Partial update of track IDs by yfukai · Pull Request #158 · royerlab/tracksdata

yfukai · 2025-09-09T00:57:03Z

This is a fresh implementation of #151. In this PR, assign_track_ids takes the node_ids argument as

rx_graph.assign_track_ids(node_ids=node_ids)

That only updates the track IDs for a subset of nodes connected to nodes specified by node_ids while maintaining the overall consistency of the ID assignment.

…odes and tests

…tribute-selection Allow attribute selection in subgraph views

This reverts commit 4abd84f.

…d-for-attribute-selection" This reverts commit dd32c64, reversing changes made to 6f19429.

…ph' into partial_update_track_id

codecov-commenter · 2025-09-09T01:04:44Z

Codecov Report

❌ Patch coverage is 83.60656% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.97%. Comparing base (8e891d2) to head (cb7fc9e).

Files with missing lines	Patch %	Lines
src/tracksdata/graph/_rustworkx_graph.py	81.25%	3 Missing and 3 partials ⚠️
src/tracksdata/graph/_base_graph.py	77.77%	2 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #158      +/-   ##
==========================================
+ Coverage   87.78%   87.97%   +0.18%     
==========================================
  Files          50       50              
  Lines        3357     3392      +35     
  Branches      570      581      +11     
==========================================
+ Hits         2947     2984      +37     
+ Misses        248      246       -2     
  Partials      162      162

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…k_id

Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com>

yfukai · 2025-09-22T04:52:00Z

This is ready, I believe! @JoOkuma
This is built upon PR #162.

JoOkuma

Hi @yfukai , thanks for the PR.
I really liked the part of trying to keep the same track ids.

I left some minor comments and a few questions.

JoOkuma · 2025-09-26T18:24:02Z

+        assert isinstance(tracks_graph, rx.PyDiGraph)
+
+    # Check that re-assigning track IDs without reset works as expected
+    graph_backend.update_node_attrs(attrs={DEFAULT_ATTR_KEYS.TRACK_ID: -1})


Suggested change

graph_backend.update_node_attrs(attrs={DEFAULT_ATTR_KEYS.TRACK_ID: -1})

Should we remove this line because of your comment says without reset?

Thanks for the comment, I intended to reset the track IDs here, so that I can check in the following line starting with tracks_graph_reassign=!
Is it clearer if I split this to another test?

Sounds good, no need to test.

JoOkuma · 2025-09-26T18:34:05Z

+        raise NotImplementedError(f"{self.__class__.__name__} backend does not support track id assignment.")
+
+    # Internal utility to compute the exact set of nodes to assign when a subset is requested
+    def _compute_track_node_ids(self, seeds: list[int] | None) -> list[int]:


I really like this function, I can see some use cases besides updating track_ids
Do you think we could rename and remove the _ prefix to make it "public"?

I'm not really good at naming functions. I thought of non_branching_connected_nodes or non_branching_connected_components, but I'm open to your suggestions.

Yeah, sounds great! I'm not sure which is better, but could connected_tracklet_nodes be an option, for example? I just wanted to find a shorter name. Or superset_tracklet_nodes?

Or possibly tracklet_nodes or all_tracklet_nodes makes sense.

@yfukai, I like tracklet_nodes the most, it's short and straight to the point, thanks for the suggestions

Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com>

… reassignment

yfukai

Hi, thank you @JoOkuma for your review! I'm happy to hear you liked the implementation, which I also like 👍
I believe I addressed the issues you found, and I'm happy to have your feedback again!

yfukai · 2025-09-27T11:05:31Z

+        assert isinstance(tracks_graph, rx.PyDiGraph)
+
+    # Check that re-assigning track IDs without reset works as expected
+    graph_backend.update_node_attrs(attrs={DEFAULT_ATTR_KEYS.TRACK_ID: -1})


Thanks for the comment, I intended to reset the track IDs here, so that I can check in the following line starting with tracks_graph_reassign=!
Is it clearer if I split this to another test?

yfukai · 2025-09-27T11:09:35Z

+        raise NotImplementedError(f"{self.__class__.__name__} backend does not support track id assignment.")
+
+    # Internal utility to compute the exact set of nodes to assign when a subset is requested
+    def _compute_track_node_ids(self, seeds: list[int] | None) -> list[int]:


Yeah, sounds great! I'm not sure which is better, but could connected_tracklet_nodes be an option, for example? I just wanted to find a shorter name. Or superset_tracklet_nodes?

JoOkuma

@yfukai, LGTM, I'm approving the PR.
Feel free to merge once you rename _compute_track_node_ids function.

yfukai · 2025-09-29T23:39:10Z

I updated the function name! I don't have the merge right but please feel free to go ahead 🙏

JoOkuma · 2025-09-30T03:12:05Z

I forgot about that again. Thanks!

yfukai added 15 commits August 24, 2025 14:30

removing the "Null" node from assign_track_ids and updated relevant c…

5fd9f0b

…odes and tests

updated pytest

2b5939d

updated test

fbf1111

further test

6f19429

Allow attribute selection without copying

dabef78

feat: add helper to normalize attribute keys

2e9ded2

Merge pull request #4 from yfukai/codex/update-subgraph-method-for-at…

dd32c64

…tribute-selection Allow attribute selection in subgraph views

_base_graph.py を更新

4abd84f

try to modify but got lost

fae8e09

Revert "_base_graph.py を更新"

7023e1b

This reverts commit 4abd84f.

Revert "Merge pull request #4 from yfukai/codex/update-subgraph-metho…

4b438f9

…d-for-attribute-selection" This reverts commit dd32c64, reversing changes made to 6f19429.

solved rustworkx problems

bd8e1e0

updating but sqlgraph is not working

049a82e

fixed bugs

d5f0ee8

Merge remote-tracking branch 'origin/remove_null_node_from_tracks_gra…

fcf288c

…ph' into partial_update_track_id

Scaffolding what to do

61c7018

yfukai changed the title ~~Partial update track IDs~~ Partial update of track IDs Sep 9, 2025

yfukai added 12 commits September 10, 2025 09:48

adding tests

3eae229

Merge remote-tracking branch 'upstream/main' into partial_update_trac…

cfa7ffd

…k_id

test passing with the codex help (while need to be reviewed)

8d367fb

updating comments

57e5fd8

wrote test

19c1a93

test passing

ffdca00

test passing and formated

89876a2

test passing with reassignment of the track IDs

a8822ad

trying to add another test cases

fbdb24b

further test case

8f138fa

added remove_edge function

1d3ca08

dealing with ruff error

64de42f

yfukai and others added 10 commits September 11, 2025 13:51

small fix

5e59da7

Merge branch 'delete_edges' into partial_update_track_id

2bc4120

fixed session scope

9633454

adding test for covering GraphView

c1767c1

Merge branch 'main' into delete_edges

cea3c78

Update src/tracksdata/graph/_graph_view.py

e0c76e2

Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com>

updated logic for the graphview

e3e14a3

reordered condition statement for sqlgraph

df68b3f

Merge branch 'delete_edges' into partial_update_track_id

004664b

Casting track_id to int to avoid type issues with updating attrs

6f4fbb1

yfukai marked this pull request as ready for review September 22, 2025 04:49

yfukai added 5 commits September 25, 2025 08:37

fixing error bugs

7a6f8ac

fixed error in view remove_edge

3c12726

patched error message for sqlgraph

662a191

organized and tested error messages

1a619b3

Merge branch 'delete_edges' into partial_update_track_id

48de8c8

JoOkuma mentioned this pull request Sep 25, 2025

Adding remove_edge function #162

Merged

Merge branch 'main' into partial_update_track_id

0c8dcbe

JoOkuma requested changes Sep 26, 2025

View reviewed changes

yfukai and others added 3 commits September 27, 2025 08:04

Update src/tracksdata/graph/_base_graph.py

d8759e6

Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com>

Update src/tracksdata/graph/_rustworkx_graph.py

90fcb7d

Co-authored-by: Jordão Bragantini <jordao.bragantini@gmail.com>

Added originally failing test and solved it by fixing the tracklet id…

9df2436

… reassignment

yfukai commented Sep 27, 2025

View reviewed changes

fixed lint

ed462ca

JoOkuma approved these changes Sep 29, 2025

View reviewed changes

renamed tracklet_nodes function

cb7fc9e

JoOkuma merged commit af26e1c into royerlab:main Sep 30, 2025
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