22 - %P 28396-28412 - %@ 1094-4087 - %D 2018 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_fitting.rst b/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_fitting.rst deleted file mode 100644 index f6eb990c7..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_fitting.rst +++ /dev/null @@ -1,92 +0,0 @@ -Ring Removal Fitting -################################################################# - -Description --------------------------- - -Method to remove stripe artefacts in a sinogram (<-> ring -artefacts in a reconstructed image) using a fitting-based method. -It's suitable for use on low-contrast sinogram and/or for removing -blurry rings. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - sigmax: - visibility: intermediate - dtype: int - description: Sigma of the Gaussian window in x-direction which controls the strength of the removal. - default: 5 - - sigmay: - visibility: intermediate - dtype: int - description: Sigma of the Gaussian window in y-direction - default: 20 - - order: - visibility: intermediate - dtype: int - description: polynomial fit order. - default: 2 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Superior techniques for eliminating ring artifacts in X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2018superior, - title = {Superior techniques for eliminating ring artifacts in X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={26}, - number={22}, - pages={28396--28412}, - year={2018}, - publisher={Optical Society of America}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Superior techniques for eliminating ring artifacts in X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 26 - %N 22 - %P 28396-28412 - %@ 1094-4087 - %D 2018 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_normalization.rst b/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_normalization.rst deleted file mode 100644 index d2db5b270..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_normalization.rst +++ /dev/null @@ -1,45 +0,0 @@ -Ring Removal Normalization -################################################################# - -Description --------------------------- - -Method to remove stripe artefacts in a sinogram (<-> ring artefacts in a -reconstructed image) using a normalization-based method. A simple -improvement to handle partial stripes is included. - - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - radius: - visibility: intermediate - dtype: int - description: Radius of the Gaussian kernel. - default: 11 - - number_of_chunks: - visibility: intermediate - dtype: int - description: Divide the sinogram to many chunks of rows - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_regularization.rst b/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_regularization.rst deleted file mode 100644 index 3b454cad7..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_regularization.rst +++ /dev/null @@ -1,86 +0,0 @@ -Ring Removal Regularization -################################################################# - -Description --------------------------- - -Method to remove stripe artefacts in a sinogram (<-> ring -artefacts in a reconstructed image) using a regularization-based -method. A simple improvement to handle partial stripes is included. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - alpha: - visibility: intermediate - dtype: float - description: The correction strength. Smaller is stronger. - default: 0.005 - - number_of_chunks: - visibility: intermediate - dtype: int - description: Divide the sinogram to many chunks of rows. - default: 1 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -An analytical formula for ring artefact suppression in X-ray tomography by Titarenko, Sofya et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{titarenko2010analytical, - title={An analytical formula for ring artefact suppression in X-ray tomography}, - author={Titarenko, Sofya and Withers, Philip J and Yagola, Anatoly}, - journal={Applied Mathematics Letters}, - volume={23}, - number={12}, - pages={1489--1495}, - year={2010}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T An analytical formula for ring artefact suppression in X-ray tomography - %A Titarenko, Sofya - %A Withers, Philip J - %A Yagola, Anatoly - %J Applied Mathematics Letters - %V 23 - %N 12 - %P 1489-1495 - %@ 0893-9659 - %D 2010 - %I Elsevier - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_sorting.rst b/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_sorting.rst deleted file mode 100644 index df4feecfc..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_sorting.rst +++ /dev/null @@ -1,79 +0,0 @@ -Ring Removal Sorting -################################################################# - -Description --------------------------- - -Method to remove stripe artefacts in a sinogram (<-> ring -artefacts in a reconstructed image) using a sorting-based method. -It works particularly well for removing partial rings. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - size: - visibility: intermediate - dtype: int - description: Size of the median filter window. Greater is stronger. - default: 31 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -Superior techniques for eliminating ring artifacts in X-ray micro-tomography by Vo, Nghia T et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{vo2018superior, - title = {Superior techniques for eliminating ring artifacts in X-ray micro-tomography}, - author={Vo, Nghia T and Atwood, Robert C and Drakopoulos, Michael}, - journal={Optics express}, - volume={26}, - number={22}, - pages={28396--28412}, - year={2018}, - publisher={Optical Society of America}} - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T Superior techniques for eliminating ring artifacts in X-ray micro-tomography - %A Vo, Nghia T - %A Atwood, Robert C - %A Drakopoulos, Michael - %J Optics express - %V 26 - %N 22 - %P 28396-28412 - %@ 1094-4087 - %D 2018 - %I Optical Society of America - - diff --git a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_waveletfft.rst b/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_waveletfft.rst deleted file mode 100644 index 9d9703416..000000000 --- a/doc/source/plugin_documentation/plugins.ring_removal.ring_removal_waveletfft.rst +++ /dev/null @@ -1,54 +0,0 @@ -Ring Removal Waveletfft -################################################################# - -Description --------------------------- - -Ring artefact removal method - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - nvalue: - visibility: intermediate - dtype: int - description: Order of the the Daubechies (DB) wavelets. - default: 5 - - sigma: - visibility: intermediate - dtype: int - description: Damping parameter. Larger is stronger. - default: 1 - - level: - visibility: intermediate - dtype: int - description: Wavelet decomposition level. - default: 3 - - padFT: - visibility: intermediate - dtype: int - description: Padding for Fourier transform - default: 20 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.savers.edf_saver.rst b/doc/source/plugin_documentation/plugins.savers.edf_saver.rst deleted file mode 100644 index 29ca70100..000000000 --- a/doc/source/plugin_documentation/plugins.savers.edf_saver.rst +++ /dev/null @@ -1,8 +0,0 @@ -Edf Saver -################################################################# - -Description --------------------------- - -A class to save xrf data to edf files. - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.savers.hdf5_saver.rst b/doc/source/plugin_documentation/plugins.savers.hdf5_saver.rst deleted file mode 100644 index 5f142e268..000000000 --- a/doc/source/plugin_documentation/plugins.savers.hdf5_saver.rst +++ /dev/null @@ -1,36 +0,0 @@ -Hdf5 Saver -################################################################# - -Description --------------------------- - -A class to save tomography data to a hdf5 file - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: none - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: none - default: [] - - pattern: - visibility: basic - dtype: str - description: "Optimise data storage to this access pattern 'optimum' will automate this process by choosing the output pattern from the previous plugin, if it exists, else the first pattern." - default: optimum - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.savers.image_saver.rst b/doc/source/plugin_documentation/plugins.savers.image_saver.rst deleted file mode 100644 index 522b2626b..000000000 --- a/doc/source/plugin_documentation/plugins.savers.image_saver.rst +++ /dev/null @@ -1,73 +0,0 @@ -Image Saver -################################################################# - -Description --------------------------- - -A class to save tomography data to image files. Run the MaxAndMin plugin -before this to rescale the data. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: none - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: none - default: [] - - pattern: - visibility: intermediate - dtype: tuple - description: How to slice the data. - default: VOLUME_XZ - - format: - visibility: intermediate - dtype: str - description: Image format. - default: tif - - num_bit: - visibility: intermediate - dtype: int - description: Bit depth of the tiff format (8, 16 or 32). - default: 16 - - max: - visibility: intermediate - dtype: float - description: Global max for tiff scaling. - default: None - - min: - visibility: intermediate - dtype: float - description: Global min for tiff scaling. - default: None - - jpeg_quality: - visibility: intermediate - dtype: range - description: JPEG encoding quality (1 is worst, 100 is best). - default: 75 - - prefix: - visibility: datasets - dtype: str - description: Override the default output jpg file prefix - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.savers.tiff_saver.rst b/doc/source/plugin_documentation/plugins.savers.tiff_saver.rst deleted file mode 100644 index eeca997c6..000000000 --- a/doc/source/plugin_documentation/plugins.savers.tiff_saver.rst +++ /dev/null @@ -1,42 +0,0 @@ -Tiff Saver -################################################################# - -Description --------------------------- - -A class to save tomography data to tiff files - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: none - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: none - default: [] - - pattern: - visibility: basic - dtype: str - description: How to slice the data - default: VOLUME_XZ - - prefix: - visibility: basic - dtype: str - description: Override the default output tiff file prefix. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.savers.xrf_saver.rst b/doc/source/plugin_documentation/plugins.savers.xrf_saver.rst deleted file mode 100644 index 9f223fcf7..000000000 --- a/doc/source/plugin_documentation/plugins.savers.xrf_saver.rst +++ /dev/null @@ -1,9 +0,0 @@ -Xrf Saver -################################################################# - -Description --------------------------- - -A class to save xrf data to Diamond Mapping .nxs format. -It can also save to edf and rgb for pymca visualisation. - \ No newline at end of file diff --git a/doc/source/plugin_documentation/plugins.segmentation.evolving_contours.morph_snakes.rst b/doc/source/plugin_documentation/plugins.segmentation.evolving_contours.morph_snakes.rst deleted file mode 100644 index 3433b3300..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.evolving_contours.morph_snakes.rst +++ /dev/null @@ -1,62 +0,0 @@ -Morph Snakes -################################################################# - -Description --------------------------- - -A Plugin to segment reconstructed data using Morphsnakes module. -When initialised with a mask, the active contour propagates to find the -minimum of energy (a possible edge countour). - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - lambda1: - visibility: basic - dtype: int - description: Weight parameter for the outer region, if lambda1 is larger than lambda2, the outer region will contain a larger range of values than the inner region. - default: 1 - - lambda2: - visibility: basic - dtype: int - description: Weight parameter for the inner region, if lambda2 is larger than lambda1, the inner region will contain a larger range of values than the outer region. - default: 1 - - smoothing: - visibility: basic - dtype: int - description: Number of times the smoothing operator is applied per iteration, reasonable values are around 1-4 and larger values lead to smoother segmentations. - default: 1 - - iterations: - visibility: basic - dtype: int - description: The number of iterations. - default: 350 - - pattern: - visibility: intermediate - dtype: str - description: Pattern to apply to this. - default: VOLUME_YZ - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.evolving_contours.morph_snakes3D.rst b/doc/source/plugin_documentation/plugins.segmentation.evolving_contours.morph_snakes3D.rst deleted file mode 100644 index abbabe7d5..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.evolving_contours.morph_snakes3D.rst +++ /dev/null @@ -1,56 +0,0 @@ -Morph Snakes3D -################################################################# - -Description --------------------------- - -A Plugin to 3D segment reconstructed data using -Morphsnakes module. When initialised with a mask, the active contour -propagates to find the minimum of energy (a possible edge countour). - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - lambda1: - visibility: basic - dtype: int - description: Weight parameter for the outer region, if lambda1 is larger than lambda2, the outer region will contain a larger range of values than the inner region. - default: 1 - - lambda2: - visibility: basic - dtype: int - description: Weight parameter for the inner region, if lambda2 is larger than lambda1, the inner region will contain a larger range of values than the outer region. - default: 1 - - smoothing: - visibility: basic - dtype: int - description: Number of times the smoothing operator is applied per iteration, reasonable values are around 1-4 and larger values lead to smoother segmentations. - default: 1 - - iterations: - visibility: basic - dtype: int - description: The number of iterations. - default: 350 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.gaussian_mixtures.gmm_segment3D.rst b/doc/source/plugin_documentation/plugins.segmentation.gaussian_mixtures.gmm_segment3D.rst deleted file mode 100644 index d105bb131..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.gaussian_mixtures.gmm_segment3D.rst +++ /dev/null @@ -1,36 +0,0 @@ -Gmm Segment3D -################################################################# - -Description --------------------------- - -A Plugin to segment data using Gaussian Mixtures from scikit - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - classes: - visibility: basic - dtype: int - description: The number of classes for GMM - default: 5 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.geo_distance.geo_distance.rst b/doc/source/plugin_documentation/plugins.segmentation.geo_distance.geo_distance.rst deleted file mode 100644 index 3a8159f3e..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.geo_distance.geo_distance.rst +++ /dev/null @@ -1,42 +0,0 @@ -Geo Distance -################################################################# - -Description --------------------------- - -Geodesic transformation of images with manual initialisation. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: The default names. - default: "['GeoDist, 'max_values']" - - lambda: - visibility: basic - dtype: float - description: Weighting between 0 and 1 - default: 0.5 - - iterations: - visibility: basic - dtype: int - description: The number of iterations for raster scanning. - default: 4 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.geo_distance.geo_distance3D.rst b/doc/source/plugin_documentation/plugins.segmentation.geo_distance.geo_distance3D.rst deleted file mode 100644 index e393b9279..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.geo_distance.geo_distance3D.rst +++ /dev/null @@ -1,42 +0,0 @@ -Geo Distance3D -################################################################# - -Description --------------------------- - -3D geodesic transformation of images with manual initialisation. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: The default names. - default: "['GeoDist']" - - lambda: - visibility: basic - dtype: float - description: Weighting between 0 and 1 - default: 0.5 - - iterations: - visibility: basic - dtype: int - description: The number of iterations for raster scanning. - default: 4 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.final_segment_i23.rst b/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.final_segment_i23.rst deleted file mode 100644 index ec5e645a1..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.final_segment_i23.rst +++ /dev/null @@ -1,36 +0,0 @@ -Final Segment I23 -################################################################# - -Description --------------------------- - -Apply at the end when all objects have been segmented independently (crystal, liquor, whole object) - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - set_classes_val: - visibility: basic - dtype: list - description: Set the values for all 4 classes (crystal, liquor, loop, vacuum). - default: [255, 128, 64, 0] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.i23_segment.rst b/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.i23_segment.rst deleted file mode 100644 index 3b974788b..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.i23_segment.rst +++ /dev/null @@ -1,46 +0,0 @@ -I23 Segment -################################################################# - -Description --------------------------- - -A Plugin to segment reconstructed data from i23 beamline. The projection data -should be first reconstructed iteratively using the ToMoBAR plugin. The goal of -the segmentation plugin is to cluster and segment data using Gaussian Mixtures -and then apply iterative model-based segmentation to further process the obtained -mask. https://github.com/dkazanc/i23seg - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Default out dataset names. - default: "['maskGMM4', 'maskGMM4_proc', 'maskGMM5', 'maskGMM5_proc']" - - correction_window: - visibility: basic - dtype: int - description: The size of the correction window - default: 9 - - iterations: - visibility: basic - dtype: int - description: The number of iterations for segmentation. - default: 10 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.i23_segment3D.rst b/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.i23_segment3D.rst deleted file mode 100644 index 8d1e5b64d..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.i23segmentation.i23_segment3D.rst +++ /dev/null @@ -1,52 +0,0 @@ -I23 Segment3D -################################################################# - -Description --------------------------- - -A Plugin to segment reconstructed data from i23 beamline. The projection data -should be first reconstructed iteratively using the ToMoBAR plugin. The goal of -the segmentation plugin is to cluster and segment data using Gaussian Mixtures -and then apply iterative model-based segmentation to further process the obtained mask -INPUT to the plugin is the result of gmm_segment plugin - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - classes: - visibility: intermediate - dtype: int - description: The number of classes for GMM. - default: 5 - - correction_window: - visibility: basic - dtype: int - description: The size of the correction (non-local) window - default: 8 - - iterations: - visibility: basic - dtype: int - description: The number of iterations for segmentation. - default: 10 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.masks_initialise.mask_initialiser.rst b/doc/source/plugin_documentation/plugins.segmentation.masks_initialise.mask_initialiser.rst deleted file mode 100644 index a4928d1c9..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.masks_initialise.mask_initialiser.rst +++ /dev/null @@ -1,58 +0,0 @@ -Mask Initialiser -################################################################# - -Description --------------------------- - -A plugin to initialise a binary mask for level sets and -distance transform segmentations. Seeds are generated by -providing coordinates of three points in 3D space (start-middle-finish) -and connecting them with a cylinder of a certain radius. -Importantly the Z coordinate is given following VOLUME_XY vertical pattern - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: The default names - default: ['INIT_MASK'] - - mask1_coordinates: - visibility: basic - dtype: list - description: X0,Y0,Z0 (start) X1,Y1,Z1 (middle) and X2,Y2,Z2 (finish) coordinates of three points. - default: [10, 10, 0, 15, 15, 15, 20, 20, 20] - - mask1_radius: - visibility: basic - dtype: int - description: Mask1 will be initialised with an ellipse of radius. - default: 5 - - mask2_coordinates: - visibility: basic - dtype: list - description: The second mask coordinates. - default: None - - mask2_radius: - visibility: basic - dtype: int - description: Mask2 will be initialised with an ellipse of radius. - default: None - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.morphological_operations.morph_proc.rst b/doc/source/plugin_documentation/plugins.segmentation.morphological_operations.morph_proc.rst deleted file mode 100644 index f2ab14751..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.morphological_operations.morph_proc.rst +++ /dev/null @@ -1,51 +0,0 @@ -Morph Proc -################################################################# - -Description --------------------------- - -A Plugin to perform morphological operations on grayscale images -(use: erosion, dilation, opening, closing) or binary images -(use: binary_erosion, binary_dilation, binary_opening, binary_closing) - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - disk_radius: - visibility: basic - dtype: int - description: The radius of the disk-shaped structuring element for morphology. - default: 5 - - morph_operation: - visibility: intermediate - dtype: int - description: The type of morphological operation. - default: binary_opening - options: ['binary_erosion', 'binary_dilation', 'binary_opening', 'binary_closing'] - - pattern: - visibility: intermediate - dtype: str - description: Pattern to apply this to. - default: VOLUME_XZ - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.morphological_operations.morph_remove_objects.rst b/doc/source/plugin_documentation/plugins.segmentation.morphological_operations.morph_remove_objects.rst deleted file mode 100644 index c7d520640..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.morphological_operations.morph_remove_objects.rst +++ /dev/null @@ -1,48 +0,0 @@ -Morph Remove Objects -################################################################# - -Description --------------------------- - -A Plugin to remove objects smaller than the specified size. - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - min_size: - visibility: basic - dtype: int - description: The smallest allowable object size. - default: 64 - - connectivity: - visibility: basic - dtype: int - description: The connectivity defining the neighborhood of a pixel. - default: 1 - - pattern: - visibility: intermediate - dtype: str - description: Pattern to apply this to. - default: VOLUME_XZ - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.segmentation.thresholding.thresh_segm.rst b/doc/source/plugin_documentation/plugins.segmentation.thresholding.thresh_segm.rst deleted file mode 100644 index c16bc21a5..000000000 --- a/doc/source/plugin_documentation/plugins.segmentation.thresholding.thresh_segm.rst +++ /dev/null @@ -1,54 +0,0 @@ -Thresh Segm -################################################################# - -Description --------------------------- - -A Plugin to segment the data by providing two scalar values for lower and upper intensities - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to create - default: [] - - min_intensity: - visibility: basic - dtype: float - description: A scalar to define lower limit for intensity, all values below are set to zero. - default: 0 - - max_intensity: - visibility: basic - dtype: float - description: A scalar to define upper limit for intensity, all values above are set to zero. - default: 0.01 - - value: - visibility: basic - dtype: int - description: An integer to set all values between min_intensity and max_intensity. - default: 1 - - pattern: - visibility: intermediate - dtype: str - description: Pattern to apply this to. - default: VOLUME_XY - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.simulation.tomo_phantom.rst b/doc/source/plugin_documentation/plugins.simulation.tomo_phantom.rst deleted file mode 100644 index fcb05238d..000000000 --- a/doc/source/plugin_documentation/plugins.simulation.tomo_phantom.rst +++ /dev/null @@ -1,152 +0,0 @@ -Tomo Phantom -################################################################# - -Description --------------------------- - -A plugin for TomoPhantom software which generates synthetic phantoms -and projection data (2D from Phantom2DLibrary.dat and 3D from -Phantom3DLibrary.dat) - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Default out dataset names. - default: "['tomo', 'model']" - - geom_model: - visibility: basic - dtype: int - description: Select a model (integer) from the library (see TomoPhantom files). - default: 1 - - geom_model_size: - visibility: basic - dtype: int - description: Set the size of the phantom. - default: 256 - - geom_projections_total: - visibility: intermediate - dtype: int - description: The total number of projections. - default: 360 - - geom_detectors_horiz: - visibility: intermediate - dtype: int - description: The size of _horizontal_ detectors. - default: 300 - - artifacts_noise_type: - visibility: intermediate - dtype: str - description: Set the noise type, Poisson or Gaussian. - default: Poisson - - artifacts_noise_sigma: - visibility: intermediate - dtype: int - description: Define noise amplitude. - default: 5000 - - artifacts_misalignment_maxamplitude: - visibility: intermediate - dtype: int - description: Incorporate misalignment into projections (in pixels). - default: None - - artifacts_zingers_percentage: - visibility: intermediate - dtype: float - description: Add broken pixels to projections, e.g. 0.25. - default: None - - artifacts_stripes_percentage: - visibility: intermediate - dtype: float - description: The amount of stripes in the data, e.g. 1.0. - default: None - - artifacts_stripes_maxthickness: - visibility: intermediate - dtype: float - description: Defines the maximal thickness of a stripe. - default: 3.0 - - artifacts_stripes_intensity: - visibility: intermediate - dtype: float - description: To incorporate the change of intensity in the stripe. - default: 0.3 - - artifacts_stripes_type: - visibility: intermediate - dtype: str - description: Set the stripe type between full and partial. - default: full - - artifacts_stripes_variability: - visibility: intermediate - dtype: float - description: The intensity variability of a stripe. - default: 0.007 - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml - -Citations --------------------------- - -TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks by Kazantsev, Daniil et al. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Bibtex -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - @article{kazantsev2018tomophantom, - title={TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks}, - author={Kazantsev, Daniil and Pickalov, Valery and Nagella, Srikanth and Pasca, Edoardo and Withers, Philip J}, - journal={SoftwareX}, - volume={7}, - pages={150--155}, - year={2018}, - publisher={Elsevier} - } - - -Endnote -"""""""""""""""""""""""""""""""""""""""""" - -.. code-block:: none - - %0 Journal Article - %T TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks - %A Kazantsev, Daniil - %A Pickalov, Valery - %A Nagella, Srikanth - %A Pasca, Edoardo - %A Withers, Philip J - %J SoftwareX - %V 7 - %P 150-155 - %@ 2352-7110 - %D 2018 - %I Elsevier - - diff --git a/doc/source/plugin_documentation/plugins.simulation.tomo_phantom_quantification.rst b/doc/source/plugin_documentation/plugins.simulation.tomo_phantom_quantification.rst deleted file mode 100644 index b77ba044f..000000000 --- a/doc/source/plugin_documentation/plugins.simulation.tomo_phantom_quantification.rst +++ /dev/null @@ -1,30 +0,0 @@ -Tomo Phantom Quantification -################################################################# - -Description --------------------------- - -A plugin to calculate some standard image quality metrics - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Default out dataset names. - default: "['quantification_values']" - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.stats.min_and_max.rst b/doc/source/plugin_documentation/plugins.stats.min_and_max.rst deleted file mode 100644 index 2e4c5cd95..000000000 --- a/doc/source/plugin_documentation/plugins.stats.min_and_max.rst +++ /dev/null @@ -1,68 +0,0 @@ -Min And Max -################################################################# - -Description --------------------------- - -A plugin to calculate the min and max values of each slice (as determined -by the pattern parameter) - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: str - description: The default names. - default: ['the_min', 'the_max'] - - pattern: - visibility: intermediate - dtype: tuple - description: How to slice the data. - default: VOLUME_XZ - - smoothing: - visibility: intermediate - dtype: bool - description: Apply a smoothing filter or not. - default: True - - masking: - visibility: intermediate - dtype: bool - description: Apply a circular mask or not. - default: True - - ratio: - visibility: intermediate - dtype: float - description: Used to calculate the circular mask. If not provided, it is calculated using the center of rotation. - default: None - - method: - visibility: intermediate - dtype: str - options: ['extrema', 'percentile'] - description: Method to find the global min and the global max. - default: percentile - - p_range: - visibility: intermediate - dtype: range - description: "Percentage range if use the 'percentile' method." - default: [0.0, 100.0] - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/source/plugin_documentation/plugins.visualisation.ortho_slice.rst b/doc/source/plugin_documentation/plugins.visualisation.ortho_slice.rst deleted file mode 100644 index 40698876f..000000000 --- a/doc/source/plugin_documentation/plugins.visualisation.ortho_slice.rst +++ /dev/null @@ -1,60 +0,0 @@ -Ortho Slice -################################################################# - -Description --------------------------- - -A plugin to calculate the centre of rotation using the Vo Method - -Parameter definitions --------------------------- - -.. code-block:: yaml - - in_datasets: - visibility: datasets - dtype: list - description: Create a list of the dataset(s) to process - default: [] - - out_datasets: - visibility: datasets - dtype: list - description: Default out dataset names. - default: "['XY','YZ','XZ']" - - xy_slices: - visibility: intermediate - dtype: int - description: which XY slices to render. - default: 100 - - yz_slices: - visibility: intermediate - dtype: int - description: which YZ slices to render. - default: 100 - - xz_slices: - visibility: intermediate - dtype: int - description: which XZ slices to render. - default: 100 - - file_type: - visibility: intermediate - dtype: str - description: File type to save as. rings and streaks - default: png - - colourmap: - visibility: hidden - dtype: str - description: Colour scheme to apply to the image. - default: magma - -Key -^^^^^^^^^^ - -.. literalinclude:: /../source/files_and_images/documentation/short_parameter_key.yaml - :language: yaml diff --git a/doc/update_api.sh b/doc/update_api.sh index de01580dc..f48b75d65 100644 --- a/doc/update_api.sh +++ b/doc/update_api.sh @@ -1,10 +1,12 @@ #!/bin/bash -python create_plugin_doc.py api_plugin plugin_autosummary.rst plugin -python create_plugin_doc.py plugin_documentation plugin_documentation.rst plugin DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" echo $DIR export SPHINX_APIDOC_OPTIONS='members,undoc-members,noindex' + +python $DIR/create_plugin_doc.py api_plugin plugin_autosummary.rst plugin +python $DIR/create_plugin_doc.py plugin_documentation plugin_documentation.rst plugin + # members will document all modules # undoc keeps modules without docstrings sphinx-apidoc -feT -o $DIR/source/api_plugin $DIR/../savu/plugins/ $DIR/../savu/plugins/*tools* $DIR/../savu/plugins/**/*tools* $DIR/../savu/plugins/**/**/*tools* $DIR/../savu/plugins/**/**/**/*tools* diff --git a/savu/data/framework_citations.py b/savu/data/framework_citations.py index 72c1a0e01..07b1c5f5e 100644 --- a/savu/data/framework_citations.py +++ b/savu/data/framework_citations.py @@ -27,7 +27,7 @@ def get_framework_citations(): cite_info = [] - cite_info.append({'name': 'Savu'}) + cite_info.append({'short_name_article': 'Savu'}) cite_info[0]['description'] = \ ("The Savu framework design is described in this paper.") cite_info[0]['bibtex'] = \ @@ -48,7 +48,7 @@ def get_framework_citations(): "%J arXiv preprint arXiv:1610.08015\n" + "%D 2016") - cite_info.append({'name': 'HDF5'}) + cite_info.append({'short_name_article': 'HDF5'}) cite_info[1]['description'] = \ ("Savu uses parallel HDF5 as a backend.") cite_info[1]['bibtex'] = \ @@ -64,7 +64,7 @@ def get_framework_citations(): "%A HDF Group\n" + "%D 2014\n") - cite_info.append({'name': 'MPI'}) + cite_info.append({'short_name_article': 'MPI'}) cite_info[2]['description'] = ("HDF5 uses the Message Passing Interface\n" + "standard for interprocess communication") cite_info[2]['bibtex'] = \ diff --git a/savu/data/plugin_list.py b/savu/data/plugin_list.py index d17c4c389..82e19a1a7 100644 --- a/savu/data/plugin_list.py +++ b/savu/data/plugin_list.py @@ -232,9 +232,9 @@ def _save_framework_citations(self, group): framework_cites = fc.get_framework_citations() count = 0 for cite in framework_cites: - citation_group = group.require_group(cite['name']) - citation = CitationInformation() - del cite['name'] + citation_group = group.require_group(cite['short_name_article']) + citation = CitationInformation(**cite) + del cite['short_name_article'] for key, value in cite.iteritems(): exec('citation.' + key + '= value') citation.write(citation_group) diff --git a/savu/plugins/basic_operations/no_process_tools.py b/savu/plugins/basic_operations/no_process_tools.py index 450fb753d..c89ac1de7 100644 --- a/savu/plugins/basic_operations/no_process_tools.py +++ b/savu/plugins/basic_operations/no_process_tools.py @@ -135,5 +135,17 @@ def define_parameters(self): dtype: pos_int description: flat data path and scale value default: 4 + algorithm: + visibility: basic + dtype: str + description: Option list + default: FBP + options: [SIRT,SART,FBP,ART,CGLS,BP,FP] + range_param: + visibility: basic + dtype: range + description: Range required + default: (0,1) + """ \ No newline at end of file diff --git a/savu/plugins/loaders/base_loader_tools.py b/savu/plugins/loaders/base_loader_tools.py index 13d8b1027..df7c463d6 100644 --- a/savu/plugins/loaders/base_loader_tools.py +++ b/savu/plugins/loaders/base_loader_tools.py @@ -17,12 +17,14 @@ def define_parameters(self): description: hidden parameter for savu template default: '<>' in_datasets: - visibility: datasets + # not inherited and not needed + visibility: not dtype: list description: Create a list of the dataset(s) to process default: [] out_datasets: - visibility: datasets + # not inherited and not needed + visibility: not dtype: list description: Create a list of the dataset(s) to create default: [] diff --git a/savu/plugins/plugin.py b/savu/plugins/plugin.py index daab4d902..20adca295 100644 --- a/savu/plugins/plugin.py +++ b/savu/plugins/plugin.py @@ -25,13 +25,11 @@ import ast import copy import logging -import inspect import numpy as np from collections import OrderedDict import savu.plugins.utils as pu import savu.plugins.docstring_parser as doc -import savu.plugins.parameter_utils as param_u from savu.plugins.plugin_datasets import PluginDatasets @@ -120,15 +118,10 @@ def _get_plugin_tools(self): def _populate_default_parameters(self): """ - This method should populate all the required parameters with default - values. it is used for checking to see if new parameter values are - appropriate - + This method should populate all the required parameters with + default values. It is used for checking to see if parameter + values are appropriate """ - # Test Plugins are: 'RemoveAllRings' 'TomobarRecon' 'Hdf5saver' - # 'NxtomoLoader' 'DarkFlatFieldCorrection' 'NoProcess' 'Astra' - # 'Vocentering' - p_tools = self._get_plugin_tools() if p_tools: self.tools = p_tools @@ -164,7 +157,8 @@ def _set_parameters(self, parameters): """ This method is called after the plugin has been created by the pipeline framework. It replaces ``self.parameters`` default values - with those given in the input process list. + with those given in the input process list. It checks for multi + parameter strings, eg. 57;68;56; :param dict parameters: A dictionary of the parameters for this \ plugin, or None if no customisation is required. @@ -172,12 +166,8 @@ def _set_parameters(self, parameters): self.initialise_parameters() for key in parameters.keys(): if key in self.parameters.keys(): - value = self.__convert_multi_params(parameters[key], key) - self.tools.modify(self.parameters, value, key) - # parameters holds current values, this is edited outside of the - # tools class so default and dependency display values are updated here - self.tools.update_defaults(self.parameters, self.p_dict, mod=key) - self.tools.check_dependencies(self.parameters, self.p_dict) + self.tools.modify(self.parameters, parameters[key], key) + self.__check_multi_params(self.parameters, parameters[key], key) else: error = ("Parameter '%s' is not valid for plugin %s. \nTry " "opening and re-saving the process list in the " @@ -185,49 +175,20 @@ def _set_parameters(self, parameters): % (key, self.name)) raise ValueError(error) - def __convert_multi_params(self, value, key): - """ Set up parameter tuning. - - Convert parameter value to a list if it uses parameter tuning and set + def __check_multi_params(self, parameters, value, key): + """ Convert parameter value to a list if it uses parameter tuning and set associated parameters, so the framework knows the new size of the data and which plugins to re-run. """ - dtype = self.p_dict[key].get('dtype') - current_parameter_details = self.p_dict[key] - - if isinstance(value, str) and ';' in value: - value = value.split(';') - if ":" in value[0]: - seq = value[0].split(':') - seq = [eval(s) for s in seq] - value = list(np.arange(seq[0], seq[1], seq[2])) - if len(value) == 0: - raise RuntimeError( - 'No values for tuned parameter "{}", ' - 'ensure start:stop:step; values are valid.'.format(key)) - - parameter_valid, error_str = param_u.is_valid(key, value[0], - current_parameter_details) - if not parameter_valid: - try: - value.remove('') - except: - pass - if isinstance(value[0], str): - value = [ast.literal_eval(i) for i in value] - - if isinstance(dtype, list): - for instance_type in dtype: - if type(value[0]) == instance_type: - # TODO Check the mapping use here - value = map(type, value) - else: - value = map(dtype, value) + # If the value is in a split string format then the value is returned + # as a list + value, error_str = pu.convert_multi_params(key, value) + if not error_str: + parameters[key] = value label = key + '_params.' + type(value[0]).__name__ self.multi_params_dict[len(self.multi_params_dict)] = \ {'label': label, 'values': value} self.extra_dims.append(len(value)) - return value def get_parameters(self, name): """ Return a plugin parameter diff --git a/savu/plugins/plugin_tools.py b/savu/plugins/plugin_tools.py index 5fb38cb38..a3747af95 100644 --- a/savu/plugins/plugin_tools.py +++ b/savu/plugins/plugin_tools.py @@ -31,7 +31,7 @@ import savu.plugins.utils as pu from savu.data.meta_data import MetaData import savu.plugins.docstring_parser as doc -import savu.plugins.parameter_utils as param_u +import scripts.config_generator.parameter_utils as param_u from savu.data.plugin_list import CitationInformation @@ -108,7 +108,6 @@ def modify(self, parameters, value, param_name): mod=param_name) # Update the list of parameters to hide those dependent on others self.check_dependencies(parameters, self.param.get_dictionary()) - parameter_valid = True else: print(error_str) print('This value has not been saved.') @@ -216,7 +215,7 @@ def _check_visibility(self, all_params, tool_class): """Make sure that the visibility choice is valid """ visibility_levels = ['basic', 'intermediate', 'advanced', - 'datasets', 'hidden'] + 'datasets', 'hidden', 'not'] visibility_valid = True for p_key, p in all_params.items(): self._check_data_keys(p_key, p) @@ -238,7 +237,7 @@ def _check_data_keys(self, p_key, p): """ datasets = ['in_datasets', 'out_datasets'] if p_key in datasets: - if p['visibility'] != 'datasets': + if p['visibility'] != 'datasets' and p['visibility'] != 'not': p['visibility'] = 'datasets' def _check_options(self, all_params, tool_class): @@ -295,23 +294,25 @@ def update_defaults(self, parameters, all_params, mod=False): temp_default = all_params[parent_param]['default'] parent_value = self._set_default(temp_default, all_params, parameters, parent_param) - if parent_value in dep_param_choices.keys(): - desc['range'] = 'The recommended value with the chosen ' \ - + str(parent_param) + ' would be ' \ - + str(dep_param_choices[parent_value]) - recommendation = 'It\'s recommended that you update ' \ - + str(p_name) + ' to ' \ - + str(dep_param_choices[parent_value]) - if mod: - if mod == p_name: - print(Fore.RED + recommendation + Fore.RESET) - else: - # If there was no modification, on loading the - # plugin set the correct default value - parameters[p_name] = dep_param_choices[parent_value] + if parent_value in dep_param_choices.keys(): + desc['range'] = 'The recommended value with the chosen ' \ + + str(parent_param) + ' would be ' \ + + str(dep_param_choices[parent_value]) + recommendation = 'It\'s recommended that you update ' \ + + str(p_name) + ' to ' \ + + str(dep_param_choices[parent_value]) + if mod: + # If a modification is being made don't automatically + # change other parameters, print a warning + if mod == p_name: + print(Fore.RED + recommendation + Fore.RESET) else: - # If there is no match - parameters[p_name] = None + # If there was no modification, on loading the + # plugin set the correct default value + parameters[p_name] = dep_param_choices[parent_value] + else: + # If there is no match + parameters[p_name] = None def check_dependencies(self, parameters, all_params): @@ -498,13 +499,13 @@ def set_doc_link(self): os.path.dirname(os.path.realpath(__file__)).split('savu')[0] # Locate documentation file - doc_folder = savu_base_path + 'doc/source/documentation/' - module = self.plugin_class.__module__.split('.') - file_ = module[-1] + '_doc' + doc_folder = savu_base_path + 'doc/source/documentation' + module_path = self.plugin_class.__module__.replace('.','/').replace('savu','') + file_ = module_path + '_doc' file_name = file_ + '.rst' file_path = doc_folder + file_name sphinx_link = 'https://savu.readthedocs.io/en/latest/' \ - 'documentation/' + file_ + 'documentation' + file_ if os.path.isfile(file_path): self.doc.set('documentation_link', sphinx_link) diff --git a/savu/plugins/reconstructions/base_recon_tools.py b/savu/plugins/reconstructions/base_recon_tools.py index 9a5b9d137..9bf59f2c2 100644 --- a/savu/plugins/reconstructions/base_recon_tools.py +++ b/savu/plugins/reconstructions/base_recon_tools.py @@ -7,11 +7,12 @@ def define_parameters(self): """ centre_of_rotation: visibility: basic - dtype: [float, int] + dtype: [float, int, str] description: Centre of rotation to use for the reconstruction. default: 0.0 - example: It could be scalar or list of centre of rotation + example: It could be a scalar, a list, or a file + containing centre of rotations init_vol: visibility: advanced diff --git a/savu/plugins/utils.py b/savu/plugins/utils.py index 812ae30f3..4333031a0 100644 --- a/savu/plugins/utils.py +++ b/savu/plugins/utils.py @@ -32,6 +32,7 @@ import inspect import itertools +import numpy as np load_tools = {} plugins = {} @@ -293,4 +294,97 @@ def set_order_by_visibility(parameters, level=False): else: keys = basic_keys + interm_keys + adv_keys + data_keys - return keys \ No newline at end of file + return keys + + +def convert_multi_params(param_name, value): + """ Check if value is a multi parameter and check if each item is valid. + Change from the input multi parameter string to a list + + :param param_name: Name of the parameter + :param value: Parameter value + :return: List or unchanged value + """ + error_str = '' + multi_parameters = (isinstance(value, str) and (';' in value) + and param_name != 'preview') + if multi_parameters: + value = value.split(';') + if ":" in value[0]: + seq = value[0].split(':') + try: + seq = [eval(s) for s in seq] + if len(value) == 0: + error_str = 'No values for tuned parameter "{}" ' \ + 'ensure start:stop:step; values are ' \ + 'valid.'.format(param_name) + elif len(seq) == 2: + value = list(np.arange(seq[0], seq[1])) + elif len(seq) > 2: + value = list(np.arange(seq[0], seq[1], seq[2])) + else: + error_str = 'Ensure start:stop:step; values are ' \ + 'valid.' + except: + error_str = 'Ensure start:stop:step; values are ' \ + 'valid.' + val_list = parse_config_string(value) if isinstance(value, str) else value + # Remove blank list entries + # Change type to int, float or str + val_list = [_cast_str_to_type(val) + for val in val_list if val] + value = val_list + return value, error_str + + +def _cast_str_to_type(value): + """ Change the string to an integer, float, tuple, list or str + """ + try: + val = int(value) + except ValueError: + try: + val = float(value) + except ValueError: + if '(' and ')' in value: + val = _cast_to_tuple(value) + elif '[' and ']' in value: + val = _cast_to_list(value) + else: + # Return the string + val = value + return val + + +def _cast_to_list(value): + # Change type to list + inner_list = value.replace('[', '').replace(']', '') + if ',' in inner_list: + list_content = inner_list.split(',') + list_content = [_cast_str_to_type(i) for i in list_content] + val = list_content + else: + val = [_cast_str_to_type(inner_list)] + return val + + +def _cast_to_tuple(value): + # Change type to tuple + inner_tuple = value.replace('(', '').replace(')', '') + if ',' in inner_tuple: + tuple_content = inner_tuple.split(',') + tuple_content = [_cast_str_to_type(i) for i in tuple_content] + val = tuple(tuple_content) + else: + inner_tuple_iterable = [_cast_str_to_type(inner_tuple)] + val = tuple(inner_tuple_iterable) + return val + + +def create_dir(file_path): + """ Check if directories provided exist at this file path. If they don't + create the directories. + """ + directory = os.path.dirname(file_path) + if not os.path.exists(directory): + os.makedirs(directory) diff --git a/savu/test/test_process_list_utils.py b/savu/test/test_process_list_utils.py index 7ef0e2143..3fc5924da 100644 --- a/savu/test/test_process_list_utils.py +++ b/savu/test/test_process_list_utils.py @@ -116,12 +116,3 @@ def get_param_value_from_file(param, in_file): value = line.split('=')[1].strip() param_list.append(value) return param_list - - -def create_dir(file_path): - """ Check if directories provided exist at this file path. If they don't - create the directories. - """ - directory = os.path.dirname(file_path) - if not os.path.exists(directory): - os.makedirs(directory) \ No newline at end of file diff --git a/savu/test/travis/framework_tests/parameter_dependency_display_test.py b/savu/test/travis/framework_tests/parameter_dependency_display_test.py new file mode 100644 index 000000000..d9edb1bbc --- /dev/null +++ b/savu/test/travis/framework_tests/parameter_dependency_display_test.py @@ -0,0 +1,213 @@ +# -*- coding: utf-8 -*- +# Copyright 2014 Diamond Light Source Ltd. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + + +""" +.. module:: parameter_dependency_display_test + :platform: Unix + :synopsis: unittest test for plugin parameter dependencies +.. moduleauthor:: Jessica Verschoyle + +""" + +from __future__ import print_function, division, absolute_import + +import unittest + +import savu.plugins.utils as pu + +class ParameterDependencyDisplayTest(unittest.TestCase): + """Test the display 'on' settings for dependent parameters. + I have included the dependency text in the docstring for clarity + """ + + def initial_setup(self): + ppath = 'savu.plugins.reconstructions.tomobar.tomobar_recon' + plugin = pu.load_class(ppath)() + plugin._populate_default_parameters() + return plugin + + def test_dependent_param_not_present(self): + # Do not display the regularisation_methodTV + ''' + regularisation_methodTV: + visibility: advanced + dtype: str + description: 0/1 - TV specific isotropic/anisotropic choice. + default: 0 + dependency: + regularisation_method: [ROF_TV, FGP_TV, PD_TV, SB_TV, NLTV] + ''' + plugin = self.initial_setup() + key = 'regularisation_method' + value = 'LLT_ROF' + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + # Check display list + display_value = plugin.p_dict['regularisation_methodTV']['display'] + self.assertTrue(display_value == 'off') + + + def test_dependent_param_present(self): + # Do display regularisation_methodTV + ''' + regularisation_methodTV: + visibility: advanced + dtype: str + description: 0/1 - TV specific isotropic/anisotropic choice. + default: 0 + dependency: + regularisation_method: [ROF_TV, FGP_TV, PD_TV, SB_TV, NLTV] + ''' + plugin = self.initial_setup() + key = 'regularisation_method' + value = 'ROF_TV' + + display_value_before = plugin.p_dict['regularisation_methodTV']['display'] + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + # Check display list + display_value = plugin.p_dict['regularisation_methodTV']['display'] + self.assertTrue(display_value=='on') + + + def test_dependent_param_none(self): + # Do NOT display regularisation_device + ''' + regularisation_device: + visibility: advanced + dtype: str + description: The device for regularisation + default: gpu + dependency: + regularisation_method: not None + ''' + plugin = self.initial_setup() + key = 'regularisation_method' + value = 'None' + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + # Check display list + display_value = plugin.p_dict['regularisation_device']['display'] + self.assertTrue(display_value == 'off') + + + def test_dependent_param_not_none(self): + # DO display regularisation_device + ''' + regularisation_device: + visibility: advanced + dtype: str + description: The device for regularisation + default: gpu + dependency: + regularisation_method: not None + ''' + plugin = self.initial_setup() + key = 'regularisation_method' + value = 'FGP_TV' + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + # Check display list + display_value = plugin.p_dict['regularisation_device']['display'] + self.assertTrue(display_value == 'on') + + + def test_default_choices(self): + # DO change reg iterations to 100 + ''' + regularisation_iterations: + visibility: basic + dtype: int + description: + summary: Total number of regularisation iterations. + The smaller the number of iterations, the smaller the effect + of the filtering is. A larger number will affect the speed + of the algorithm. + range: Recommended value dependent upon method. + default: + regularisation_method: + ROF_TV: 1000 + FGP_TV: 500 + PD_TV: 100 + SB_TV: 100 + LLT_ROF: 1000 + NDF: 1000 + Diff4th: 1000 + TGV: 80 + NLTV: 80 + dependency: + regularisation_method: not None + ''' + plugin = self.initial_setup() + key = 'regularisation_method' + value = 'PD_TV' + + # TODO try on load in comparison to modify as modify does not change default.. + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + # Check display list + display_value = plugin.p_dict['regularisation_iterations']['display'] + self.assertTrue(display_value=='on') + + + def test_default_choices2(self): + # Do not display regularisation_iterations + ''' + regularisation_iterations: + visibility: basic + dtype: int + description: + summary: Total number of regularisation iterations. + The smaller the number of iterations, the smaller the effect + of the filtering is. A larger number will affect the speed + of the algorithm. + range: Recommended value dependent upon method. + default: + regularisation_method: + ROF_TV: 1000 + FGP_TV: 500 + PD_TV: 100 + SB_TV: 100 + LLT_ROF: 1000 + NDF: 1000 + Diff4th: 1000 + TGV: 80 + NLTV: 80 + dependency: + regularisation_method: not None + ''' + plugin = self.initial_setup() + key = 'regularisation_method' + value = 'None' + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + # Check display list + display_value = plugin.p_dict['regularisation_iterations']['display'] + self.assertTrue(display_value == 'off') + + +if __name__ == "__main__": + unittest.main() diff --git a/savu/test/travis/framework_tests/parameter_type_test.py b/savu/test/travis/framework_tests/parameter_type_test.py index 7f40f815f..b63dfec33 100644 --- a/savu/test/travis/framework_tests/parameter_type_test.py +++ b/savu/test/travis/framework_tests/parameter_type_test.py @@ -27,7 +27,6 @@ import unittest import savu.plugins.utils as pu -import savu.plugins.parameter_utils as param_u class ParameterTypeTest(unittest.TestCase): @@ -170,5 +169,235 @@ def test_pos_int_1(self): valid_modification = plugin.tools.modify(plugin.parameters, value, key) self.assertFalse(valid_modification) + def test_options(self): + # Check that valid options are accepted + plugin = self.initial_setup() + key = 'algorithm' + value = 'SIRT' + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + def test_options_1(self): + # Check that invalid options of correct type are not accepted + plugin = self.initial_setup() + key = 'algorithm' + value = 'SARTT' + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + def test_options_2(self): + # Check that the invalid type int is not accepted + plugin = self.initial_setup() + key = 'algorithm' + value = 4 + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + def test_multi_param(self): + # Check that multiple integers are accepted + plugin = self.initial_setup() + key = 'positive_test' + value = '2;4;64' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = [2,4,64] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + + def test_multi_param_1(self): + # Check that negative integers within the list are not accepted + plugin = self.initial_setup() + key = 'positive_test' + value = '-2;5;4' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = [-2, 5, 4] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + + def test_multi_param_2(self): + # Check that invalid options are not accepted + plugin = self.initial_setup() + key = 'algorithm' + value = 'SIRT;SART;SLING' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = ['SIRT','SART','SLING'] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + def test_multi_param_3(self): + # Check that multiple strings are accepted + plugin = self.initial_setup() + key = 'algorithm' + value = 'FP;BP;SIRT' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = ['FP','BP','SIRT'] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + + def test_multi_param_4(self): + # Check that multiple strings are accepted + plugin = self.initial_setup() + key = 'algorithm' + value = 'FP;' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = ['FP'] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + + def test_multi_param_5(self): + # ;; is ignored and the two options are seperated + plugin = self.initial_setup() + key = 'algorithm' + value = 'FP;;SART' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = ['FP', 'SART'] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + + def test_multi_param_6(self): + # ; is ignored and options are checked as a list + plugin = self.initial_setup() + key = 'algorithm' + value = ';FP' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = ['FP'] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + + def test_multi_param_7(self): + # Check that syntax fails + plugin = self.initial_setup() + key = 'algorithm' + value = ':FP' + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + def test_multi_param_8(self): + # Check that syntax works. If colon included in the first item + # then this overwrites items after ; + plugin = self.initial_setup() + key = 'other' + value = '1:30:1;' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, + 23, 24, 25, 26, 27, 28, 29] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + + def test_multi_param_9(self): + # Check that syntax fails + plugin = self.initial_setup() + key = 'other' + value = '1:3a;' + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + def test_multi_param_10(self): + # Check that tuple list is accepted + plugin = self.initial_setup() + key = 'vocentering_search_area' + value = '(2,4);(5,65);(86,87);' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = [(2,4),(5,65),(86,87)] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + def test_multi_param_11(self): + plugin = self.initial_setup() + key = 'ica_w_init' + value = '[8,8,9];[78,89];[78,0,0];[9]' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = [[8,8,9],[78,89],[78,0,0],[9]] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + def test_multi_param_12(self): + # Range should fail as length should be 2 + plugin = self.initial_setup() + key = 'range_param' + value = '(2,7);(3,8);(0,4,6)' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = [(2,7),(3,8),(0,4,6)] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + def test_multi_param_13(self): + # One tuple, one list, should fail + plugin = self.initial_setup() + key = 'range_param' + value = '(2,7);[3,8];(0,4)' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertFalse(valid_modification) + + + def test_multi_param_14(self): + # Check that one value inside a tuple list is accepted + plugin = self.initial_setup() + key = 'vocentering_search_area' + value = '(4,5);(7);' + + # Check the multi parameter value is changed to a list correctly + val_list, error_str = pu.convert_multi_params(key, value) + result = [(4,5),(7,)] + self.assertEqual(val_list, result) + + valid_modification = plugin.tools.modify(plugin.parameters, value, key) + self.assertTrue(valid_modification) + + if __name__ == "__main__": unittest.main() diff --git a/savu/test/travis/framework_tests/yaml_parameter_test.py b/savu/test/travis/framework_tests/yaml_parameter_test.py index 3a97a1651..2e4f6e159 100644 --- a/savu/test/travis/framework_tests/yaml_parameter_test.py +++ b/savu/test/travis/framework_tests/yaml_parameter_test.py @@ -34,8 +34,8 @@ class YamlParameterTest(unittest.TestCase): def initial_setup(self, test_function): """ - Create the parameter class and set plugin parameters based - upon the docstring of the passed in function + Create a testing parameter class and set plugin parameters based + upon the docstring of the passed in function - define_parameters :param test_function: The function containing the docstring text for the test @@ -198,6 +198,57 @@ def test_parameter_indent(self): in str(context.exception)) + def test_parameter_options(self): + """ + # Options + parameter: + visibility: basic + dtype: str + description: An option list + default: FBP + options: [FBP, SIRT, SART] + + """ + # No error message + param_dict = self.initial_setup(self.test_parameter_options) + + + def test_parameter_options_1(self): + """ + # Options as tuple + parameter: + visibility: basic + dtype: str + description: An option list + default: FBP + options: (FBP, SIRT, SART) + + """ + # No error message at the moment, but to be read in correctly + # options must be surrounded by square brackets + param_dict = self.initial_setup(self.test_parameter_options_1) + + def test_parameter_options_2(self): + """ + # Invalid option choice in description + parameter: + visibility: basic + dtype: str + description: + summary: An option list + options: + SIRT: One description + SLING: Invalid option choice + FBP: A description + default: FBP + options: [FBP, SIRT, SART] + + """ + # Error message + with self.assertRaises(Exception): + param_dict = self.initial_setup(self.test_parameter_options_2) + + class PluginToolTestingClass(PluginTools): """A testing class""" def define_parameters(self): diff --git a/scripts/config_generator/config_utils.py b/scripts/config_generator/config_utils.py index 757ee12f0..37f416a74 100644 --- a/scripts/config_generator/config_utils.py +++ b/scripts/config_generator/config_utils.py @@ -172,6 +172,21 @@ def _populate_plugin_list(content, pfilter=""): content.add(key, str(count)) count += 1 +def _search_plugin_file(module_name, pfilter): + """Check for string inside file""" + string_found = False + + savu_base_path = \ + os.path.dirname(os.path.realpath(__file__)).split('scripts')[0] + file_dir = module_name.replace('.', '/') + file_path = savu_base_path + file_dir + '.py' + if os.path.isfile(file_path): + plugin_file = open(file_path, "r") + data = plugin_file.read().split() + if pfilter in data: + string_found = True + plugin_file.close() + return string_found def __get_filtered_plugins(pfilter): """ Get a sorted, filter list of plugins. """ @@ -187,6 +202,10 @@ def __get_filtered_plugins(pfilter): key_list.append(key) elif pfilter in value.__module__ or pfilter in value.__name__: key_list.append(key) + else: + # Check if the word is present in the file + if _search_plugin_file(value.__module__, pfilter): + key_list.append(key) key_list.sort() return key_list diff --git a/scripts/config_generator/display_formatter.py b/scripts/config_generator/display_formatter.py index 3d55b5610..ed67116a3 100644 --- a/scripts/config_generator/display_formatter.py +++ b/scripts/config_generator/display_formatter.py @@ -247,12 +247,16 @@ def _append_description(self, desc, key, p_dict, str_margin, width, for k, v in desc[key]['options'].items() if v} if opt in options_desc.keys(): + # Append the description opt_d = unicode_bullet_point + str(opt) + ': ' \ + options_desc[opt] - option_verbose +='\n' + opt_d - option_verbose=self._get_equal_lines(option_verbose, - width, verbose_color, c_off, - opt_margin, option_colour=colour) + else: + # No description if the field is blank + opt_d = unicode_bullet_point + str(opt) + ': ' + option_verbose += '\n' + opt_d + option_verbose = self._get_equal_lines(option_verbose, + width, verbose_color, c_off, + opt_margin, option_colour=colour) else: option_verbose = unicode_bullet_point + str(opt) option_verbose = self._get_equal_lines(option_verbose, diff --git a/savu/plugins/parameter_utils.py b/scripts/config_generator/parameter_utils.py similarity index 78% rename from savu/plugins/parameter_utils.py rename to scripts/config_generator/parameter_utils.py index c88d12ddf..2ecc122db 100644 --- a/savu/plugins/parameter_utils.py +++ b/scripts/config_generator/parameter_utils.py @@ -31,6 +31,8 @@ from colorama import Fore import savu.plugins.loaders.utils.yaml_utils as yu +from savu.plugins.utils import parse_config_string as parse_str +from savu.plugins.utils import convert_multi_params def _intlist(value): '''['int'] ''' @@ -331,32 +333,97 @@ def is_valid(param_name, value, current_parameter_details): If the items in options have not been type checked, or have errors, it may cause problems. """ + option_error_str = '' + type_error_str = '' + dtype = current_parameter_details['dtype'] default_value = current_parameter_details['default'] # If a default value is used, this is a valid option pvalid = _check_default(value, default_value) - type_error_str = '' + if pvalid is False: if isinstance(dtype, list): - # This is a list of possible types + # If there are multiple possible types for individual_type in dtype: - pvalid = type_dict[individual_type](value) + # Errors can be overwitten as later types may match the value type + pvalid, type_error_str = \ + _check_type(individual_type, param_name, value, + current_parameter_details) if pvalid is True: + # If the value type matches one of the possible types then exit break - - elif dtype not in type_dict.keys(): - type_error_str = 'That type definition is not configured properly.' - pvalid = False else: - pvalid = type_dict[dtype](value) + pvalid, type_error_str = _check_type(dtype, param_name, value, + current_parameter_details) # Then check if the option is valid - pvalid, option_error_str = _check_options(current_parameter_details, value, pvalid) + if not _is_multi_param(param_name, value): + # If it is a multi parameter, each item is checked individually + pvalid, option_error_str = _check_options\ + (current_parameter_details, value, pvalid) if pvalid is False: - type_error_str = option_error_str if option_error_str else _error_message(dtype, param_name) + # If an option error exists then use this error message + type_error_str = option_error_str if option_error_str \ + else _error_message(dtype, param_name) + + return pvalid, type_error_str + +def _check_type(dtype, param_name, value, current_parameter_details): + """ Check if the provided value matches the required date type + + :param dtype: The required data type + :param param_name: The parameter name + :param value: The new value + :param current_parameter_details: Paramter detail dictionary + :return: pvalid, True if the value type matches the required dtype + type_error_str, Error message + """ + if dtype not in type_dict.keys(): + type_error_str = 'That type definition is not configured properly.' + pvalid = False + elif _is_multi_param(param_name, value): + # If there are multiple parameters, check each individually + pvalid, type_error_str = _check_multi_params(param_name, value, + current_parameter_details) + else: + pvalid = type_dict[dtype](value) + type_error_str = '' return pvalid, type_error_str + +def _check_multi_params(param_name, value, + current_parameter_details): + """ Check if value is a multi parameter and check if each item is valid. + Change from the input multi parameter string to a list + + :param param_name: Name of the parameter + :param value: Parameter value + :param current_parameter_details: Parameter dictionary + :return: boolean True if all parameters are valid + An error string + """ + type_error_str = '' + parameter_valid = False + if _is_multi_param(param_name, value): + val_list, type_error_str = convert_multi_params(param_name, value) + if not type_error_str: + for item in val_list: + parameter_valid, type_error_str = is_valid(param_name, item, + current_parameter_details) + if parameter_valid == False: + # If one value inside the list is not valid, then return false + break + + return parameter_valid, type_error_str + + +def _is_multi_param(param_name, value): + """Return True if the value is made up of multiple parameters""" + return (isinstance(value, str) and (';' in value) + and param_name != 'preview') + + def _check_default(value, default_value): """ Return true if the new value is either a match for the default parameter value or the string 'default' @@ -390,5 +457,6 @@ def _error_message(dtype, param_name): ' the type {}.'.format(param_name, type_options) else: error_str = 'Your input for the parameter \'{}\' must match' \ - ' the type \'{}\'.'.format(param_name, type_error_dict[dtype]) + ' the type \'{}\'.'.format(param_name, + type_error_dict[dtype]) return error_str \ No newline at end of file diff --git a/scripts/plugin_generator/savu_plugin_generator.py b/scripts/plugin_generator/savu_plugin_generator.py index c3a9bf07f..35e4ad309 100644 --- a/scripts/plugin_generator/savu_plugin_generator.py +++ b/scripts/plugin_generator/savu_plugin_generator.py @@ -24,11 +24,9 @@ from __future__ import print_function, division import os -import sys import string import argparse -import savu.test.test_process_list_utils as tplu import warnings with warnings.catch_warnings(): warnings.simplefilter("ignore") @@ -181,9 +179,9 @@ def create_documentation_template(file_path, module, savu_base_path): print('A documentation file exists at ' + file_str) else: # Create the file directory for the documentation if it doesn't exist - tplu.create_dir(file_str) + pu.create_dir(file_str) # Create the file for the documentation images - tplu.create_dir(doc_image_folder) + pu.create_dir(doc_image_folder) doc_image_folder_inline = doc_image_folder.split('files_and_images/')[1] with open(file_str, 'w+') as new_rst_file: new_rst_file.write(':orphan:\n\n') @@ -297,7 +295,7 @@ def main(): savu_base_path = \ os.path.dirname(os.path.realpath(__file__)).split('scripts')[0] file_path = module.replace('.', '/') - if args.delete == True: + if args.delete: remove_plugin_files(file_path, module, savu_base_path) else: create_plugin_template(file_path, module, args.quick, savu_base_path) diff --git a/scripts/plugin_generator_tests/savu_plugin_generator_test.py b/scripts/plugin_generator_tests/savu_plugin_generator_test.py index 3728f3972..46fd0cb06 100644 --- a/scripts/plugin_generator_tests/savu_plugin_generator_test.py +++ b/scripts/plugin_generator_tests/savu_plugin_generator_test.py @@ -25,7 +25,7 @@ import os import unittest - +import savu.plugins.utils as pu import savu.test.test_process_list_utils as tplu import savu.test.travis.framework_tests.plugin_coverage_test as pct @@ -122,8 +122,8 @@ def create_plugin_directories(self, savu_base_path, plugin_files): for file in plugin_files: doc_dir = doc_path + file image_dir = doc_image_path + file - tplu.create_dir(doc_dir) - tplu.create_dir(image_dir) + pu.create_dir(doc_dir) + pu.create_dir(image_dir) if __name__ == "__main__":