def load_nifti(self):
#Path files
T1_file = os.path.join(config.T1Path, 'T1W3DTFESENSE.nii.gz')
#Load nifti images T1
img = nib.load(T1_file)
#Get data images
img_data = img.get_data()
#Transpose matrix
img_data = np.transpose(img_data, (2, 1, 0))
#Image shape
img_data_shape = img_data.shape
#Get affine matrix
affine_matrix = transform.getTransformMatrix(img)
print affine_matrix
#Data Importer
dataImporter = vtk.vtkImageImport()
dataImporter.SetDataScalarTypeToShort()
data_string = img_data.flatten(order='F').tostring()
dataImporter.SetNumberOfScalarComponents(1)
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
dataImporter.SetDataExtent(0, img_data_shape[0] - 1, 0, img_data_shape[1] - 1, 0, img_data_shape[2] - 1)
dataImporter.SetWholeExtent(0, img_data_shape[0] - 1, 0, img_data_shape[1] - 1, 0, img_data_shape[2] - 1)
dataImporter.Update()
temp_data = dataImporter.GetOutput()
#Create and copy new vtkImageData Object
new_data_temp = vtk.vtkImageData()
new_data_temp.DeepCopy(temp_data)
print new_data_temp.GetOrigin()
print new_data_temp.GetSpacing()
print new_data_temp.GetExtent()
#
#Reslice new vtkImageData Object with voxel size using affine_matrix from header
new_data = vtk.vtkImageData()
#new_data = transform.resliceImage(new_data_temp, affine_matrix)
transform_tal = braviztransforms.readFreeSurferTransform(config.talPath)
new_data = braviztransforms.applyTransform(new_data_temp, affine_matrix)
#new_data = new_data_temp
#Start ImagePlaneWidget
#Outline
outline=vtk.vtkOutlineFilter()
outline.SetInputData(new_data)
outlineMapper=vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
#Picker
picker = vtk.vtkCellPicker()
picker.SetTolerance(0.005)
#PlaneWidget
planeWidgetX = vtk.vtkImagePlaneWidget()
planeWidgetX.DisplayTextOn()
planeWidgetX.SetInputData(new_data)
planeWidgetX.SetPlaneOrientationToXAxes()
planeWidgetX.SetSliceIndex(100)
planeWidgetX.SetPicker(picker)
planeWidgetX.SetKeyPressActivationValue("x")
prop1 = planeWidgetX.GetPlaneProperty()
prop1.SetColor(1, 0, 0)
#PlaneWidget Y
planeWidgetY = vtk.vtkImagePlaneWidget()
planeWidgetY.DisplayTextOn()
planeWidgetY.SetInputData(new_data)
planeWidgetY.SetPlaneOrientationToYAxes()
planeWidgetY.SetSliceIndex(100)
planeWidgetY.SetPicker(picker)
planeWidgetY.SetKeyPressActivationValue("y")
prop2 = planeWidgetY.GetPlaneProperty()
prop2.SetColor(1, 1, 0)
planeWidgetY.SetLookupTable(planeWidgetX.GetLookupTable())
#PlaneWidget Z
planeWidgetZ = vtk.vtkImagePlaneWidget()
planeWidgetZ.DisplayTextOn()
planeWidgetZ.SetInputData(new_data)
planeWidgetZ.SetPlaneOrientationToZAxes()
planeWidgetZ.SetSliceIndex(100)
planeWidgetZ.SetPicker(picker)
planeWidgetZ.SetKeyPressActivationValue("z")
prop2 = planeWidgetY.GetPlaneProperty()
prop2.SetColor(0, 0, 1)
planeWidgetZ.SetLookupTable(planeWidgetX.GetLookupTable())
#Add outlineactor in render window
self.ren.AddActor(outlineActor)
#Load widget interactors and enable
planeWidgetX.SetInteractor(self.iren)
planeWidgetX.On()
planeWidgetY.SetInteractor(self.iren)
planeWidgetY.On()
planeWidgetZ.SetInteractor(self.iren)
planeWidgetZ.On()
#Load nifti images, T1 and orig img = nib.load(T1_file) img_orig = nib.load(orig_file) #Nifti header img_header = img.get_header() #Get data images img_data = img.get_data() #Images shapes img_data_shape = img_data.shape #Get affine matrix affine_matrix = transform.getTransformMatrix(img) #Voxel center vox_center = (np.array(img_data.shape) - 1) / 2 uno = np.array([0,0,0]) dos = np.array([0,0,1]) tres = np.array([0,0,2]) ultimo = np.array([0,0,310]) #Applying affine result_affine = apply_affine(affine_matrix, vox_center) result_affine2 = apply_affine(affine_matrix, uno) result_affine3 = apply_affine(affine_matrix, dos) result_affine4 = apply_affine(affine_matrix, tres) result_affine5 = apply_affine(affine_matrix, ultimo) print result_affine2
