def __init__(self):
self.slicerVolumesLogic = slicer.vtkSlicerVolumesLogic()
self.slicerVolumesLogic.SetMRMLScene(slicer.mrmlScene)
self.dwiconvert_parameter_node = None
self.diffusionweightedvolumemasking_parameter_node = None
self.diffusiontensorestimation_parameter_node = None
self.seeding_parameter_node = None
def mapFromCrosshair(self, targetNode=None):
"""Create a distance map based on the current location of the crosshair node"""
self.volumeStatistics()
if targetNode is None:
targetNode = slicer.vtkSlicerVolumesLogic().CloneVolume(
slicer.mrmlScene, self.nodes['dtd_covariance_MD'],
'distanceVolume')
crosshairNode = slicer.util.getNode('vtkMRMLCrosshairNodedefault')
crosshairRAS = crosshairNode.GetCrosshairRAS()
crosshairIndex = self.indexAt(targetNode, crosshairRAS)
print(f'RAS {crosshairRAS}')
for nodeName in self.names:
node = self.nodes[nodeName]
sample = self.sampleAtRAS(node, crosshairRAS)
print(f'{nodeName}: {sample}')
targetArray = slicer.util.arrayFromVolume(targetNode)
for element in numpy.ndenumerate(targetArray):
index = element[0]
distance = self.standardizedDistanceBetweenIndices(
index, crosshairIndex)
targetArray[index] = distance
targetArray = slicer.util.updateVolumeFromArray(
targetNode, targetArray)
def loadVoi(self,filePath,segmentationNode,motionState=0,voi=None):
if not segmentationNode:
print "No segmentation node"
return
if voi.slicerNodeID[motionState]:
return voi.slicerNodeID[motionState]
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()
segLogic = slicer.modules.segmentations.logic()
segLogic.SetMRMLScene(slicer.mrmlScene)
voi.slicerNodeID[motionState]=None
if not filePath or not os.path.isfile(filePath):
#Try to execute hed2nrrd.sh
filePrefix, fileExtension = os.path.splitext(filePath)
hed2nrrd = "/u/motion/share/bin/hed2nrrd.sh"
dirName = os.path.dirname(os.path.realpath(filePath) )
if os.path.isfile(hed2nrrd):
#If you have write access, nrrd file is created
if os.access(dirName, os.W_OK):
os.system(hed2nrrd + " " + dirName)
else:
print "No write access to " + dirName +"\n Either create .nrrd files or get write permission."
if not filePath or not os.path.isfile(filePath):
print "No file!" + filePath
return None
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetMRMLScene(slicer.mrmlScene)
slicerVolumeName = voi.name + "_" + str(motionState)
slicerVolume = volumesLogic.AddArchetypeVolume(filePath,slicerVolumeName,1)
#success, midV = slicer.util.loadVolume(os.path.basename(filePath),
#properties = {'name' : "Helo", 'labelmap' : True}, returnNode = True)
slicerVolume.SetOrigin(voi.getSlicerOrigin())
if not slicerVolume:
print "Can't load volume " + os.path.basename(filePath)
return None
colorNode = slicer.util.getNode("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
colorIndex = colorNode.GetColorIndexByName(voi.name.lower())
color = [0,0,0,1]
if colorIndex < 2:
colorIndex = colorNode.GetColorIndexByName("region 11")
if not colorNode.GetColor(colorIndex,color):
print "Can't set color for " + voi.name.lower()
color = [0,0,0,1]
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
displayNode.SetColor(color[0:3])
slicer.mrmlScene.AddNode(displayNode)
slicerVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
try:
array = slicer.util.array(slicerVolume.GetID())
except AttributeError:
import sys
sys.stderr.write('Cannot get array.')
array[:] = ( array[:] >> voi.motionStateBit[motionState] ) & 1
if colorIndex > -1:
array[:] *= colorIndex
slicerVolume.GetImageData().Modified()
if not slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode(slicerVolume,segmentationNode):
print "Can't load volume in segmentation"
return None
else:
print "Added " + slicerVolume.GetName() + " to " + segmentationNode.GetName()
return slicerVolume.GetID()
grayMaker = slicer.modules.grayscalemodelmaker
slicer.cli.run(grayMaker, None, parameters)
# Volume from the sample data that works with our CLI
v = getNode('MRHead')
grayModel(v)
### Numpy, VTK, matplotlib example
import vtk
import slicer
mrml = slicer.vtkMRMLScene()
vl = slicer.vtkSlicerVolumesLogic()
vl.SetAndObserveMRMLScene(mrml)
n = vl.AddArchetypeVolume('../../Testing/Data/Input/MRHeadResampled.nhdr', 'CTC')
i = n.GetImageData()
print (i.GetScalarRange())
import vtk.util.numpy_support
a = vtk.util.numpy_support.vtk_to_numpy(i.GetPointData().GetScalars())
print(a.min(),a.max())
# Matplotlib doesn't come with Slicer, must be installed separately
import matplotlib
import matplotlib.pyplot
n, bins, patches = matplotlib.pyplot.hist(a, 50, facecolor='g', alpha=0.75)
matplotlib.pyplot.show()
