helper function of padding inside label

tools/helpers/imageManipulation.py

@@ -498,7 +498,6 @@ def slicePadded(im, startStop, createMask = False):
 
     return imSliced
 
-
 # private functions
 #def _mask2D(im, erosion=False, structure=None, ):
     #"""

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=False):
+def getLabel(labelledVolume, label, boundingBoxes=None, centresOfMass=None, margin=0, 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.
@@ -543,8 +543,8 @@ def getLabel(labelledVolume, label, boundingBoxes=None, centresOfMass=None, marg
                 offset = int(extractCubeSize)
 
             # if a margin is set, add it to offset
-            if margin is not None:
-                offset += margin
+            #if margin is not None:
+            offset += margin
 
             offset = int(offset)
 
@@ -558,32 +558,32 @@ def getLabel(labelledVolume, label, boundingBoxes=None, centresOfMass=None, marg
                                       int(comRound[1] + offset + 1),
                                       int(comRound[2] + offset + 1)])
 
-            sliceLimited, sliceOffset = _checkSlice(topOfSlice, botOfSlice, [0, 0, 0], numpy.array(labelledVolume.shape))
+            #sliceLimited, sliceOffset = _checkSlice(topOfSlice, botOfSlice, [0, 0, 0], numpy.array(labelledVolume.shape))
 
-            output['sliceCube'] = sliceLimited
+            labSubVol = spam.helpers.slicePadded(labelledVolume, [topOfSlice[0], botOfSlice[0], topOfSlice[1], botOfSlice[1], topOfSlice[2], botOfSlice[2]])
+            #output['sliceCube'] = sliceLimited
+            output['sliceCube'] = (slice(topOfSlice[0], botOfSlice[0]), slice(topOfSlice[1], botOfSlice[1]), slice(topOfSlice[2], botOfSlice[2]))
 
-            output['centreOfMassREL'] = com - [sliceLimited[0].start - sliceOffset[0].start,
-                                               sliceLimited[1].start - sliceOffset[1].start,
-                                               sliceLimited[2].start - sliceOffset[2].start]
-
-            labSubVol[sliceOffset] = labelledVolume[sliceLimited].copy()
+            output['centreOfMassREL'] = com - topOfSlice
 
         # We have a bounding box, let's extract it.
         else:
-            if margin is None:
-                margin = 0
+            topOfSlice = numpy.array([int(bbo[0] - margin),
+                                      int(bbo[2] - margin),
+                                      int(bbo[4] - margin)])
+            botOfSlice = numpy.array([int(bbo[1] + margin + 1),
+                                      int(bbo[3] + margin + 1),
+                                      int(bbo[5] + margin + 1)])
 
-            sliceLimited = (slice(max(int(bbo[0] - margin),     0), min(int(bbo[1] + 1 + margin), labelledVolume.shape[0])),
-                            slice(max(int(bbo[2] - margin),     0), min(int(bbo[3] + 1 + margin), labelledVolume.shape[1])),
-                            slice(max(int(bbo[4] - margin),     0), min(int(bbo[5] + 1 + margin), labelledVolume.shape[2])))
+            #sliceLimited = (slice(max(int(bbo[0] - margin),     0), min(int(bbo[1] + 1 + margin), labelledVolume.shape[0])),
+                            #slice(max(int(bbo[2] - margin),     0), min(int(bbo[3] + 1 + margin), labelledVolume.shape[1])),
+                            #slice(max(int(bbo[4] - margin),     0), min(int(bbo[5] + 1 + margin), labelledVolume.shape[2])))
 
-            output['slice'] = sliceLimited
+            labSubVol = spam.helpers.slicePadded(labelledVolume, [topOfSlice[0], botOfSlice[0], topOfSlice[1], botOfSlice[1], topOfSlice[2], botOfSlice[2]])
 
-            output['centreOfMassREL'] = com - [sliceLimited[0].start,
-                                               sliceLimited[1].start,
-                                               sliceLimited[2].start]
+            output['slice'] = (slice(topOfSlice[0], botOfSlice[0]), slice(topOfSlice[1], botOfSlice[1]), slice(topOfSlice[2], botOfSlice[2]))
 
-            labSubVol = labelledVolume[sliceLimited].copy()
+            output['centreOfMassREL'] = com - topOfSlice
 
         # Get mask for this label
         maskLab = labSubVol == label