Code

Update 4.2 AI build#16

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Merged

emilroz merged 195 commits intoglencoesoftware:compat-4-2-aiglencoesoftware/CellProfiler:compat-4-2-aifrom DavidStirling:compat-4-2-aiDavidStirling/CellProfiler:compat-4-2-aiCopy head branch name to clipboardApr 26, 2024

+3,606-853

Commits

Commits on Oct 22, 2021

• crop the volume before computing SA for big speed increases (CellProfiler#4472)

  bethac07

  authored
  0278c17

• don't convert images after masking (CellProfiler#4473)

  bethac07

  authored
  d1831ca

Commits on Nov 4, 2021

• Improve JSON handling

  DavidStirling

  committed
  b300b4d

Commits on Nov 5, 2021

• Merge pull request CellProfiler#4479 from CellProfiler/jsonpipe

  Show description for a90e17e
  alicelucas

  authored
  a90e17e

Commits on Jan 18, 2022

• Update threshold.py (CellProfiler#4468)

  bethac07

  authored
  95d4343

Commits on Jan 19, 2022

• Improve java detection in builds (CellProfiler#4444)

  Show description for f8506d2
  

  DavidStirling

  and

  David Stirling

  authored
  f8506d2

• Ensure rescaled GrayToColor images remain within float range (CellProfiler#4445)

  Show description for 8e961a0
  

  DavidStirling

  and

  David Stirling

  authored
  8e961a0

• Fix post_group LAP crash when a frame lacks data (CellProfiler#4450)

  Show description for 394f229
  

  DavidStirling

  and

  David Stirling

  authored
  394f229

• Revise workspace viewer default colors (CellProfiler#4455)

  Show description for 7392dc4
  

  DavidStirling

  and

  David Stirling

  authored
  7392dc4

• Support display of text-based measurements (CellProfiler#4447)

  Show description for 145ed68
  

  DavidStirling

  and

  David Stirling

  authored
  145ed68

• ExportToDatabase bug fixes (CellProfiler#4449)

  Show description for 9226ca2
  

  DavidStirling

  and

  David Stirling

  authored
  9226ca2

• Add convex hull mode to FillObjects (CellProfiler#4451)

  Show description for 8cb000b
  

  Jihyeon-Je

  and

  David Stirling

  authored
  8cb000b

• Fix interpolation functions (CellProfiler#4454)

  Show description for bc5764f
  

  DavidStirling

  and

  David Stirling

  authored
  bc5764f

• Add debug interpreter (CellProfiler#4458)

  Show description for 93ec31a
  

  3 peopleauthored
  93ec31a

• Added Z coordinates and 3D flag to exporttodatabase (CellProfiler#4474)

  Show description for c5b6caf
  rsenft1

  authored
  c5b6caf

• Fix issue with downsampling when advanced watershed features are on (CellProfiler#4478)

  Show description for d98e553
  rsenft1

  authored
  d98e553

• Reduce the memory usage of MeasureObjectNeighbors (CellProfiler#4483)

  Show description for 5c990f2
  LukeOZN

  authored
  5c990f2

Commits on Feb 1, 2022

• updated marching_cubes function name (CellProfiler#4499)

  Show description for 6dee40c
  

  callum-jpg

  and

  Callum Tromans-Coia

  authored
  6dee40c

Commits on Feb 14, 2022

• Update resize.py

  Show description for b65928a
  bdiazroh

  committed
  b65928a

• Update resizeobjects.py

  Show description for 196e1eb
  bdiazroh

  committed
  196e1eb

Commits on Feb 15, 2022

• Update resize.py

  bdiazroh

  committed
  fda2792

• Update resizeobjects.py

  bdiazroh

  committed
  2872ab2

Commits on Feb 16, 2022

• Update upgrade_settings

  bdiazroh

  committed
  fde416e

Commits on Feb 17, 2022

• Allow build with Python 3.9.x (CellProfiler#4503)

  ximion

  authored
  1203165

• fix composite image test (CellProfiler#4500)

  bethac07

  authored
  edc572d

• Add option to disable bit depth conversion in SaveImages (CellProfiler#4452)

  Show description for 723cc1e
  

  3 peopleauthored
  723cc1e

• Resolves CellProfiler#4490 by adding in a description of correspondence vectors for MeasureTexture (CellProfiler#4504)

  Show description for cd72894
  rsenft1

  authored
  cd72894

• fixed 3d cmap (CellProfiler#4510)

  Show description for 7fd8c1c
  

  callum-jpg

  and

  Callum Tromans-Coia

  authored
  7fd8c1c

• Update resize.py

  bdiazroh

  committed
  d649355

Commits on Feb 18, 2022

• Add tests for resize volume

  bdiazroh

  committed
  ae6351f

• Merge pull request CellProfiler#4508 from bdiazroh/master

  Show description for a7a16b3
  gnodar01

  authored
  a7a16b3

Commits on Mar 15, 2022

• Fix an error introduced in commit 7fd8c1c (CellProfiler#4516)

  Show description for 30a7871
  callum-jpg

  authored
  30a7871

Commits on Jul 11, 2022

• Include tifffile dependency short term fix for CellProfiler#4549 (CellProfiler#4553)

  rsenft1

  authored
  d275def

• Fix issue in displayScatterPlot causing Y axis objects to grab the x axis value (CellProfiler#4561)

  rsenft1

  authored
  250c48c

• Fixed typo: "Alican blue" -> "Alcian blue" (CellProfiler#4520)

  Show description for 9a42d1e
  crisluengo

  authored
  9a42d1e

• Fix tests related to CellProfiler#4520 (CellProfiler#4562)

  Show description for 53e0f48
  bethac07

  authored
  53e0f48

• Update signing certificate (CellProfiler#4521)

  bethac07

  authored
  1e4e8a7

Commits on Jul 15, 2022

• Added ExpandOrShrink, CombineObjects and MedialAxis to cellprofiler-library (CellProfiler#4554)

  Show description for 69d4f26
  

  callum-jpg

  and

  bethac07

  authored
  69d4f26

• Issues/4436 rsctc (CellProfiler#4532)

  Show description for 5e81f52
  

  rsenft1

  and

  callum-jpg

  authored
  5e81f52

• Issues/4542 (CellProfiler#4543)

  Show description for 1bef0ff
  vbruttin

  authored
  1bef0ff

• Use correct scaler, populate choices

  bethac07

  committed
  a109f9d

Commits on Jul 16, 2022

• Fix grid range in 3D

  Show description for e2a1799
  bethac07

  committed
  e2a1799

• Add image ordering info to documentation

  bethac07

  committed
  2a3ef11

• Check if volumetric in imshow_color

  bethac07

  committed
  01e351c

• Fix upgrade_settings

  bethac07

  committed
  9dfb8b6

• Pass in volumetric and normalize

  bethac07

  committed
  2381774

• fix failing test

  bethac07

  committed
  f3a11e7

• Force z planes to stay in range

  bethac07

  committed
  d7151f4

Commits on Jul 17, 2022

• Allow fuzzy column matching in FilterObjects

  bethac07

  committed
  271c8fd

• Index with tuples rather than lists

  Show description for efbb28e
  gnodar01

  committed
  efbb28e

Commits on Jul 18, 2022

• Resolve final non-tuple MD indexing error

  Show description for 572d597
  gnodar01

  committed
  572d597

• Display data on image enhancement (CellProfiler#4539)

  Show description for 2685598
  callum-jpg

  authored
  2685598

• dont' need to elongate names to pass

  bethac07

  committed
  948e64e

• Fix version typo in comments

  gnodar01

  committed
  4320055

• Fix values check

  Show description for d36f2a5
  gnodar01

  committed
  d36f2a5

• Refactor so that fuzzy settings live in Rules

  bethac07

  committed
  45ec7c8

• Merge pull request CellProfiler#4576 from CellProfiler/numpy123support

  Show description for ab0c508
  gnodar01

  authored
  ab0c508

• Remove unused constants

  Show description for 95b6ac4
  gnodar01

  committed
  95b6ac4

• Cosmetic fixes

  bethac07

  committed
  65d48df

• Merge pull request CellProfiler#4578 from CellProfiler/core-100

  Show description for f62dbd2
  gnodar01

  authored
  f62dbd2

• FlagImage, at least for rules

  bethac07

  committed
  6b1f00f

• ClassifyObjects

  bethac07

  committed
  1aa69fc

• Added more information about saving images in subfolders (CellProfiler#4579)

  rsenft1

  authored
  e0163c6

• Add fuzzy measurements for loading

  bethac07

  committed
  38848af

Commits on Jul 19, 2022

• Finally working version

  bethac07

  committed
  c0fa851

• Avoid case where the object_count is nan

  bethac07

  committed
  e391505

• Add test

  bethac07

  committed
  a8cb292

Commits on Jul 20, 2022

• GUI pref for ignoring errors, flag for headless

  bethac07

  committed
  54efee3

• Force per-parent labels to be consecutive

  bethac07

  committed
  d40af5f

Commits on Jul 21, 2022

• Make sure required columns for GCTs are exported

  bethac07

  committed
  a40bcc5

• New way to make batch commands

  bethac07

  committed
  b50d8fb

Commits on Jul 22, 2022

• Set up test workflow (CellProfiler#4584)

  Show description for 002747e
  gnodar01

  authored
  002747e

• Don't kill other tests if one fails

  bethac07

  authored
  130308a

• Merge pull request CellProfiler#4592 from CellProfiler/finish_tests

  Show description for 11b8cd4
  gnodar01

  authored
  11b8cd4

• fix index issue, refactor

  bethac07

  committed
  909aa5c

• Don't run on draft PRs, run on pushes to other PRs

  bethac07

  authored
  d0d54f8

Commits on Jul 25, 2022

• Merge pull request CellProfiler#4595 from CellProfiler/update_test_runner

  Show description for 6748913
  gnodar01

  authored
  6748913

• Fix syntax error

  gnodar01

  committed
  c2bd53a

• Merge pull request CellProfiler#4596 from CellProfiler/update_test_runner

  Show description for 16853bd
  gnodar01

  authored
  16853bd

• Add classifier tests

  bethac07

  committed
  c44a3f8

• catch "0 objects to classify" errors

  bethac07

  committed
  afd3a5d

Commits on Jul 26, 2022

• Make a minor formatting adjustment

  gnodar01

  committed
  725d10a

• Merge pull request CellProfiler#4569 from CellProfiler/issues/4424

  Show description for 50cf1f9
  gnodar01

  authored
  50cf1f9

• Add link to ASCII character codes wiki

  gnodar01

  committed
  7256a1c

• Merge pull request CellProfiler#4568 from CellProfiler/issues/4382

  Show description for 6da16a9
  gnodar01

  authored
  6da16a9

• Merge pull request CellProfiler#4572 from CellProfiler/issues/4571

  Show description for 5c1b072
  gnodar01

  authored
  5c1b072

• Merge pull request CellProfiler#4573 from CellProfiler/issues/4567

  Show description for d910c5f
  gnodar01

  authored
  d910c5f

• Merge pull request CellProfiler#4570 from CellProfiler/issues/4530

  Show description for a153c9d
  gnodar01

  authored
  a153c9d

• Merge pull request CellProfiler#4574 from CellProfiler/issues/4480

  Show description for 20a3c61
  gnodar01

  authored
  20a3c61

• Merge pull request CellProfiler#4575 from CellProfiler/issues/4370

  Show description for 0f4c42d
  gnodar01

  authored
  0f4c42d

Commits on Jul 27, 2022

• Merge pull request CellProfiler#4582 from CellProfiler/issues/4467

  Show description for 0d4f4d7
  gnodar01

  authored
  0d4f4d7

• Merge pull request CellProfiler#4587 from CellProfiler/issues/4586

  Show description for ec60333
  gnodar01

  authored
  ec60333

• Merge pull request CellProfiler#4588 from CellProfiler/issues/4548

  Show description for 7e98b5d
  gnodar01

  authored
  7e98b5d

Commits on Jul 28, 2022

• Merge pull request CellProfiler#4585 from CellProfiler/issues/4527

  Show description for 6ab8a82
  gnodar01

  authored
  6ab8a82

• Rename old function

  bethac07

  committed
  1869020

• Merge pull request CellProfiler#4589 from CellProfiler/issues/4413

  Show description for cc9e038
  gnodar01

  authored
  cc9e038

• Remove CPA and add CP3 and CP4 citations (CellProfiler#4598)

  Show description for 128e6ec
  rsenft1

  authored
  128e6ec

• passing measuremnet feature to library eos

  callum-jpg

  committed
  bcfd0ca

• added measurement for expand and shrink

  callum-jpg

  committed
  065200d

• bump centrosome

  bethac07

  committed
  120ce8d

Commits on Jul 29, 2022

• Merge pull request CellProfiler#4600 from CellProfiler/centrosome_121

  Show description for fae1c32
  gnodar01

  authored
  fae1c32

• Merge pull request CellProfiler#4599 from CellProfiler/eos-measurement-library

  Show description for 6c6aa1d
  gnodar01

  authored
  6c6aa1d

• Bump CP version (CellProfiler#4601)

  Show description for e2a2d66
  gnodar01

  authored
  e2a2d66

• bump pyinstaller

  bethac07

  authored
  4d07188

• Bump numpy to 1.23

  bethac07

  authored
  69db4fe

• Updated setup-java, use LTS

  bethac07

  authored
  6a637d6

Commits on Aug 1, 2022

• Put validate in "if", remove print

  bethac07

  committed
  25ca710

• Fix java location

  bethac07

  authored
  3b45fff

• Merge pull request CellProfiler#4603 from CellProfiler/issues/4602

  Show description for e700994
  gnodar01

  authored
  e700994

• Add widget_inspector option

  Show description for 6fbc3fa
  gnodar01

  committed
  6fbc3fa

Commits on Aug 2, 2022

• Fix hyperlink

  gnodar01

  committed
  83a9452

• Merge pull request CellProfiler#4607 from CellProfiler/quick_docs_fix

  Show description for 1f9f94a
  gnodar01

  authored
  1f9f94a

• Add widget inspector to preferences

  gnodar01

  committed
  28d4fb8

• Inject widget inspector on set

  gnodar01

  committed
  a58d30b

• Generalize dynamic menu injection/removal

  gnodar01

  committed
  0b09b4c

• Add documentation for widget inspector

  gnodar01

  committed
  6a791be

Commits on Aug 3, 2022

• Merge pull request CellProfiler#4605 from CellProfiler/debugger_flag

  Show description for f56bd10
  gnodar01

  authored
  f56bd10

• Added additional save features to SaveCroppedObjects (CellProfiler#4545)

  Show description for a8d6a8b
  

  3 peopleauthored
  a8d6a8b

Commits on Aug 9, 2022

• [Refactoring] making the code more Pythonic (CellProfiler#4610)

  Show description for 5b70c43
  maldil

  authored
  5b70c43

• Bump python-bioformats to 4.0.6 (CellProfiler#4612)

  bethac07

  authored
  1868db3

Commits on Aug 10, 2022

• Bump version refs to 4.2.3rc1 (CellProfiler#4613)

  gnodar01

  authored
  6cfc321

• Update welcome screen links (CellProfiler#4614)

  bethac07

  authored
  adad818

• Bump to 4.2.3 (CellProfiler#4615)

  bethac07

  authored
  83652bd

• library needs an init to be packaged (CellProfiler#4616)

  bethac07

  authored
  0253f00

Commits on Aug 11, 2022

• Create __init__.py

  bethac07

  authored
  059e1ea

• v4.2.4rc1

  bethac07

  committed
  8eaf28d

• v4.2.4

  bethac07

  committed
  fd829f8

Commits on Aug 15, 2022

• Make pip upgrade and setuptools and wheel install on Windows (CellProfiler#4622)

  Show description for 534b646
  bethac07

  authored
  534b646

• Add --no-use-pep517 to Windows

  bethac07

  authored
  4e353fa

Commits on Nov 23, 2022

• fix subsample values >1 overwriting input image

  callum-jpg

  committed
  31867e3

Commits on Dec 13, 2022

• Merge pull request CellProfiler#4697 from CellProfiler/issues/CellProfiler#4670

  Show description for 9c15cb3
  bethac07

  authored
  9c15cb3

• pin skimage due to 4663

  bethac07

  authored
  834bd8a

Commits on Dec 14, 2022

• Patch headless creation of properties files (CellProfiler#4698)

  bethac07

  authored
  6f3e091

• Update resize.py (CellProfiler#4701)

  bdiazroh

  authored
  a5bcc12

• Catch "no objects of any type" (CellProfiler#4699)

  bethac07

  authored
  7083ea7

• v4.2.5

  bethac07

  committed
  898a2f0

• Use distribution 4.2.x branch

  bethac07

  committed
  00fe315

• Bump java version

  bethac07

  committed
  15f1bc4

• Build on Mac 11

  bethac07

  committed
  bd0d2ed

Commits on Dec 15, 2022

• Pin scipy for build machine

  bethac07

  authored
  f8e6a83

Commits on Aug 8, 2023

• Tighten some pins, loosen others (CellProfiler#4801)

  Show description for 5234d0b
  bethac07

  authored
  5234d0b

• Bump java, don't fail fast

  bethac07

  authored
  4f8d188

• Pin wx on build machine

  bethac07

  authored
  65763aa

• Recreate CellProfiler#4638 in 4.2.x (CellProfiler#4803)

  Show description for f5b06d1
  bethac07

  authored
  f5b06d1

Commits on Aug 9, 2023

• Unpin wx on build machine

  bethac07

  authored
  cafb847

• Revert changes that are breaking Metadata

  bethac07

  committed
  e84f45c

• Pin matplotlib on build machine

  bethac07

  committed
  e3696cb

• Pin wxPython on the build machine again, but only for Windows

  bethac07

  authored
  fab976c

Commits on Sep 14, 2023

• Support 3D images in FlagImage

  

  bethac07

  authored and

  gnodar01

  committed
  e3fe294

• Don't check perimeter when area is 0

  

  bethac07

  authored and

  gnodar01

  committed
  9f05a02

Commits on Feb 26, 2024

• Merge branch 'compat-4-2-ai' into 4.2.x

  DavidStirling

  authored
  0ac8bb7

• Rebase onto 4.2.6 series

  Show description for a9f36b1
  DavidStirling

  authored
  a9f36b1

Commits on Feb 28, 2024

• Update dependencies

  DavidStirling

  committed
  71f3bc4

• RunCellpose plugin revisions for V3

  DavidStirling

  committed
  19a23c4

• Remove timer

  DavidStirling

  committed
  dc32386

• Pin stardist

  DavidStirling

  committed
  7cbbe19

Commits on Feb 29, 2024

• Add model caching

  DavidStirling

  committed
  bcbe019

• Update module, implement caching

  DavidStirling

  committed
  d480b5a

Commits on Mar 1, 2024

• Upgrade function

  DavidStirling

  committed
  1c8e6b0

• Drop tests actions script

  DavidStirling

  committed
  130c2d6

Commits on Mar 6, 2024

• Set JDK home

  DavidStirling

  committed
  e2c522d

• Drop comments

  DavidStirling

  committed
  b51af5e

• Revert java ver to 11

  DavidStirling

  committed
  ee0141a

• Macos 11

  DavidStirling

  committed
  deb6c78

• Use var for java iss packing

  DavidStirling

  committed
  fe61e7f

Commits on Mar 7, 2024

• Pin pyinstaller hooks, bump macos version

  DavidStirling

  committed
  e5a027c

• Install cython on macos

  DavidStirling

  committed
  bdb571b

• Bump mysqlclient

  DavidStirling

  committed
  0a5bd41

• Install mysqlclient earlier

  DavidStirling

  committed
  7343e01

• Do mysqlclient after brew

  DavidStirling

  committed
  1290bd5

• Pin mysql itself

  DavidStirling

  committed
  02f022a

• Link mysql

  DavidStirling

  committed
  1f98105

• Pin create-dmg (not on brew)

  DavidStirling

  committed
  6dd1115

• Include orb descriptors

  DavidStirling

  committed
  3344df1

• wxpy 4.1 incompatible with macos-12, try macos-11

  DavidStirling

  committed
  51c675c

• That failed, try wx 4.2

  DavidStirling

  committed
  2a075e6

• Fix stardist settings loader

  DavidStirling

  committed
  97020a3

• Bundle torch dependencies

  DavidStirling

  committed
  39c98dc

• Pin tensorflow

  DavidStirling

  committed
  d27caca

• Reduce pyinstaller hook pin

  DavidStirling

  committed
  8e65bac

• Increase recusion limits

  DavidStirling

  committed
  66b05cd

• Allow macos to continue even if dmg does not unmount

  DavidStirling

  committed
  8fb07ed

• Debug dmg creation

  DavidStirling

  committed
  b59687c

Commits on Mar 8, 2024

• Bump pyinstaller test

  DavidStirling

  committed
  f8dc596

Commits on Mar 18, 2024

• Try shutting down malware scanning during dmg creation

  DavidStirling

  committed
  6926c38

• Test alternate dmg maker

  DavidStirling

  committed
  16bd5b5

• Uncomment

  DavidStirling

  committed
  6d35e26

• Tweak workflow for alt dmg generator

  DavidStirling

  committed
  b2895ab

• Disable dmg signing

  DavidStirling

  committed
  a2a43ed

• Ignore signing status

  DavidStirling

  committed
  f3048df

Commits on Mar 22, 2024

• Pin wx back on Windows

  DavidStirling

  committed
  30dd61f

• Remove unwanted jvm dll from Windows bootloader

  DavidStirling

  committed
  b247c20

• Remove unwanted jvm dll from Windows bootloader

  DavidStirling

  committed
  abeaa8c

Commits on Mar 26, 2024

• Correct version

  DavidStirling

  committed
  b4311e4

Commits on Apr 5, 2024

• Add lxml dep

  DavidStirling

  committed
  1b07044