def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self)
self._imageReslice = vtk.vtkImageReslice()
self._imageReslice.SetInterpolationModeToCubic()
self._matrixToHT = vtk.vtkMatrixToHomogeneousTransform()
self._matrixToHT.Inverse()
module_utils.setup_vtk_object_progress(self, self._imageReslice,
'Resampling volume')
self._viewFrame = self._createViewFrame(
{'Module (self)' : self,
'vtkImageReslice' : self._imageReslice})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.syncViewWithLogic()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# initialise any mixins we might have
NoConfigModuleMixin.__init__(self)
self._imageReslice = vtk.vtkImageReslice()
self._imageReslice.SetInterpolationModeToCubic()
self._matrixToHT = vtk.vtkMatrixToHomogeneousTransform()
self._matrixToHT.Inverse()
module_utils.setup_vtk_object_progress(self, self._imageReslice,
'Resampling volume')
self._viewFrame = self._createViewFrame({
'Module (self)':
self,
'vtkImageReslice':
self._imageReslice
})
# pass the data down to the underlying logic
self.config_to_logic()
# and all the way up from logic -> config -> view to make sure
self.syncViewWithLogic()
def reslice(img, transform, data):
reslicer=vtk.vtkImageReslice()
reslicer.SetInputData(img)
transform = numpy2vtkMatrix(transform)
vtkTrans = vtk.vtkMatrixToHomogeneousTransform()
vtkTrans.SetInput(transform)
reslicer.SetResliceTransform(vtkTrans)
reslicer.SetOutputOrigin(data.GetOrigin())
reslicer.SetOutputSpacing(data.GetSpacing())
reslicer.SetOutputExtent(data.GetExtent())
def xform_mesh(mesh, xform_4x4):
xform_4x4_vtk = vtkMatrix4x4()
for i in range(4):
for j in range(4):
xform_4x4_vtk.SetElement(i, j, xform_4x4[i, j])
mat_to_xform = vtkMatrixToHomogeneousTransform()
mat_to_xform.SetInput(xform_4x4_vtk)
xform_polydata = vtkTransformPolyDataFilter()
xform_polydata.SetInputData(mesh)
xform_polydata.SetTransform(mat_to_xform)
xform_polydata.Update()
return xform_polydata.GetOutput()
a12 = vtk.vtkActor() a12.SetMapper(m12) a12.GetProperty().SetColor(0.9, 0.9, 0) a12.GetProperty().SetRepresentationToWireframe() ren12 = vtk.vtkRenderer() ren12.SetViewport(0.0, 0.0, 0.25, 0.5) ren12.ResetCamera(-0.5, 0.5, -0.5, 0.5, -1, 1) ren12.AddActor(a12) renWin.AddRenderer(ren12) #-------------------------- # perspective transform matrix m2 = vtk.vtkMatrix4x4() m2.SetElement(3, 0, -0.11) m2.SetElement(3, 1, 0.3) m2.SetElement(3, 2, 0.2) t2 = vtk.vtkMatrixToHomogeneousTransform() t2.SetInput(m2) f21 = vtk.vtkTransformPolyDataFilter() f21.SetInputConnection(ap.GetOutputPort()) f21.SetTransform(t2) m21 = vtk.vtkDataSetMapper() m21.SetInputConnection(f21.GetOutputPort()) a21 = vtk.vtkActor() a21.SetMapper(m21) a21.GetProperty().SetColor(1, 0, 0) a21.GetProperty().SetRepresentationToWireframe() ren21 = vtk.vtkRenderer() ren21.SetViewport(0.25, 0.5, 0.50, 1.0) ren21.ResetCamera(-0.5, 0.5, -0.5, 0.5, -1, 1) ren21.AddActor(a21) renWin.AddRenderer(ren21)
a12 = vtk.vtkActor() a12.SetMapper(m12) a12.GetProperty().SetColor(0.9,0.9,0) a12.GetProperty().SetRepresentationToWireframe() ren12 = vtk.vtkRenderer() ren12.SetViewport(0.0,0.0,0.25,0.5) ren12.ResetCamera(-0.5,0.5,-0.5,0.5,-1,1) ren12.AddActor(a12) renWin.AddRenderer(ren12) #-------------------------- # perspective transform matrix m2 = vtk.vtkMatrix4x4() m2.SetElement(3,0,-0.11) m2.SetElement(3,1,0.3) m2.SetElement(3,2,0.2) t2 = vtk.vtkMatrixToHomogeneousTransform() t2.SetInput(m2) f21 = vtk.vtkTransformPolyDataFilter() f21.SetInputConnection(ap.GetOutputPort()) f21.SetTransform(t2) m21 = vtk.vtkDataSetMapper() m21.SetInputConnection(f21.GetOutputPort()) a21 = vtk.vtkActor() a21.SetMapper(m21) a21.GetProperty().SetColor(1,0,0) a21.GetProperty().SetRepresentationToWireframe() ren21 = vtk.vtkRenderer() ren21.SetViewport(0.25,0.5,0.50,1.0) ren21.ResetCamera(-0.5,0.5,-0.5,0.5,-1,1) ren21.AddActor(a21) renWin.AddRenderer(ren21)
def resliceImage(img, transform, origin2=None, dimension2=None, spacing2=None, interpolate=True):
if isinstance(transform, (np.matrix, np.ndarray)):
transform = numpy2vtkMatrix(transform)
print 'bu'
if isinstance(transform, vtk.vtkMatrix4x4):
vtkTrans = vtk.vtkMatrixToHomogeneousTransform()
vtkTrans.SetInput(transform)
if spacing2 is None or origin2 is None:
transform_i = transform.NewInstance()
transform_i.DeepCopy(transform)
transform_i.Invert()
if spacing2 is None:
org = np.array(transform_i.MultiplyDoublePoint((0,0,0,1)))
next_pt = np.array(transform_i.MultiplyDoublePoint((1,1,1,1)))
delta = (org[0:3]/org[3]) - (next_pt[0:3]/next_pt[3])
spacing2 = delta
#spacing2 = [transform_i.GetElement(0, 0), transform_i.GetElement(1, 1), transform_i.GetElement(2, 2)]
if origin2 is None or spacing2 is None:
if origin2 is None:
# TODO: Use a better strategy to find the new origin; this doesn't
# work with large rotations or reflections
x_min, x_max, y_min, y_max, z_min, z_max = img.GetBounds()
corners = [(x_min, y_min, z_min), (x_min, y_min, z_max), (x_min, y_max, z_min),
(x_min, y_max, z_max),
(x_max, y_min, z_min), (x_max, y_min, z_max), (x_max, y_max, z_min),
(x_max, y_max, z_max)]
corners2 = []
for c in corners:
ch = c + (1,)
corners2.append(transform_i.MultiplyDoublePoint(ch))
x2_min, y2_min, z2_min, _ = np.min(corners2, axis=0)
x2_max, y2_max, z2_max, _ = np.max(corners2, axis=0)
origin2 = [0, 0, 0]
origin2[0] = x2_min if spacing2[0] >= 0 else x2_max
origin2[1] = y2_min if spacing2[1] >= 0 else y2_max
origin2[2] = z2_min if spacing2[2] >= 0 else z2_max
if dimension2 is None:
dimension2 = [0, 0, 0]
dimension2[0] = int(np.ceil(np.abs((x2_min - x2_max) / spacing2[0])))
dimension2[1] = int(np.ceil(np.abs((y2_min - y2_max) / spacing2[1])))
dimension2[2] = int(np.ceil(np.abs((z2_min - z2_max) / spacing2[2])))
elif isinstance(transform, vtk.vtkAbstractTransform):
vtkTrans = transform
if None == spacing2 or None == origin2:
log = logging.getLogger(__name__)
log.error(
"spacing2 and origin2 are required when using a general transform")
raise Exception(
"spacing2 and origin2 are required when using a general transform")
else:
log = logging.getLogger(__name__)
log.error("Method not implemented for %s transform" % type(transform))
raise Exception(
"Method not implemented for %s transform" % type(transform))
if None == dimension2:
dimension2 = img.GetDimensions()
#=============================Finished parsing arguments===============
reslicer = vtk.vtkImageReslice()
reslicer.SetResliceTransform(vtkTrans)
reslicer.SetInputData(img)
outData = vtk.vtkImageData()
outData.SetOrigin(origin2)
outData.SetDimensions(dimension2)
outData.SetSpacing(spacing2)
reslicer.SetInformationInput(outData)
if interpolate is False:
reslicer.SetInterpolationModeToNearestNeighbor()
else:
reslicer.SetInterpolationModeToCubic()
reslicer.Update()
outImg = reslicer.GetOutput()
# print dimension2
return outImg