def quickComputeFillFromEllipseCenters(inputVolume1, contourList, fillMethod):
"""
Uses shellActiveContourWrapper to perform level set initiated at all contours in contourList.
Parameters:
inputVolume1: guides the level set operation
contourList: list of seed contours
fillMethod: specifies the fill method, use 'shellActiveContour'
"""
global numpyBufferFromPyBufferClass
global img
InternalPixelType = itk.F
Dimension = 3
ImageType = itk.Image[InternalPixelType, Dimension]
converter = itk.PyBuffer[ImageType]
IT = itk.Image.F3
img = IT.New(Regions=[inputVolume1.shape[2], inputVolume1.shape[1], inputVolume1.shape[0]])
img.Allocate()
img.FillBuffer(0)
InternalImageType = IT
OutputImageType = IT
numpyBufferFromPyBufferClass = itk.PyBuffer[IT].GetArrayFromImage(img)
numpyBufferFromPyBufferClass[:, :, :] = inputVolume1
centerList = []
contourCount = 0
print "number of contours", len(contourList)
erodedContoursNode = GroupNode('ErodedContours')
#file = open("o:\\temp\\contours.txt", 'w')
for contour in contourList:
center = contour.bestFitEllipse.center
#centerList.append(center)
#print "starting erosion", contourCount
#print dir(copy_module)
#locations = copy_module.deepcopy(contour.locations())
#print locations
#file.write(str(locations))
#print "number of points", len(locations)
erodedContourSet = erosion.erosion_polygon(contour.locations(), 10)
erodedContourSet = erodedContourSet +\
erosion.erosion_polygon(contour.locations(), 20)
#print "completed erosion"
for erodedContour in erodedContourSet:
erodedContourObject = Contour()
erodedContourObject.addNumpyPoints(erodedContour)
erodedContoursNode.addObject(erodedContourObject)
#for point in contour.locations():
for point in erodedContour:
#centerList.append(((array(point) - array(center)) / 2.0) + array(center))
centerList.append(array(point))
contourCount += 1
#file.close()
count = 0
#todo: check if this center variable needs to be here
if len(contourList) > 0:
center = contour.bestFitEllipse.center
print "compute fill", count, "total", len(contourList)
inputVolume = converter.GetImageFromArray(numpyBufferFromPyBufferClass)
inputVolumeFileName = os.path.join(default_path.defaultOutputPath, "hello.nrrd")
# Writing and reading from file works around a WrapITK bug
itk.write(inputVolume, inputVolumeFileName)
reader1 = itk.ImageFileReader[InternalImageType].New(FileName=inputVolumeFileName)
image1 = reader1.GetOutput()
if fillMethod == 'fastMarch':
#resultItkArray = fastMarch(image1, center, contour, inputVolume)
raise Exception, "not implemented"
elif fillMethod == 'shellActiveContour':
#resultItkArray = shellActiveContourWrapper(image1, centerList, contour, inputVolume)
resultItkArray = shellActiveContourWrapper(image1, centerList, None, inputVolume)
else: raise Exception, "Invalid fill method"
tempFileName = os.path.join(default_path.defaultOutputPath, "fillResult.nrrd")
print "writing file", tempFileName
itk.write(resultItkArray, tempFileName)
resultVolume = numpy.array(converter.GetArrayFromImage(resultItkArray))
if 1:
#contour.features['fastMarchFromEllipseCenter'] = resultVolume
blob = Blob()
#binaryResult = resultVolume < 10000000
binaryResult = resultVolume < 0.5
if 0:
print "starting flood fill"
pointList = floodFill(binaryResult, center)
print "flood fill finished"
blob.setPoints(pointList)
if count == 0:
sumVolume = (1.0 * binaryResult)
else:
sumVolume += (1.0 * binaryResult)
#contour.features['fastMarchBlobFromEllipseCenter'] = blob
print "result volume"
count += 1
return sumVolume, erodedContoursNode
def computeFillFromEllipseCenters(inputVolume1, contourList, fillMethod):
"""
Uses shellActiveContourWrapper to perform level set separately at each contour.
Nolonger using this function.
"""
global numpyBufferFromPyBufferClass
global img
InternalPixelType = itk.F
Dimension = 3
ImageType = itk.Image[InternalPixelType, Dimension]
converter = itk.PyBuffer[ImageType]
IT = itk.Image.F3
img = IT.New(Regions=[inputVolume1.shape[2], inputVolume1.shape[1], inputVolume1.shape[0]])
img.Allocate()
img.FillBuffer(0)
InternalImageType = IT
OutputImageType = IT
numpyBufferFromPyBufferClass = itk.PyBuffer[IT].GetArrayFromImage(img)
numpyBufferFromPyBufferClass[:, :, :] = inputVolume1
count = 0
for contour in contourList:
center = contour.bestFitEllipse.center
print "compute fill", count, "total", len(contourList)
inputVolume = converter.GetImageFromArray(numpyBufferFromPyBufferClass)
inputVolumeFileName = os.path.join(default_path.defaultOutputPath, "hello.nrrd")
# Writing and reading from file works around a WrapITK bug
itk.write(inputVolume, inputVolumeFileName)
reader1 = itk.ImageFileReader[InternalImageType].New(FileName=inputVolumeFileName)
image1 = reader1.GetOutput()
if fillMethod == 'fastMarch':
resultItkArray = fastMarch(image1, center, contour, inputVolume)
elif fillMethod == 'shellActiveContour':
resultItkArray = shellActiveContourWrapper(image1, center, contour, inputVolume)
else: raise Exception, "Invalid fill method"
tempFileName = os.path.join(default_path.defaultOutputPath, "fillResult.nrrd")
print "writing file", tempFileName
itk.write(resultItkArray, tempFileName)
resultVolume = numpy.array(converter.GetArrayFromImage(resultItkArray))
if 1:
#contour.features['fastMarchFromEllipseCenter'] = resultVolume
blob = Blob()
#binaryResult = resultVolume < 10000000
binaryResult = resultVolume < 0.5
if 0:
print "starting flood fill"
pointList = floodFill(binaryResult, center)
print "flood fill finished"
blob.setPoints(pointList)
if count == 0:
sumVolume = (1.0 * binaryResult)
else:
sumVolume += (1.0 * binaryResult)
#contour.features['fastMarchBlobFromEllipseCenter'] = blob
print "result volume"
count += 1
return sumVolume
