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Feature/geff io#37

Merged
lxenard merged 75 commits into
mainfrom
feature/geff_io
Mar 20, 2026
Merged

Feature/geff io#37
lxenard merged 75 commits into
mainfrom
feature/geff_io

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@lxenard

@lxenard lxenard commented Sep 10, 2025

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GEFF reader and writer

lxenard and others added 28 commits July 25, 2025 16:32
@lxenard
Add geff files to gitignore
b62ec95
@lxenard
Add folder structure for geff io
e409be5
@lxenard
Put explicit units in TM XML files
341f1ef
@lxenard
Move check_fusions() to utils.py
37e0030 
This function will be used by different loaders.
@lxenard
Add pytest.ini_options
99632df
@lxenard
Rename and move common functions in loaders and tests
558df05
@lxenard
Extract update feature names related functions from TM loader, rename…
6428ecd 
… and move to io.utils
@lxenard
Improve _update_node_feature_key()
947a568
@lxenard
Reimplement _update_lineage_ID_key() into _update_lineages_IDs_key()
373c37d
@lxenard
WIP geff loader main
1fcd697
@lxenard
WIP GEFF loader
60c352b
@lxenard
Merge branch 'main' into feature/geff_io
30cbd00
@lxenard
Replace features by properties
075c271
@lxenard
WIP extraction of lineage props metadata
3eda3b4
@lxenard
Finalize extraction of properties metadata
3ef02e5
@lxenard
Add missing docstrings
8025f0a
@lxenard
Raise Error when geff graph is undirected
87ba1f8
@lxenard
WIP GEFF exporter
c55fd89
@lxenard
Update pyproject.toml with geff
e3c4da1
@lxenard
Add Model.has_cycle_data() method
ae71656
@lxenard
Working GEFF exporter
28b9925
@lxenard
Add missing info in __init__.py files
8c80a1e
@lxenard
Ugly WIP on GEFF loader
d91f806
@lxenard
Less wonky GEFF loader
dcf29a5
@lxenard
Fix incorrect typing
5058277
@lxenard
Fix incorrect docstrings and imports order
0e884d8
@lxenard
Small improvments on GEFF exporter
c05e31e
@lxenard
Add parameter to control validation of GEFF schema
d4b2738
@JoOkuma

JoOkuma commented Feb 10, 2026

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Hi @lxenard, how far are you from merging this?
I'm recommending pycellin to a user, but they would need the geff io to use it.
All the best,
Jordao

@lxenard

lxenard commented Feb 11, 2026

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Hi @JoOkuma, funny that you ask me that, because I've started working on it again just yesterday!
I need to merge the branch api/time-key first, then wrap-up things here. So before the end of the month I would say?
(and March to get a more friendly documentation)

lxenard and others added 26 commits March 6, 2026 10:17
@lxenard
WIP test loader GEFF
223e1c8
@lxenard
Test + debug _extract_props_metadata()
bcb7f29
@lxenard
Test + debug _extract_lin_props_metadata()
3aab815
@lxenard
Test + debug _build_props_metadata()
06f9fb3
@lxenard
Fix for when property ids collide: now data is also updated
8791437
@lxenard
Fix redudant lineage_ID assignment
2c4dfb1
@lxenard
Test + debug _split_graph_into_lineages()
d077f64
@lxenard
More precise error message when plotting
338a541
@lxenard
Test + debug _standardize_properties_data()
ad4b0f9
@lxenard
Test + debug _standardize_props_metadata()
9f7caba
@lxenard
Cleaning load_GEFF()
fcd8329
@lxenard
Update notebook with GEFF import/export
1d543d8
@lxenard
Add sample GEFF file
cb09d0a
@lxenard
WIP multi-type properties
9f89206
@lxenard
Test + debug PropertyType
418dff8
@lxenard
Update io for multi-type properties
67bd419
@lxenard
Updated pickle file example
287b9da
@lxenard
Fix CTC loader that was relying on frame instead of timepoint
e83f635
@lxenard
Add __str__ to PropertyType
21b50cf
@lxenard
Small fixes for GEFF and TrackMate IO
aaa0b4f
@lxenard
Fix docstring
74ab52f
@lxenard
Fix Model._categorize_props()
73994cb
@lxenard
More robust frame_prop identification in TM exporter
ac7dbc8
@lxenard
More robust way to deal with missing position properties in TM exporter
390e859
@lxenard
More robust Model.propagate_cycle_properties()
d2da8e4
@lxenard
Update notebooks and output data
94710e1
@lxenard lxenard marked this pull request as ready for review March 20, 2026 17:05
@lxenard lxenard merged commit c0b32ed into main Mar 20, 2026
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@lxenard

lxenard commented Mar 24, 2026

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Hi @JoOkuma, just letting you know that I've finally released a new version that includes the GEFF IO. It should be quite robust, but if you or your user run into any issue, please let me know!

@lxenard lxenard deleted the feature/geff_io branch April 7, 2026 13:01
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2 participants

@lxenard @JoOkuma