Bugfix in calculation of particle stats

analysis/particleeditor.py

@@ -143,7 +143,8 @@ class ParticleEditor(QtCore.QObject):
         print(f'Combining particles {contourIndices} into {newAssignment}')
         contours = self.particleContainer.getParticleContoursByIndex(contourIndices)
         newContour = self.mergeContours(contours.copy())        
-        stats = self.characterizeParticle(newContour)
+        pixelscale = self.viewparent.dataset.getPixelScale()
+        stats = self.characterizeParticle(newContour, pixelscale)
 
         self.particleContainer.mergeParticles(contourIndices, newContour, stats, newAssignment=newAssignment)
         for ind in contourIndices:
@@ -178,7 +179,8 @@ class ParticleEditor(QtCore.QObject):
         
     def acceptPaintedResult(self):
         newContour = self.mergeContours(self.particlePainter.contours.copy())
-        stats = self.characterizeParticle(newContour)
+        pixelscale = self.viewparent.dataset.getPixelScale()
+        stats = self.characterizeParticle(newContour, pixelscale)
         
         self.particleContainer.mergeParticles(self.storedIndices, newContour, stats, newAssignment=self.storedAssignmend)
         for ind in self.storedIndices:
@@ -237,7 +239,7 @@ class ParticleEditor(QtCore.QObject):
             
         return newContour
         
-    def characterizeParticle(self, contours):
+    def characterizeParticle(self, contours, pixelscale):
         ##characterize particle
         longellipse, shortellipse = np.nan, np.nan
         
@@ -251,8 +253,10 @@ class ParticleEditor(QtCore.QObject):
         long, short = rect[1]
         if short>long:
             long, short = short, long
+        
+        area = cv2.contourArea(cnt)
     
-        return long, short, longellipse, shortellipse, cv2.contourArea(cnt)
+        return long*pixelscale, short*pixelscale, longellipse*pixelscale, shortellipse*pixelscale, area*pixelscale**2
 
     @QtCore.pyqtSlot(list)
     def deleteParticles(self, contourIndices):