def showTextureOnModel(self, modelNode, textureImageNode): modelDisplayNode = modelNode.GetDisplayNode() modelDisplayNode.SetBackfaceCulling(0) textureImageFlipVert = vtk.vtkImageFlip() textureImageFlipVert.SetFilteredAxis(1) textureImageFlipVert.SetInputConnection(textureImageNode.GetImageDataConnection()) modelDisplayNode.SetTextureImageDataConnection(textureImageFlipVert.GetOutputPort())
def showTextureOnModel(self, modelNode, textureImageNode): modelDisplayNode = modelNode.GetDisplayNode() modelDisplayNode.SetBackfaceCulling(0) textureImageFlipVert = vtk.vtkImageFlip() textureImageFlipVert.SetFilteredAxis(1) textureImageFlipVert.SetInputConnection(textureImageNode.GetImageDataConnection()) modelDisplayNode.SetTextureImageDataConnection(textureImageFlipVert.GetOutputPort())
def showTextureOnModel(self, modelNode, textureImageNode): modelDisplayNode=modelNode.GetDisplayNode() # Get model display node modelDisplayNode.SetBackfaceCulling(0) # In computer graphics, back-face culling determines whether a polygon of a graphical object is visible. textureImageFlipVert=vtk.vtkImageFlip() # vtkImageFlip will reflect the data along the filtered axis. textureImageFlipVert.SetFilteredAxis(1) # Specify which axis will be flipped. This must be an integer between 0 (for x) and 2 (for z). Initial value is 0. textureImageFlipVert.SetInputConnection(textureImageNode.GetImageDataConnection()) # Set the connection for the given input port index. Each input port of a filter has a specific purpose. A port may have zero or more connections and the required number is specified by each filter. Setting the connection with this method removes all other connections from the port. modelDisplayNode.SetTextureImageDataConnection(textureImageFlipVert.GetOutputPort()) # Set and observe the texture image data port.
def ConvertTextureToPointAttribute(modelNode, textureImageNode):
polyData=modelNode.GetPolyData()
textureImageFlipVert=vtk.vtkImageFlip()
textureImageFlipVert.SetFilteredAxis(1)
textureImageFlipVert.SetInputConnection(textureImageNode.GetImageDataConnection())
textureImageFlipVert.Update()
textureImageData=textureImageFlipVert.GetOutput()
pointData=polyData.GetPointData()
tcoords=pointData.GetTCoords()
numOfPoints=pointData.GetNumberOfTuples()
assert numOfPoints==tcoords.GetNumberOfTuples(), "Number of texture coordinates does not equal number of points"
textureSamplingPointsUv=vtk.vtkPoints()
textureSamplingPointsUv.SetNumberOfPoints(numOfPoints)
for pointIndex in xrange(numOfPoints):
uv=tcoords.GetTuple2(pointIndex)
textureSamplingPointsUv.SetPoint(pointIndex, uv[0], uv[1], 0)
textureSamplingPointDataUv=vtk.vtkPolyData()
uvToXyz=vtk.vtkTransform()
textureImageDataSpacingSpacing=textureImageData.GetSpacing()
textureImageDataSpacingOrigin=textureImageData.GetOrigin()
textureImageDataSpacingDimensions=textureImageData.GetDimensions()
uvToXyz.Scale(textureImageDataSpacingDimensions[0]/textureImageDataSpacingSpacing[0], textureImageDataSpacingDimensions[1]/textureImageDataSpacingSpacing[1], 1)
uvToXyz.Translate(textureImageDataSpacingOrigin)
textureSamplingPointDataUv.SetPoints(textureSamplingPointsUv)
transformPolyDataToXyz=vtk.vtkTransformPolyDataFilter()
transformPolyDataToXyz.SetInputData(textureSamplingPointDataUv)
transformPolyDataToXyz.SetTransform(uvToXyz)
probeFilter=vtk.vtkProbeFilter()
probeFilter.SetInputConnection(transformPolyDataToXyz.GetOutputPort())
probeFilter.SetSourceData(textureImageData)
probeFilter.Update()
rgbPoints=probeFilter.GetOutput().GetPointData().GetArray('ImageScalars')
colorArrayRed=vtk.vtkDoubleArray()
colorArrayRed.SetName('ColorRed')
colorArrayRed.SetNumberOfTuples(numOfPoints)
colorArrayGreen=vtk.vtkDoubleArray()
colorArrayGreen.SetName('ColorGreen')
colorArrayGreen.SetNumberOfTuples(numOfPoints)
colorArrayBlue=vtk.vtkDoubleArray()
colorArrayBlue.SetName('ColorBlue')
colorArrayBlue.SetNumberOfTuples(numOfPoints)
for pointIndex in xrange(numOfPoints):
rgb=rgbPoints.GetTuple3(pointIndex)
colorArrayRed.SetValue(pointIndex,rgb[0])
colorArrayGreen.SetValue(pointIndex,rgb[1])
colorArrayBlue.SetValue(pointIndex,rgb[2])
colorArrayRed.Modified()
colorArrayGreen.Modified()
colorArrayBlue.Modified()
pointData.AddArray(colorArrayRed)
pointData.AddArray(colorArrayGreen)
pointData.AddArray(colorArrayBlue)
pointData.Modified()
polyData.Modified()
def convertTextureToPointAttribute(self, modelNode, textureImageNode,
colorAsVector):
polyData = modelNode.GetPolyData()
textureImageFlipVert = vtk.vtkImageFlip()
textureImageFlipVert.SetFilteredAxis(1)
textureImageFlipVert.SetInputConnection(
textureImageNode.GetImageDataConnection())
textureImageFlipVert.Update()
textureImageData = textureImageFlipVert.GetOutput()
pointData = polyData.GetPointData()
tcoords = pointData.GetTCoords()
numOfPoints = pointData.GetNumberOfTuples()
assert numOfPoints == tcoords.GetNumberOfTuples(
), "Number of texture coordinates does not equal number of points"
textureSamplingPointsUv = vtk.vtkPoints()
textureSamplingPointsUv.SetNumberOfPoints(numOfPoints)
for pointIndex in range(numOfPoints):
uv = tcoords.GetTuple2(pointIndex)
textureSamplingPointsUv.SetPoint(pointIndex, uv[0], uv[1], 0)
textureSamplingPointDataUv = vtk.vtkPolyData()
uvToXyz = vtk.vtkTransform()
textureImageDataSpacingSpacing = textureImageData.GetSpacing()
textureImageDataSpacingOrigin = textureImageData.GetOrigin()
textureImageDataSpacingDimensions = textureImageData.GetDimensions()
uvToXyz.Scale(
textureImageDataSpacingDimensions[0] /
textureImageDataSpacingSpacing[0],
textureImageDataSpacingDimensions[1] /
textureImageDataSpacingSpacing[1], 1)
uvToXyz.Translate(textureImageDataSpacingOrigin)
textureSamplingPointDataUv.SetPoints(textureSamplingPointsUv)
transformPolyDataToXyz = vtk.vtkTransformPolyDataFilter()
transformPolyDataToXyz.SetInputData(textureSamplingPointDataUv)
transformPolyDataToXyz.SetTransform(uvToXyz)
probeFilter = vtk.vtkProbeFilter()
probeFilter.SetInputConnection(transformPolyDataToXyz.GetOutputPort())
probeFilter.SetSourceData(textureImageData)
probeFilter.Update()
rgbPoints = probeFilter.GetOutput().GetPointData().GetArray(
'ImageScalars')
if colorAsVector:
colorArray = vtk.vtkDoubleArray()
colorArray.SetName('Color')
colorArray.SetNumberOfComponents(3)
colorArray.SetNumberOfTuples(numOfPoints)
for pointIndex in range(numOfPoints):
rgb = rgbPoints.GetTuple3(pointIndex)
colorArray.SetTuple3(pointIndex, rgb[0] / 255., rgb[1] / 255.,
rgb[2] / 255.)
colorArray.Modified()
pointData.AddArray(colorArray)
else:
colorArrayRed = vtk.vtkDoubleArray()
colorArrayRed.SetName('ColorRed')
colorArrayRed.SetNumberOfTuples(numOfPoints)
colorArrayGreen = vtk.vtkDoubleArray()
colorArrayGreen.SetName('ColorGreen')
colorArrayGreen.SetNumberOfTuples(numOfPoints)
colorArrayBlue = vtk.vtkDoubleArray()
colorArrayBlue.SetName('ColorBlue')
colorArrayBlue.SetNumberOfTuples(numOfPoints)
for pointIndex in range(numOfPoints):
rgb = rgbPoints.GetTuple3(pointIndex)
colorArrayRed.SetValue(pointIndex, rgb[0])
colorArrayGreen.SetValue(pointIndex, rgb[1])
colorArrayBlue.SetValue(pointIndex, rgb[2])
colorArrayRed.Modified()
colorArrayGreen.Modified()
colorArrayBlue.Modified()
pointData.AddArray(colorArrayRed)
pointData.AddArray(colorArrayGreen)
pointData.AddArray(colorArrayBlue)
pointData.Modified()
polyData.Modified()
def onCompute(self):
slicer.app.processEvents()
import time
# Show the status bar
self.progressBar.show()
# Initilize various parameters
self.bone_labels = np.fromstring(self.lineedit.text,
dtype=int,
sep=',')
# Check to see if self.bone_labels is set to negative on and if so set to the default labels
if self.bone_labels[0] == -1:
# Use the minimum and maximum of the Ref_Bone_Slider (which is based on the minimum and maximum label in the first image)
self.bone_labels = range(int(self.Ref_Bone_Slider.minimum),
int(self.Ref_Bone_Slider.maximum) + 1)
self.max_bone_label = np.max(self.bone_labels)
# Find all the files in the input folder
self.files = os.listdir(self.directory_path)
# Sort the files to be in order now
self.files.sort(key=self.alphanum_key)
if self.num_files > len(self.files):
self.num_files = len(self.files)
# Initilize a list of file indicies
if self.num_files == -1:
self.file_list = range(0, len(self.files))
else:
self.file_list = range(0, int(self.num_files))
# Initilize Python list to hold all of the polydata
# One index for each bone label (ranges from 1 to 9)
polydata_list = []
for i in range(0, self.max_bone_label + 1):
polydata_list.append([])
# Load all of the images from the input folder
images_list = []
for curr_file in self.file_list:
# Update the status bar
self.progressBar.setValue(
float(curr_file) / len(self.file_list) * 100 /
10) # Use 10% of the status bar for loading the images
slicer.app.processEvents()
slicer.util.showStatusMessage("Loading Images...")
if self.files[curr_file][-3:] == 'nii':
print(str('Running file number ' + str(curr_file)))
# Load the nifti (.nii) or analyze image (.img/.hdr) using SimpleITK
filename = os.path.join(self.directory_path,
self.files[curr_file])
image = self.load_image(filename)
# It's upside-down when loaded, so add a flip filter
if self.flip_image_vertically.checked == True:
imflip = vtk.vtkImageFlip()
try:
imflip.SetInputData(image.GetOutput())
except:
imflip.SetInputData(image)
imflip.SetFilteredAxis(1)
imflip.Update()
image = imflip.GetOutput()
# If the images are flipped left/right so use a flip filter
if self.flip_image_horizontally.checked == True:
imflip = vtk.vtkImageFlip()
try:
imflip.SetInputData(image.GetOutput())
except:
imflip.SetInputData(image)
imflip.SetFilteredAxis(0)
imflip.Update()
image = imflip.GetOutput()
# Append the loaded image to the images_list
images_list.append(image)
# Temporarily push the image to Slicer (to have the correct class type for the model maker Slicer module)
if self.debug_show_images.checked == True:
image = sitk.ReadImage(filename)
sitkUtils.PushToSlicer(image,
str(curr_file),
0,
overwrite=True)
node = slicer.util.getNode(str(curr_file))
# If there is a non .nii file in the folder the images_list will be shorter than file_list
# Redefine the file_list here
self.file_list = range(0, len(images_list))
iter = 0 # For status bar
# Extract the surface from each image (i.e. the polydata)
for label in self.bone_labels:
for curr_file in self.file_list:
# Update the status bar (start at 10%)
self.progressBar.setValue(
10 + float(iter) /
(len(self.bone_labels) * len(self.file_list)) * 100 /
5) # Use 20% of the bar for this
slicer.app.processEvents()
iter = iter + 1
slicer.util.showStatusMessage("Extracting Surfaces...")
polydata = self.Extract_Surface(images_list[curr_file], label)
polydata_list[label].append(polydata)
# Create model node ("Extract_Shapes") and add to scene
if self.show_extracted_shapes.checked == True:
Extract_Shapes = slicer.vtkMRMLModelNode()
Extract_Shapes.SetAndObservePolyData(polydata)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(
True) # Show in slice view
modelDisplay.SetVisibility(True) # Show in 3D view
slicer.mrmlScene.AddNode(modelDisplay)
Extract_Shapes.SetAndObserveDisplayNodeID(
modelDisplay.GetID())
slicer.mrmlScene.AddNode(Extract_Shapes)
# Save each registered bone separately?
if self.Save_Extracted_Bones_Separately.checked == True:
for label in self.bone_labels:
for i in range(0, len(self.file_list)):
path = os.path.join(
self.output_directory_path,
'Bone_' + str(label) + '_position_' + str(i) + '.ply')
plyWriter = vtk.vtkPLYWriter()
plyWriter.SetFileName(path)
plyWriter.SetInputData(polydata_list[label][i])
plyWriter.Write()
print('Saved: ' + path)
# If this is set to true, stop the computation after extracting and smoothing the bones
if self.Skip_Registration.checked == True:
# Set the status bar to 100%
self.progressBar.setValue(100)
slicer.app.processEvents()
slicer.util.showStatusMessage("Skipping Registration Step...")
# Hide the status bar
self.progressBar.hide()
# Reset the status message on bottom of 3D Slicer
slicer.util.showStatusMessage(" ")
return 0
# Update the status bar (start at 30%)
self.progressBar.setValue(30 + 20) # Use 20% of the bar for this
slicer.app.processEvents()
slicer.util.showStatusMessage("Calculating Reference Shapes...")
# Don't use the mean shapes
# Use the bone shapes from volunteer 1 instead of the mean shape for each bone
# Initialize a Python list to hold the reference shapes
reference_shapes = []
# One index for each bone label (ranges from 1 to 9)
for i in range(0, self.max_bone_label + 1):
reference_shapes.append([])
# Get the bone shapes from the first volunteer and save them
for label in self.bone_labels:
reference_shapes[label].append(polydata_list[label][0])
######### Register the reference shape to each bone position #########
iter_bar = 0 # For status bar
for label in self.bone_labels:
for i in range(0, len(self.file_list)):
# Update the status bar (start at 50%)
self.progressBar.setValue(
50 + float(iter_bar) /
(len(self.bone_labels) * len(self.file_list)) * 100 /
5) # Use 20% of the bar for this
slicer.app.processEvents()
iter_bar = iter_bar + 1
slicer.util.showStatusMessage(
"Registering Reference Shapes...")
transformedSource = self.IterativeClosestPoint(
target=polydata_list[label][i],
source=reference_shapes[label][0])
# Replace the surface of file i and label with the registered reference shape for that particular bone
polydata_list[label][i] = transformedSource
iter_bar = 0 # For status bar
######### Register the reference bone (usually the radius for the wrist) for all the volunteers together #########
for label in self.bone_labels:
for i in range(0, len(self.file_list)):
# !! IMPORTANT !! Register the reference bone last (or else the bones afterwards will not register correctly)
# Skip the reference label for now (register after all the other bones are registered)
if label != self.ref_label:
# Update the status bar (start at 70%)
self.progressBar.setValue(
70 + float(iter_bar) /
(len(self.bone_labels) * len(self.file_list)) * 100 /
5) # Use 20% of the bar for this
slicer.app.processEvents()
iter_bar = iter_bar + 1
slicer.util.showStatusMessage(
"Registering Radius Together...")
polydata_list[label][i] = self.IterativeClosestPoint(
target=polydata_list[self.ref_label][0],
source=polydata_list[self.ref_label][i],
reference=polydata_list[label][i])
# Now register the reference label bones together
for i in range(0, len(self.file_list)):
polydata_list[self.ref_label][i] = self.IterativeClosestPoint(
target=polydata_list[self.ref_label][0],
source=polydata_list[self.ref_label][i],
reference=polydata_list[self.ref_label][i])
######### Save the output #########
# Should the reference bone be remove (i.e. not saved) in the final PLY surface file?
if self.Remove_Ref_Bone.checked == True:
index = np.argwhere(self.bone_labels == self.ref_label)
self.bone_labels = np.delete(self.bone_labels, index)
# Combine the surfaces of the wrist for each person and save as a .PLY file
for i in range(0, len(self.file_list)):
temp_combine_list = []
# Update the status bar (start at 90%)
self.progressBar.setValue(90 + float(i) / len(self.file_list) *
100 / 10) # Use 10% of the bar for this
slicer.app.processEvents()
iter_bar = iter_bar + 1
slicer.util.showStatusMessage("Saving Output Surfaces...")
total_points = [0]
# Get all the bones in a Python list for volunteer 'i'
for label in self.bone_labels:
temp_combine_list.append(polydata_list[label][i])
# Print the number of surface points for this bone
num_points = polydata_list[label][i].GetNumberOfPoints()
print("Bone " + str(label) + " points: " + str(num_points))
total_points.append(total_points[-1] + num_points)
print("Total Cumulative Points" + str(total_points))
# Combined the surfaces in the list into a single polydata surface
combined_polydata = self.Combine_Surfaces(temp_combine_list)
# Create model node ("ICP_Result") and add to scene
if self.show_registered_shapes.checked == True:
ICP_Result = slicer.vtkMRMLModelNode()
ICP_Result.SetAndObservePolyData(combined_polydata)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(
True) # Show in slice view
modelDisplay.SetVisibility(True) # Show in 3D view
slicer.mrmlScene.AddNode(modelDisplay)
ICP_Result.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(ICP_Result)
# Write the combined polydata surface to a .PLY file
plyWriter = vtk.vtkPLYWriter()
path = os.path.join(self.output_directory_path,
str(self.files[i][:-4]) + '_combined.ply')
plyWriter.SetFileName(path)
plyWriter.SetInputData(combined_polydata)
plyWriter.Write()
print('Saved: ' + path)
# Save each registered bone separately as well?
if self.Save_Registered_Bones_Separately.checked == True:
for label in self.bone_labels:
path = os.path.join(
self.output_directory_path,
'Position_' + str(i) + '_bone_' + str(label) + '.ply')
plyWriter.SetFileName(path)
plyWriter.SetInputData(polydata_list[label][i])
plyWriter.Write()
print('Saved: ' + path)
# Set the status bar to 100%
self.progressBar.setValue(100)
# Hide the status bar
self.progressBar.hide()
# Reset the status message on bottom of 3D Slicer
slicer.util.showStatusMessage(" ")
return 0
