Optimizations, closes #1070 by Teranis · Pull Request #1071 · SchmollerLab/Cell_ACDC

Teranis · 2026-04-07T14:09:47Z

updated RP to
- Cache centroids
- Estimate centroids based on bbox if exact is not important
- Ability to update only the cutout of the entire lab (GUI can use bbox of "old" obj before change, current view or custom bbox
  - handles border touching correctly (ignore if specific IDs are provided and not part of it, otherwise label them with mask)
- Apply assignment changes (Just ID swaps, for example, from tracker) and avoid recomputing RP altogether
- Apply deletions (similar to assignments)
updated CellACDC trackers to
- return assignments for real-time tracking
- Handle tracking for only a subset of IDs inside the tracker itself
updated GUI:
- Integration of new RP functionality
- Left some comments to review together with @ElpadoCan
- Updated swapping and assigning IDs to use RP (merge safe!)
- Clear border uses its own implementation
- Set Lost centroids now look for the closest pixel with the correct ID
- Loading optimisation from acdc_df (minor, but nice for 3D)
- Segm metadata, loading of data if applicable
Updated debugutils to have a line benchmark decorator for nice execution time stats
Drawing missing IDs now uses bulk, significant speedup and memory save for many new obj

Questions:
Is update_rp always called? Also, when modifying unvisited frames?

… locations

Co-authored-by: Copilot <copilot@github.com>

…ACDC into optimizations

Co-authored-by: Copilot <copilot@github.com>

Copilot

Pull request overview

Copilot reviewed 24 out of 39 changed files in this pull request and generated 5 comments.

Comments suppressed due to low confidence (1)

cellacdc/workers.py:185

These accesses assume data_dict['regionprops'] is an acdcRegionprops with .IDs/.IDs_set. If older/alternate code paths still store a plain skimage.measure.regionprops list here, this will raise AttributeError even when lab is present. Consider using a small helper like IDs = rp.IDs if hasattr(rp, 'IDs') else [obj.label for obj in rp] (and similarly for IDs_set).

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Copilot · 2026-04-28T11:20:41Z

+precompiled_import_success = False
+try:
+    from cellacdc.precompiled.precompiled_functions import (
+        find_all_objects_2D,
+        find_all_objects_3D,
+        calc_IoA_matrix_2D,
+        calc_IoA_matrix_3D,
+    )
+    precompiled_import_success = True
+except Exception as err:
+    import traceback
+    print('[WARNING]: could not import precompiled functions, falling back to pure python versions. ')
+    traceback.print_exc()
+
+if precompiled_import_success:
+    print('Precompiled functions imported successfully.')


Importing cellacdc now prints to stdout/stderr (warning + full traceback on ImportError, and a success message on success). Import-time prints are noisy in CLI/GUI contexts and can break tools that rely on clean stdout. Consider using the project logger (or warnings.warn) and avoid printing tracebacks unless an explicit debug flag/environment variable is enabled.

Copilot · 2026-04-28T11:20:41Z

+            IDs = data_dict['regionprops'].IDs
            checker = core.CcaIntegrityChecker(cca_df, lab, IDs)



IDs = data_dict['regionprops'].IDs assumes regionprops is an acdcRegionprops. If it is ever a plain list of RegionProperties (e.g., legacy cached state), this will raise AttributeError and prevent integrity checks from running. Use the same fallback pattern as elsewhere (e.g., hasattr(rp, 'IDs')).

Copilot · 2026-04-28T11:20:42Z

+        self.ID_to_idx = {obj.label: idx for idx, obj in enumerate(self._rp)}
+        # Update IDs and IDs_set separately and explicitly
+        self.IDs_set = set(self.ID_to_idx)
+        self.IDs = list(self.IDs_set)


set_attributes builds self.IDs from list(self.IDs_set). Since sets are unordered, this makes rp.IDs nondeterministic between runs, which can lead to flaky behavior in callers that iterate rp.IDs. Prefer preserving region order (e.g., list(self.ID_to_idx) / [obj.label for obj in self._rp]) or explicitly sorting.

Suggested change

self.IDs = list(self.IDs_set)

self.IDs = list(self.ID_to_idx)

Co-authored-by: Copilot <copilot@github.com>

…ACDC into optimizations

Co-authored-by: Copilot <copilot@github.com>

Copilot

Pull request overview

Copilot reviewed 24 out of 39 changed files in this pull request and generated 4 comments.

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Co-authored-by: Copilot <copilot@github.com>

…ACDC into optimizations

Teranis and others added 27 commits April 6, 2026 20:16

WIP: RP, draw new objects, etc

87222a0

WIP: tracker opt

1cbb398

feat: updated RP, updated tracking, updated lab modifications in many…

94c8bb4

… locations

WIP: fix regionprops local cutouts

4ebeab5

WIP: Fix assignment update

5e9de08

fix: set self.lab to avoid stale lab

5f3f62e

fix: merge and separate IDs

a7de6e1

feat: cython implementation for find_all_objects

2b5fe62

Co-authored-by: Copilot <copilot@github.com>

feat: update rp factory to use own find obj function

881038d

Co-authored-by: Copilot <copilot@github.com>

feat: further opt, update gh workflow

3583929

Co-authored-by: Copilot <copilot@github.com>

fix: updated gh action

e97eae1

Co-authored-by: Copilot <copilot@github.com>

fix: updated gh action 2

2f3a240

fix: add setup.py

908a084

Co-authored-by: Copilot <copilot@github.com>

fix: updated gh action 3

c3dcf5d

Co-authored-by: Copilot <copilot@github.com>

fix: updated gh action 4

8838861

Co-authored-by: Copilot <copilot@github.com>

feat: contour caching, Io cython

370c241

fix: cython workflow

e7af3a9

Update .gitignore

c46b521

ci: update precompiled Cython extensions [skip ci]

dc6d599

Merge branch 'main' into optimizations

0641f0a

Co-authored-by: Copilot <copilot@github.com>

ci: update precompiled Cython extensions [skip ci]

48632ab

feat: update unit tests

255bb43

Co-authored-by: Copilot <copilot@github.com>

Merge branch 'optimizations' of https://github.com/SchmollerLab/Cell_…

99f7e91

…ACDC into optimizations

fix: remove unused zslices rp

d45140c

WIP/feat: contour 3D caching inside rp, 3D for hull and fill holes

901565c

Co-authored-by: Copilot <copilot@github.com>

feat: add most common projection

dff33e1

Co-authored-by: Copilot <copilot@github.com>

Merge branch 'main' into optimizations

e9f8974

Teranis marked this pull request as ready for review April 27, 2026 17:54

Teranis requested review from ElpadoCan and Copilot April 27, 2026 17:54

Copilot started reviewing on behalf of Teranis April 28, 2026 11:14 View session

Copilot AI reviewed Apr 28, 2026

View reviewed changes

Teranis and others added 13 commits April 28, 2026 13:46

feat: opt finding most common label on proj, tooltips

2606508

Co-authored-by: Copilot <copilot@github.com>

fix: correct getBaseAcdcDf IDs init

d7defed

feat: getBaseAcdcDf better decision when to include z_centroid

25d4f17

Co-authored-by: Copilot <copilot@github.com>

ci: update precompiled Cython extensions [skip ci]

0d36b0f

ci: update precompiled Cython extensions [skip ci]

ea783d5

fix: gh workflow compile

3acd5f7

Co-authored-by: Copilot <copilot@github.com>

Merge branch 'optimizations' of https://github.com/SchmollerLab/Cell_…

f11f577

…ACDC into optimizations

ci: update precompiled Cython extensions [skip ci]

329f265

test: delete binaries

f06800e

Merge branch 'optimizations' of https://github.com/SchmollerLab/Cell_…

4a25124

…ACDC into optimizations

ci: update precompiled Cython extensions [skip ci]

1da1626

fix: always commit binaries

b04f2b2

Co-authored-by: Copilot <copilot@github.com>

ci: update precompiled Cython extensions [skip ci]

dadf0fe

Teranis requested a review from Copilot April 28, 2026 12:23

Copilot started reviewing on behalf of Teranis April 28, 2026 12:23 View session

Copilot AI reviewed Apr 28, 2026

View reviewed changes

Comment thread cellacdc/trackers/CellACDC/CellACDC_tracker.py

Comment thread cellacdc/regionprops.py

Comment thread cellacdc/regionprops.py

Comment thread cellacdc/load.py

Teranis and others added 12 commits April 28, 2026 14:36

fix: check that getSingleTimepointSegmSize is not None

a9e741f

Co-authored-by: Copilot <copilot@github.com>

fix: 2 step tracker

f05499e

Co-authored-by: Copilot <copilot@github.com>

feat: add most_common_projection_3D to binary verification

5d30f61

review: fixes and changes after reviewing

d3800d2

fix: 2 steps tracker, keep objects

1a4f651

Co-authored-by: Copilot <copilot@github.com>

Merge branch 'optimizations' of https://github.com/SchmollerLab/Cell_…

f96894c

…ACDC into optimizations

fix: stale myutils.exec_time import

b1ca41f

Merge branch 'main' into optimizations

cc65daa

Merge branch 'optimizations' of https://github.com/SchmollerLab/Cell_…

90d4c56

…ACDC into optimizations

fix: rp None for fresh segm

e4062a4

fix: lint error

5384dc7

fix: init rp for not timelapse data

07cd77b

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Optimizations, closes #1070#1071

Optimizations, closes #1070#1071
Teranis wants to merge 57 commits intomainfrom
optimizations

Teranis commented Apr 7, 2026 •

edited

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		IDs = data_dict['regionprops'].IDs
		checker = core.CcaIntegrityChecker(cca_df, lab, IDs)

	self.IDs = list(self.IDs_set)
	self.IDs = list(self.ID_to_idx)

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Teranis commented Apr 7, 2026 •

edited

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