default value

tools/label/contacts.py

@@ -820,7 +820,7 @@ def _markerCorrection(markers, numMarkers, distanceMap, volBin, peakDistance=5,
             peakDistance = int(peakDistance*1.3)
             localMaxi = skimage.feature.peak_local_max(distanceMap, min_distance=peakDistance, indices=False, exclude_border = False, labels=volBin, num_peaks=2)
             markers, numMarkers = scipy.ndimage.measurements.label(localMaxi,structure=struc)
-    
+
     # If there are no markers, decrease peakDistance
     while (numpy.any(markers)==False or numpy.amax(markers) < 2):
         if (counter > 10 ):
@@ -830,7 +830,7 @@ def _markerCorrection(markers, numMarkers, distanceMap, volBin, peakDistance=5,
         localMaxi = skimage.feature.peak_local_max(distanceMap, min_distance=peakDistance, indices=False, exclude_border = False, labels=volBin, num_peaks=2)
         markers, numMarkers = scipy.ndimage.measurements.label(localMaxi,structure=struc)
         counter = counter + 1
-        
+
     if (numpy.amax(markers) > 2):
         centerOfMass = scipy.ndimage.measurements.center_of_mass(markers, labels=markers, index=range(1,numMarkers+1))
         distances = numpy.zeros((numMarkers,numMarkers))

tools/label/label.py

@@ -411,7 +411,7 @@ def _checkSlice(topOfSlice, botOfSlice, topLimit, botLimit):
     return returnSliceLimited, returnSliceOffset
 
 
-def getLabel(labelledVolume, label, boundingBoxes=None, centresOfMass=None, margin=None, extractCube=False, extractCubeSize=None, maskOtherLabels=True, labelDilate=0, labelDilateMaskOtherLabels=True):
+def getLabel(labelledVolume, label, boundingBoxes=None, centresOfMass=None, margin=None, extractCube=False, extractCubeSize=None, maskOtherLabels=True, labelDilate=0, labelDilateMaskOtherLabels=False):
     """
     Helper function to extract labels from a labelled image/volume.
     A dictionary is returned with the a subvolume around the particle.
@@ -588,7 +588,7 @@ def getLabel(labelledVolume, label, boundingBoxes=None, centresOfMass=None, marg
                     maskLab[numpy.logical_and(labSubVol!=label, labSubVol!=0)] = 0
             if labelDilate < 0:
                 strucuringElement = spam.mesh.structuringElement(radius=-1*labelDilate, order=2, dim=3)
-                maskLab = scipy.ndimage.morphology.binary_erosion( maskLab, structure=strucuringElement, iterations=1)
+                maskLab = scipy.ndimage.morphology.binary_erosion(maskLab, structure=strucuringElement, iterations=1)
 
             # Just overwrite "labSubVol"
             labSubVol = maskLab