def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageWriter(), 'Writing vtkImage.',
('vtkImage',), (),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def MeshToVolume(Filename):
reader = vtk.vtkPolyDataReader()
pol2stenc = vtk.vtkPolyDataToImageStencil()
imgstenc = vtk.vtkImageStencil()
reader.SetFileName(os.path.join(subjects_dir,subject_dir,Filename))
reader.Update()
ref_mesh = reader.GetOutput()
ref_volume = vtk.vtkImageData()
# define output volume dimension
spacing = (0.5,0.5,0.5)
ref_volume.SetSpacing(spacing)
bounds = ref_mesh.GetBounds()
dim = [math.ceil(bounds[ii*2+1] - bounds[ii*2] / spacing[ii]) for ii in range(0,3)]
origin = [bounds[ii*2] + spacing[ii] / 2 for ii in range(0,3)]
extent = (0,dim[0] - 1,0,dim[1] -1 ,0,dim[2]-1)
ref_volume.SetOrigin(origin)
ref_volume.SetDimensions(dim)
ref_volume.SetExtent(extent)
ref_volume.SetScalarTypeToUnsignedChar()
ref_volume.AllocateScalars()
# Fill the image with white voxels
for i in range(0,ref_volume.GetNumberOfPoints()):
ref_volume.GetPointData().GetScalars().SetTuple1(i,255)
print ref_volume.GetNumberOfPoints()
pol2stenc.SetInput(ref_mesh)
pol2stenc.SetOutputOrigin(origin)
pol2stenc.SetOutputSpacing(spacing)
pol2stenc.SetOutputWholeExtent(ref_volume.GetExtent())
pol2stenc.Update()
imgstenc.SetInput(ref_volume)
imgstenc.SetStencil(pol2stenc.GetOutput())
imgstenc.ReverseStencilOff()
imgstenc.SetBackgroundValue(0)
imgstenc.Update()
tmp = imgstenc.GetOutput()
writer = vtk.vtkImageWriter()
writer.SetFileName('prova.nii.gz')
writer.SetInput(ref_volume)
writer.Update()
out = v2n(tmp.GetPointData().GetScalars())
return np.reshape(out, (dim[0],dim[1],dim[2]))
def saveRawImage(name, image):
"""
save a Raw Image (.img,.raw) from a vtkImageData
"""
writer = vtk.vtkImageWriter()
writer.SetFileName(name)
writer.SetInput(image)
writer.SetFileDimensionality(3)
writer.Write()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageWriter(),
'Writing vtkImage.', ('vtkImage', ),
(),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def saveRawImage(name, image, coding='uchar'):
"""
save a Raw Image (.img,.raw) from a vtkImageData
"""
imgCast = castImage(image, coding)
writer = vtk.vtkImageWriter()
writer.SetFileName(name)
writer.SetInput(imgCast)
writer.SetFileDimensionality(3)
writer.Write()
def average_all_images(image_datas, fname='average_image.raw'):
# how cool is this, this class was from my masters' thesis.
# though the new vtk coding is not recognizable anymore...
sum = vtk.vtkImageWeightedSum()
weights = vtk.vtkDoubleArray()
for image in image_datas:
weights.InsertNextTuple1(1.0)
sum.AddInput(image)
sum.SetWeights(weights)
sum.NormalizeByWeightOn()
sum.Update()
writer = vtk.vtkImageWriter()
writer.SetInput(sum.GetOutput())
writer.SetFileName(fname)
writer.SetFileDimensionality(3)
writer.Write()
return(sum.GetOutput())
def writeImage(
image,
filename,
verbose=1):
myVTK.myPrint(verbose, "*** writeImage: " + filename + " ***")
if ('vtk' in filename):
image_writer = vtk.vtkImageWriter()
elif ('vti' in filename):
image_writer = vtk.vtkXMLImageDataWriter()
else:
assert 0, "File must be .vtk or .vti. Aborting."
image_writer.SetFileName(filename)
image_writer.SetInputData(image)
image_writer.Update()
image_writer.Write()
def writeImage(image, filename, verbose=0):
myVTK.myPrint(verbose, "*** writeImage: " + filename + " ***")
if ('vtk' in filename):
image_writer = vtk.vtkImageWriter()
elif ('vti' in filename):
image_writer = vtk.vtkXMLImageDataWriter()
else:
assert 0, "File must be .vtk or .vti. Aborting."
myVTK.myPrint(verbose - 1, "n_points = " + str(image.GetNumberOfPoints()))
image_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_writer.SetInputData(image)
else:
image_writer.SetInput(image)
image_writer.Update()
image_writer.Write()
def writeImage(
image,
filename,
verbose=0):
mypy.my_print(verbose, "*** writeImage: "+filename+" ***")
if ('vtk' in filename):
image_writer = vtk.vtkImageWriter()
elif ('vti' in filename):
image_writer = vtk.vtkXMLImageDataWriter()
else:
assert 0, "File must be .vtk or .vti. Aborting."
mypy.my_print(verbose, "n_points = "+str(image.GetNumberOfPoints()))
image_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_writer.SetInputData(image)
else:
image_writer.SetInput(image)
image_writer.Update()
image_writer.Write()
idx = numpy.nonzero(data_fiber_counts[sidx])
LI = numpy.zeros(data_fiber_counts[0].shape)
LI[idx] = numpy.divide(data_fiber_LI[sidx][idx], data_fiber_counts[sidx][idx])
sum_LI += LI
sum_LIR[LI > 0] += LI[LI > 0]
sum_LIL[LI < 0] += LI[LI < 0]
flip_sum_LIL = sum_LIL[::-1,:,:]
symm_LIL = sum_LIL + flip_sum_LIL
flip_sum_LIR = sum_LIR[::-1,:,:]
symm_LIR = sum_LIR + flip_sum_LIR
right_img = wma.filter.array_to_vtk(symm_LIR)
writer = vtk.vtkImageWriter()
writer.SetFilePrefix('right')
writer.SetInput(right_img)
writer.SetFileDimensionality(2)
writer.SetFilePattern('%s.%03d')
writer.Write()
left_img = wma.filter.array_to_vtk(symm_LIL)
writer.SetFilePrefix('left')
writer.SetInput(left_img)
writer.Write()
# Read groups file, in theory
handedness = numpy.array([75, 85, 55, -35, -90, -85, -95, 70, -75, -25, 60, -70, 75, 100, 75, -35, -45, 90, 85, -75, 5, -80, 50, -40, -95, 100])
def writeImageData(self, fname):
writer = vtk.vtkImageWriter()
writer.SetInput(self.reader.GetOutput())
writer.SetFileName(fname)
writer.SetFileDimensionality(3)
writer.Write()
def MeshToVolume(Filename):
reader = vtk.vtkPolyDataReader()
pol2stenc = vtk.vtkPolyDataToImageStencil()
imgstenc = vtk.vtkImageStencil()
reader.SetFileName(os.path.join(subjects_dir, subject_dir, Filename))
reader.Update()
ref_mesh = reader.GetOutput()
ref_volume = vtk.vtkImageData()
# define output volume dimension
spacing = (0.5, 0.5, 0.5)
ref_volume.SetSpacing(spacing)
bounds = ref_mesh.GetBounds()
dim = [
math.ceil(bounds[ii * 2 + 1] - bounds[ii * 2] / spacing[ii])
for ii in range(0, 3)
]
origin = [bounds[ii * 2] + spacing[ii] / 2 for ii in range(0, 3)]
extent = (0, dim[0] - 1, 0, dim[1] - 1, 0, dim[2] - 1)
ref_volume.SetOrigin(origin)
ref_volume.SetDimensions(dim)
ref_volume.SetExtent(extent)
ref_volume.SetScalarTypeToUnsignedChar()
ref_volume.AllocateScalars()
# Fill the image with white voxels
for i in range(0, ref_volume.GetNumberOfPoints()):
ref_volume.GetPointData().GetScalars().SetTuple1(i, 255)
print ref_volume.GetNumberOfPoints()
pol2stenc.SetInput(ref_mesh)
pol2stenc.SetOutputOrigin(origin)
pol2stenc.SetOutputSpacing(spacing)
pol2stenc.SetOutputWholeExtent(ref_volume.GetExtent())
pol2stenc.Update()
imgstenc.SetInput(ref_volume)
imgstenc.SetStencil(pol2stenc.GetOutput())
imgstenc.ReverseStencilOff()
imgstenc.SetBackgroundValue(0)
imgstenc.Update()
tmp = imgstenc.GetOutput()
writer = vtk.vtkImageWriter()
writer.SetFileName('prova.nii.gz')
writer.SetInput(ref_volume)
writer.Update()
out = v2n(tmp.GetPointData().GetScalars())
return np.reshape(out, (dim[0], dim[1], dim[2]))