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Changelog

0.15.2 - 2023-08-28

Bug Fixes

  • Fix range threshold selection of algorithms (#1009)
  • When run batch check if file extension is supported by loader (#1016)
  • Do not allow to select and render corrupted batch plans (#1015)

Testing

  • [Automatic] Constraints upgrades: imagecodecs, ipykernel, magicgui, psygnal, scipy, superqt, tifffile (#1011)
  • [Automatic] Constraints upgrades: imageio, pyinstaller, tifffile (#1018)

Ci

  • Use faster version of black (#1010)
  • [pre-commit.ci] pre-commit autoupdate (#1013)

0.15.1 - 2023-08-09

Bug Fixes

  • Fix possible problem of double registration napari plugin in PartSeg bundle (#974)
  • Bump OS versions for part of testing workflows. (#977)
  • Bump os version for main tests workflow. (#979)
  • Ensure that the module PartSegCore.channel_class is present in bundle (#980)
  • Lower npe2 schema version to work with older napari version (#981)
  • Generate test report per platfom (#978)
  • Importing plugins in bundle keeping proper module names (#983)
  • Fix napari repo workflow (#985)
  • Fix bug in read tiff files with double Q in axes but one related to dummy dimmension (#992)
  • Fix bug that lead to corupted state when saving calculation plan to excel file (#995)
  • Enable python 3.11 test on CI, fix minor errors (#869)

Features

  • Allow to save multiple napari image layers to single tiff file (#1000)
  • Add option to export batch project with data (#996)

Testing

  • [Automatic] Constraints upgrades: imageio, ipython, psygnal, scipy, sentry-sdk (#975)
  • [Automatic] Constraints upgrades: h5py, imagecodecs, imageio, ipykernel, napari, numpy, pandas, pydantic, pyinstaller, scipy, sentry-sdk, tifffile, vispy (#986)
  • [Automatic] Constraints upgrades: imagecodecs, sentry-sdk, tifffile (#997)
  • [Automatic] Constraints upgrades: ipykernel, pydantic (#1002)
  • [Automatic] Constraints upgrades: numpy, pygments, sentry-sdk, superqt (#1007)

Ci

  • [pre-commit.ci] pre-commit autoupdate (#973)
  • [pre-commit.ci] pre-commit autoupdate (#982)
  • [pre-commit.ci] pre-commit autoupdate (#987)
  • [pre-commit.ci] pre-commit autoupdate (#988)
  • [pre-commit.ci] pre-commit autoupdate (#991)
  • [pre-commit.ci] pre-commit autoupdate (#998)
  • [pre-commit.ci] pre-commit autoupdate (#1004)
  • Change markdown linter from pre-commit to mdformat (#1006)

0.15.0 - 2023-05-30

Bug Fixes

  • Print all exceptions instead of the latest one in exception dialog (#799)
  • Fix ROIExtractionResult __str__and __repr__ to use ROIExtractionResult not SegmentationResult (#810)
  • Fix code to address changes in the napari repository (#817)
  • Fix the problem with resize of multiline widgets (#832)
  • Fix tox configuration to run all required tests (#840)
  • Fix MSO step_limit description in GUI (#843)
  • Fix redefined-while-unusedimport code for python 3.9.7 (#844)
  • Fix warnings reported by Deepsource (#846)
  • Ensure that "ROI" layer is in the proper place for proper visualization (#856)
  • Fix tests of napari widgets (#862)
  • Fix build of the bundle for a new psygnal release (#863)
  • Fix minimal requirements pipeline (#877)
  • Fix bug with generation of form for the model with hidden field (#920)
  • Update pyinstaller configuration (#926)
  • Use text icon, not pixmap icon in colormap and labels list (#938)
  • Resolve warnings when testing custom save dialog. (#941)
  • Add padding zeros for component num when load Mask seg file to ROI GUI (#944)
  • Proper calculate bounds for watershed napari widget (#969)
  • Fix bug in the wrong order of axis saved in napari contribution (#972)

Dependency

  • [Automatic] Dependency upgrades (#824)
  • [Automatic] Dependency upgrades (#828)
  • [Automatic] Dependency upgrades: ipykernel, packaging (#838)
  • [Automatic] Dependency upgrades: imageio, ipykernel, napari, numpy, sentry (#850)
  • [Automatic] Dependency upgrades: imagecodecs, ipykernel, numpy, psygnal (#859)
  • [Automatic] Dependency upgrades: pydantic, pygments, xlsxwriter (#874)
  • [Automatic] Dependency upgrades: imageio, packaging, scipy, xlsxwriter (#878)
  • [Automatic] Dependency upgrades: ipykernel, requests, sentry, xlsxwriter (#884)
  • [Automatic] Dependency upgrades: h5py, imagecodecs, imageio, ipykernel, pandas, sentry, tifffile (#889)
  • [Automatic] Dependency upgrades: ipython, pyqt5 (#893)
  • [Automatic] Dependency upgrades: imageio, ipykernel, ipython, numpy, openpyxl, psygnal, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, tifffile, xlsxwriter (#897)
  • [Automatic] Dependency upgrades: imageio, psygnal (#905)
  • [Automatic] Dependency upgrades: ipython, magicgui, scipy, sentry-sdk, tifffile (#906)
  • [Automatic] Dependency upgrades: imagecodecs, imageio, ipykernel, openpyxl, pydantic, pyinstaller, qtawesome, qtconsole, sentry-sdk, tifffile, xlsxwriter (#908)
  • [Automatic] Dependency upgrades: imageio, ipykernel, ipython, pandas, psygnal, pydantic, pygments, pyinstaller, qtpy, sentry-sdk, tifffile (#917)

Documentation

  • Update README and project metadata (#805)

Features

  • Add PARTSEG_SENTRY_URL env variable support and basic documentation about error reporting (#802)
  • Allow to see underlying exception when show warning caused by exception (#829)
  • Add voxel size measurement and allow to overwrite voxel size in batch (#853)
  • Add alpha support for Qt6 (#866)
  • Add option to create projection alongside z-axis (#919)
  • Add napari image custom representation for better error report via sentry (#861)
  • Add import and export operation for labels and colormaps (#936)
  • Implement napari widgets for colormap and lables control (#935)
  • Add forget all button to multiple files widget (#942)
  • Do not abort processing whole mask segmentation project during exception on single component (#943)
  • Add distance based watersheed to flow methods (#915)
  • Add napari widgets for all group of algoritms (#958)
  • Add napari widget to copy lables along z-axis (#968)

Miscellaneous Tasks

  • Improve ruff configuration, remove isort (#815)
  • Use fail_on_no_env feature from tox-gh-actions (#842)
  • Add python 3.11 to list of supported versions (#867)
  • Disable python 3.11 test because of timeout (#870)
  • Bump ruff to 0.0.218, remove flake8 from pre-commit (#880)
  • Replace GabrielBB/xvfb-action@v1 by aganders3/headless-gui, part 2 (#887)
  • Better minimal requirements test (#888)
  • Improve regexp for proper generate list of packages in update report (#894)
  • Add check for PR title (#933)
  • Migrate from nme to local_migrator (#951)

Refactor

  • Simplify and refactor github workflows. (#864)
  • Better load Mask project in Roi Analysis (#921)
  • Use more descriptive names in pylint: disable (#922)
  • Remove pkg_resources usage as it is deprecated (#967)
  • Convert napari plugin to npe2 (#966)

Security

  • Bump peter-evans/create-pull-request from 4 to 5 (#928)

Styling

  • Change default theme to dark, remove blinking windows on startup. (#809)

Testing

  • [Automatic] Dependency upgrades: packaging, pyinstaller, pyopengl-accelerate, tifffile, xlsxwriter (#932)
  • [Automatic] Constraints upgrades: fonticon-fontawesome6, imageio, numpy, partsegcore-compiled-backend, pygments, sentry-sdk (#937)
  • [Automatic] Constraints upgrades: imageio, ipython, pandas, requests, sentry-sdk (#948)
  • [Automatic] Constraints upgrades: ipython, nme, qtconsole, requests, sentry-sdk (#955)
  • [Automatic] Constraints upgrades: ipykernel, local-migrator, pyinstaller, sentry-sdk, sympy (#957)
  • [Automatic] Constraints upgrades: sentry-sdk, xlsxwriter (#959)
  • [Automatic] Constraints upgrades: requests (#961)

Ci

  • Update codecov configuration to wait on two reports before post information (#934)
  • [pre-commit.ci] pre-commit autoupdate (#945)
  • [pre-commit.ci] pre-commit autoupdate (#956)
  • [pre-commit.ci] pre-commit autoupdate (#964)

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