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Trackmate version bump & added default values to missing features to trackmate #191

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merged 1 commit into from
Feb 7, 2025
Merged

Trackmate version bump & added default values to missing features to trackmate #191

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4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,8 @@ test = [
"pre-commit >=3.2.2",
"pytest >=7.3.1",
"pytest-qt >=4.2.0",
"pytrackmate @ git+https://github.com/hadim/pytrackmate.git",
"napari[testing] > 0.4.18",
"pytrackmate >=1.3.4",
"napari[testing] >0.4.18",
"pyqt5 >=5.15.4",
]

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12 changes: 12 additions & 0 deletions ultrack/core/export/trackmate.py
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Expand Up @@ -206,8 +206,20 @@ def tracks_layer_to_trackmate(
spot_elem.set("name", str(spot_id))
spot_elem.set("FRAME", str(int(entry["t"])))
spot_elem.set("RADIUS", "5.0")
spot_elem.set("POSITION_T", str(entry["t"]))
spot_elem.set("POSITION_X", str(entry["x"]))
spot_elem.set("POSITION_Y", str(entry["y"]))
# features with default values
spot_elem.set("MANUAL_COLOR", "1"),
spot_elem.set("MEAN_INTENSITY", "1.0"),
spot_elem.set("MEDIAN_INTENSITY", "1.0"),
spot_elem.set("MIN_INTENSITY", "1.0"),
spot_elem.set("MAX_INTENSITY", "1.0"),
spot_elem.set("TOTAL_INTENSITY", "1.0"),
spot_elem.set("STANDARD_DEVIATION", "1.0"),
spot_elem.set("ESTIMATED_DIAMETER", "10.0"),
spot_elem.set("CONTRAST", "0.0"),
spot_elem.set("SNR", "0.0"),
if has_z:
spot_elem.set("POSITION_Z", str(entry["z"]))
else:
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