Fix issues with TrackMate

.github/codecov.yml

@@ -0,0 +1,11 @@
+coverage:
+  precision: 0
+  round: nearest
+  range: "0...75"
+  # notification blocks
+  # https://docs.codecov.io/docs/codecovyml-reference#section-coverage-notify
+  notify:
+  status:
+    project:
+    patch:
+    changes:

src/imcflibs/imagej/trackmate.py

@@ -8,15 +8,14 @@
 
 from fiji.plugin.trackmate import Logger, Model, SelectionModel, Settings, TrackMate
 from fiji.plugin.trackmate.action import LabelImgExporter
+from fiji.plugin.trackmate.action.LabelImgExporter import LabelIdPainting
 from fiji.plugin.trackmate.cellpose import CellposeDetectorFactory
 from fiji.plugin.trackmate.cellpose.CellposeSettings import PretrainedModel
 from fiji.plugin.trackmate.detection import LogDetectorFactory
 from fiji.plugin.trackmate.features import FeatureFilter
 from fiji.plugin.trackmate.stardist import StarDistDetectorFactory
 from fiji.plugin.trackmate.tracking.jaqaman import SparseLAPTrackerFactory
-
 from ij import IJ
-
 from java.lang import Double
 
 from .. import pathtools
@@ -347,7 +346,7 @@
 
     if not settings.trackerFactory:
         # Create a Sparse LAP Tracker if no Tracker has been created
-        settings = sparseLAP_tracker(settings)
+        settings = sparse_lap_tracker(settings)
 
     ok = trackmate.checkInput()
     if not ok:
@@ -376,9 +375,10 @@
 
     exportSpotsAsDots = False
     exportTracksOnly = False
+    labelIdPainting = LabelIdPainting.LABEL_IS_TRACK_ID
     # implus2.close()
     label_imp = LabelImgExporter.createLabelImagePlus(
-        trackmate, exportSpotsAsDots, exportTracksOnly, False
+        trackmate, exportSpotsAsDots, exportTracksOnly, labelIdPainting
     )
     label_imp.setCalibration(cal)
     label_imp.setDimensions(dims[2], dims[3], dims[4])