ENH: improved handling of labels with different orientation

* geometry checks now include direction matrix consistency check
* conversion script now includes resampling pre-processing step
   to enforce consistent ordering of the pixel data between the image
   and label volumes

Py/SlicerReportingModuleWidgetHelper.py

@@ -477,12 +477,21 @@ def GeometriesMatch(vol1, vol2):
     dim1 = image1.GetDimensions()
     dim2 = image2.GetDimensions()
 
-    print dim1,' ',dim2
+    if dim1[0] != dim2[0] or dim1[1] != dim2[1] or dim1[2] != dim2[2]:
+      return False
 
-    if dim1[0] == dim2[0] and dim1[1] == dim2[1] and dim1[2] == dim2[2]:
-      return True
+    # check orientation
+    dir1 = vtk.vtkMatrix4x4()
+    dir2 = vtk.vtkMatrix4x4()
+    vol1.GetIJKToRASDirectionMatrix(dir1)
+    vol2.GetIJKToRASDirectionMatrix(dir2)
 
-    return False
+    for i in range(4):
+      for j in range(4):
+        if dir1.GetElement(i,j) != dir2.GetElement(i,j):
+          return False
+
+    return True
 
   @staticmethod
   def getEditorParameterNode():

Util/LabelToDICOMSEGConverterScript.py

@@ -44,14 +44,15 @@
 
 from __main__ import slicer, vtk, ctk
 import sys, glob, shutil, qt
-# import args
+import SimpleITK as sitk
 
 from DICOMLib import DICOMPlugin
 from DICOMLib import DICOMLoadable
 
 def DoIt(inputDir, labelFile, outputDir, forceLabel):
 
   dbDir1 = slicer.app.temporaryPath+'/LabelConverter'
+  reportingLogic = slicer.modules.reporting.logic()
 
   print('Temporary directory location: '+dbDir1)
   qt.QDir().mkpath(dbDir1)
@@ -88,6 +89,7 @@ def DoIt(inputDir, labelFile, outputDir, forceLabel):
       exit()
 
     inputVolume = scalarVolumePlugin.load(loadables[0])
+    slicer.mrmlScene.AddNode(inputVolume)
     print('Input volume loaded!')
 
     # read the label volume
@@ -110,25 +112,37 @@ def DoIt(inputDir, labelFile, outputDir, forceLabel):
       thresh.Update()
       labelImage = thresh.GetOutput()
       labelVolume.SetAndObserveImageData(labelImage)
-
-    reportingLogic = slicer.modules.reporting.logic()
+
+    slicer.mrmlScene.AddNode(labelVolume)
+
+    # resample label to the input volume raster
+    resampledLabel = slicer.vtkMRMLScalarVolumeNode()
+    slicer.mrmlScene.AddNode(resampledLabel)
+    eye = slicer.vtkMRMLLinearTransformNode()
+    slicer.mrmlScene.AddNode(eye)
+    parameters = {}
+    parameters['inputVolume'] = labelVolume.GetID()
+    parameters['referenceVolume'] = inputVolume.GetID()
+    parameters['outputVolume'] = resampledLabel.GetID()
+    parameters['warpTransform'] = eye.GetID()
+    parameters['interpolationMode'] = 'NearestNeighbor'
+    parameters['pixelType'] = 'ushort'
+    cliNode = None
+    cliNode = slicer.cli.run(slicer.modules.brainsresample, None, parameters, 1)
+    labelVolume = resampledLabel
 
     displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
     displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
     slicer.mrmlScene.AddNode(displayNode)
-    slicer.mrmlScene.AddNode(labelVolume)
+
+    labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
+    labelVolume.LabelMapOn()
     labelVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
-    print('Display node set up, ID = '+str(displayNode.GetID()))
-
-    # save as DICOM SEG
+
+    # initialize the DICOM DB for Reporting logic, save as DICOM SEG
     labelCollection = vtk.vtkCollection()
     labelCollection.AddItem(labelVolume)
 
-    slicer.mrmlScene.AddNode(inputVolume)
-    labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
-
-    # initialize the DICOM DB for Reporting logic
-
     print('About to write DICOM SEG!')
     dbFileName = slicer.dicomDatabase.databaseFilename
     reportingLogic.InitializeDICOMDatabase(dbFileName)