def initializeMetadata( self ):
try:
self.fieldData = vtk.vtkDataSetAttributes()
mdarray = getStringDataArray( 'metadata' )
self.fieldData.AddArray( mdarray )
# diagnosticWriter.log( self, ' initialize field data in ispec[%x] ' % id(self) )
except Exception, err:
print>>sys.stderr, "Error initializing metadata"
def initializeMetadata(self):
try:
self.fieldData = vtk.vtkDataSetAttributes()
mdarray = getStringDataArray('metadata')
self.fieldData.AddArray(mdarray)
# diagnosticWriter.log( self, ' initialize field data in ispec[%x] ' % id(self) )
except Exception, err:
print >> sys.stderr, "Error initializing metadata"
def sliceDown(self):
# Warp using the normals
warp = vtk.vtkWarpVector()
warp.SetInputData(fixMesh(downsample(self.currentPeel))) # fixMesh here updates normals needed for warping
warp.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes().NORMALS)
warp.SetScaleFactor(-1)
warp.Update()
out = vtk.vtkPolyData()
out = upsample(warp.GetPolyDataOutput())
out = smooth(out)
out = fixMesh(out)
out = cleanMesh(out)
self.currentPeel = out
#!/usr/bin/env python
import vtk
dsa = vtk.vtkDataSetAttributes()
for array in "Bit Char Double Float Int Long Short UnsignedChar UnsignedInt UnsignedLong UnsignedShort".split(
):
var = eval('vtk.vtk' + array + 'Array')()
var.Allocate(1, 1)
var.SetNumberOfComponents(3)
var.SetNumberOfTuples(4)
var.SetName("a" + array + "Array")
# SetComponent
k = 0
i = 0
while i < var.GetNumberOfTuples():
j = 0
while j < var.GetNumberOfComponents():
var.SetComponent(i, j, 1)
k = k + 1
j = j + 1
i = i + 1
dsa.AddArray(var)
del var
pass
anotherFloatArray = vtk.vtkFloatArray()
anotherFloatArray.Allocate(1, 1)
def main():
colors = vtk.vtkNamedColors()
file_name, start_label, end_label = get_program_parameters()
if start_label > end_label:
end_label, start_label = start_label, end_label
# Generate cubes from labels
# 1) Read the meta file
# 2) Convert point data to cell data
# 3) Convert to geometry and display
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_name)
reader.Update()
# Pad the volume so that we can change the point data into cell
# data.
extent = reader.GetOutput().GetExtent()
pad = vtk.vtkImageWrapPad()
pad.SetInputConnection(reader.GetOutputPort())
pad.SetOutputWholeExtent(extent[0], extent[1] + 1, extent[2], extent[3] + 1, extent[4], extent[5] + 1)
pad.Update()
# Copy the scalar point data of the volume into the scalar cell data
pad.GetOutput().GetCellData().SetScalars(reader.GetOutput().GetPointData().GetScalars())
selector = vtk.vtkThreshold()
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_CELLS,
vtk.vtkDataSetAttributes().SCALARS)
selector.SetInputConnection(pad.GetOutputPort())
selector.ThresholdBetween(start_label, end_label)
selector.Update()
# Shift the geometry by 1/2
transform = vtk.vtkTransform()
transform.Translate(-0.5, -0.5, -0.5)
transform_model = vtk.vtkTransformFilter()
transform_model.SetTransform(transform)
transform_model.SetInputConnection(selector.GetOutputPort())
geometry = vtk.vtkGeometryFilter()
geometry.SetInputConnection(transform_model.GetOutputPort())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(geometry.GetOutputPort())
mapper.SetScalarRange(start_label, end_label)
mapper.SetScalarModeToUseCellData()
mapper.SetColorModeToMapScalars()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window.SetSize(640, 480)
render_window.SetWindowName('GenerateCubesFromLabels')
render_window_interactor = vtk.vtkRenderWindowInteractor()
render_window_interactor.SetRenderWindow(render_window)
renderer.AddActor(actor)
renderer.SetBackground(colors.GetColor3d('DarkSlateBlue'))
render_window.Render()
camera = renderer.GetActiveCamera()
camera.SetPosition(42.301174, 939.893457, -124.005030)
camera.SetFocalPoint(224.697134, 221.301653, 146.823706)
camera.SetViewUp(0.262286, -0.281321, -0.923073)
camera.SetDistance(789.297581)
camera.SetClippingRange(168.744328, 1509.660206)
render_window_interactor.Start()
#!/usr/bin/env python
import vtk
dsa = vtk.vtkDataSetAttributes()
for array in "Bit Char Double Float Int Long Short UnsignedChar UnsignedInt UnsignedLong UnsignedShort".split():
var = eval('vtk.vtk'+ array +'Array')()
var.Allocate(1,1)
var.SetNumberOfComponents(3)
var.SetNumberOfTuples(4)
var.SetName("a"+array+"Array")
# SetComponent
k = 0
i = 0
while i < var.GetNumberOfTuples():
j = 0
while j < var.GetNumberOfComponents():
var.SetComponent(i,j,1)
k = k + 1
j = j + 1
i = i + 1
dsa.AddArray(var)
del var
pass
anotherFloatArray = vtk.vtkFloatArray()
anotherFloatArray.Allocate(1,1)
anotherFloatArray.SetNumberOfComponents(3)
def main():
# vtkDiscreteFlyingEdges3D was introduced in VTK >= 8.2
use_flying_edges = vtk_version_ok(8, 2, 0)
file_name, start_label, end_label = get_program_parameters()
if start_label > end_label:
end_label, start_label = start_label, end_label
# Create all of the classes we will need
reader = vtk.vtkMetaImageReader()
histogram = vtk.vtkImageAccumulate()
if use_flying_edges:
try:
using_marching_cubes = False
discrete_cubes = vtk.vtkDiscreteFlyingEdges3D()
except AttributeError:
using_marching_cubes = True
discrete_cubes = vtk.vtkDiscreteMarchingCubes()
else:
using_marching_cubes = True
discrete_cubes = vtk.vtkDiscreteMarchingCubes()
smoother = vtk.vtkWindowedSincPolyDataFilter()
selector = vtk.vtkThreshold()
scalars_off = vtk.vtkMaskFields()
geometry = vtk.vtkGeometryFilter()
writer = vtk.vtkXMLPolyDataWriter()
# Define all of the variables
file_prefix = 'Label'
smoothing_iterations = 15
pass_band = 0.001
feature_angle = 120.0
# Generate models from labels
# 1) Read the meta file
# 2) Generate a histogram of the labels
# 3) Generate models from the labeled volume
# 4) Smooth the models
# 5) Output each model into a separate file
reader.SetFileName(file_name)
histogram.SetInputConnection(reader.GetOutputPort())
histogram.SetComponentExtent(0, end_label, 0, 0, 0, 0)
histogram.SetComponentOrigin(0, 0, 0)
histogram.SetComponentSpacing(1, 1, 1)
histogram.Update()
discrete_cubes.SetInputConnection(reader.GetOutputPort())
discrete_cubes.GenerateValues(end_label - start_label + 1, start_label, end_label)
smoother.SetInputConnection(discrete_cubes.GetOutputPort())
smoother.SetNumberOfIterations(smoothing_iterations)
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.SetFeatureAngle(feature_angle)
smoother.SetPassBand(pass_band)
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.Update()
selector.SetInputConnection(smoother.GetOutputPort())
if use_flying_edges:
if using_marching_cubes:
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_CELLS,
vtk.vtkDataSetAttributes().SCALARS)
else:
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes().SCALARS)
else:
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_CELLS,
vtk.vtkDataSetAttributes().SCALARS)
# Strip the scalars from the output
scalars_off.SetInputConnection(selector.GetOutputPort())
scalars_off.CopyAttributeOff(vtk.vtkMaskFields().POINT_DATA,
vtk.vtkDataSetAttributes().SCALARS)
scalars_off.CopyAttributeOff(vtk.vtkMaskFields().CELL_DATA,
vtk.vtkDataSetAttributes().SCALARS)
geometry.SetInputConnection(scalars_off.GetOutputPort())
writer.SetInputConnection(geometry.GetOutputPort())
for i in range(start_label, end_label + 1):
# see if the label exists, if not skip it
frequency = histogram.GetOutput().GetPointData().GetScalars().GetTuple1(i)
if frequency == 0.0:
continue
# select the cells for a given label
selector.ThresholdBetween(i, i)
# output the polydata
output_fn = '{:s}{:d}.vtp'.format(file_prefix, i)
print('{:s} writing {:s}'.format(os.path.basename(sys.argv[0]), output_fn))
writer.SetFileName(output_fn)
writer.Write()