def mhd2npy(fn):
# back the other way:
r = vtk.vtkMetaImageReader()
r.SetFileName(fn)
r.Update()
image = r.GetOutput()
vtk_data = image.GetPointData().GetScalars()
numpy_data = ns.vtk_to_numpy(vtk_data)
dims = image.GetDimensions()
numpy_data = numpy_data.reshape(dims[2], dims[1], dims[0])
numpy_data = numpy_data.transpose(2, 1, 0)
return numpy_data
def mhd2npy(fn):
# back the other way:
r = vtk.vtkMetaImageReader()
r.SetFileName(fn)
r.Update()
image = r.GetOutput()
vtk_data = image.GetPointData().GetScalars()
numpy_data = ns.vtk_to_numpy(vtk_data)
dims = image.GetDimensions()
numpy_data = numpy_data.reshape(dims[2], dims[1], dims[0])
numpy_data = numpy_data.transpose(2, 1, 0)
return numpy_data
def loadSingleFile(self):
loader = self.fileLoader
loader.loadFile()
if loader.accepted:
loader.setDir(os.path.dirname(str(loader.selectedFile)))
self.disableSlider()
self.dicomReader = vtkgdcm.vtkGDCMImageReader()
self.dicomReader.SetFileName(str(loader.selectedFile))
print(dir(self.dicomReader))
print(self.dicomReader.GetScale())
self.dicomReader.Update()
imageData = self.dicomReader.GetOutput()
size = imageData.GetDimensions()
width = size[0]
height = size[1]
self.vtkWidget.setMaximumSize(QtCore.QSize(width, height))
self.vtkWidget.setMinimumSize(QtCore.QSize(width, height))
RefDs = dicom.read_file(str(loader.selectedFile))
ConstPixelDims = (int(RefDs.Rows), int(RefDs.Columns), 1)
pointData = imageData.GetPointData()
arrayData = pointData.GetArray(0)
arrayDicom = numpy_support.vtk_to_numpy(arrayData)
arrayDicom = arrayDicom.reshape(ConstPixelDims, order='F')
shape = arrayDicom.shape
wtf = arrayDicom.reshape(shape[0], shape[1])
wtf = numpy.fliplr(wtf).transpose()
max = numpy.max(wtf)
min = numpy.min(wtf)
print(numpy.max(wtf))
print(numpy.min(wtf))
grad = numpy.gradient(wtf)
print(wtf)
computed = numpy.sqrt(numpy.square(grad[0]) + numpy.square(grad[1]))
#self.proc.start()
ax = self.figure.add_subplot(111)
ax.imshow(wtf, interpolation="nearest", cmap=plt.get_cmap('gray'), vmin=0, vmax=max)
self.canvas.draw()
#points = vtk.vtkPoints()
#points.SetNumberOfPoints(2)
#points.Allocate(2)
#points.InsertPoint(0, 100, 100, 0.001)
#points.InsertPoint(0, 200, 200, 0.001)
#cells = vtk.vtkCellArray()
#cells.Initialize()
#line = vtk.vtkLine()
#line.GetPointIds().SetId(0,0)
#line.GetPointIds().SetId(1,1)
#cells.InsertNextCell(line)
#poly = vtk.vtkPolyData()
#poly.Initialize()
#poly.SetPoints(points)
#poly.SetLines(cells)
#poly.Modified()
#mapper = vtk.vtkPolyDataMapper2D()
#print(dir(mapper))
#mapper.SetInput(poly)
#mapper.ScalarVisibilityOn()
#mapper.SetScalarModeToUsePointData()
#mapper.Update()
#self.drawLine([(200,200), (300,300)])
#actor = vtk.vtkActor2D()
#actor.SetMapper(mapper)
blend = vtk.vtkImageBlend()
blend.AddInputConnection(self.dicomReader.GetOutputPort())
#blend.AddInputConnection(actor.GetOutputPort())
self.viewer.SetInputConnection(blend.GetOutputPort())
#print(dir(self.viewer.GetRenderer()))
#self.viewer.GetRenderer().AddActor2D(actor)
#self.viewer.SetInputConnection(self.dicomReader.GetOutputPort())
self.viewer.SetZSlice(0)
self.getMedicalData()
self.iren.ReInitialize()
self.iren.Render()
self.iren.Start()
#actor = vtk.vtkImageActor()
#self.viewer.GetRenderer().AddActor(actor)
self.viewer.GetRenderer().Render()
