def assemble_neuron(neuron_num):
print(f"Processing neuron {neuron_num}")
files = glob.glob("meshes-with-axons-filled/*_n%03d.vtp" % neuron_num)
out_filename = "meshes-with-axons-filled-assembled/n%02d.vtp" % neuron_num
appendFilter = vtk.vtkAppendPolyData()
for file in files:
_, basename = os.path.split(file)
x, y, z = int(basename[1]), int(basename[3]), int(basename[5])
print(x, y, z)
# Prepare to read the file.
readerVolume = vtk.vtkXMLPolyDataReader()
readerVolume.SetFileName(file)
readerVolume.Update()
# Set up the transform filter
translation = vtk.vtkTransform()
translation.Translate(x * 1023.0, y * 1023.0, z * 1023.0 * 2.49)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputConnection(readerVolume.GetOutputPort())
transformFilter.SetTransform(translation)
transformFilter.Update()
appendFilter.AddInputData(transformFilter.GetOutput())
appendFilter.Update()
writer = vtk.vtkXMLDataSetWriter()
writer.SetFileName(out_filename)
writer.SetInputData(appendFilter.GetOutput())
writer.Write()
def main():
filenames = list()
uGrids = list()
uGrids.append(MakeUnstructuredGrid(vtk.vtkVertex()))
filenames.append("Vertex.vtu")
uGrids.append(MakePolyVertex())
filenames.append("PolyVertex.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkLine()))
filenames.append("Line.vtu")
uGrids.append(MakePolyLine())
filenames.append("PolyLine.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkTriangle()))
filenames.append("Triangle.vtu")
uGrids.append(MakeTriangleStrip())
filenames.append("TriangleStrip.vtu")
uGrids.append(MakePolygon())
filenames.append("Polygon.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkPixel()))
filenames.append("Pixel.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkQuad()))
filenames.append("Quad.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkTetra()))
filenames.append("Tetra.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkVoxel()))
filenames.append("Voxel.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkHexahedron()))
filenames.append("Hexahedron.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkWedge()))
filenames.append("Wedge.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkPyramid()))
filenames.append("Pyramid.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkPentagonalPrism()))
filenames.append("PentagonalPrism.vtu")
uGrids.append(MakeUnstructuredGrid(vtk.vtkHexagonalPrism()))
filenames.append("HexagonalPrism.vtu")
# Write each grid into a file
for i in range(0, len(uGrids)):
print("Writing: ", filenames[i])
writer = vtk.vtkXMLDataSetWriter()
writer.SetFileName(filenames[i])
writer.SetInputData(uGrids[i])
writer.Write()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkXMLDataSetWriter(),
'Writing vtkXMLDataSet.',
('vtkXMLDataSet', ), (),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def write_vtk_data(_data, _path_to_file):
fu.ensure_dir_exists(_path_to_file)
writer = vtk.vtkXMLDataSetWriter()
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(_data)
else:
writer.SetInputData(_data)
writer.SetFileName(_path_to_file)
writer.Update()
writer.Write()
def write(self, filename):
if filename[-4:] == '.vtu':
filename = filename[:-4]
writer = vtk.vtkXMLDataSetWriter()
writer.SetDataModeToAscii()
for t in xrange(0, self.num_times):
filename_time = '{:s}.{:03d}.vtu'.format(filename, t)
print "printing {:s} ...".format(filename_time)
writer.SetInputData(self.grid[t])
writer.SetFileName(filename_time)
writer.Write()
def save(mesh: geo.Mesh, out_dir: str, name: str):
out = pathlib.Path(out_dir)
out.mkdir(exist_ok=True)
out /= pathlib.Path(f'{name}.vtu')
grid = mesh.make_vtu_grid()
writer = vtkXMLDataSetWriter()
writer.SetFileName(str(out.absolute()))
writer.SetInputData(grid)
writer.Write()
def write(self, filename):
if filename[-4:] == '.vtu':
filename = filename[:-4]
writer = vtk.vtkXMLDataSetWriter()
writer.SetDataModeToAscii()
for t in xrange(0, self.num_times):
filename_time = '{:s}.{:03d}.vtu'.format(filename, t)
print "printing {:s} ...".format(filename_time)
writer.SetInputData(self.grid[t])
writer.SetFileName(filename_time)
writer.Write()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self,
module_manager,
vtk.vtkXMLDataSetWriter(),
"Writing vtkXMLDataSet.",
("vtkXMLDataSet",),
(),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None,
)
def write_vtk_data(_data, _path_to_file):
fu.ensure_dir_exists(_path_to_file)
file_ext = fu.get_file_extension(_path_to_file)
if (file_ext == "stl"):
writer = vtk.vtkSTLWriter()
writer.SetFileTypeToBinary()
else:
writer = vtk.vtkXMLDataSetWriter()
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(_data)
else:
writer.SetInputData(_data)
writer.SetFileName(_path_to_file)
writer.Write()
sys.stdout.write('Attempting read ' + type + ' from junk file.\n')
reader.Update()
sys.stdout.write('Attempting read P' + type + ' from junk file.\n')
preader.Update()
del input
del writer
del reader
del pwriter
del preader
# Test the data set writers.
for t in types:
type = t[0]
ext = t[1]
writer = vtk.vtkXMLDataSetWriter()
pwriter = vtk.vtkXMLPDataSetWriter()
input = eval('vtk.vtk' + type + '()')
writer.SetFileName('empty' + type + 'DataSet.' + ext)
sys.stdout.write('Attempting DataSet ' + type + ' write with no input.\n')
writer.Write()
sys.stdout.write('Attempting DataSet ' + type + ' write with empty input.\n')
writer.SetInputData(input)
writer.Write()
pwriter.SetFileName('emptyP' + type + 'DataSet.p' + ext)
sys.stdout.write('Attempting DataSet ' + type + ' write with no input.\n')
pwriter.SetNumberOfPieces(1)
pwriter.Write()
sys.stdout.write('Attempting DataSet ' + type + ' write with empty input.\n')
def main():
colors = vtk.vtkNamedColors()
ifn, index = get_program_parameters()
# Prepare to read the file.
readerVolume = vtk.vtkXdmfReader()
readerVolume.SetFileName(ifn)
readerVolume.Update()
# Extract the region of interest.
voi = vtk.vtkExtractVOI()
voi.SetInputConnection(readerVolume.GetOutputPort())
voi.SetVOI(0, 1023, 0, 1023, 0, 1023)
voi.SetSampleRate(1, 1, 1)
voi.Update() # Necessary for GetScalarRange().
srange = voi.GetOutput().GetScalarRange() # Needs Update() before!
print("Range", srange)
# Prepare surface generation.
contour = vtk.vtkDiscreteMarchingCubes() # For label images.
contour.SetInputConnection(voi.GetOutputPort())
# contour.ComputeNormalsOn()
print("Doing label", index)
contour.SetValue(0, index)
contour.Update() # Needed for GetNumberOfPolys()!!!
print("Done contour")
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(contour.GetOutputPort())
smoother.SetNumberOfIterations(20) # This has little effect on the error!
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
# smoother.SetFeatureAngle(120.0)
smoother.SetPassBand(.001) # This increases the error a lot!
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.GenerateErrorScalarsOn()
# smoother.GenerateErrorVectorsOn()
smoother.Update()
smoothed_polys = smoother.GetOutput()
print(smoothed_polys)
smoother_error = smoothed_polys.GetPointData().GetScalars()
writer = vtk.vtkXMLDataSetWriter()
writer.SetFileName("out.vtp")
writer.SetInputData(smoothed_polys)
writer.Write()
# Find min and max z.
se_range = smoother_error.GetRange()
print("Smoother error range:", se_range)
minz = se_range[0] # min(smoother_error)
maxz = se_range[1] # max(smoother_error)
if maxz > 1:
print("Big smoother error: min/max:", minz, maxz)
# minz = 0.3 # This way colours of different particles are comparable.
# maxz = 1
minz = 0.3
maxz = 0.6
#smoothed_polys = contour.GetOutput()
# Create the color map.
colorLookupTable = vtk.vtkLookupTable()
colorLookupTable.SetTableRange(
minz,
maxz) # This does nothing, use mapper.SetScalarRange(minz, maxz).
colorLookupTable.SetHueRange(2 / 3.0, 1)
# colorLookupTable.SetSaturationRange(0, 0)
# colorLookupTable.SetValueRange(1, 0)
# colorLookupTable.SetNumberOfColors(256) #256 default
colorLookupTable.Build()
# Calculate cell normals.
triangleCellNormals = vtk.vtkPolyDataNormals()
triangleCellNormals.SetInputData(smoothed_polys)
triangleCellNormals.ComputeCellNormalsOn()
triangleCellNormals.ComputePointNormalsOff()
triangleCellNormals.ConsistencyOn()
triangleCellNormals.AutoOrientNormalsOn()
triangleCellNormals.Update() # Creates vtkPolyData.
mapper = vtk.vtkPolyDataMapper()
# mapper.SetInput(smoothed_polys) # This has no normals.
mapper.SetInputConnection(
triangleCellNormals.GetOutputPort()) # this is better for vis;-)
mapper.ScalarVisibilityOn() # Show colour.
mapper.SetScalarRange(minz, maxz)
# mapper.SetScalarModeToUseCellData() # Contains the label eg. 31
mapper.SetScalarModeToUsePointData(
) # The smoother error relates to the verts.
mapper.SetLookupTable(colorLookupTable)
# Take the isosurface data and create geometry.
actor = vtk.vtkLODActor()
actor.SetNumberOfCloudPoints(100000)
actor.SetMapper(mapper)
# Create the renderer.
ren = vtk.vtkRenderer()
ren.SetBackground(colors.GetColor3d("DimGray"))
ren.AddActor(actor)
# Create a window for the renderer of size 600X600
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(600, 600)
# Set a user interface interactor for the render window.
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Start the initialization and rendering.
iren.Initialize()
renWin.Render()
ren.GetActiveCamera().SetPosition(255, 255, -128)
ren.GetActiveCamera().SetFocalPoint(255, 255, 256)
ren.GetActiveCamera().SetViewUp(0.844464, 0.227883, 0.484716)
ren.ResetCameraClippingRange()
renWin.Render()
iren.Start()
sys.stdout.write('Attempting read ' + type + ' from junk file.\n')
reader.Update()
sys.stdout.write('Attempting read P' + type + ' from junk file.\n')
preader.Update()
del input
del writer
del reader
del pwriter
del preader
# Test the data set writers.
for t in types:
type = t[0]
ext = t[1]
writer = vtk.vtkXMLDataSetWriter()
pwriter = vtk.vtkXMLPDataSetWriter()
input = eval('vtk.vtk' + type + '()')
writer.SetFileName('empty' + type + 'DataSet.' + ext)
sys.stdout.write('Attempting DataSet ' + type + ' write with no input.\n')
writer.Write()
sys.stdout.write('Attempting DataSet ' + type + ' write with empty input.\n')
writer.SetInputData(input)
writer.Write()
pwriter.SetFileName('emptyP' + type + 'DataSet.p' + ext)
sys.stdout.write('Attempting DataSet ' + type + ' write with no input.\n')
pwriter.SetNumberOfPieces(1)
pwriter.Write()
sys.stdout.write('Attempting DataSet ' + type + ' write with empty input.\n')
def process_one_chunk(filename, out_filename):
print(f"Processing file {filename}")
xdmf_template = "chunk_template.xdmf"
_, basename = os.path.split(filename)
xdmf_out = f"xdmf/{basename}.xdmf"
copy_and_replace(xdmf_template, xdmf_out, replacement='../' + filename)
cube = h5py.File(filename, 'r')
neuron_ids = np.array(cube['neuron_ids'])
cube.close()
# Prepare to read the file.
readerVolume = vtk.vtkXdmfReader()
readerVolume.SetFileName(xdmf_out)
readerVolume.Update()
# Extract the region of interest.
# voi = vtk.vtkExtractVOI()
# voi.SetInputConnection(readerVolume.GetOutputPort())
# voi.SetVOI(0, 1023, 0, 1023, 0, 1023)
# voi.SetSampleRate(1, 1, 1)
# voi.Update() # Necessary for GetScalarRange().
for index in neuron_ids:
full_out_name = out_filename % index
if os.path.exists(full_out_name):
print("Skipping neuron %d" % index)
continue
print("Processing neuron %d" % index)
# Prepare surface generation.
contour = vtk.vtkDiscreteMarchingCubes() # For label images.
contour.SetInputConnection(readerVolume.GetOutputPort())
contour.SetValue(0, index)
contour.Update() # Needed for GetNumberOfPolys()!!!
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(contour.GetOutputPort())
smoother.SetNumberOfIterations(15)
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.SetPassBand(.01)
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.GenerateErrorScalarsOn()
smoother.Update()
decimate = vtk.vtkDecimatePro()
decimate.SetInputData(smoother.GetOutput())
decimate.SetTargetReduction(.8)
decimate.PreserveTopologyOn()
decimate.BoundaryVertexDeletionOff()
decimate.Update()
smoothed_polys = decimate.GetOutput()
writer = vtk.vtkXMLDataSetWriter()
writer.SetFileName(full_out_name)
writer.SetInputData(smoothed_polys)
writer.Write()
return 1
