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Bug fix and improvement in TrackMate export #90

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merged 3 commits into from
Feb 29, 2024
Merged

Bug fix and improvement in TrackMate export #90

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185cebd
Fix SPOT_SOURCE_ID bug and improve TrackMate export
qin-yu Feb 28, 2024
1896af8
Highlight the limitation of TrackMate export test
qin-yu Feb 29, 2024
fc393a5
Improve TrackMate export
qin-yu Feb 29, 2024
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6 changes: 5 additions & 1 deletion ultrack/core/export/_test/test_trackmate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,11 @@
pytrackmate = pytest.importorskip("pytrackmate")


def test_trackmate_writer(tmp_path: Path) -> None:
def test_trackmate_export_spot_match(tmp_path: Path) -> None:
"""Check if the spots (objects) match between the tracks and the exported trackmate xml file.

This test cannot check if the exported tracking is valid.
"""
tracks_outpath = tmp_path / "tracks.xml"

tracks_df = pd.DataFrame(
Expand Down
57 changes: 55 additions & 2 deletions ultrack/core/export/trackmate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ def tracks_layer_to_trackmate(
) -> str:
"""
Convert a pandas DataFrame representation of Napari track layer to TrackMate XML format.
`<ImageData/>` need to be set manually in the output XML.

Parameters
----------
Expand All @@ -32,8 +33,61 @@ def tracks_layer_to_trackmate(
-------
str
A string representation of the XML in the TrackMate format.

Examples
--------
>>> tracks_df = pd.DataFrame(
... [[1,0,12.0,49.0,49.0,1000001,-1,-1],
... [1,1,12.0,49.0,32.0,2000001,-1,1000001],
... [2,1,12.0,49.0,66.0,2000002,-1,1000001]],
... columns=['track_id','t','z','y','x','id','parent_track_id','parent_id']
... )
>>> print(tracks_df)
track_id t z y x id parent_track_id parent_id
0 1 0 12.0 49.0 49.0 1000001 -1 -1
1 1 1 12.0 49.0 32.0 2000001 -1 1000001
2 2 1 12.0 49.0 66.0 2000002 -1 1000001
>>> tracks_layer_to_trackmate(tracks_df)
<?xml version="1.0" ?>
<TrackMate version="7.11.1">
<Model spatialunits="pixels" timeunits="frames">
<AllTracks>
<Track TRACK_ID="1" NUMBER_SPOTS="2" NUMBER_GAPS="0" TRACK_START="0" TRACK_STOP="1" name="Track_1">
<Edge SPOT_SOURCE_ID="1000001" SPOT_TARGET_ID="2000001" EDGE_TIME="0.5"/>
</Track>
<Track TRACK_ID="2" NUMBER_SPOTS="1" NUMBER_GAPS="0" TRACK_START="1" TRACK_STOP="1" name="Track_2">
<Edge SPOT_SOURCE_ID="1000001" SPOT_TARGET_ID="2000002" EDGE_TIME="0.5"/>
</Track>
</AllTracks>
<FilteredTracks>
<TrackID TRACK_ID="1"/>
<TrackID TRACK_ID="2"/>
</FilteredTracks>
<AllSpots>
<SpotsInFrame frame="0">
<Spot ID="1000001" QUALITY="1.0" VISIBILITY="1" name="1000001" FRAME="0" RADIUS="5.0" POSITION_X="49.0" POSITION_Y="49.0" POSITION_Z="12.0"/>
</SpotsInFrame>
<SpotsInFrame frame="1">
<Spot ID="2000001" QUALITY="1.0" VISIBILITY="1" name="2000001" FRAME="1" RADIUS="5.0" POSITION_X="32.0" POSITION_Y="49.0" POSITION_Z="12.0"/>
<Spot ID="2000002" QUALITY="1.0" VISIBILITY="1" name="2000002" FRAME="1" RADIUS="5.0" POSITION_X="66.0" POSITION_Y="49.0" POSITION_Z="12.0"/>
</SpotsInFrame>
</AllSpots>
<FeatureDeclarations>
...
</FeatureDeclarations>
</Model>
<Settings>
<InitialSpotFilter feature="QUALITY" value="0.0" isabove="true"/>
<SpotFilterCollection/>
<TrackFilterCollection/>
<ImageData filename="None" folder="None" width="0" height="0" depth="0" nslices="1" nframes="2" pixelwidth="1.0" pixelheight="1.0" voxeldepth="1.0" timeinterval="1.0"/>
</Settings>
</TrackMate>
"""
tracks_df["id"] = tracks_df["id"].astype(int)
if not tracks_df["id"].is_unique:
raise ValueError("The 'id' column must be unique.")
tracks_df.set_index("id", inplace=True)
tracks_df["parent_id"] = tracks_df["parent_id"].astype(int)
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tracks_df["track_id"] = tracks_df["track_id"].astype(int)

Expand Down Expand Up @@ -101,7 +155,6 @@ def tracks_layer_to_trackmate(
elem.set("dimension", dimension)
elem.set("isint", isint)

# Create edge features
# Create edge features
edge_features_elem = ET.SubElement(features_elem, "EdgeFeatures")
edge_features = [
Expand Down Expand Up @@ -172,7 +225,7 @@ def tracks_layer_to_trackmate(

ET.SubElement(filtered_tracks_elem, "TrackID").set("TRACK_ID", str(track_id))

for spot_id, entry in group.iterrows():
for spot_id, entry in group.iterrows(): # spot_id is the DataFrame row index
parent_id = int(entry["parent_id"])
if parent_id == NO_PARENT:
continue
Expand Down
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