def GetSlices(self, orientation, slice_number):
if self.buffer_slices[orientation].index == slice_number:
if self.buffer_slices[orientation].vtk_image:
image = self.buffer_slices[orientation].vtk_image
else:
n_image = self.get_image_slice(orientation, slice_number)
image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
ww_wl_image = self.do_ww_wl(image)
image = self.do_colour_image(ww_wl_image)
if self.current_mask and self.current_mask.is_shown:
if self.buffer_slices[orientation].vtk_mask:
print "Getting from buffer"
mask = self.buffer_slices[orientation].vtk_mask
else:
print "Do not getting from buffer"
n_mask = self.get_mask_slice(orientation, slice_number)
mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
mask = self.do_colour_mask(mask)
self.buffer_slices[orientation].mask = n_mask
final_image = self.do_blend(image, mask)
self.buffer_slices[orientation].vtk_mask = mask
else:
final_image = image
self.buffer_slices[orientation].vtk_image = image
else:
n_image = self.get_image_slice(orientation, slice_number)
image = converters.to_vtk(n_image, self.spacing, slice_number, orientation)
ww_wl_image = self.do_ww_wl(image)
image = self.do_colour_image(ww_wl_image)
if self.current_mask and self.current_mask.is_shown:
n_mask = self.get_mask_slice(orientation, slice_number)
mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
mask = self.do_colour_mask(mask)
final_image = self.do_blend(image, mask)
else:
n_mask = None
final_image = image
mask = None
self.buffer_slices[orientation].index = slice_number
self.buffer_slices[orientation].image = n_image
self.buffer_slices[orientation].mask = n_mask
self.buffer_slices[orientation].vtk_image = image
self.buffer_slices[orientation].vtk_mask = mask
return final_image
def LoadImage(self):
slice_data = slice_.Slice()
n_array = slice_data.matrix
spacing = slice_data.spacing
slice_number = 0
orientation = 'AXIAL'
image = converters.to_vtk(n_array, spacing, slice_number, orientation)
self.image = image
def LoadImage(self):
slice_data = slice_.Slice()
n_array = slice_data.matrix
spacing = slice_data.spacing
slice_number = 0
orientation = 'AXIAL'
image = converters.to_vtk(n_array, spacing, slice_number, orientation)
self.image = image
def CreateSurface(self, roi):
if self.from_binary:
a_mask = numpy.array(self.mask[roi.start + 1: roi.stop + 1,
1:, 1:])
image = converters.to_vtk(a_mask, self.spacing, roi.start,
"AXIAL")
del a_mask
else:
a_image = numpy.array(self.image[roi])
if self.algorithm == u'InVesalius 3.b2':
a_mask = numpy.array(self.mask[roi.start + 1: roi.stop + 1,
1:, 1:])
a_image[a_mask == 1] = a_image.min() - 1
a_image[a_mask == 254] = (self.min_value + self.max_value) / 2.0
image = converters.to_vtk(a_image, self.spacing, roi.start,
"AXIAL")
gauss = vtk.vtkImageGaussianSmooth()
gauss.SetInput(image)
gauss.SetRadiusFactor(0.3)
gauss.ReleaseDataFlagOn()
gauss.Update()
del image
image = gauss.GetOutput()
del gauss
del a_mask
else:
image = converters.to_vtk(a_image, self.spacing, roi.start,
"AXIAL")
del a_image
if self.imagedata_resolution:
# image = iu.ResampleImage3D(image, self.imagedata_resolution)
image = ResampleImage3D(image, self.imagedata_resolution)
flip = vtk.vtkImageFlip()
flip.SetInput(image)
flip.SetFilteredAxis(1)
flip.FlipAboutOriginOn()
flip.ReleaseDataFlagOn()
flip.Update()
del image
image = flip.GetOutput()
del flip
#filename = tempfile.mktemp(suffix='_%s.vti' % (self.pid))
#writer = vtk.vtkXMLImageDataWriter()
#writer.SetInput(mask_vtk)
#writer.SetFileName(filename)
#writer.Write()
#print "Writing piece", roi, "to", filename
# Create vtkPolyData from vtkImageData
#print "Generating Polydata"
#if self.mode == "CONTOUR":
#print "Contour"
contour = vtk.vtkContourFilter()
contour.SetInput(image)
#contour.SetInput(flip.GetOutput())
if self.from_binary:
contour.SetValue(0, 127) # initial threshold
else:
contour.SetValue(0, self.min_value) # initial threshold
contour.SetValue(1, self.max_value) # final threshold
contour.ComputeScalarsOn()
contour.ComputeGradientsOn()
contour.ComputeNormalsOn()
contour.ReleaseDataFlagOn()
contour.Update()
#contour.AddObserver("ProgressEvent", lambda obj,evt:
# self.SendProgress(obj, _("Generating 3D surface...")))
polydata = contour.GetOutput()
del image
del contour
#else: #mode == "GRAYSCALE":
#mcubes = vtk.vtkMarchingCubes()
#mcubes.SetInput(flip.GetOutput())
#mcubes.SetValue(0, self.min_value)
#mcubes.SetValue(1, self.max_value)
#mcubes.ComputeScalarsOff()
#mcubes.ComputeGradientsOff()
#mcubes.ComputeNormalsOff()
#mcubes.AddObserver("ProgressEvent", lambda obj,evt:
#self.SendProgress(obj, _("Generating 3D surface...")))
#polydata = mcubes.GetOutput()
#triangle = vtk.vtkTriangleFilter()
#triangle.SetInput(polydata)
#triangle.AddObserver("ProgressEvent", lambda obj,evt:
#self.SendProgress(obj, _("Generating 3D surface...")))
#triangle.Update()
#polydata = triangle.GetOutput()
#if self.decimate_reduction:
##print "Decimating"
#decimation = vtk.vtkDecimatePro()
#decimation.SetInput(polydata)
#decimation.SetTargetReduction(0.3)
#decimation.AddObserver("ProgressEvent", lambda obj,evt:
#self.SendProgress(obj, _("Generating 3D surface...")))
##decimation.PreserveTopologyOn()
#decimation.SplittingOff()
#decimation.BoundaryVertexDeletionOff()
#polydata = decimation.GetOutput()
self.pipe.send(None)
filename = tempfile.mktemp(suffix='_%s.vtp' % (self.pid))
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInput(polydata)
writer.SetFileName(filename)
writer.Write()
print "Writing piece", roi, "to", filename
del polydata
del writer
self.q_out.put(filename)
def bitmap2memmap(files, slice_size, orientation, spacing, resolution_percentage):
"""
From a list of dicom files it creates memmap file in the temp folder and
returns it and its related filename.
"""
message = _("Generating multiplanar visualization...")
update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = "ProgressDialog")
temp_file = tempfile.mktemp()
if orientation == 'SAGITTAL':
if resolution_percentage == 1.0:
shape = slice_size[1], slice_size[0], len(files)
else:
shape = math.ceil(slice_size[1]*resolution_percentage),\
math.ceil(slice_size[0]*resolution_percentage), len(files)
elif orientation == 'CORONAL':
if resolution_percentage == 1.0:
shape = slice_size[1], len(files), slice_size[0]
else:
shape = math.ceil(slice_size[1]*resolution_percentage), len(files),\
math.ceil(slice_size[0]*resolution_percentage)
else:
if resolution_percentage == 1.0:
shape = len(files), slice_size[1], slice_size[0]
else:
shape = len(files), math.ceil(slice_size[1]*resolution_percentage),\
math.ceil(slice_size[0]*resolution_percentage)
if resolution_percentage == 1.0:
matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape)
cont = 0
max_scalar = None
min_scalar = None
xy_shape = None
first_resample_entry = False
for n, f in enumerate(files):
image_as_array = bitmap_reader.ReadBitmap(f)
image = converters.to_vtk(image_as_array, spacing=spacing,\
slice_number=1, orientation=orientation.upper())
if resolution_percentage != 1.0:
image_resized = ResampleImage2D(image, px=None, py=None,\
resolution_percentage = resolution_percentage, update_progress = None)
yx_shape = image_resized.GetDimensions()[1], image_resized.GetDimensions()[0]
if not(first_resample_entry):
shape = shape[0], yx_shape[0], yx_shape[1]
matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape)
first_resample_entry = True
image = image_resized
min_aux, max_aux = image.GetScalarRange()
if min_scalar is None or min_aux < min_scalar:
min_scalar = min_aux
if max_scalar is None or max_aux > max_scalar:
max_scalar = max_aux
array = numpy_support.vtk_to_numpy(image.GetPointData().GetScalars())
if array.dtype == 'uint16':
array = array - 32768/2
array = array.astype("int16")
if orientation == 'CORONAL':
array.shape = matrix.shape[0], matrix.shape[2]
matrix[:, n, :] = array[:,::-1]
elif orientation == 'SAGITTAL':
array.shape = matrix.shape[0], matrix.shape[1]
# TODO: Verify if it's necessary to add the slices swapped only in
# sagittal rmi or only in # Rasiane's case or is necessary in all
# sagittal cases.
matrix[:, :, n] = array[:,::-1]
else:
array.shape = matrix.shape[1], matrix.shape[2]
matrix[n] = array
update_progress(cont,message)
cont += 1
matrix.flush()
scalar_range = min_scalar, max_scalar
return matrix, scalar_range, temp_file
def CreateSurface(self, roi):
if self.from_binary:
a_mask = numpy.array(self.mask[roi.start + 1:roi.stop + 1, 1:, 1:])
image = converters.to_vtk(a_mask, self.spacing, roi.start, "AXIAL")
del a_mask
else:
a_image = numpy.array(self.image[roi])
if self.algorithm == u'InVesalius 3.b2':
a_mask = numpy.array(self.mask[roi.start + 1:roi.stop + 1, 1:,
1:])
a_image[a_mask == 1] = a_image.min() - 1
a_image[a_mask == 254] = (self.min_value +
self.max_value) / 2.0
image = converters.to_vtk(a_image, self.spacing, roi.start,
"AXIAL")
gauss = vtk.vtkImageGaussianSmooth()
gauss.SetInput(image)
gauss.SetRadiusFactor(0.3)
gauss.ReleaseDataFlagOn()
gauss.Update()
del image
image = gauss.GetOutput()
del gauss
del a_mask
else:
image = converters.to_vtk(a_image, self.spacing, roi.start,
"AXIAL")
del a_image
if self.imagedata_resolution:
# image = iu.ResampleImage3D(image, self.imagedata_resolution)
image = ResampleImage3D(image, self.imagedata_resolution)
flip = vtk.vtkImageFlip()
flip.SetInput(image)
flip.SetFilteredAxis(1)
flip.FlipAboutOriginOn()
flip.ReleaseDataFlagOn()
flip.Update()
del image
image = flip.GetOutput()
del flip
#filename = tempfile.mktemp(suffix='_%s.vti' % (self.pid))
#writer = vtk.vtkXMLImageDataWriter()
#writer.SetInput(mask_vtk)
#writer.SetFileName(filename)
#writer.Write()
#print "Writing piece", roi, "to", filename
# Create vtkPolyData from vtkImageData
#print "Generating Polydata"
#if self.mode == "CONTOUR":
#print "Contour"
contour = vtk.vtkContourFilter()
contour.SetInput(image)
#contour.SetInput(flip.GetOutput())
if self.from_binary:
contour.SetValue(0, 127) # initial threshold
else:
contour.SetValue(0, self.min_value) # initial threshold
contour.SetValue(1, self.max_value) # final threshold
contour.ComputeScalarsOn()
contour.ComputeGradientsOn()
contour.ComputeNormalsOn()
contour.ReleaseDataFlagOn()
contour.Update()
#contour.AddObserver("ProgressEvent", lambda obj,evt:
# self.SendProgress(obj, _("Generating 3D surface...")))
polydata = contour.GetOutput()
del image
del contour
#else: #mode == "GRAYSCALE":
#mcubes = vtk.vtkMarchingCubes()
#mcubes.SetInput(flip.GetOutput())
#mcubes.SetValue(0, self.min_value)
#mcubes.SetValue(1, self.max_value)
#mcubes.ComputeScalarsOff()
#mcubes.ComputeGradientsOff()
#mcubes.ComputeNormalsOff()
#mcubes.AddObserver("ProgressEvent", lambda obj,evt:
#self.SendProgress(obj, _("Generating 3D surface...")))
#polydata = mcubes.GetOutput()
#triangle = vtk.vtkTriangleFilter()
#triangle.SetInput(polydata)
#triangle.AddObserver("ProgressEvent", lambda obj,evt:
#self.SendProgress(obj, _("Generating 3D surface...")))
#triangle.Update()
#polydata = triangle.GetOutput()
#if self.decimate_reduction:
##print "Decimating"
#decimation = vtk.vtkDecimatePro()
#decimation.SetInput(polydata)
#decimation.SetTargetReduction(0.3)
#decimation.AddObserver("ProgressEvent", lambda obj,evt:
#self.SendProgress(obj, _("Generating 3D surface...")))
##decimation.PreserveTopologyOn()
#decimation.SplittingOff()
#decimation.BoundaryVertexDeletionOff()
#polydata = decimation.GetOutput()
self.pipe.send(None)
filename = tempfile.mktemp(suffix='_%s.vtp' % (self.pid))
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInput(polydata)
writer.SetFileName(filename)
writer.Write()
print "Writing piece", roi, "to", filename
del polydata
del writer
self.q_out.put(filename)
