Watershed workflow

.gitignore

@@ -5,6 +5,7 @@ tests/*.h5
 !tests/data/inputdata/smallVideoSimpleSegmentation.h5
 !tests/data/inputdata/mitocheck_2d+t/mitocheck_small_2D+t.h5
 !tests/data/inputdata/mitocheck_2d+t/mitocheck_small_2D+t_export.h5
+session.vim
 
 *.pyc
 *.goutputstream

docs/.gitignore

@@ -0,0 +1,2 @@
+session.vim
+_build

docs/Makefile

@@ -3,14 +3,15 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
+SPHINXBUILD   = sphinx-build2
 PAPER         =
 BUILDDIR      = _build
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+#ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -D graphviz_dot=/user/bin/dot
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 

docs/appletExample.rst

@@ -0,0 +1,159 @@
+================================================================================
+Building your own applet using the watershedSegmentation applet
+================================================================================
+
+This applet gets images for RawData, Boundaries and Seeds and 
+returns the calculated watershed segmentation and the used Labels. 
+
+More information on how you can use this applet can be found in 
+`Link <http://ilastik.org/documentation/>`_ under ILASTIK WORKFLOWS.
+
+
+Basic File Structure
+========================================
+
+#. __init__.py 
+
+        .. literalinclude:: ../ilastik/applets/watershedSegmentation/__init__.py
+           :linenos:
+           :language: python
+
+#. opWatershedSegmentation.py
+
+   * This file includes the InputSlots and OutputSlots and how they are used internally. 
+
+   * The main calculations can be found here as well.
+
+   * more Information, how you can implement or use operators can be looked up in the lazyflow 
+     documentation under the point of 'operator overview' and 'advanced concepts' 
+     which is worth reading for a better understanding
+
+#. watershedSegmentationApplet.py
+
+   * Handles what happens when the applet is created. 
+
+   * Mainly only the function broadcastingSlots should be changed, in particular only the return value. 
+     Look at the function description for more information.
+
+     .. currentmodule:: ilastik.applets.watershedSegmentation.watershedSegmentationApplet
+     .. autoattribute:: WatershedSegmentationApplet.broadcastingSlots
+
+
+#. watershedSegmentationSerializer.py
+
+   * Handles which OutputSlots shall be serialized. This means, that these slots have the same content
+     after project restart. 
+
+   * For more information see the following documentation and the code and the comments in its __init__ function.
+
+     .. currentmodule:: ilastik.applets.watershedSegmentation.watershedSegmentationSerializer
+     .. autoclass:: WatershedSegmentationSerializer
+             :members: __init__
+
+
+#. watersehdSegmentationGui.py
+
+   * handles the graphical user interface and the slots, that are 
+
+   * handles the views of the layer
+
+   * this file is discussed in more detail in :ref:`the Gui <applet_gui>`.
+
+
+#. addtional files:
+
+   Normally these files above are sufficient. Sometimes classes or cached versions of operators are 
+   excluded into addtional files. This is only for a better overview and maintenance.
+
+
+.. _applet_gui:
+
+Basic Structure in watershedSegmentationGui
+====================================================
+
+.. currentmodule:: ilastik.applets.watershedSegmentation.watershedSegmentationGui
+
+#. Inheritance
+
+        The Gui inherits from the WatershedLabelingGui which handles all about the labels.
+
+        Inheritance-tree:
+
+        LayerViewerGui->LabelingGui->WatershedLabelingGui
+
+        More information can be found in the :ref:`watershed labeling gui <applet_labeling_gui>` section.
+
+
+        The Gui uses mainly these functions:
+
+#. setupLayers
+
+   .. automethod:: WatershedSegmentationGui.setupLayers
+   .. currentmodule:: ilastik.applets.layerViewer.layerViewerGui
+   .. automethod:: LayerViewerGui._initLayer
+   .. currentmodule:: ilastik.applets.watershedSegmentation.watershedSegmentationGui
+
+#. __init__
+
+   Includes all the functionality that you can use with the side panel within your applet. 
+   Some parts can be used of existing classes, some need to be done manually.
+
+   * The slots for the base class for the labels are initialized here.
+     Only needed for LabelingGui or WatershedLabelingGui.
+
+     Otherwise you have to supply your own userinterface and their functionality. 
+
+
+   * Handling what happens when you push a button, click on a checkbox or any other action.
+
+
+
+.. _applet_labeling_gui:
+
+Basic Structure in watershedLabelingGui (gui base class)
+==============================================================
+
+The whole functionality of everything that depends on labeling 
+is handled within this class. 
+
+The labeling gui is an applet itself, so it has a serializer, an operator and so on. 
+But most of the things can be used from the superclass. 
+
+For other applets, another base class like LayerViewerGui can be sufficient, e.g. see the seeds applet.
+
+
+WatershedLabelingGui inherits from LabelingGui. First of all it is sufficient to understand what happens in the LabelingGui. 
+
+
+LabelingGui 
+----------------------------------------------------
+
+
+.. currentmodule:: ilastik.applets.labeling.labelingGui
+
+#. In the beginning, there are lots of properties and setters. 
+
+
+#.     
+       .. automethod:: LabelingGui.__init__
+                :noindex:
+       .. automethod:: LabelingGui._initLabelUic
+
+#. The rest is more or less the structure and methods that make this class work well. 
+   It is not essential for the main understanding of this class but for detailed information.
+
+
+
+Changes in WatershedLabelingGui compared to the LabelingGui
+--------------------------------------------------------------------
+
+All changes in the WatershedLabelingGui compared to the LabelingGui:
+
+.. currentmodule:: ilastik.applets.watershedLabeling.watershedLabelingGui
+.. autoclass:: WatershedLabelingGui
+        :members: _defineModel, _changeInteractionMode, _onLabelSelected, _defineLabel, _beforeLabelRemoved, _onLabelRemoved, getNextLabelName, getNextLabelColor, getNextLabelNumber
+
+
+
+To supply the WatershedLabelingGui with a LabelListModel that displays the value of the labels, a new class was necessary, the LabelListModelWithNumber. 
+

docs/applet_api.rst

@@ -82,8 +82,9 @@ Applet Base Class
 
    .. automethod:: __init__
 
-.. autoclass:: ControlCommand
-   :members:
+.. TODO this class isn't existing anymore
+        .. autoclass:: ControlCommand
+           :members:
 
 .. autoclass:: ShellRequest
    :members:

docs/applet_library.rst

@@ -110,9 +110,10 @@ Batch Output
    :scale: 100  %
    :alt: Batch Output Top-Level Operator
 
-.. currentmodule:: ilastik.applets.batchIo.batchIoApplet
-.. autoclass:: BatchIoApplet
-   :members:
+.. TODO doesn't work in the original docu as well 
+        .. currentmodule:: ilastik.applets.batchIo.batchIoApplet
+        .. autoclass:: BatchIoApplet
+           :members:
 
 
 Workflow-specific Applets
@@ -174,9 +175,11 @@ with object features can be found in the $ILASTIK/examples directory.
 To get your plugins discovered by ilastik, you have to add their path 
 to the .ilastikrc file in your home directory. The file should look
 as follows:
-    [ilastik]
-
-    plugin_directories: /path/to/cool_features
+.. code::
+
+        [ilastik]
+
+        plugin_directories: /path/to/cool_features
 
 The cool_features directory in this case should contain the .py and the .yapsy-plugin files.
 
@@ -201,8 +204,9 @@ The cool_features directory in this case should contain the .py and the .yapsy-p
 .. autoclass:: OpRegionFeatures
    :members:
 
-.. autoclass:: OpRegionFeatures3d
-   :members:
+.. TODO this class isn't existing anymore
+        .. autoclass:: OpRegionFeatures3d
+           :members:
 
 .. autoclass:: OpObjectCenterImage
    :members:

docs/conf.py

@@ -11,12 +11,32 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+# caution, don't remove this from here
+# matplotlib needs to use the qt4 version, otherwise there are about 20 errors in the compiling
+from PyQt4 import QtGui, QtCore
+import matplotlib #new line
+matplotlib.use("Qt4Agg") #new line
+
 import sys, os
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('..'))
+sys.path.append(os.path.abspath('../../lazyflow'))
+sys.path.append(os.path.abspath('../../volumina'))
+#sys.path.append(os.path.abspath('../../lazyflow/lazyflow'))
+#sys.path.append(os.path.abspath('../../lazyflow/lazyflow/utility'))
+# necessary for the 'ImportError: No module named ilastik_feature_selection'
+# adjust this to your own needs
+sys.path.append('/home/andreas/miniconda2/envs/ilastik-devel/lib/python2.7/site-packages')
+
+
+# necessary for ImportError: No module named qimage2ndarray
+# adjust this to your own needs
+sys.path.append('/home/andreas/qimage2ndarray/qimage2ndarray-master')
+
+#print sys.path
 
 # -- General configuration -----------------------------------------------------
 
@@ -25,7 +45,8 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.viewcode', 'sphinx.ext.autodoc']
+#extensions = ['sphinx.ext.viewcode', 'sphinx.ext.autodoc']
+extensions = ['sphinx.ext.viewcode', 'sphinx.ext.autodoc', 'sphinx.ext.graphviz']
 
 autodoc_member_order = 'bysource'
 
@@ -43,7 +64,7 @@
 
 # General information about the project.
 project = u'ilastik'
-copyright = u'2012, Christoph Straehle, Bernhard X. Kausler, Thorben Kröger, Ullrich Köthe , Fred A. Hamprecht, Anna Kreshuk, Luca Fiaschi, Stuart Berg'
+copyright = u'2012-2017, Christoph Straehle, Bernhard X. Kausler, Thorben Kröger, Ullrich Köthe , Fred A. Hamprecht, Anna Kreshuk, Luca Fiaschi, Stuart Berg, Andreas Haller'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -52,7 +73,7 @@
 # The short X.Y version.
 version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0'
+release = '1.0.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -188,7 +209,7 @@
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
   ('index', 'ilastik.tex', u'ilastik Documentation',
-   u'Christoph Sommer \\and Christoph Straehle \\and Bernhard X. Kausler \\and Thorben Kröger \\and Ullrich Köthe  \\and Fred A. Hamprecht \\and Anna Kreshuk \\and Luca Fiaschi \\and Stuart Berg',
+   u'Christoph Sommer \\and Christoph Straehle \\and Bernhard X. Kausler \\and Thorben Kröger \\and Ullrich Köthe  \\and Fred A. Hamprecht \\and Anna Kreshuk \\and Luca Fiaschi \\and Stuart Berg \\and Andreas Haller',
    'manual'),
 ]
 
@@ -219,7 +240,7 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'ilastik', u'ilastik Documentation',
-     [u'Christoph Sommer, Christoph Straehle, Bernhard X. Kausler, Thorben Kröger, Ullrich Köthe , Fred A. Hamprecht, Anna Kreshuk, Luca Fiaschi, Stuart Berg'], 1)
+     [u'Christoph Sommer, Christoph Straehle, Bernhard X. Kausler, Thorben Kröger, Ullrich Köthe , Fred A. Hamprecht, Anna Kreshuk, Luca Fiaschi, Stuart Berg, Andreas Haller'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -233,7 +254,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
   ('index', 'ilastik', u'ilastik Documentation',
-   u'Christoph Sommer, Christoph Straehle, Bernhard X. Kausler, Thorben Kröger, Ullrich Köthe , Fred A. Hamprecht, Anna Kreshuk, Luca Fiaschi, Stuart Berg', 'ilastik', 'One line description of project.',
+   u'Christoph Sommer, Christoph Straehle, Bernhard X. Kausler, Thorben Kröger, Ullrich Köthe , Fred A. Hamprecht, Anna Kreshuk, Luca Fiaschi, Stuart Berg, Andreas Haller', 'ilastik', 'One line description of project.',
    'Miscellaneous'),
 ]