Use GEFF as the main file format of TrackMate - #352

Draft

tinevez wants to merge 58 commits into

v9from

Commits on Jul 20, 2026

Move the GEFF writer to its package,
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046daa3
Don't write useless features.
tinevez
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0180109
Serialize DisplaySettings to a Json tree.
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a9ddc96
Rework the GEFF writer.
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86d4855
Also save TrackMate version.
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c1e1b35
WIP: Serialize Settings class to Json
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ffc8753
In Settings, reorder fields and add nchannels.
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9077d2f
Fully serialize a Settings object to GEFF.
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84c0be7

Commits on Jul 21, 2026

Mark a few fields of FeatureModel transient
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d2be336
Serialize feature declarations to GEFF.
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5b90aa2
Serialize display_hints.
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88a227d
Serialize relative path to image as a related object.
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e089621
Write TRACKMATE ID and 'radius' for spots.
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e297330
Save the trackID to GEFF.
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641236e
Read a TrackMate model from a GEFF file.
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c0c3351
Read feature declarations.
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83f0711
Simplify writing feature values.
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b21a5e5
Properly read edge features.
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6452170
Deserializing Settings from Json updates an existing instance.
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d6e5d5d
Read Settings and ImagePlus from GEFF.
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cb7ca44
Read display settings from GEFF.
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01e1f4e
Read GUI state.
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31b3a6f
Post-process the deserialized Settings
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3c2f90e
Change the green color for readability.
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ec67b6c
Update the paper list.
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52e272f
Use common key to save log.
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55d1489
Give deserialized spots a default name
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daaddcc
Deserialize the log.
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e63083a
Update the GEFF test drive.
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94d721d
DisplayHints for time must match the time axis, which is FRAME now.
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72785d4
We want to save all spots, even the invisible ones.
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fb11e84
Don't write metadata for props that won't have a value.
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c093279
Properly serialize int feature values.
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5d49795
Only add metadata on edge features that are used at least once.
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6efa940
WIP: Serialize spot names.
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a7a4ac3

Commits on Jul 22, 2026

Commits on Jul 23, 2026

Don't transform units to Zarr units.
tinevez
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490f100
Don't deserialize the TRACK_ID val into a Spot feature.
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5858326
Deserialize default edge Z position
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c875d1e
Don't store or use the 'score' and 'distance' edge props.
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a5e3b03
Add Assertj dep to test scope.
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7f62cd9
Test for model equality after saving and reloading to/from GEFF.
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2ed9638
Remove the nchannels field from Settings.
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000ddf5
WIP: Test for Settings equality after GEFF de/serialization.
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5c81b11

Commits on Jul 24, 2026

Remove the 'BLOCKING_VALUE' parameter from LAP trackers settings.
tinevez
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4a296cc
Also test for log, GUI state and display settings equality.
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58e7496
Move the GEFF demo to a geff package.
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dca6465
When reading from GEFF, put Z to 0 in 2D for all spot types.
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2c3f282
Use the same GEFF test in a test deserializing SpotRois.
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de627df
Use the SpotRoi test case in the demo.
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db0eae5
Also deserialize the RADIUS prop for all spot types.
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2867f6a
Make a specific test comparison for SpotRoi
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87a752a
Rename the GEFF demo
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8b7374d
Test GEFF de/serialization with mixed spot types.
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108fabf
Demo the mixed model.
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2d74a5b