From 6de5786a8c4964bcb8e4e036add12f7c71c4fc3e Mon Sep 17 00:00:00 2001 From: Gabriel Iltis Date: Wed, 10 Dec 2014 02:02:26 -0500 Subject: [PATCH 1/5] DEV: Added basic functions to modules.yaml for mrg Tool sets added thus far include: Thresholding Filtering Morphology Transformation --- vttools/vtmods/import_lists/modules.yaml | 110 +++++++++++++++++++++++ 1 file changed, 110 insertions(+) diff --git a/vttools/vtmods/import_lists/modules.yaml b/vttools/vtmods/import_lists/modules.yaml index 26888f6..e342a75 100644 --- a/vttools/vtmods/import_lists/modules.yaml +++ b/vttools/vtmods/import_lists/modules.yaml @@ -74,6 +74,116 @@ autowrap_func: - func_name: estimate_d_blind module_path: skxray.calibration namespace: calibration +#- func_name: find_ring_center_acorr_iD +# module_path: skxray.image +# namespace: image +# FF IMAGE PROCESSING: FILTER TOOLS +- func_name: gaussian_filter + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: median_filter + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: minimum_filter + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: maximum_filter + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: gaussian_gradient_magnitude + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: gaussian_laplace + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: laplace + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: percentile_filter + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: sobel + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: prewitt + module_path: skxray.api.ff_image + namespace: image_processing | filtering +- func_name: rank_filter + module_path: skxray.api.ff_image + namespace: image_processing | filtering +# FF IMAGE PROCESSING: HISTOGRAM TOOLS +- func_name: hist_make + module_path: skxray.api.ff_image + namespace: image_processing | histogram +- func_name: rescale_intensity_values + module_path: skxray.api.ff_image + namespace: image_processing | histogram +# FF IMAGE PROCESSING: MORPHOLOGY MANIPULATION +- func_name: binary_opening + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: binary_closing + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: binary_erosion + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: binary_dilation + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: grey_opening + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: grey_closing + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: grey_erosion + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: grey_dilation + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: binary_fill_holes + module_path: skxray.api.ff_image + namespace: image_processing | morphology +- func_name: binary_propagation + module_path: skxray.api.ff_image + namespace: image_processing | morphology +# FF IMAGE PROCESSING: THRESHOLDING TOOLS +- func_name: thresh_globalGT + module_path: skxray.api.ff_image + namespace: image_processing | thresholding +- func_name: thresh_globalLT + module_path: skxray.api.ff_image + namespace: image_processing | thresholding +- func_name: thresh_bounded + module_path: skxray.api.ff_image + namespace: image_processing | thresholding +- func_name: thresh_adapt + module_path: skxray.api.ff_image + namespace: image_processing | thresholding +- func_name: thresh_otsu + module_path: skxray.api.ff_image + namespace: image_processing | thresholding +- func_name: thresh_yen + module_path: skxray.api.ff_image + namespace: image_processing | thresholding +- func_name: thresh_isodata + module_path: skxray.api.ff_image + namespace: image_processing | thresholding +# FF IMAGE PROCESSING: TRANSFORMATION TOOLS +- func_name: swap_axes + module_path: skxray.api.ff_image + namespace: image_processing | transform +- func_name: flip_axis + module_path: skxray.api.ff_image + namespace: image_processing | transform +- func_name: crop_volume + module_path: skxray.api.ff_image + namespace: image_processing | transform +- func_name: rotate_volume + module_path: skxray.api.ff_image + namespace: image_processing | transform #- {func_name: emission_line_search, module_path: skxray.constants, namespace: core, add_input_dict: true} From 1adec48bdabcde6d516cf04ffdd06d1e57cacd7c Mon Sep 17 00:00:00 2001 From: Gabriel Iltis Date: Wed, 10 Dec 2014 18:21:32 -0500 Subject: [PATCH 2/5] DEV: Added read_amiraMesh and read_netCDF to modules.yaml --- vttools/vtmods/import_lists/modules.yaml | 46 ++++++++++++++++++++++-- 1 file changed, 43 insertions(+), 3 deletions(-) diff --git a/vttools/vtmods/import_lists/modules.yaml b/vttools/vtmods/import_lists/modules.yaml index e342a75..56315ae 100644 --- a/vttools/vtmods/import_lists/modules.yaml +++ b/vttools/vtmods/import_lists/modules.yaml @@ -18,6 +18,17 @@ import_modules: # list of functions to autowrap autowrap_func: +# FILE I/O +- func_name: read_binary + module_path: skxray.io.binary + namespace: io +- func_name: read_amiraMesh + module_path: skxray.io.avizo_io + namespace: io +- func_name: read_netCDF + module_path: skxray.io.net_cdf_io + namespace: io + - func_name: grid3d module_path: skxray.core namespace: core @@ -49,9 +60,6 @@ autowrap_func: - func_name : pixel_to_phi module_path: skxray.core namespace: core -- func_name: read_binary - module_path: skxray.io.binary - namespace: io - func_name: convolve module_path: numpy namespace: numpy @@ -184,6 +192,38 @@ autowrap_func: - func_name: rotate_volume module_path: skxray.api.ff_image namespace: image_processing | transform +# FF IMAGE PROCESSING: LOGICAL OPERATIONS +- func_name: logical_and + module_path: skxray.api.ff_image + namespace: image_processing | math | logic +- func_name: logical_or + module_path: skxray.api.ff_image + namespace: image_processing | math | logic +- func_name: logical_not + module_path: skxray.api.ff_image + namespace: image_processing | math | logic +- func_name: logical_xor + module_path: skxray.api.ff_image + namespace: image_processing | math | logic +- func_name: logical_nand + module_path: skxray.api.ff_image + namespace: image_processing | math | logic +- func_name: logical_subtract + module_path: skxray.api.ff_image + namespace: image_processing | math | logic +# FF IMAGE PROCESSING: ARITHMETIC OPERATIONS +- func_name: add + module_path: skxray.api.ff_image + namespace: image_processing | math | arithmetic +- func_name: subtract + module_path: skxray.api.ff_image + namespace: image_processing | math | arithmetic +- func_name: multiply + module_path: skxray.api.ff_image + namespace: image_processing | math | arithmetic +- func_name: divide + module_path: skxray.api.ff_image + namespace: image_processing | math | arithmetic #- {func_name: emission_line_search, module_path: skxray.constants, namespace: core, add_input_dict: true} From e9180774a17386b5491b276a5f7c0f2abef06484 Mon Sep 17 00:00:00 2001 From: Gabriel Iltis Date: Tue, 6 Jan 2015 15:37:59 -0500 Subject: [PATCH 3/5] DEV: Updated modules.yaml to match import functions specified by API Functions added focus on image processing --- vttools/vtmods/import_lists/modules.yaml | 32 ++++++++++++++++-------- 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/vttools/vtmods/import_lists/modules.yaml b/vttools/vtmods/import_lists/modules.yaml index 56315ae..6b32089 100644 --- a/vttools/vtmods/import_lists/modules.yaml +++ b/vttools/vtmods/import_lists/modules.yaml @@ -28,6 +28,12 @@ autowrap_func: - func_name: read_netCDF module_path: skxray.io.net_cdf_io namespace: io +- func_name: read_tiff + module_path: skxray.io.tiff_io + namespace: io +- func_name: save_tiff + module_path: skxray.io.tiff_io + namespace: io - func_name: grid3d module_path: skxray.core @@ -129,34 +135,40 @@ autowrap_func: # FF IMAGE PROCESSING: MORPHOLOGY MANIPULATION - func_name: binary_opening module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | binary - func_name: binary_closing module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | binary - func_name: binary_erosion module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | binary - func_name: binary_dilation module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | binary - func_name: grey_opening module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | grayscale - func_name: grey_closing module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | grayscale - func_name: grey_erosion module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | grayscale - func_name: grey_dilation module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | grayscale - func_name: binary_fill_holes module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | binary - func_name: binary_propagation module_path: skxray.api.ff_image - namespace: image_processing | morphology + namespace: image_processing | morphology | binary +- func_name: extract_material + module_path: skxray.api.ff_image + namespace: image_processing | morphology | material manipulation +- func_name: extract_all_else + module_path: skxray.api.ff_image + namespace: image_processing | morphology | material manipulation # FF IMAGE PROCESSING: THRESHOLDING TOOLS - func_name: thresh_globalGT module_path: skxray.api.ff_image From 6f6935bd22974efbd37de7710bdcc7edc796d9fd Mon Sep 17 00:00:00 2001 From: Gabriel Iltis Date: Tue, 20 Jan 2015 03:10:35 -0500 Subject: [PATCH 4/5] DEV: Restructured image processing tool inclusion in the API Removed the ff_image api structure file and reorganized the image processing tools and functions in accordance with the changes incorporated into wrap_lib. Image processing tools are now included according to tool function or category. --- vt_config/NSLS-II/init.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/vt_config/NSLS-II/init.py b/vt_config/NSLS-II/init.py index 74813c1..068e8fd 100644 --- a/vt_config/NSLS-II/init.py +++ b/vt_config/NSLS-II/init.py @@ -108,6 +108,13 @@ def get_modules(): 'skxray.io.binary', 'skxray.api.diffraction', 'vttools.to_wrap.fitting', + 'skxray.api.image_processing.arithmetic.basic_math', + 'skxray.api.image_processing.arithmetic.logic', + 'skxray.api.image_processing.filtering', + 'skxray.api.image_processing.histogram', + 'skxray.api.image_processing.morphology', + 'skxray.api.image_processing.thresholding', + 'skxray.api.image_processing.transformation' ] for mod_name in mod_targets: From 1062d058075329b71c80a18a014d9bddfd8ad8ba Mon Sep 17 00:00:00 2001 From: Gabriel Iltis Date: Wed, 25 Feb 2015 12:00:36 -0500 Subject: [PATCH 5/5] DEV: Added vtk_tools module to package index for autowrapping --- vt_config/NSLS-II/init.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/vt_config/NSLS-II/init.py b/vt_config/NSLS-II/init.py index 068e8fd..17814a9 100644 --- a/vt_config/NSLS-II/init.py +++ b/vt_config/NSLS-II/init.py @@ -106,6 +106,10 @@ def get_modules(): 'skxray.core', 'skxray.recip', 'skxray.io.binary', + 'skxray.io.avizo_io', + 'skxray.io.net_cdf_io', + 'skxray.io.tiff_io', + 'skxray.io.vtk_tools', 'skxray.api.diffraction', 'vttools.to_wrap.fitting', 'skxray.api.image_processing.arithmetic.basic_math',