display adjustment and auto-increment

MontpellierRessourcesImagerie · Jan 25, 2024 · 5d75614 · 5d75614
1 parent 5b75a4d
commit 5d75614
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Showing 4 changed files with 2 additions and 9 deletions.
diff --git a/volker/toolsets/spine_analyzer/replace_label.py b/volker/toolsets/spine_analyzer/replace_label.py
@@ -19,7 +19,7 @@ def main():
     spineChannel = segmentation.getLabelChannelIndex()
     segmentation.replaceLabel(X, Y, Z, FRAME, NEW_LABEL)
     image.setC(spineChannel)
-    image.setDisplayRange(0, 255)
+    image.resetDisplayRange()
     image.setC(originalC)
     image.updateAndDraw()
 

diff --git a/volker/toolsets/spine_analyzer/segment_spine.py b/volker/toolsets/spine_analyzer/segment_spine.py
@@ -92,7 +92,7 @@ def main():
     else:
         segmentation.addFromAutoThresholdInRoi(roi, threshold=threshold)
     inputImage.setC(spineChannel)
-    inputImage.setDisplayRange(0, 255)
+    inputImage.resetDisplayRange()
     inputImage.setC(originalC)
     inputImage.updateAndDraw()
 

diff --git a/volker/toolsets/spine_analyzer/segmentation.py b/volker/toolsets/spine_analyzer/segmentation.py
@@ -65,7 +65,6 @@ def __init__(self, image, nextLabel=0):
         """Create a new instance segmentation for the given image. If the image already has a label-channel it is used for the
         instance segmentation, otherwise an empty label-channel is added to the image.
         """
-        ImagePlus.setDefault16bitRange(15)      # 15 avoids reset when auto-adjust is called on other channels
         self.maxDistance = self.MAX_DISTANCE
         self.setLUT(self.DEFAULT_LUT_NAME)
         self.setThresholdingMethod(self.DEFAULT_THRESHOLDING_METHOD)

diff --git a/volker/toolsets/spine_analyzer/stackutil.py b/volker/toolsets/spine_analyzer/stackutil.py
@@ -74,11 +74,7 @@ def copyStackTo(image, stack, channel, frame, lut=None, overwrite=False, startSl
         if not rangeEnd:
             rangeEnd = stack.getStack().size()
         stackSliceNumber = 1
-        print("rangeStart", rangeStart)
-        print("rangeEnd", rangeEnd)
         for sliceNumber in range(rangeStart, rangeEnd + 1): 
-            print("sliceNumber", sliceNumber)
-            print("stackSliceNumber", stackSliceNumber)
             image.getStack().getProcessor(offset + ((sliceNumber-1) * nChannels)).copyBits(stack.getStack().getProcessor(stackSliceNumber), 0, 0, pasteMethod)
             stackSliceNumber = stackSliceNumber + 1
         image.setC(channel)
@@ -107,11 +103,9 @@ def segmentObjectInRegion(image, roi, method="Default", firstZ=None, lastZ=None,
             processor = maskImage.getStack().getProcessor(z)
             processor.fillOutside(roi)
         if threshold:
-            print("using threshold value: ", threshold)
             IJ.setRawThreshold(maskImage, threshold, 65535)
             IJ.run(maskImage, "Convert to Mask", "background=Dark Black")
         else:
-            print("using auto-threshold mathod:", method)
             IJ.setAutoThreshold(maskImage, method + " dark stack");
             IJ.run(maskImage, "Convert to Mask", "method="+method+" background=Dark black")
         labelsImage = LabelImages.regionComponentsLabeling(maskImage, 255, 6, 32)