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Changelog

All notable changes to this project will be documented in this file.

0.16.0 - 2024-10-22

This release drop support for python 3.8 and napari below 0.4.19.

🐛 Bug Fixes

  • Fix error when image changed during segmentation (#1218)
  • Fix pre release tests (#1219)

🧪 Testing

  • [Automatic] Constraints upgrades: h5py, imageio, ipython, napari, numpy, sentry-sdk (#1201)
  • [Automatic] Constraints upgrades: sentry-sdk (#1214)

⚙️ Miscellaneous Tasks

  • Stop using mambaforge in tests (#1203)
  • [pre-commit.ci] pre-commit autoupdate (#1202)
  • [pre-commit.ci] pre-commit autoupdate (#1204)
  • Remove defining default version of language in pre-commit configuration (#1208)
  • [pre-commit.ci] pre-commit autoupdate (#1209)
  • Drop python 3.8 (#1206)
  • Use PublishPipelineArtifact in place of PublishBuildArtifacts to reduce CI fragility (#1213)
  • Update CI configuration to use more modern OS and python versions (#1207)
  • Fix upgrade-dependencies.yamldocs constraints (#1215)
  • [pre-commit.ci] pre-commit autoupdate (#1216)

0.15.4 - 2024-09-27

🚀 Features

  • Add preview of image metadata (#1154)
  • Add option to combine channels using sum and max (#1159)
  • Add metadata viewer as napari widget (#1195)
  • Read channel colors from *.czi metadata (#1198)
  • Use image color when add layer to napari (#1200)

🐛 Bug Fixes

  • Fix selection of custom label colors for napari 0.5.0 (#1138)
  • Add pint call to enforce initialization of unit registry (#1146)
  • Workaround for lack of zsd support in czifile (#1142)
  • Fix preparing data for mahotas.haralick to avoid overflow problem (#1150)
  • Fix use_convex type from int to bool for segmentation algorithms (#1152)
  • Prevent propagation of decreasing contrast limits set by user (#1166)
  • Prevent error on searching component if there is no component (#1167)
  • Fix checking if channel requested by MeasurementProfile exists (#1165)
  • Fix trying to access to just deleted measurement profile from edit window. (#1168)
  • Fix bug in code for checking for survey file (#1174)
  • Fix plugin discovery in bundle to register them in napari viewer (#1175)
  • Fix problem with setting range of auto-generated widget (#1187)
  • Fix reading channel names from single channel czi files (#1194)

🚜 Refactor

  • Make warnings error in tests (#1192)
  • Merge all channel-specific attributes of the Image class (#1191)

📚 Documentation

  • Change homepage URL (#1139)
  • Add link for download macOS arm bundle (#1140)
  • Add changelog for 0.15.4 release
  • Update changelog (#1176)

🧪 Testing

  • [Automatic] Constraints upgrades: napari, sentry-sdk, sympy (#1128)
  • [Automatic] Constraints upgrades: mahotas, numpy, sentry-sdk, sympy (#1145)
  • [Automatic] Constraints upgrades: numpy, tifffile (#1163)
  • [Automatic] Constraints upgrades: napari, sentry-sdk, tifffile (#1169)
  • [Automatic] Constraints upgrades: magicgui, sentry-sdk (#1172)
  • [Automatic] Constraints upgrades: sympy, tifffile (#1177)
  • [Automatic] Constraints upgrades: imageio, napari, numpy (#1180)
  • Constraints upgrades: sentry-sdk and fix tests (#1182)
  • napari==0.5.3 related fixes, Constraints upgrades: imageio, ipython, numpy, qtconsole, scipy, simpleitk, tifffile (#1183)
  • [Automatic] Constraints upgrades: numpy, pydantic (#1188)
  • [Automatic] Constraints upgrades: imagecodecs, pandas, pydantic, sentry-sdk, sympy, tifffile (#1190)

⚙️ Miscellaneous Tasks

  • Speedup tests by use tox-uv (#1141)
  • Get additional dict from PR branch for checking PR title (#1144)
  • Relax numpy constraint (#1143)
  • Allow to skip spellchecking PR title (#1147)
  • [pre-commit.ci] pre-commit autoupdate (#1149)
  • Create only archive with version in name on azures pipeline (#1151)
  • Fix tests for napari from repository (#1148)
  • Use python 3.11 to determine updated packages in PR description (#1160)
  • [pre-commit.ci] pre-commit autoupdate (#1164)
  • [pre-commit.ci] pre-commit autoupdate (#1170)
  • Disable thumbnail generation in napari layer as it is fragile and not used (#1171)
  • [pre-commit.ci] pre-commit autoupdate (#1173)
  • [pre-commit.ci] pre-commit autoupdate (#1178)
  • Fix call of logger to properly pass arguments to messages (#1179)
  • Fix coverage files upload by enable hidden files upload (#1186)
  • [pre-commit.ci] pre-commit autoupdate (#1184)
  • Use PyQt6 in pre-tests (#1196)
  • Add missed code from #1191 (#1197)
  • [pre-commit.ci] pre-commit autoupdate (#1189)
  • Auto add "skip check PR title" label in update dependencies PR (#1199)

Build

  • Remove PyOpenGL-accelerate from dependencies because of numpy incompatibility (#1155)
  • Update install constraints on numpy and qt packages (#1157)
  • Enforce napari 0.5.0 for Qt6 bindings (#1161)
  • Require napari>=0.5.0 only for python 3.9+ (#1162)

0.15.3 - 2024-07-08

🚀 Features

  • Pydantic 2 compatibility (#1084)

🐛 Bug Fixes

  • Fix rendering icons in colormap preview (#1040)
  • Fix test for validation length of message for sentry-sdk 2.0 release (#1098)
  • When fix reader check lowercase extension for validate compatibility (#1097)
  • Fix napari 0.5.0 compatibility (#1116)

🚜 Refactor

  • Fix Qt flags (#1041)
  • Fix qt flags in roi mask code (#1042)
  • Fix qt flags in roi analysis (#1043)
  • Migrate from setup.cfg to pyproject.toml (#1070)

📚 Documentation

  • Allow to use newer release of build docs dependencies (#1057)

🧪 Testing

  • [Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, ipython, numpy, oiffile, pandas, psygnal, pyinstaller, qtconsole, qtpy, sentry-sdk, simpleitk, superqt, tifffile, xlsxwriter (#1020)
  • [Automatic] Constraints upgrades: h5py, imageio, ipython, numpy, packaging, pydantic, pyinstaller, pyqt5, scipy, sentry-sdk, superqt, tifffile, xlsxwriter (#1027)
  • [Automatic] Constraints upgrades: imageio, magicgui, xlsxwriter (#1030)
  • [Automatic] Constraints upgrades: ipykernel, pandas, qtpy (#1032)
  • [Automatic] Constraints upgrades: imageio, ipykernel, ipython, numpy, pandas, psygnal, pygments, pyinstaller, qtconsole, scipy, sentry-sdk, simpleitk (#1035)
  • [Automatic] Constraints upgrades: imagecodecs, imageio, ipykernel, magicgui, pandas, pyinstaller, qtawesome, sentry-sdk, tifffile (#1048)
  • [Automatic] Constraints upgrades: ipykernel, numpy, pandas, partsegcore-compiled-backend, pydantic, scipy, sentry-sdk (#1058)
  • Improve test of PartSegImage (#1072)
  • Improve test suite for PartSegCore (#1077)
  • [Automatic] Constraints upgrades: imageio, ipykernel, local-migrator, napari, numpy, pandas, partsegcore-compiled-backend, pyinstaller, sentry-sdk, tifffile, vispy, xlsxwriter (#1063)
  • [Automatic] Constraints upgrades: magicgui, packaging, psygnal, pyinstaller, sentry-sdk, superqt (#1086)
  • [Automatic] Constraints upgrades: psygnal, pydantic, sentry-sdk, vispy (#1090)
  • [Automatic] Constraints upgrades: h5py, ipykernel, mahotas, pandas, psygnal, pydantic, pyinstaller, qtawesome, scipy, sentry-sdk, superqt (#1092)
  • [Automatic] Constraints upgrades: imageio, tifffile (#1100)
  • [Automatic] Constraints upgrades: pydantic, sentry-sdk, superqt, tifffile (#1102)
  • [Automatic] Constraints upgrades: psygnal, pygments, qtconsole, sentry-sdk, superqt, tifffile (#1105)
  • [Automatic] Constraints upgrades: imagecodecs, magicgui, oiffile, openpyxl, packaging, pydantic, pyinstaller, requests, scipy, sentry-sdk, superqt, sympy, tifffile, vispy (#1107)
  • [Automatic] Constraints upgrades: pydantic (#1112)

⚙️ Miscellaneous Tasks

  • [pre-commit.ci] pre-commit autoupdate (#1019)
  • Remove plugin page preview as it is no longer maintained (#1021)
  • [pre-commit.ci] pre-commit autoupdate (#1022)
  • [pre-commit.ci] pre-commit autoupdate (#1026)
  • [pre-commit.ci] pre-commit autoupdate (#1031)
  • [pre-commit.ci] pre-commit autoupdate (#1034)
  • Use new semgrep configuration (#1039)
  • Upload raw coverage information (#1044)
  • [pre-commit.ci] pre-commit autoupdate (#1036)
  • Run coverage upload in separate steep (#1053)
  • Generate local report in Tests workflow and use proper script for fetch report (#1054)
  • Move coverage back to main workflow (#1055)
  • [pre-commit.ci] pre-commit autoupdate (#1056)
  • [pre-commit.ci] pre-commit autoupdate (#1059)
  • Update actions/upload-artifact and actions/download-artifact from 3 to 4 (#1062)
  • [pre-commit.ci] pre-commit autoupdate (#1064)
  • Group actions update (#1065)
  • [pre-commit.ci] pre-commit autoupdate (#1068)
  • Remove requirement of 2 builds upload to codecov.io (#1073)
  • Re add tests to coverage report (#1074)
  • Switch from setup.cfg to pyproject.toml in workflows (#1076)
  • Fix compiling pyinstaller pre-deps (#1075)
  • Add codespell to pre-commit and fix pointed bugs (#1078)
  • Add new ruff rules and apply them (#1079)
  • [pre-commit.ci] pre-commit autoupdate (#1080)
  • [pre-commit.ci] pre-commit autoupdate (#1081)
  • Fix upgrade depenecies workflow (#1083)
  • Block using mpmath==1.4.0a0 and sentry-sdk 2.0.0a1/a2 in pre-test (#1085)
  • [pre-commit.ci] pre-commit autoupdate (#1089)
  • Fix jupyter failing test by using constraints (#1093)
  • [pre-commit.ci] pre-commit autoupdate (#1091)
  • [pre-commit.ci] pre-commit autoupdate (#1096)
  • Add python 3.12 testing (#1087)
  • Exclude pyside2 on python 3.11 and 3.12 from testing (#1099)
  • [pre-commit.ci] pre-commit autoupdate (#1101)
  • [pre-commit.ci] pre-commit autoupdate (#1103)
  • Bump macos runners to macos-13 (both azure and GHA) (#1113)
  • [pre-commit.ci] pre-commit autoupdate (#1108)
  • Remove pyqt5 from constraints (#1118)
  • Add workflow for releases from GHA (#1117)
  • Add actionlint to CI to early prevent bug in github workflows (#1119)
  • Fix release workflow, by update permissions
  • Check if release notes are properly created (#1122)
  • Proper use enum in checking new version (#1123)
  • Refactor and simplify menu bar creation, add workaround for macOS numpy problem (#1124)
  • Simplify release workflow (#1126)
  • Fix make_release.yml to proper detect release, attempt 3 (#1127)

🛡️ Security

  • (deps) Bump actions/checkout from 3 to 4 (#1029)
  • (deps) Bump conda-incubator/setup-miniconda from 2 to 3 (#1038)
  • (deps) Bump aganders3/headless-gui from 1 to 2 (#1047)
  • (deps) Bump actions/checkout from 3 to 4 (#1045)
  • (deps) Bump hynek/build-and-inspect-python-package from 1 to 2 (#1050)
  • (deps) Bump actions/setup-python from 4 to 5 (#1046)
  • (deps) Bump github/codeql-action from 2 to 3 (#1051)
  • (deps) Bump peter-evans/create-pull-request from 5 to 6 (#1067)
  • (deps) Bump codecov/codecov-action from 3 to 4 (#1066)

Build

  • Fix not bundling Font Awesome 6 Free-Solid-900.otf file to executable (#1114)
  • Update readme and release to point to GitHub releases (#1115)
  • Do not create archive twice when create bundle (#1120)
  • Enable macOS-arm bundle builds (#1121)

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)

⚙️ Miscellaneous Tasks

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

0.15.1 - 2023-08-08

🚀 Features

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

🐛 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 platform (#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 dimension (#992)
  • Fix bug that lead to corrupted state when saving calculation plan to excel file (#995)
  • Enable python 3.11 test on CI, fix minor errors (#869)

🧪 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)

⚙️ Miscellaneous Tasks

  • [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)
  • [pre-commit.ci] pre-commit autoupdate (#1008)

0.15.0 - 2023-05-30

🚀 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 labels 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 algorithms (#958)
  • Add napari widget to copy labels along z-axis (#968)

🐛 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 napari repository (#817)
  • Fix 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 proper place for proper visualization (#856)
  • Fix tests of napari widgets (#862)
  • Fix build of bundle for a new psygnal release (#863)
  • Fix minimal requirements pipeline (#877)
  • 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)

🚜 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)

📚 Documentation

  • Update README and project metadata (#805)
  • Create release notes for PartSeg 0.15.0 (#971)

🎨 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)
  • [Automatic] Constraints upgrades: imageio, pandas, pydantic, pyopengl-accelerate, sentry-sdk, xlsxwriter (#970)

⚙️ 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)
  • Update codecov configuration to wait on two reports before post information (#934)
  • [pre-commit.ci] pre-commit autoupdate (#945)
  • Migrate from nme to local_migrator (#951)
  • [pre-commit.ci] pre-commit autoupdate (#956)
  • [pre-commit.ci] pre-commit autoupdate (#964)

🛡️ Security

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

Bugfix

  • Fix bug with generation of form for model with hidden field (#920)

Dep

  • [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)

0.14.6 - 2022-11-13

🐛 Bug Fixes

  • Fix bug when loading already created project causing hide of ROI layer (#787)

0.14.5 - 2022-11-09

🚀 Features

  • Add option for ensure type in EventedDict and use it to validate profiles structures (#776)
  • Add option to create issue from error report dialog (#782)
  • Add option for multiline field in algorithm parameters (#766)

🐛 Bug Fixes

  • Fix scalebar color (#774)
  • Fix bug when saving segmentation parameters in mask analysis (#781)
  • Fix multiple error related to loading new file in interactive mode (#784)

🚜 Refactor

  • Optimize CLI actions (#772)
  • Clean warnings about threshold methods (#783)

Build

  • (deps) Bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6 (#775)

0.14.4 - 2022-10-24

🚀 Features

  • Load alternatives labeling when open PartSeg projects in napari (#731)
  • Add option to toggle scale bar (#733)
  • Allow customize 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 background in ROI Analysis (#768)

🐛 Bug Fixes

  • Fix typos
  • Fix get_theme calls to prepare for napari 0.4.17 (#729)
  • Fix saving pipeline from GUI (#756)
  • Fix profile export/import dialogs (#761)
  • Enable compare button if ROI is available (#765)
  • Fix bug in cut with roi to do not make black artifacts (#767)

🧪 Testing

  • Add new build and inspect wheel action (#747)

⚙️ Miscellaneous Tasks

  • Prepare pyinstaller configuration for napari 0.4.17 (#748)
  • Add ruff linter (#754)

Bugfix

  • Fix sentry tests (#742)
  • Fix reporting error in load settings from drive (#725)

Build

  • (deps) Bump actions/checkout from 2 to 3 (#716)
  • (deps) Bump actions/download-artifact from 1 to 3 (#709)

0.14.3 - 2022-08-18

🐛 Bug Fixes

  • Delay setting image if an algorithm is still running (#627)
  • Wrong error report when no component is found in restartable segmentation algorithm. (#633)
  • Fix process of build 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)

Build

  • (deps) Bump qtpy from 2.0.1 to 2.1.0 in /requirements (#613)
  • (deps) Bump pyinstaller from 5.0.1 to 5.1 in /requirements (#629)
  • (deps) Bump tifffile from 2022.4.28 to 2022.5.4 in /requirements (#619)
  • (deps) Bump codecov/codecov-action from 1 to 3 (#637)
  • (deps) Bump requests from 2.27.1 to 2.28.0 in /requirements (#647)
  • (deps) Bump actions/setup-python from 3 to 4 (#648)
  • (deps) Bump pyqt5 from 5.15.6 to 5.15.7 in /requirements (#652)
  • (deps) Bump sentry-sdk from 1.5.12 to 1.6.0 in /requirements (#659)
  • (deps) Bump numpy from 1.22.4 to 1.23.0 in /requirements (#660)
  • (deps) Bump lxml from 4.9.0 to 4.9.1 in /requirements (#665)
  • (deps) Bump mahotas from 1.4.12 to 1.4.13 in /requirements (#662)
  • (deps) Bump pyinstaller from 5.1 to 5.2 in /requirements (#667)

0.14.2 - 2022-05-05

🐛 Bug Fixes

  • Fix bug in save label colors between sessions (#610)
  • Register PartSeg plugins before start napari widgets. (#611)
  • Mouse interaction with components work 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)

📚 Documentation

  • Update changelog (#621)

🧪 Testing

  • Speedup test by setup cache for pip (#604)
  • Setup cache for azure pipelines workflows (#606)

Build

  • (deps) Bump sentry-sdk from 1.5.10 to 1.5.11 in /requirements (#615)

0.14.1 - 2022-04-27

🚀 Features

  • Use pygments for coloring code in exception window (#591)
  • Add option to calculate Measurement per Mask component (#590)

🐛 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 compatybility bug for conda Pyside2 version (#595)
  • Error when synchronization is loaded and new iloaded image has different dimensionality than currently loaded. (#598)

🚜 Refactor

  • Refactor the create batch plan widgets and add test for it (#587)
  • Drop napari below 0.4.12 (#592)
  • Update the order of ROI Mask algorithms to be the same as in older PartSeg versions (#600)

Build

  • (deps) Bump partsegcore-compiled-backend from 0.13.11 to 0.14.0 in /requirements (#582)
  • (deps) Bump simpleitk from 2.1.1 to 2.1.1.2 in /requirements (#589)
  • (deps) Bump pyinstaller from 4.10 to 5.0 in /requirements (#586)

0.14.0 - 2022-04-14

🚀 Features

  • Allow to set zoom factor from 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 batch plan (#568)
  • Allow import calculation plan from batch result excel file (#567)
  • Improve error reporting when fail to deserialize data (#574)
  • Launch PartSeg GUI from napari (#581)

🐛 Bug Fixes

  • Fix "Show selected" rendering mode in PartSeg ROI Mask (#565)

🚜 Refactor

  • Store PartSegImage.Image channels as separated arrays (#554)
  • Remove deprecated modules. (#429)
  • Switch serialization backen to nme (#569)

📚 Documentation

  • Update changelog and add new badges to readme (#580)

🧪 Testing

  • Add test of creating AboutDialog (#539)
  • Setup test for python 3.10. Disable class_generator test for this python (#570)

Bugfix

  • Add access by operator [] to pydantic.BaseModel base structures for keep backward compatybility (#579)

Build

  • (deps) Bump sentry-sdk from 1.5.2 to 1.5.3 in /requirements (#512)
  • (deps) Bump ipython from 8.0.0 to 8.0.1 in /requirements (#513)
  • (deps) Bump pandas from 1.3.5 to 1.4.0 in /requirements (#514)
  • (deps) Bump oiffile from 2021.6.6 to 2022.2.2 in /requirements (#521)
  • (deps) Bump numpy from 1.22.1 to 1.22.2 in /requirements (#524)
  • (deps) Bump tifffile from 2021.11.2 to 2022.2.2 in /requirements (#523)
  • (deps) Bump qtpy from 2.0.0 to 2.0.1 in /requirements (#522)
  • (deps) Bump sentry-sdk from 1.5.3 to 1.5.4 in /requirements (#515)
  • (deps) Bump pyinstaller from 4.8 to 4.10 in /requirements (#545)
  • (deps) Bump pillow from 9.0.0 to 9.0.1 in /requirements (#549)
  • (deps) Bump sphinx from 4.4.0 to 4.5.0 in /requirements (#561)
  • (deps) Bump tifffile from 2022.2.9 to 2022.3.25 in /requirements (#562)
  • (deps) Bump sympy from 1.10 to 1.10.1 in /requirements (#556)
  • (deps) Bump sentry-sdk from 1.5.7 to 1.5.8 in /requirements (#557)

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 writer 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