From d465b4bedf27d7cd640ca12e01dfcba67fb1d3f9 Mon Sep 17 00:00:00 2001 From: Laurent Guerard Date: Tue, 8 Apr 2025 14:18:05 +0200 Subject: [PATCH 1/3] Fix call to create LAP tracker --- src/imcflibs/imagej/trackmate.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/imcflibs/imagej/trackmate.py b/src/imcflibs/imagej/trackmate.py index 9fe8ce99..b17a13f7 100644 --- a/src/imcflibs/imagej/trackmate.py +++ b/src/imcflibs/imagej/trackmate.py @@ -347,7 +347,7 @@ def run_trackmate( 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: From 4f89cbefe054cd8fc970359b2cee5b0f9dc8aeec Mon Sep 17 00:00:00 2001 From: Laurent Guerard Date: Tue, 8 Apr 2025 14:18:42 +0200 Subject: [PATCH 2/3] Change to more recent call for creating label image --- src/imcflibs/imagej/trackmate.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/imcflibs/imagej/trackmate.py b/src/imcflibs/imagej/trackmate.py index b17a13f7..4433a8b7 100644 --- a/src/imcflibs/imagej/trackmate.py +++ b/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 @@ -376,9 +375,10 @@ def run_trackmate( 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]) From 43b2352f60fdfbfe82d0f8061093608471935d00 Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Tue, 8 Apr 2025 15:06:09 +0200 Subject: [PATCH 3/3] Attempt to configure codecov reports With the lack of possible unit-testing for the Java-only parts, we unfortunately need to have ultra-relaxed coverage reports, otherwise they will quickly become annoying and disliked. --- .github/codecov.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 .github/codecov.yml diff --git a/.github/codecov.yml b/.github/codecov.yml new file mode 100644 index 00000000..40446366 --- /dev/null +++ b/.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: