patch to develop

.gitignore

@@ -450,7 +450,7 @@ Session.vim
 # auto-generated tag files
 tags
 
-package/PartSeg/utils/color_image/color_image\.c
+package/PartSegCore/color_image/color_image\.c
 
 !notebooks/
 notebooks/*
@@ -465,11 +465,11 @@ test_data/
 !launcher.spec
 /test_data_all/
 /test_data.tbz2
-!/package/PartSeg/utils/segmentation/multiscale_opening/*.cpp
-/package/PartSeg/utils/segmentation/multiscale_opening/*.gch
-package/PartSeg/utils/multiscale_opening/\.vscode/
+!/PartSegCore/segmentation/multiscale_opening/*.cpp
+/PartSegCore/segmentation/multiscale_opening/*.gch
+package/PartSegCore/multiscale_opening/\.vscode/
 
-package/PartSeg/utils/multiscale_opening/\.vscode/
+package/PartSegCore/multiscale_opening/\.vscode/
 /tutorials/tutorial-chromosome-1/tutorial-chromosome1.pdf
 !/package/tests/test_data/measurements_profile.json
 

MANIFEST.in

@@ -1,5 +1,5 @@
 global-include *.pyx
 global-include *.pxd
-include package/PartSeg/utils/distance_in_structure/*.h
-include package/PartSeg/utils/multiscale_opening/*.h
+include package/PartSegCore/distance_in_structure/*.h
+include package/PartSegCore/multiscale_opening/*.h
 include Readme.md

Readme.md

@@ -1,5 +1,5 @@
 # PartSeg
-[![Build Status](https://travis-ci.com/4DNucleome/PartSeg.svg?branch=master)](https://travis-ci.com/4DNucleome/PartSeg)
+[![Build Status](https://travis-ci.org/4DNucleome/PartSeg.svg?branch=master)](https://travis-ci.org/4DNucleome/PartSeg) 
 [![PyPI version](https://badge.fury.io/py/PartSeg.svg)](https://badge.fury.io/py/PartSeg)
 [![Documentation Status](https://readthedocs.org/projects/partseg/badge/?version=latest)](https://partseg.readthedocs.io/en/latest/?badge=latest)
 [![Build Status](https://dev.azure.com/PartSeg/PartSeg/_apis/build/status/4DNucleome.PartSeg?branchName=master)](https://dev.azure.com/PartSeg/PartSeg/_build/latest?definitionId=1&branchName=master)

azure-pipelines.yml

@@ -37,7 +37,7 @@ stages:
           displayName: 'Use Python $(python.version)'
           inputs:
             versionSpec: '$(python.version)'
-        - script: sudo apt-get update && sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0
+        - script: sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0
           displayName: "install libs"
         - task: DownloadPipelineArtifact@2
           inputs:
@@ -108,7 +108,7 @@ stages:
         variables:
           CIBW_BUILD: cp36-manylinux1_x86_64 cp37-manylinux1_x86_64
           CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMAND: pytest {project}/package/tests --ignore={project}/package/tests/test_gui
+          CIBW_TEST_COMMAND: pytest {project}/package/tests --ignore={project}/package/tests/test_qt_part
         steps:
           - task: UsePythonVersion@0
           - task: DownloadPipelineArtifact@2
@@ -127,7 +127,7 @@ stages:
       - job: macos_wheel
         pool: {vmImage: 'macOS-10.13'}
         variables:
-          CIBW_BUILD: cp36-*intel cp37-*intel
+          CIBW_BUILD: cp36-* cp37-*
           CIBW_TEST_REQUIRES: pytest pytest-qt
           CIBW_TEST_COMMAND: pytest {project}/package/tests
         steps:
@@ -173,14 +173,15 @@ stages:
               python -m pip install -r requirements_pyinstaller.txt
               python -m pip install .
               python  build_utils/create_build.py
-          - script: sudo apt-get update && sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0
+          - script: sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0
             displayName: "install libs"
-          - script: xvfb-run dist/PartSeg/PartSeg_exec _test
-            displayName: TestBuild
+
           - task: PublishBuildArtifacts@1
             inputs:
               pathToPublish: dist2
               artifactName: execs
+          - script: xvfb-run dist/PartSeg/PartSeg_exec _test
+            displayName: TestBuild
 
       - job: macos_pyinstaller
         pool: {vmImage: 'macOS-10.13'}
@@ -191,12 +192,12 @@ stages:
               python -m pip install -r requirements_pyinstaller.txt
               python -m pip install .
               python  build_utils/create_build.py
-          - script: dist/PartSeg/PartSeg_exec _test
-            displayName: TestBuild
           - task: PublishBuildArtifacts@1
             inputs:
               pathToPublish: dist2
               artifactName: execs
+          - script: dist/PartSeg/PartSeg_exec _test
+            displayName: TestBuild
 
       - job: windows_pyinstaller
         pool: {vmImage: 'vs2017-win2016'}
@@ -212,3 +213,43 @@ stages:
               artifactName: execs
           - script: dist\PartSeg\PartSeg_exec _test
             displayName: TestBuild
+
+      - job: help
+        pool: {vmImage: 'Ubuntu-16.04'}
+        steps:
+          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.6', architecture: x64}}
+          - bash: |
+              python -m pip install -r requirements_pyinstaller.txt
+              python -m pip install .
+              python -m pip install sphinx
+            displayName: InstallDeps
+          - bash: make -C docs html
+            displayName: BuildDocs
+          - bash: |
+              mkdir docs_result
+              cd docs/_build; zip -r ../../docs_result/PartSeg_documentation_`python -c "import PartSeg; print(PartSeg.__version__)"`.zip html; cd ../..
+          - task: PublishBuildArtifacts@1
+            inputs:
+              pathToPublish: docs_result
+              artifactName: docs
+
+      - job: Notebook_check
+        pool: {vmImage: 'Ubuntu-16.04'}
+        continueOnError: true
+        variables:
+          DATA_PATH: typy_neuronow2
+        steps:
+          - {task: UsePythonVersion@0, inputs: {versionSpec: '3.6', architecture: x64}}
+          - bash: |
+              wget -q -N https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/typy_neuronow2.zip
+              unzip typy_neuronow2.zip
+              ls typy_neuronow2
+            displayName: GetData
+          - bash: |
+              python -m pip install -r requirements_pyinstaller.txt
+              python -m pip install .
+              python -m pip install jupyter[all]
+              python -m pip install matplotlib
+            displayName: InstallDeps
+          - bash: DATA_PATH=${PWD}/typy_neuronow2 jupyter nbconvert --to notebook --execute tutorials/tutorial_neuron_types/Neuron_types_example.ipynb
+            displayName: BuildDocs

changelog.md

@@ -1,13 +1,20 @@
 # Changelog 
 
+## 0.9.4
+ - read mask segmentation projects 
+ - choose source type in batch
+ - add support to CZI file format
+ - extract utils to PartSegCore module
+ - add automated tests of example notebook
+ - reversed mask
+ - load segemtation parameters in mask segmentation
+
 ## 0.9.3
  - start automated build documentation
  - change color map backend and allow for user to create custom color map. 
  - segmentation compare
  - update test engines
  - support of PySide2 
-
-
 
 ## 0.9.2.3
  - refactor code to make easier create plugin for mask segmentation 
@@ -17,7 +24,7 @@
 
 ## 0.9.2.2
  - extract static data to separated package
- - update marker of fix range and add mark of gauus in channel control 
+ - update marker of fix range and add mark of gauss in channel control 
 
 ## 0.9.2.1
  - add VoteSmooth and add choosing of smooth algorithm

docs/PartSegCore/analysis/base.rst

@@ -0,0 +1,11 @@
+PartSegCore.analysis
+====================
+
+This module contains all utils specific for segmentation analysis task
+
+PartSegCore.analysis.algorithm_description
+---------------------------------------------------
+
+.. automodule:: PartSegCore.analysis.algorithm_description
+   :members:
+   :show-inheritance:

docs/PartSegCore/analysis/batch_processing.rst

@@ -0,0 +1,19 @@
+PartSegCore.analysis.batch_processing
+=====================================
+
+This module contains utils for parallel batch processing
+
+PartSegCore.analysis.batch_processing.batch_backend
+---------------------------------------------------
+
+.. automodule:: PartSegCore.analysis.batch_processing.batch_backend
+   :members:
+   :show-inheritance:
+
+
+PartSegCore.analysis.batch_processing.parallel_backend
+------------------------------------------------------
+
+.. automodule:: PartSegCore.analysis.batch_processing.parallel_backend
+   :members:
+   :show-inheritance:

docs/PartSegCore/analysis/calculation_plan.rst

@@ -0,0 +1,7 @@
+PartSegCore.analysis.calculation_plan
+=====================================
+
+
+.. automodule:: PartSegCore.analysis.calculation_plan
+   :members:
+   :show-inheritance:

docs/PartSegCore/base.rst

@@ -0,0 +1,52 @@
+PartSegCore base
+================
+
+On this page there are described base classes of PartSegCore module
+
+.algorithm_describe_base
+------------------------
+.. automodule:: PartSegCore.algorithm_describe_base
+   :members:
+
+.channel_class
+--------------
+.. automodule:: PartSegCore.channel_class
+   :members:
+   :show-inheritance:
+
+.image_operations
+-----------------
+.. automodule:: PartSegCore.image_operations
+   :members:
+   :show-inheritance:
+
+.json_hooks
+-----------
+.. automodule:: PartSegCore.json_hooks
+   :members:
+   :show-inheritance:
+
+
+.mask_create
+------------
+.. automodule:: PartSegCore.mask_create
+   :members:
+   :show-inheritance:
+
+
+.register
+---------
+.. automodule:: PartSegCore.register
+   :members:
+
+.. data:: base_class_dict
+
+   dict with base class for given type of algorithm, keys are :py:class:`RegisterEnum` members
+
+
+.mask_partition_utils
+---------------------
+
+.. automodule:: PartSegCore.mask_partition_utils
+   :members:
+   :show-inheritance:

docs/PartSegCore/color_image.rst

@@ -0,0 +1,20 @@
+PartSegCore.color_image
+=======================
+
+This module contains utils needed for transform multichannel image to RGB
+
+.. automodule:: PartSegCore.color_image
+   :members:
+   :inherited-members:
+   :show-inheritance:
+
+.. py:data:: resolution
+
+    Constraint equal to 1024. This is information with which accuracy the colormaps are prepared.
+    1024 means that there will interpolated to 1024 values.
+
+.. py:data:: default_colormap_dict
+
+   Dict with default colormaps avaliable in PartSeg.
+
+a

docs/PartSegCore/distance_in_structure.rst

@@ -0,0 +1,32 @@
+PartSegCore.distance_in_structure
+=================================
+
+.find_split
+-----------
+
+.. automodule:: PartSegCore.distance_in_structure.find_split
+   :members:
+
+.euclidean_cython
+-----------------
+
+.. automodule:: PartSegCore.distance_in_structure.euclidean_cython
+   :members:
+
+.fuzzy_distance
+---------------
+
+.. automodule:: PartSegCore.distance_in_structure.fuzzy_distance
+   :members:
+
+.path_sprawl_cython
+-------------------
+
+.. automodule:: PartSegCore.distance_in_structure.path_sprawl_cython
+   :members:
+
+.sprawl_utils
+-------------
+
+.. automodule:: PartSegCore.distance_in_structure.sprawl_utils
+   :members:

docs/PartSegCore/index.rst

@@ -0,0 +1,16 @@
+PartSegCore
+===========
+
+This package contains calculation backend of PartSeg
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   base
+   color_image
+   distance_in_structure
+   segmentation
+   analysis/base
+   analysis/batch_processing
+   analysis/calculation_plan

docs/PartSegCore/segmentation.rst

@@ -0,0 +1,25 @@
+PartSegCore.segmentation
+==========================
+Here we describe base classes for segmentation
+
+Base classes
+------------------------
+.. automodule:: PartSegCore.segmentation
+   :members:
+   :inherited-members:
+   :show-inheritance:
+
+.sprawl
+-------
+
+.. automodule:: PartSegCore.segmentation.sprawl
+   :members:
+   :inherited-members:
+   :show-inheritance:
+
+.restartable_segmentation_algorithms
+------------------------------------
+
+.. automodule:: PartSegCore.segmentation.restartable_segmentation_algorithms
+   :members:
+   :show-inheritance:

docs/PartSegImage.rst

@@ -9,12 +9,17 @@ PartSegImage
 
 PartSegImage.image_reader
 -------------------------
-.. autoclass:: PartSegImage.image_reader.MyTiffPage
-    :members: asarray
 
 .. automodule:: PartSegImage.image_reader
    :members:
    :exclude-members: ImageReader, MyTiffPage
    :show-inheritance:
 
 
+PartSegImage.tifffile_fixes
+---------------------------
+
+.. autoclass:: PartSegImage.tifffile_fixes.MyTiffPage
+    :members: asarray
+
+