fixed the 255 labels limit

MontpellierRessourcesImagerie · Nov 13, 2024 · dfc81cc · dfc81cc
1 parent 77be61a
commit dfc81cc
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/volker/toolsets/spine_analyzer/segment_spine.py b/volker/toolsets/spine_analyzer/segment_spine.py
@@ -78,7 +78,7 @@ def main():
     if spineChannel and currentC == spineChannel:
         IJ.error("Please run the segmentation on a greyscale channel!")
         sys.exit()
-    roi = inputImage.getRoi();
+    roi = inputImage.getRoi()
     if not roi:
         IJ.error("Please draw a ROI around a spine!")
         sys.exit()

diff --git a/volker/toolsets/spine_analyzer/segmentation.py b/volker/toolsets/spine_analyzer/segmentation.py
@@ -45,6 +45,7 @@
 from ij.process import LUT 
 from ij.process import ImageStatistics
 from ij.process import StackStatistics
+from ij.process import ImageConverter
 from fr.cnrs.mri.cialib.stackutil import HyperstackUtils
 from inra.ijpb.binary import BinaryImages
 from inra.ijpb.label import LabelImages
@@ -140,6 +141,11 @@ def getMaxLabel(self):
     def addFromMask(self, mask, startSlice=None, endSlice=None):
         """Add the biggest connected object in the mask as a an object to the segmentation with the next unused label.
         """
+        doScaling = ImageConverter.getDoScaling()
+        ImageConverter.setDoScaling(False)
+        imageConverter = ImageConverter(mask)
+        imageConverter.convertToGray16()
+        ImageConverter.setDoScaling(doScaling)
         LabelImages.replaceLabels(mask, [255], self.nextLabel)
         HyperstackUtils.copyStackTo(self.image, mask, self.labelChannelIndex,  self.image.getT(), lut=self.lut, startSlice=startSlice, endSlice=endSlice)
         self.nextLabel = self.nextLabel + 1