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diff --git a/python-partseg.spec b/python-partseg.spec new file mode 100644 index 0000000..8e2f74e --- /dev/null +++ b/python-partseg.spec @@ -0,0 +1,2099 @@ +%global _empty_manifest_terminate_build 0 +Name: python-PartSeg +Version: 0.14.6 +Release: 1 +Summary: PartSeg is python GUI and set of napari plugins for bio imaging analysis especially nucleus analysis, +License: BSD-3-Clause +URL: https://4dnucleome.cent.uw.edu.pl/PartSeg/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/98/98/0504d6ffbbd38b91f03a46caf8f9a1c5b0c9488809184615a3f997b9207f/PartSeg-0.14.6.tar.gz +BuildArch: noarch + +Requires: python3-IPython +Requires: python3-PartSegCore-compiled-backend +Requires: python3-PartSegData +Requires: python3-QtAwesome +Requires: python3-QtPy +Requires: python3-SimpleITK +Requires: python3-appdirs +Requires: python3-czifile +Requires: python3-defusedxml +Requires: python3-h5py +Requires: python3-imagecodecs +Requires: python3-imageio +Requires: python3-ipykernel +Requires: python3-magicgui +Requires: python3-mahotas +Requires: python3-napari +Requires: python3-nme +Requires: python3-numpy +Requires: python3-oiffile +Requires: python3-openpyxl +Requires: python3-packaging +Requires: python3-pandas +Requires: python3-psygnal +Requires: python3-pydantic +Requires: python3-pygments +Requires: python3-qtconsole +Requires: python3-requests +Requires: python3-scipy +Requires: python3-sentry-sdk +Requires: python3-six +Requires: python3-superqt +Requires: python3-sympy +Requires: python3-tifffile +Requires: python3-traceback-with-variables +Requires: python3-vispy +Requires: python3-xlrd +Requires: python3-xlsxwriter +Requires: python3-importlib-metadata +Requires: python3-typing-extensions +Requires: python3-vispy +Requires: python3-PyOpenGL-accelerate +Requires: python3-PyOpenGL-accelerate +Requires: python3-PyQt5 +Requires: python3-autodoc-pydantic +Requires: python3-sphinx +Requires: python3-sphinx-autodoc-typehints +Requires: python3-sphinx-qt-documentation +Requires: python3-PyQt5 +Requires: python3-PyQt5 +Requires: python3-PySide2 +Requires: python3-PySide2 +Requires: python3-codecov +Requires: python3-lxml +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-pytest-qt +Requires: python3-pytest-timeout +Requires: python3-scikit-image +Requires: python3-tox + +%description +# PartSeg + + +[](https://badge.fury.io/py/PartSeg) +[](https://anaconda.org/conda-forge/partseg) +[](https://pypi.org/project/partseg) +[](https://partseg.readthedocs.io/en/latest/?badge=latest) +[](https://dev.azure.com/PartSeg/PartSeg/_build/latest?definitionId=1&branchName=develop) +[](https://zenodo.org/badge/latestdoi/166421141) +[](https://doi.org/10.1186/s12859-021-03984-1) +[](https://github.com/4DNucleome/PartSeg/blob/master/License.txt) +[](https://github.com/pre-commit/pre-commit) +[](https://github.com/psf/black) + +[](https://lgtm.com/projects/g/4DNucleome/PartSeg/alerts/) +[](https://lgtm.com/projects/g/4DNucleome/PartSeg/context:python) +[](https://www.codacy.com/gh/4DNucleome/PartSeg/dashboard?utm_source=github.com&utm_medium=referral&utm_content=4DNucleome/PartSeg&utm_campaign=Badge_Grade) +[](https://codecov.io/gh/4DNucleome/PartSeg) +[](https://deepsource.io/gh/4DNucleome/PartSeg/?ref=repository-badge) + +PartSeg is a GUI and a library for segmentation algorithms. PartSeg also provide napari plugins for IO and labels measurement. + +This application is designed to help biologist with segmentation based on threshold and connected components. + + + +## Tutorials + +- Tutorial: **Chromosome 1 (as gui)** [link](https://github.com/4DNucleome/PartSeg/blob/master/tutorials/tutorial-chromosome-1/tutorial-chromosome1_16.md) +- Data for chromosome 1 tutorial [link](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg_samples.zip) +- Tutorial: **Different neuron types (as library)** [link](https://github.com/4DNucleome/PartSeg/blob/master/tutorials/tutorial_neuron_types/Neuron_types_example.ipynb) + +## Installation + +- From binaries: + - [Windows](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-windows.zip) (build on Windows 10) + - [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-linux.zip) (build on Ubuntu 18.04) + - [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-macos.zip) (build on MacOS Mojave) + +- With pip: + - From pypi: `pip install PartSeg[all]` + - From repository: `pip install git+https://github.com/4DNucleome/PartSeg.git` + +Installation troubleshooting information could be found in wiki: [wiki](https://github.com/4DNucleome/PartSeg/wiki/Instalation-troubleshoot). +If this information does not solve problem you can open [issue](https://github.com/4DNucleome/PartSeg/issues). + +## Running + +If you downloaded binaries, run the `PartSeg` (or `PartSeg.exe` for Windows) file inside the `PartSeg` folder + +If you installed from repository or from pip, you can run it with `PartSeg` command or `python -m PartSeg`. +First option does not work on Windows. + +PartSeg export few commandline options: + +- `--no_report` - disable error reporting +- `--no_dialog` - disable error reporting and error dialog. Use only when running from terminal. +- `segmentation_analysis` - skip launcher and start analysis gui +- `segmentation` - skip launcher and start segmentation gui + +## napari plugin + +PartSeg provides napari plugins for io to allow reading projects format in napari viewer. + +## Save Format + +Saved projects are tar files compressed with gzip or bz2. + +Metadata is saved in data.json file (in json format). +Images/masks are saved as *.npy (numpy array format). + +## Interface + +Launcher. Choose the program that you will launch: + + + +Main window of Segmentation Analysis: + + + +Main window of Segmentation Analysis with view on measurement result: + + + +Window for creating a set of measurements: + + + +Main window of Mask Segmentation: + + + +## Laboratory + +Laboratory of Functional and Structural Genomics +[http://4dnucleome.cent.uw.edu.pl/](http://4dnucleome.cent.uw.edu.pl/) + +## Cite as + +Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction +from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021). +[https://doi.org/10.1186/s12859-021-03984-1](https://doi.org/10.1186/s12859-021-03984-1) + + +## Changelog + +### 0.14.6 - 2022-11-13 + +#### Bug Fixes + +- Fix bug when loading already created project causing hide of ROI layer (#787) + +#### Features + +- Improve error message if segmentation do not fit in ROI Mask (#788) + +### 0.14.5 - 2022-11-09 + +#### Bug Fixes + +- Fix scalebar color (#774) +- Fix bug when saving segmentation parameters in mask analysis (#781) +- Fix multiple errors related to loading a new file in interactive mode (#784) + +#### Features + +- Add an option for ensuring type in EventedDict and use it to validate profiles structures (#776) +- Add an option to create an issue from the error report dialog (#782) +- Add option for the multiline field in algorithm parameters (#766) + +#### Refactor + +- Optimize CLI actions (#772) +- Clean warnings about threshold methods (#783) + +#### Build + +- Bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6 (#775) + +### 0.14.4 - 2022-10-24 + +#### Bug Fixes + +- Fix `get_theme` calls to prepare for napari 0.4.17 (#729) +- Fix sentry tests (#742) +- Fix reporting error in load settings from the drive (#725) +- Fix saving pipeline from GUI (#756) +- Fix profile export/import dialogs (#761) +- Enable the "Compare" button if ROI is available (#765) +- Fix bug in cut with ROI to not make black artifacts (#767) + +#### Features + +- Load alternatives labeling when opening PartSeg projects in napari (#731) +- Add option to toggle scale bar (#733) +- Allow customizing the settings directory using the `PARTSEG_SETTINGS_DIR` environment variable (#751) +- Separate recent algorithms from general application settings (#752) +- Add multiple otsu as threshold method with selection range of components (#710) +- Add function to load components from Mask Segmentation with a background in ROI Analysis (#768) + +#### Miscellaneous Tasks + +- Prepare pyinstaller configuration for napari 0.4.17 (#748) +- Add ruff linter (#754) + +#### Testing + +- Add new build and inspect wheel action (#747) + +#### Build + +- Bump actions/checkout from 2 to 3 (#716) +- Bump actions/download-artifact from 1 to 3 (#709) + +### 0.14.3 - 2022-08-18 + +#### Bug Fixes + +- Fix lack of rendering ROI when load image from segmentation (#694) +- Fix running ROI extraction from napari widget (#695) +- Delay setting image if an algorithm is still running (#627) +- Wrong error report when no component is found in restartable segmentation algorithm. (#633) +- Fix the process of building documentation (#653) + +#### Refactor + +- Clean potential vulnerabilities (#630) + +#### Testing + +- Add more tests for common GUI elements (#622) +- Report coverage per package. (#639) +- Update conda environment to not use PyQt5 in test (#646) +- Add tests files to calculate coverage (#655) + +### 0.14.2 - 2022-05-05 + +#### Bug Fixes + +- Fix bug in save label colors between sessions (#610) +- Register PartSeg plugins before starting napari widgets. (#611) +- Mouse interaction with components works again after highlight. (#620) + +#### Refactor + +- Limit test run (#603) +- Filter and solve warnings in tests (#607) +- Use QAbstractSpinBox.AdaptiveDecimalStepType in SpinBox instead of hardcoded bounds (#616) +- Clean and test `PartSeg.common_gui.universal_gui_part` (#617) + +#### Testing + +- Speedup test by setup cache for pip (#604) +- Setup cache for azure pipelines workflows (#606) + +### 0.14.1 - 2022-04-27 + +#### Bug Fixes + +- Update build wheels and sdist to have proper version tag (#583) +- Fix removing the first measurement entry in the napari Measurement widget (#584) +- Fix compatibility bug for conda Pyside2 version (#595) +- Error when synchronization is loaded, and newly loaded image has different dimensionality than currently loaded. (#598) + +#### Features + +- Use pygments for coloring code in exception window (#591) +- Add option to calculate Measurement per Mask component (#590) + +#### Refactor + +- Refactor the creation batch plan widgets and add tests for it (#587) +- Drop napari bellow 0.4.12 (#592) +- Update the order of ROI Mask algorithms to be the same as in older PartSeg versions (#600) + +### 0.14.0 - 2022-04-14 + +#### Bug Fixes + +- Fix "Show selected" rendering mode in PartSeg ROI Mask (#565) +- Add access by operator `[]` to `pydantic.BaseModel` base structures for keeping backward compatibility (#579) + +#### Features + +- Allow setting zoom factor from the interface in Search Label napari plugin (#538) +- Add controlling of zoom factor of search ROI in main GUI (#540) +- Better serialization mechanism allow for declaration data structure migration locally (#462) +- Make `*.obsep" file possible to load in PartSeg Analysis (#564) +- Add option to extract measurement profile or ROI extraction profile from the batch plan (#568) +- Allow import calculation plan from batch result excel file (#567) +- Improve error reporting when failing to deserialize data (#574) +- Launch PartSeg GUI from napari #581 + +#### Refactor + +- Store PartSegImage.Image channels as separated arrays (#554) +- Remove deprecated modules. (#429) +- Switch serialization backend to `nme` (#569) + +#### Testing + +- Add test of creating AboutDialog (#539) +- Setup test for python 3.10. Disable `class_generator` test for this python (#570) + +### 0.13.15 + +#### Bug Fixes + +- Using `translation` instead of `translation_grid` for shifting layers. (#474) +- Bugs in napari plugins (#478) +- Missing mask when using roi extraction from napari (#479) +- Fix segmentation fault on macos machines (#487) +- Fixes for napari 0.4.13 (#506) + +#### Documentation + +- Create 0.13.15 release (#511) +- Add categories and preview page workflow for the napari hub (#489) + +#### Features + +- Assign properties to mask layer in napari measurement widget (#480) + +#### Build + +- Bump qtpy from 1.11.3 to 2.0.0 in /requirements (#498) +- Bump pydantic from 1.8.2 to 1.9.0 in /requirements (#496) +- Bump sentry-sdk from 1.5.1 to 1.5.2 in /requirements (#497) +- Bump sphinx from 4.3.1 to 4.3.2 in /requirements (#500) +- Bump pyinstaller from 4.7 to 4.8 in /requirements (#502) +- Bump pillow from 8.4.0 to 9.0.0 in /requirements (#501) +- Bump requests from 2.26.0 to 2.27.1 in /requirements (#495) +- Bump numpy from 1.21.4 to 1.22.0 in /requirements (#499) +- Bump numpy from 1.22.0 to 1.22.1 in /requirements (#509) +- Bump sphinx from 4.3.2 to 4.4.0 in /requirements (#510) + +### 0.13.14 + +#### Bug Fixes + +- ROI alternative representation (#471) +- Change additive to translucent in rendering ROI and Mask (#472) + +#### Features + +- Add morphological watershed segmentation (#469) +- Add Bilateral image filter (#470) + +### 0.13.13 + +#### Bug Fixes + +- Fix bugs in the generation process of the changelog for release. (#428) +- Restoring ROI on home button click in compare viewer (#443) +- Fix Measurement name prefix in bundled PartSeg. (#458) +- Napari widgets registration in pyinstaller bundle (#465) +- Hide points button if no points are loaded, hide Mask checkbox if no mask is set (#463) +- Replace Label data instead of adding/removing layers - fix blending layers (#464) + +#### Features + +- Add threshold information in layer annotation in the Multiple Otsu ROI extraction method (#430) +- Add option to select rendering method for ROI (#431) +- Add callback mechanism to ProfileDict, live update of ROI render parameters (#432) +- Move the info bar on the bottom of the viewer (#442) +- Add options to load recent files in multiple files widget (#444) +- Add ROI annotations as properties to napari labels layer created by ROI Extraction widgets (#445) +- Add signals to ProfileDict, remove redundant synchronization mechanisms (#449) +- Allow ignoring updates for 21 days (#453) +- Save all components if no components selected in mask segmentation (#456) +- Add modal dialog for search ROI components (#459) +- Add full measurement support as napari widget (#460) +- Add search labels as napari widget (#467) + +#### Refactor + +- Export common code for load/save dialog to one place (#437) +- Change most of call QFileDialog to more generic code (#440) + +#### Testing + +- Add test for `PartSeg.common_backend` module (#433) + +### 0.13.12 + +#### Bug Fixes + +- Importing the previous version of settings (#406) +- Cutting without masking data (#407) +- Save in subdirectory in batch plan (#414) +- Loading plugins for batch processing (#423) + +#### Features + +- Add randomization option for correlation calculation (#421) +- Add Imagej TIFF writter for image. (#405) +- Mask create widget for napari (#395) +- In napari roi extraction method show information from roi extraction method (#408) +- Add `*[0-9].tif` button in batch processing window (#412) +- Better label representation in 3d view (#418) + +#### Refactor + +- Use Font Awesome instead of custom symbols (#424) + +### 0.13.11 + +#### Bug Fixes + +- Adding mask in Prepare Plan for batch (#383) +- Set proper completion mode in SearchComboBox (#384) +- Showing warnings on the error with ROI load (#385) + +#### Features + +- Add CellFromNucleusFlow "Cell from nucleus flow" cell segmentation method (#367) +- When cutting components in PartSeg ROI mask allow not masking outer data (#379) +- Theme selection in GUI (#381) +- Allow return points from ROI extraction algorithm (#382) +- Add measurement to get ROI annotation by name. (#386) +- PartSeg ROI extraction algorithms as napari plugins (#387) +- Add Pearson, Mander's, Intensity, Spearman colocalization measurements (#392) +- Separate standalone napari settings from PartSeg embedded napari settings (#397) + +#### Performance + +- Use faster calc bound function (#375) + +#### Refactor + +- Remove CustomApplication (#389) + +### 0.13.10 + +- change tiff save backend to ome-tiff +- add `DistanceROIROI` and `ROINeighbourhoodROI` measurements + +### 0.13.9 + +- annotation show bugfix + +### 0.13.8 + +- napari deprecation fixes +- speedup simple measurement +- bundle plugins initial support + +### 0.13.7 + +- add measurements widget for napari +- fix bug in pipeline usage + +### 0.13.6 + +- Hotfix release +- Prepare for a new napari version + +### 0.13.5 + +- Small fixes for error reporting +- Fix mask segmentation + +### 0.13.4 + +- Bugfix for outdated profile/pipeline preview + +### 0.13.3 + +- Fix saving roi_info in multiple files and history + +### 0.13.2 + +- Fix showing label in select label tab + +### 0.13.1 + +- Add Haralick measurements +- Add obsep file support + +### 0.13.0 + +- Add possibility of custom input widgets for algorithms +- Switch to napari Colormaps instead of custom one +- Add points visualization +- Synchronization widget for builtin (View menu) napari viewer +- Drop Python 3.6 + +### 0.12.7 + +- Fixes for napari 0.4.6 + +### 0.12.6 + +- Fix prev_mask_get +- Fix cache mechanism on mask change +- Update PyInstaller build + +### 0.12.5 + +- Fix bug in pipeline execute + +### 0.12.4 + +- Fix ROI Mask windows related build (signal not properly connected) + +### 0.12.3 + +- Fix ROI Mask + +### 0.12.2 + +- Fix windows bundle + +### 0.12.1 + +- History of last opened files +- Add ROI annotation and ROI alternatives +- Minor bugfix + +### 0.12.0 + +- Toggle multiple files widget in View menu +- Toggle Left panel in ROI Analysis in View Menu +- Rename Mask Segmentation to ROI Mask +- Add documentation for interface +- Add Batch processing tutorial +- Add information about errors to batch processing output file +- Load image from the batch prepare window +- Add search option in part of list and combo boxes +- Add drag and drop mechanism to load list of files to batch window. + +### 0.11.5 + +- add side view to viewer +- fix horizontal view for Measurements result table + +### 0.11.4 + +- bump to napari 0.3.8 in bundle +- fix bug with not presented segmentation loaded from project +- add frame (1 pix) to image cat from base one based on segmentation +- pin to Qt version to 5.14 + +### 0.11.3 + +- prepare for napari 0.3.7 +- split napari io plugin on multiple part +- better reporting for numpy array via sentry +- fix setting color for mask marking + +### 0.11.2 + +- Speedup image set in viewer using async calls +- Fix bug in long name of sheet with parameters + +### 0.11.1 + +- Add screenshot option in View menu +- Add Voxels measurements + +### 0.11.0 + +- Make sprawl algorithm name shorter +- Unify capitalisation of measurement names +- Add simple measurements to mask segmentation +- Use napari as viewer +- Add possibility to preview additional output of algorithms (In View menu) +- Update names of available Algorithm and Measurement to be more descriptive. + +### 0.10.8 + +- fix synchronisation between viewers in Segmentation Analysis +- fix batch crash on error during batch run, add information about file on which calculation fails +- add changelog preview in Help > About + +### 0.10.7 + +- in measurements, on empty list of components mean will return 0 + +### 0.10.6 + +- fix border rim preview +- fix problem with size of image preview +- zoom with scroll and moving if rectangle zoom is not marked + +### 0.10.5 + +- make PartSeg PEP517 compatible. +- fix multiple files widget on Windows (path normalisation) + +### 0.10.4 + +- fix slow zoom + +### 0.10.3 + +- deterministic order of elements in batch processing. + +### 0.10.2 + +- bugfixes + +### 0.10.1 + +- bugfixes + +### 0.10.0 + +- Add creating custom label coloring. +- Change execs interpreter to python 3.7. +- Add masking operation in Segmentation Mask. +- Change license to BSD. +- Allow select root type in batch processing. +- Add median filter in preview. + +### 0.9.7 + +- fix bug in compare mask + +### 0.9.6 + +- fix bug in loading project with mask +- upgrade PyInstaller version (bug GHSA-7fcj-pq9j-wh2r) + +### 0.9.5 + +- fix bug in loading project in "Segmentation analysis" + +### 0.9.4 + +- read mask segmentation projects +- choose source type in batch +- add initial support to OIF and CZI file format +- extract utils to PartSegCore module +- add automated tests of example notebook +- reversed mask +- load segmentation parameters in mask segmentation +- allow use sprawl in segmentation tool +- add radial split of mask for measurement +- add all measurement results in batch, per component sheet + +### 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 +- create class base updater for update outdated algorithm description +- fix save functions +- fix different bugs + +### 0.9.2.2 + +- extract static data to separated package +- 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 + +### 0.9.2 + +- add pypi base check for update + +- remove resetting image state when change state in same image + +- in stack segmentation add options to picking components from segmentation's + +- in mask segmentation add: + + - preview of segmentation parameters per component, + - save segmentation parameters in save file + - new implementation of batch mode. + +### 0.9.1 + +- Add multiple files widget + +- Add Calculating distances between segmented object and mask + +- Batch processing plan fixes: + + - Fix adding pipelines to plan + - Redesign mask widget + +- modify measurement backend to allow calculate multi channel measurements. + +### 0.9 + +Begin of changelog + + +%package -n python3-PartSeg +Summary: PartSeg is python GUI and set of napari plugins for bio imaging analysis especially nucleus analysis, +Provides: python-PartSeg +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-PartSeg +# PartSeg + + +[](https://badge.fury.io/py/PartSeg) +[](https://anaconda.org/conda-forge/partseg) +[](https://pypi.org/project/partseg) +[](https://partseg.readthedocs.io/en/latest/?badge=latest) +[](https://dev.azure.com/PartSeg/PartSeg/_build/latest?definitionId=1&branchName=develop) +[](https://zenodo.org/badge/latestdoi/166421141) +[](https://doi.org/10.1186/s12859-021-03984-1) +[](https://github.com/4DNucleome/PartSeg/blob/master/License.txt) +[](https://github.com/pre-commit/pre-commit) +[](https://github.com/psf/black) + +[](https://lgtm.com/projects/g/4DNucleome/PartSeg/alerts/) +[](https://lgtm.com/projects/g/4DNucleome/PartSeg/context:python) +[](https://www.codacy.com/gh/4DNucleome/PartSeg/dashboard?utm_source=github.com&utm_medium=referral&utm_content=4DNucleome/PartSeg&utm_campaign=Badge_Grade) +[](https://codecov.io/gh/4DNucleome/PartSeg) +[](https://deepsource.io/gh/4DNucleome/PartSeg/?ref=repository-badge) + +PartSeg is a GUI and a library for segmentation algorithms. PartSeg also provide napari plugins for IO and labels measurement. + +This application is designed to help biologist with segmentation based on threshold and connected components. + + + +## Tutorials + +- Tutorial: **Chromosome 1 (as gui)** [link](https://github.com/4DNucleome/PartSeg/blob/master/tutorials/tutorial-chromosome-1/tutorial-chromosome1_16.md) +- Data for chromosome 1 tutorial [link](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg_samples.zip) +- Tutorial: **Different neuron types (as library)** [link](https://github.com/4DNucleome/PartSeg/blob/master/tutorials/tutorial_neuron_types/Neuron_types_example.ipynb) + +## Installation + +- From binaries: + - [Windows](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-windows.zip) (build on Windows 10) + - [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-linux.zip) (build on Ubuntu 18.04) + - [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-macos.zip) (build on MacOS Mojave) + +- With pip: + - From pypi: `pip install PartSeg[all]` + - From repository: `pip install git+https://github.com/4DNucleome/PartSeg.git` + +Installation troubleshooting information could be found in wiki: [wiki](https://github.com/4DNucleome/PartSeg/wiki/Instalation-troubleshoot). +If this information does not solve problem you can open [issue](https://github.com/4DNucleome/PartSeg/issues). + +## Running + +If you downloaded binaries, run the `PartSeg` (or `PartSeg.exe` for Windows) file inside the `PartSeg` folder + +If you installed from repository or from pip, you can run it with `PartSeg` command or `python -m PartSeg`. +First option does not work on Windows. + +PartSeg export few commandline options: + +- `--no_report` - disable error reporting +- `--no_dialog` - disable error reporting and error dialog. Use only when running from terminal. +- `segmentation_analysis` - skip launcher and start analysis gui +- `segmentation` - skip launcher and start segmentation gui + +## napari plugin + +PartSeg provides napari plugins for io to allow reading projects format in napari viewer. + +## Save Format + +Saved projects are tar files compressed with gzip or bz2. + +Metadata is saved in data.json file (in json format). +Images/masks are saved as *.npy (numpy array format). + +## Interface + +Launcher. Choose the program that you will launch: + + + +Main window of Segmentation Analysis: + + + +Main window of Segmentation Analysis with view on measurement result: + + + +Window for creating a set of measurements: + + + +Main window of Mask Segmentation: + + + +## Laboratory + +Laboratory of Functional and Structural Genomics +[http://4dnucleome.cent.uw.edu.pl/](http://4dnucleome.cent.uw.edu.pl/) + +## Cite as + +Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction +from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021). +[https://doi.org/10.1186/s12859-021-03984-1](https://doi.org/10.1186/s12859-021-03984-1) + + +## Changelog + +### 0.14.6 - 2022-11-13 + +#### Bug Fixes + +- Fix bug when loading already created project causing hide of ROI layer (#787) + +#### Features + +- Improve error message if segmentation do not fit in ROI Mask (#788) + +### 0.14.5 - 2022-11-09 + +#### Bug Fixes + +- Fix scalebar color (#774) +- Fix bug when saving segmentation parameters in mask analysis (#781) +- Fix multiple errors related to loading a new file in interactive mode (#784) + +#### Features + +- Add an option for ensuring type in EventedDict and use it to validate profiles structures (#776) +- Add an option to create an issue from the error report dialog (#782) +- Add option for the multiline field in algorithm parameters (#766) + +#### Refactor + +- Optimize CLI actions (#772) +- Clean warnings about threshold methods (#783) + +#### Build + +- Bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6 (#775) + +### 0.14.4 - 2022-10-24 + +#### Bug Fixes + +- Fix `get_theme` calls to prepare for napari 0.4.17 (#729) +- Fix sentry tests (#742) +- Fix reporting error in load settings from the drive (#725) +- Fix saving pipeline from GUI (#756) +- Fix profile export/import dialogs (#761) +- Enable the "Compare" button if ROI is available (#765) +- Fix bug in cut with ROI to not make black artifacts (#767) + +#### Features + +- Load alternatives labeling when opening PartSeg projects in napari (#731) +- Add option to toggle scale bar (#733) +- Allow customizing the settings directory using the `PARTSEG_SETTINGS_DIR` environment variable (#751) +- Separate recent algorithms from general application settings (#752) +- Add multiple otsu as threshold method with selection range of components (#710) +- Add function to load components from Mask Segmentation with a background in ROI Analysis (#768) + +#### Miscellaneous Tasks + +- Prepare pyinstaller configuration for napari 0.4.17 (#748) +- Add ruff linter (#754) + +#### Testing + +- Add new build and inspect wheel action (#747) + +#### Build + +- Bump actions/checkout from 2 to 3 (#716) +- Bump actions/download-artifact from 1 to 3 (#709) + +### 0.14.3 - 2022-08-18 + +#### Bug Fixes + +- Fix lack of rendering ROI when load image from segmentation (#694) +- Fix running ROI extraction from napari widget (#695) +- Delay setting image if an algorithm is still running (#627) +- Wrong error report when no component is found in restartable segmentation algorithm. (#633) +- Fix the process of building documentation (#653) + +#### Refactor + +- Clean potential vulnerabilities (#630) + +#### Testing + +- Add more tests for common GUI elements (#622) +- Report coverage per package. (#639) +- Update conda environment to not use PyQt5 in test (#646) +- Add tests files to calculate coverage (#655) + +### 0.14.2 - 2022-05-05 + +#### Bug Fixes + +- Fix bug in save label colors between sessions (#610) +- Register PartSeg plugins before starting napari widgets. (#611) +- Mouse interaction with components works again after highlight. (#620) + +#### Refactor + +- Limit test run (#603) +- Filter and solve warnings in tests (#607) +- Use QAbstractSpinBox.AdaptiveDecimalStepType in SpinBox instead of hardcoded bounds (#616) +- Clean and test `PartSeg.common_gui.universal_gui_part` (#617) + +#### Testing + +- Speedup test by setup cache for pip (#604) +- Setup cache for azure pipelines workflows (#606) + +### 0.14.1 - 2022-04-27 + +#### Bug Fixes + +- Update build wheels and sdist to have proper version tag (#583) +- Fix removing the first measurement entry in the napari Measurement widget (#584) +- Fix compatibility bug for conda Pyside2 version (#595) +- Error when synchronization is loaded, and newly loaded image has different dimensionality than currently loaded. (#598) + +#### Features + +- Use pygments for coloring code in exception window (#591) +- Add option to calculate Measurement per Mask component (#590) + +#### Refactor + +- Refactor the creation batch plan widgets and add tests for it (#587) +- Drop napari bellow 0.4.12 (#592) +- Update the order of ROI Mask algorithms to be the same as in older PartSeg versions (#600) + +### 0.14.0 - 2022-04-14 + +#### Bug Fixes + +- Fix "Show selected" rendering mode in PartSeg ROI Mask (#565) +- Add access by operator `[]` to `pydantic.BaseModel` base structures for keeping backward compatibility (#579) + +#### Features + +- Allow setting zoom factor from the interface in Search Label napari plugin (#538) +- Add controlling of zoom factor of search ROI in main GUI (#540) +- Better serialization mechanism allow for declaration data structure migration locally (#462) +- Make `*.obsep" file possible to load in PartSeg Analysis (#564) +- Add option to extract measurement profile or ROI extraction profile from the batch plan (#568) +- Allow import calculation plan from batch result excel file (#567) +- Improve error reporting when failing to deserialize data (#574) +- Launch PartSeg GUI from napari #581 + +#### Refactor + +- Store PartSegImage.Image channels as separated arrays (#554) +- Remove deprecated modules. (#429) +- Switch serialization backend to `nme` (#569) + +#### Testing + +- Add test of creating AboutDialog (#539) +- Setup test for python 3.10. Disable `class_generator` test for this python (#570) + +### 0.13.15 + +#### Bug Fixes + +- Using `translation` instead of `translation_grid` for shifting layers. (#474) +- Bugs in napari plugins (#478) +- Missing mask when using roi extraction from napari (#479) +- Fix segmentation fault on macos machines (#487) +- Fixes for napari 0.4.13 (#506) + +#### Documentation + +- Create 0.13.15 release (#511) +- Add categories and preview page workflow for the napari hub (#489) + +#### Features + +- Assign properties to mask layer in napari measurement widget (#480) + +#### Build + +- Bump qtpy from 1.11.3 to 2.0.0 in /requirements (#498) +- Bump pydantic from 1.8.2 to 1.9.0 in /requirements (#496) +- Bump sentry-sdk from 1.5.1 to 1.5.2 in /requirements (#497) +- Bump sphinx from 4.3.1 to 4.3.2 in /requirements (#500) +- Bump pyinstaller from 4.7 to 4.8 in /requirements (#502) +- Bump pillow from 8.4.0 to 9.0.0 in /requirements (#501) +- Bump requests from 2.26.0 to 2.27.1 in /requirements (#495) +- Bump numpy from 1.21.4 to 1.22.0 in /requirements (#499) +- Bump numpy from 1.22.0 to 1.22.1 in /requirements (#509) +- Bump sphinx from 4.3.2 to 4.4.0 in /requirements (#510) + +### 0.13.14 + +#### Bug Fixes + +- ROI alternative representation (#471) +- Change additive to translucent in rendering ROI and Mask (#472) + +#### Features + +- Add morphological watershed segmentation (#469) +- Add Bilateral image filter (#470) + +### 0.13.13 + +#### Bug Fixes + +- Fix bugs in the generation process of the changelog for release. (#428) +- Restoring ROI on home button click in compare viewer (#443) +- Fix Measurement name prefix in bundled PartSeg. (#458) +- Napari widgets registration in pyinstaller bundle (#465) +- Hide points button if no points are loaded, hide Mask checkbox if no mask is set (#463) +- Replace Label data instead of adding/removing layers - fix blending layers (#464) + +#### Features + +- Add threshold information in layer annotation in the Multiple Otsu ROI extraction method (#430) +- Add option to select rendering method for ROI (#431) +- Add callback mechanism to ProfileDict, live update of ROI render parameters (#432) +- Move the info bar on the bottom of the viewer (#442) +- Add options to load recent files in multiple files widget (#444) +- Add ROI annotations as properties to napari labels layer created by ROI Extraction widgets (#445) +- Add signals to ProfileDict, remove redundant synchronization mechanisms (#449) +- Allow ignoring updates for 21 days (#453) +- Save all components if no components selected in mask segmentation (#456) +- Add modal dialog for search ROI components (#459) +- Add full measurement support as napari widget (#460) +- Add search labels as napari widget (#467) + +#### Refactor + +- Export common code for load/save dialog to one place (#437) +- Change most of call QFileDialog to more generic code (#440) + +#### Testing + +- Add test for `PartSeg.common_backend` module (#433) + +### 0.13.12 + +#### Bug Fixes + +- Importing the previous version of settings (#406) +- Cutting without masking data (#407) +- Save in subdirectory in batch plan (#414) +- Loading plugins for batch processing (#423) + +#### Features + +- Add randomization option for correlation calculation (#421) +- Add Imagej TIFF writter for image. (#405) +- Mask create widget for napari (#395) +- In napari roi extraction method show information from roi extraction method (#408) +- Add `*[0-9].tif` button in batch processing window (#412) +- Better label representation in 3d view (#418) + +#### Refactor + +- Use Font Awesome instead of custom symbols (#424) + +### 0.13.11 + +#### Bug Fixes + +- Adding mask in Prepare Plan for batch (#383) +- Set proper completion mode in SearchComboBox (#384) +- Showing warnings on the error with ROI load (#385) + +#### Features + +- Add CellFromNucleusFlow "Cell from nucleus flow" cell segmentation method (#367) +- When cutting components in PartSeg ROI mask allow not masking outer data (#379) +- Theme selection in GUI (#381) +- Allow return points from ROI extraction algorithm (#382) +- Add measurement to get ROI annotation by name. (#386) +- PartSeg ROI extraction algorithms as napari plugins (#387) +- Add Pearson, Mander's, Intensity, Spearman colocalization measurements (#392) +- Separate standalone napari settings from PartSeg embedded napari settings (#397) + +#### Performance + +- Use faster calc bound function (#375) + +#### Refactor + +- Remove CustomApplication (#389) + +### 0.13.10 + +- change tiff save backend to ome-tiff +- add `DistanceROIROI` and `ROINeighbourhoodROI` measurements + +### 0.13.9 + +- annotation show bugfix + +### 0.13.8 + +- napari deprecation fixes +- speedup simple measurement +- bundle plugins initial support + +### 0.13.7 + +- add measurements widget for napari +- fix bug in pipeline usage + +### 0.13.6 + +- Hotfix release +- Prepare for a new napari version + +### 0.13.5 + +- Small fixes for error reporting +- Fix mask segmentation + +### 0.13.4 + +- Bugfix for outdated profile/pipeline preview + +### 0.13.3 + +- Fix saving roi_info in multiple files and history + +### 0.13.2 + +- Fix showing label in select label tab + +### 0.13.1 + +- Add Haralick measurements +- Add obsep file support + +### 0.13.0 + +- Add possibility of custom input widgets for algorithms +- Switch to napari Colormaps instead of custom one +- Add points visualization +- Synchronization widget for builtin (View menu) napari viewer +- Drop Python 3.6 + +### 0.12.7 + +- Fixes for napari 0.4.6 + +### 0.12.6 + +- Fix prev_mask_get +- Fix cache mechanism on mask change +- Update PyInstaller build + +### 0.12.5 + +- Fix bug in pipeline execute + +### 0.12.4 + +- Fix ROI Mask windows related build (signal not properly connected) + +### 0.12.3 + +- Fix ROI Mask + +### 0.12.2 + +- Fix windows bundle + +### 0.12.1 + +- History of last opened files +- Add ROI annotation and ROI alternatives +- Minor bugfix + +### 0.12.0 + +- Toggle multiple files widget in View menu +- Toggle Left panel in ROI Analysis in View Menu +- Rename Mask Segmentation to ROI Mask +- Add documentation for interface +- Add Batch processing tutorial +- Add information about errors to batch processing output file +- Load image from the batch prepare window +- Add search option in part of list and combo boxes +- Add drag and drop mechanism to load list of files to batch window. + +### 0.11.5 + +- add side view to viewer +- fix horizontal view for Measurements result table + +### 0.11.4 + +- bump to napari 0.3.8 in bundle +- fix bug with not presented segmentation loaded from project +- add frame (1 pix) to image cat from base one based on segmentation +- pin to Qt version to 5.14 + +### 0.11.3 + +- prepare for napari 0.3.7 +- split napari io plugin on multiple part +- better reporting for numpy array via sentry +- fix setting color for mask marking + +### 0.11.2 + +- Speedup image set in viewer using async calls +- Fix bug in long name of sheet with parameters + +### 0.11.1 + +- Add screenshot option in View menu +- Add Voxels measurements + +### 0.11.0 + +- Make sprawl algorithm name shorter +- Unify capitalisation of measurement names +- Add simple measurements to mask segmentation +- Use napari as viewer +- Add possibility to preview additional output of algorithms (In View menu) +- Update names of available Algorithm and Measurement to be more descriptive. + +### 0.10.8 + +- fix synchronisation between viewers in Segmentation Analysis +- fix batch crash on error during batch run, add information about file on which calculation fails +- add changelog preview in Help > About + +### 0.10.7 + +- in measurements, on empty list of components mean will return 0 + +### 0.10.6 + +- fix border rim preview +- fix problem with size of image preview +- zoom with scroll and moving if rectangle zoom is not marked + +### 0.10.5 + +- make PartSeg PEP517 compatible. +- fix multiple files widget on Windows (path normalisation) + +### 0.10.4 + +- fix slow zoom + +### 0.10.3 + +- deterministic order of elements in batch processing. + +### 0.10.2 + +- bugfixes + +### 0.10.1 + +- bugfixes + +### 0.10.0 + +- Add creating custom label coloring. +- Change execs interpreter to python 3.7. +- Add masking operation in Segmentation Mask. +- Change license to BSD. +- Allow select root type in batch processing. +- Add median filter in preview. + +### 0.9.7 + +- fix bug in compare mask + +### 0.9.6 + +- fix bug in loading project with mask +- upgrade PyInstaller version (bug GHSA-7fcj-pq9j-wh2r) + +### 0.9.5 + +- fix bug in loading project in "Segmentation analysis" + +### 0.9.4 + +- read mask segmentation projects +- choose source type in batch +- add initial support to OIF and CZI file format +- extract utils to PartSegCore module +- add automated tests of example notebook +- reversed mask +- load segmentation parameters in mask segmentation +- allow use sprawl in segmentation tool +- add radial split of mask for measurement +- add all measurement results in batch, per component sheet + +### 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 +- create class base updater for update outdated algorithm description +- fix save functions +- fix different bugs + +### 0.9.2.2 + +- extract static data to separated package +- 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 + +### 0.9.2 + +- add pypi base check for update + +- remove resetting image state when change state in same image + +- in stack segmentation add options to picking components from segmentation's + +- in mask segmentation add: + + - preview of segmentation parameters per component, + - save segmentation parameters in save file + - new implementation of batch mode. + +### 0.9.1 + +- Add multiple files widget + +- Add Calculating distances between segmented object and mask + +- Batch processing plan fixes: + + - Fix adding pipelines to plan + - Redesign mask widget + +- modify measurement backend to allow calculate multi channel measurements. + +### 0.9 + +Begin of changelog + + +%package help +Summary: Development documents and examples for PartSeg +Provides: python3-PartSeg-doc +%description help +# PartSeg + + +[](https://badge.fury.io/py/PartSeg) +[](https://anaconda.org/conda-forge/partseg) +[](https://pypi.org/project/partseg) +[](https://partseg.readthedocs.io/en/latest/?badge=latest) +[](https://dev.azure.com/PartSeg/PartSeg/_build/latest?definitionId=1&branchName=develop) +[](https://zenodo.org/badge/latestdoi/166421141) +[](https://doi.org/10.1186/s12859-021-03984-1) +[](https://github.com/4DNucleome/PartSeg/blob/master/License.txt) +[](https://github.com/pre-commit/pre-commit) +[](https://github.com/psf/black) + +[](https://lgtm.com/projects/g/4DNucleome/PartSeg/alerts/) +[](https://lgtm.com/projects/g/4DNucleome/PartSeg/context:python) +[](https://www.codacy.com/gh/4DNucleome/PartSeg/dashboard?utm_source=github.com&utm_medium=referral&utm_content=4DNucleome/PartSeg&utm_campaign=Badge_Grade) +[](https://codecov.io/gh/4DNucleome/PartSeg) +[](https://deepsource.io/gh/4DNucleome/PartSeg/?ref=repository-badge) + +PartSeg is a GUI and a library for segmentation algorithms. PartSeg also provide napari plugins for IO and labels measurement. + +This application is designed to help biologist with segmentation based on threshold and connected components. + + + +## Tutorials + +- Tutorial: **Chromosome 1 (as gui)** [link](https://github.com/4DNucleome/PartSeg/blob/master/tutorials/tutorial-chromosome-1/tutorial-chromosome1_16.md) +- Data for chromosome 1 tutorial [link](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg_samples.zip) +- Tutorial: **Different neuron types (as library)** [link](https://github.com/4DNucleome/PartSeg/blob/master/tutorials/tutorial_neuron_types/Neuron_types_example.ipynb) + +## Installation + +- From binaries: + - [Windows](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-windows.zip) (build on Windows 10) + - [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-linux.zip) (build on Ubuntu 18.04) + - [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.14.6-macos.zip) (build on MacOS Mojave) + +- With pip: + - From pypi: `pip install PartSeg[all]` + - From repository: `pip install git+https://github.com/4DNucleome/PartSeg.git` + +Installation troubleshooting information could be found in wiki: [wiki](https://github.com/4DNucleome/PartSeg/wiki/Instalation-troubleshoot). +If this information does not solve problem you can open [issue](https://github.com/4DNucleome/PartSeg/issues). + +## Running + +If you downloaded binaries, run the `PartSeg` (or `PartSeg.exe` for Windows) file inside the `PartSeg` folder + +If you installed from repository or from pip, you can run it with `PartSeg` command or `python -m PartSeg`. +First option does not work on Windows. + +PartSeg export few commandline options: + +- `--no_report` - disable error reporting +- `--no_dialog` - disable error reporting and error dialog. Use only when running from terminal. +- `segmentation_analysis` - skip launcher and start analysis gui +- `segmentation` - skip launcher and start segmentation gui + +## napari plugin + +PartSeg provides napari plugins for io to allow reading projects format in napari viewer. + +## Save Format + +Saved projects are tar files compressed with gzip or bz2. + +Metadata is saved in data.json file (in json format). +Images/masks are saved as *.npy (numpy array format). + +## Interface + +Launcher. Choose the program that you will launch: + + + +Main window of Segmentation Analysis: + + + +Main window of Segmentation Analysis with view on measurement result: + + + +Window for creating a set of measurements: + + + +Main window of Mask Segmentation: + + + +## Laboratory + +Laboratory of Functional and Structural Genomics +[http://4dnucleome.cent.uw.edu.pl/](http://4dnucleome.cent.uw.edu.pl/) + +## Cite as + +Bokota, G., Sroka, J., Basu, S. et al. PartSeg: a tool for quantitative feature extraction +from 3D microscopy images for dummies. BMC Bioinformatics 22, 72 (2021). +[https://doi.org/10.1186/s12859-021-03984-1](https://doi.org/10.1186/s12859-021-03984-1) + + +## Changelog + +### 0.14.6 - 2022-11-13 + +#### Bug Fixes + +- Fix bug when loading already created project causing hide of ROI layer (#787) + +#### Features + +- Improve error message if segmentation do not fit in ROI Mask (#788) + +### 0.14.5 - 2022-11-09 + +#### Bug Fixes + +- Fix scalebar color (#774) +- Fix bug when saving segmentation parameters in mask analysis (#781) +- Fix multiple errors related to loading a new file in interactive mode (#784) + +#### Features + +- Add an option for ensuring type in EventedDict and use it to validate profiles structures (#776) +- Add an option to create an issue from the error report dialog (#782) +- Add option for the multiline field in algorithm parameters (#766) + +#### Refactor + +- Optimize CLI actions (#772) +- Clean warnings about threshold methods (#783) + +#### Build + +- Bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6 (#775) + +### 0.14.4 - 2022-10-24 + +#### Bug Fixes + +- Fix `get_theme` calls to prepare for napari 0.4.17 (#729) +- Fix sentry tests (#742) +- Fix reporting error in load settings from the drive (#725) +- Fix saving pipeline from GUI (#756) +- Fix profile export/import dialogs (#761) +- Enable the "Compare" button if ROI is available (#765) +- Fix bug in cut with ROI to not make black artifacts (#767) + +#### Features + +- Load alternatives labeling when opening PartSeg projects in napari (#731) +- Add option to toggle scale bar (#733) +- Allow customizing the settings directory using the `PARTSEG_SETTINGS_DIR` environment variable (#751) +- Separate recent algorithms from general application settings (#752) +- Add multiple otsu as threshold method with selection range of components (#710) +- Add function to load components from Mask Segmentation with a background in ROI Analysis (#768) + +#### Miscellaneous Tasks + +- Prepare pyinstaller configuration for napari 0.4.17 (#748) +- Add ruff linter (#754) + +#### Testing + +- Add new build and inspect wheel action (#747) + +#### Build + +- Bump actions/checkout from 2 to 3 (#716) +- Bump actions/download-artifact from 1 to 3 (#709) + +### 0.14.3 - 2022-08-18 + +#### Bug Fixes + +- Fix lack of rendering ROI when load image from segmentation (#694) +- Fix running ROI extraction from napari widget (#695) +- Delay setting image if an algorithm is still running (#627) +- Wrong error report when no component is found in restartable segmentation algorithm. (#633) +- Fix the process of building documentation (#653) + +#### Refactor + +- Clean potential vulnerabilities (#630) + +#### Testing + +- Add more tests for common GUI elements (#622) +- Report coverage per package. (#639) +- Update conda environment to not use PyQt5 in test (#646) +- Add tests files to calculate coverage (#655) + +### 0.14.2 - 2022-05-05 + +#### Bug Fixes + +- Fix bug in save label colors between sessions (#610) +- Register PartSeg plugins before starting napari widgets. (#611) +- Mouse interaction with components works again after highlight. (#620) + +#### Refactor + +- Limit test run (#603) +- Filter and solve warnings in tests (#607) +- Use QAbstractSpinBox.AdaptiveDecimalStepType in SpinBox instead of hardcoded bounds (#616) +- Clean and test `PartSeg.common_gui.universal_gui_part` (#617) + +#### Testing + +- Speedup test by setup cache for pip (#604) +- Setup cache for azure pipelines workflows (#606) + +### 0.14.1 - 2022-04-27 + +#### Bug Fixes + +- Update build wheels and sdist to have proper version tag (#583) +- Fix removing the first measurement entry in the napari Measurement widget (#584) +- Fix compatibility bug for conda Pyside2 version (#595) +- Error when synchronization is loaded, and newly loaded image has different dimensionality than currently loaded. (#598) + +#### Features + +- Use pygments for coloring code in exception window (#591) +- Add option to calculate Measurement per Mask component (#590) + +#### Refactor + +- Refactor the creation batch plan widgets and add tests for it (#587) +- Drop napari bellow 0.4.12 (#592) +- Update the order of ROI Mask algorithms to be the same as in older PartSeg versions (#600) + +### 0.14.0 - 2022-04-14 + +#### Bug Fixes + +- Fix "Show selected" rendering mode in PartSeg ROI Mask (#565) +- Add access by operator `[]` to `pydantic.BaseModel` base structures for keeping backward compatibility (#579) + +#### Features + +- Allow setting zoom factor from the interface in Search Label napari plugin (#538) +- Add controlling of zoom factor of search ROI in main GUI (#540) +- Better serialization mechanism allow for declaration data structure migration locally (#462) +- Make `*.obsep" file possible to load in PartSeg Analysis (#564) +- Add option to extract measurement profile or ROI extraction profile from the batch plan (#568) +- Allow import calculation plan from batch result excel file (#567) +- Improve error reporting when failing to deserialize data (#574) +- Launch PartSeg GUI from napari #581 + +#### Refactor + +- Store PartSegImage.Image channels as separated arrays (#554) +- Remove deprecated modules. (#429) +- Switch serialization backend to `nme` (#569) + +#### Testing + +- Add test of creating AboutDialog (#539) +- Setup test for python 3.10. Disable `class_generator` test for this python (#570) + +### 0.13.15 + +#### Bug Fixes + +- Using `translation` instead of `translation_grid` for shifting layers. (#474) +- Bugs in napari plugins (#478) +- Missing mask when using roi extraction from napari (#479) +- Fix segmentation fault on macos machines (#487) +- Fixes for napari 0.4.13 (#506) + +#### Documentation + +- Create 0.13.15 release (#511) +- Add categories and preview page workflow for the napari hub (#489) + +#### Features + +- Assign properties to mask layer in napari measurement widget (#480) + +#### Build + +- Bump qtpy from 1.11.3 to 2.0.0 in /requirements (#498) +- Bump pydantic from 1.8.2 to 1.9.0 in /requirements (#496) +- Bump sentry-sdk from 1.5.1 to 1.5.2 in /requirements (#497) +- Bump sphinx from 4.3.1 to 4.3.2 in /requirements (#500) +- Bump pyinstaller from 4.7 to 4.8 in /requirements (#502) +- Bump pillow from 8.4.0 to 9.0.0 in /requirements (#501) +- Bump requests from 2.26.0 to 2.27.1 in /requirements (#495) +- Bump numpy from 1.21.4 to 1.22.0 in /requirements (#499) +- Bump numpy from 1.22.0 to 1.22.1 in /requirements (#509) +- Bump sphinx from 4.3.2 to 4.4.0 in /requirements (#510) + +### 0.13.14 + +#### Bug Fixes + +- ROI alternative representation (#471) +- Change additive to translucent in rendering ROI and Mask (#472) + +#### Features + +- Add morphological watershed segmentation (#469) +- Add Bilateral image filter (#470) + +### 0.13.13 + +#### Bug Fixes + +- Fix bugs in the generation process of the changelog for release. (#428) +- Restoring ROI on home button click in compare viewer (#443) +- Fix Measurement name prefix in bundled PartSeg. (#458) +- Napari widgets registration in pyinstaller bundle (#465) +- Hide points button if no points are loaded, hide Mask checkbox if no mask is set (#463) +- Replace Label data instead of adding/removing layers - fix blending layers (#464) + +#### Features + +- Add threshold information in layer annotation in the Multiple Otsu ROI extraction method (#430) +- Add option to select rendering method for ROI (#431) +- Add callback mechanism to ProfileDict, live update of ROI render parameters (#432) +- Move the info bar on the bottom of the viewer (#442) +- Add options to load recent files in multiple files widget (#444) +- Add ROI annotations as properties to napari labels layer created by ROI Extraction widgets (#445) +- Add signals to ProfileDict, remove redundant synchronization mechanisms (#449) +- Allow ignoring updates for 21 days (#453) +- Save all components if no components selected in mask segmentation (#456) +- Add modal dialog for search ROI components (#459) +- Add full measurement support as napari widget (#460) +- Add search labels as napari widget (#467) + +#### Refactor + +- Export common code for load/save dialog to one place (#437) +- Change most of call QFileDialog to more generic code (#440) + +#### Testing + +- Add test for `PartSeg.common_backend` module (#433) + +### 0.13.12 + +#### Bug Fixes + +- Importing the previous version of settings (#406) +- Cutting without masking data (#407) +- Save in subdirectory in batch plan (#414) +- Loading plugins for batch processing (#423) + +#### Features + +- Add randomization option for correlation calculation (#421) +- Add Imagej TIFF writter for image. (#405) +- Mask create widget for napari (#395) +- In napari roi extraction method show information from roi extraction method (#408) +- Add `*[0-9].tif` button in batch processing window (#412) +- Better label representation in 3d view (#418) + +#### Refactor + +- Use Font Awesome instead of custom symbols (#424) + +### 0.13.11 + +#### Bug Fixes + +- Adding mask in Prepare Plan for batch (#383) +- Set proper completion mode in SearchComboBox (#384) +- Showing warnings on the error with ROI load (#385) + +#### Features + +- Add CellFromNucleusFlow "Cell from nucleus flow" cell segmentation method (#367) +- When cutting components in PartSeg ROI mask allow not masking outer data (#379) +- Theme selection in GUI (#381) +- Allow return points from ROI extraction algorithm (#382) +- Add measurement to get ROI annotation by name. (#386) +- PartSeg ROI extraction algorithms as napari plugins (#387) +- Add Pearson, Mander's, Intensity, Spearman colocalization measurements (#392) +- Separate standalone napari settings from PartSeg embedded napari settings (#397) + +#### Performance + +- Use faster calc bound function (#375) + +#### Refactor + +- Remove CustomApplication (#389) + +### 0.13.10 + +- change tiff save backend to ome-tiff +- add `DistanceROIROI` and `ROINeighbourhoodROI` measurements + +### 0.13.9 + +- annotation show bugfix + +### 0.13.8 + +- napari deprecation fixes +- speedup simple measurement +- bundle plugins initial support + +### 0.13.7 + +- add measurements widget for napari +- fix bug in pipeline usage + +### 0.13.6 + +- Hotfix release +- Prepare for a new napari version + +### 0.13.5 + +- Small fixes for error reporting +- Fix mask segmentation + +### 0.13.4 + +- Bugfix for outdated profile/pipeline preview + +### 0.13.3 + +- Fix saving roi_info in multiple files and history + +### 0.13.2 + +- Fix showing label in select label tab + +### 0.13.1 + +- Add Haralick measurements +- Add obsep file support + +### 0.13.0 + +- Add possibility of custom input widgets for algorithms +- Switch to napari Colormaps instead of custom one +- Add points visualization +- Synchronization widget for builtin (View menu) napari viewer +- Drop Python 3.6 + +### 0.12.7 + +- Fixes for napari 0.4.6 + +### 0.12.6 + +- Fix prev_mask_get +- Fix cache mechanism on mask change +- Update PyInstaller build + +### 0.12.5 + +- Fix bug in pipeline execute + +### 0.12.4 + +- Fix ROI Mask windows related build (signal not properly connected) + +### 0.12.3 + +- Fix ROI Mask + +### 0.12.2 + +- Fix windows bundle + +### 0.12.1 + +- History of last opened files +- Add ROI annotation and ROI alternatives +- Minor bugfix + +### 0.12.0 + +- Toggle multiple files widget in View menu +- Toggle Left panel in ROI Analysis in View Menu +- Rename Mask Segmentation to ROI Mask +- Add documentation for interface +- Add Batch processing tutorial +- Add information about errors to batch processing output file +- Load image from the batch prepare window +- Add search option in part of list and combo boxes +- Add drag and drop mechanism to load list of files to batch window. + +### 0.11.5 + +- add side view to viewer +- fix horizontal view for Measurements result table + +### 0.11.4 + +- bump to napari 0.3.8 in bundle +- fix bug with not presented segmentation loaded from project +- add frame (1 pix) to image cat from base one based on segmentation +- pin to Qt version to 5.14 + +### 0.11.3 + +- prepare for napari 0.3.7 +- split napari io plugin on multiple part +- better reporting for numpy array via sentry +- fix setting color for mask marking + +### 0.11.2 + +- Speedup image set in viewer using async calls +- Fix bug in long name of sheet with parameters + +### 0.11.1 + +- Add screenshot option in View menu +- Add Voxels measurements + +### 0.11.0 + +- Make sprawl algorithm name shorter +- Unify capitalisation of measurement names +- Add simple measurements to mask segmentation +- Use napari as viewer +- Add possibility to preview additional output of algorithms (In View menu) +- Update names of available Algorithm and Measurement to be more descriptive. + +### 0.10.8 + +- fix synchronisation between viewers in Segmentation Analysis +- fix batch crash on error during batch run, add information about file on which calculation fails +- add changelog preview in Help > About + +### 0.10.7 + +- in measurements, on empty list of components mean will return 0 + +### 0.10.6 + +- fix border rim preview +- fix problem with size of image preview +- zoom with scroll and moving if rectangle zoom is not marked + +### 0.10.5 + +- make PartSeg PEP517 compatible. +- fix multiple files widget on Windows (path normalisation) + +### 0.10.4 + +- fix slow zoom + +### 0.10.3 + +- deterministic order of elements in batch processing. + +### 0.10.2 + +- bugfixes + +### 0.10.1 + +- bugfixes + +### 0.10.0 + +- Add creating custom label coloring. +- Change execs interpreter to python 3.7. +- Add masking operation in Segmentation Mask. +- Change license to BSD. +- Allow select root type in batch processing. +- Add median filter in preview. + +### 0.9.7 + +- fix bug in compare mask + +### 0.9.6 + +- fix bug in loading project with mask +- upgrade PyInstaller version (bug GHSA-7fcj-pq9j-wh2r) + +### 0.9.5 + +- fix bug in loading project in "Segmentation analysis" + +### 0.9.4 + +- read mask segmentation projects +- choose source type in batch +- add initial support to OIF and CZI file format +- extract utils to PartSegCore module +- add automated tests of example notebook +- reversed mask +- load segmentation parameters in mask segmentation +- allow use sprawl in segmentation tool +- add radial split of mask for measurement +- add all measurement results in batch, per component sheet + +### 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 +- create class base updater for update outdated algorithm description +- fix save functions +- fix different bugs + +### 0.9.2.2 + +- extract static data to separated package +- 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 + +### 0.9.2 + +- add pypi base check for update + +- remove resetting image state when change state in same image + +- in stack segmentation add options to picking components from segmentation's + +- in mask segmentation add: + + - preview of segmentation parameters per component, + - save segmentation parameters in save file + - new implementation of batch mode. + +### 0.9.1 + +- Add multiple files widget + +- Add Calculating distances between segmented object and mask + +- Batch processing plan fixes: + + - Fix adding pipelines to plan + - Redesign mask widget + +- modify measurement backend to allow calculate multi channel measurements. + +### 0.9 + +Begin of changelog + + +%prep +%autosetup -n PartSeg-0.14.6 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-PartSeg -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Apr 11 2023 Python_Bot <Python_Bot@openeuler.org> - 0.14.6-1 +- Package Spec generated |