Example #1
0
 def __init__(self, module_manager):
     SimpleVTKClassModuleBase.__init__(
         self, module_manager,
         vtk.vtkImageWriter(), 'Writing vtkImage.',
         ('vtkImage',), (),
         replaceDoc=True,
         inputFunctions=None, outputFunctions=None)
Example #2
0
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]))
Example #3
0
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()
Example #4
0
 def __init__(self, module_manager):
     SimpleVTKClassModuleBase.__init__(self,
                                       module_manager,
                                       vtk.vtkImageWriter(),
                                       'Writing vtkImage.', ('vtkImage', ),
                                       (),
                                       replaceDoc=True,
                                       inputFunctions=None,
                                       outputFunctions=None)
Example #5
0
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()
Example #8
0
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()
Example #9
0
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])
Example #11
0
 def writeImageData(self, fname):
     writer = vtk.vtkImageWriter()
     writer.SetInput(self.reader.GetOutput())
     writer.SetFileName(fname)
     writer.SetFileDimensionality(3)
     writer.Write()
Example #12
0
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]))