def __init__(self,
layer_dist=1.115,
number_of_cells_per_side_=1,
surface_density=0.1,
unit_cell_size_=300):
molar.pdb.Pdb.__init__(self)
self.layer_dist = layer_dist
self.step_num = int(32)
self.marching_cubes = vtk.vtkMarchingCubes()
self.poly_data = vtk.vtkPolyData()
self.data = vtk.vtkDataObject()
self.unit_cell_size = unit_cell_size_
self.form = "G"
self.number_of_cells_per_side = number_of_cells_per_side_
self.cerebroside = False
self.Update()
self.units = []
self.units_transed = []
self.points = vtk.vtkPoints() #for visualization
self.surf_dens = surface_density
self.total_area = 0
self.total_pair = 0
for f in FILES:
self.units.append(molar.pdb.Pdb())
self.units[-1].ReadFile(PATH + f)
for f in FILES:
self.units_transed.append(molar.pdb.Pdb())
self.units_transed[-1].ReadFile(PATH + f)
self.units_transed[-1].RotateX(180)
self.units[-1].BringToNegativeY()
def __init__(self, number_of_cells_per_side_=1, unit_cell_size_=200):
molar.pdb.Pdb.__init__(self)
self.surface_density = SURFACE_DENSITY
self.step_num = int(32)
self.marching_cubes = vtk.vtkMarchingCubes()
self.poly_data = vtk.vtkPolyData()
self.data = vtk.vtkDataObject()
self.unit_cell_size = unit_cell_size_
self.form = "G"
self.number_of_cells_per_side = number_of_cells_per_side_
self.cerebroside = False
self.Update()
self.units = []
self.units_transed = []
self.points = vtk.vtkPoints() #for visualization
self.attempt = 0
self.collisioncounter = 0
self.total_area = 0
self.total_pair = 0
for f in FILES:
self.units.append(molar.pdb.Pdb())
self.units[-1].ReadFile(PATH + f)
for f in FILES:
self.units_transed.append(molar.pdb.Pdb())
self.units_transed[-1].ReadFile(PATH + f)
self.units_transed[-1].RotateX(180)
self.pointlocator = vtk.vtkPointLocator()
self.pointlocator.Initialize()
self.pointlocator.SetDataSet(vtk.vtkPolyData())
self.pointlocator.InitPointInsertion(
vtk.vtkPoints(),
[0, unit_cell_size_, 0, unit_cell_size_, 0, unit_cell_size_])
def xyplot(points, title='', c='b', corner=1, lines=False):
"""
Return a vtkActor that is a plot of 2D points in x and y.
Use corner to assign its position:
1=topleft,
2=topright,
3=bottomleft,
4=bottomright.
"""
c = vc.getColor(c) # allow different codings
array_x = vtk.vtkFloatArray()
array_y = vtk.vtkFloatArray()
array_x.SetNumberOfTuples(len(points))
array_y.SetNumberOfTuples(len(points))
for i, p in enumerate(points):
array_x.InsertValue(i, p[0])
array_y.InsertValue(i, p[1])
field = vtk.vtkFieldData()
field.AddArray(array_x)
field.AddArray(array_y)
data = vtk.vtkDataObject()
data.SetFieldData(field)
plot = vtk.vtkXYPlotActor()
plot.AddDataObjectInput(data)
plot.SetDataObjectXComponent(0, 0)
plot.SetDataObjectYComponent(0, 1)
plot.SetXValuesToValue()
plot.SetXTitle(title)
plot.SetYTitle('')
plot.ExchangeAxesOff()
plot.PlotPointsOn()
if not lines: plot.PlotLinesOff()
plot.GetProperty().SetPointSize(5)
plot.GetProperty().SetLineWidth(2)
plot.SetNumberOfXLabels(3) #not working
plot.GetProperty().SetColor(0, 0, 0)
plot.GetProperty().SetOpacity(0.7)
plot.SetPlotColor(0, c[0], c[1], c[2])
tprop = plot.GetAxisLabelTextProperty()
tprop.SetColor(0, 0, 0)
tprop.SetOpacity(0.7)
tprop.SetFontFamily(0)
tprop.BoldOff()
tprop.ItalicOff()
tprop.ShadowOff()
tprop.SetFontSize(3) #not working
plot.SetAxisTitleTextProperty(tprop)
plot.SetAxisLabelTextProperty(tprop)
plot.SetTitleTextProperty(tprop)
if corner == 1: plot.GetPositionCoordinate().SetValue(.0, .8, 0)
if corner == 2: plot.GetPositionCoordinate().SetValue(.7, .8, 0)
if corner == 3: plot.GetPositionCoordinate().SetValue(.0, .0, 0)
if corner == 4: plot.GetPositionCoordinate().SetValue(.7, .0, 0)
plot.GetPosition2Coordinate().SetValue(.3, .2, 0)
return plot
def GetSample(obj, ev):
# Get the observed plane and bind it
planeX = GetSample.planeX
imageActor2.SetInputData(planeX.GetResliceOutput())
ren2.AddActor(imageActor2)
renWin.AddRenderer(ren2)
# Set the number of scalar components to 3,
# otherwise vtkImageAccumulate can't process it.
# planeX.GetResliceOutput().AllocateScalars(vtk.VTK_INT, 3)
# Set the input data for histogram
histogram.SetInputData(planeX.GetResliceOutput())
histogram.Update()
# Construct an array to store the histogram
red = [1, 0, 0]
frequencies = vtk.vtkIntArray()
frequencies.SetNumberOfComponents(1)
frequencies.SetNumberOfTuples(256)
o = histogram.GetOutput()
output = o.GetPointData().GetScalars()
j = 0
while j < 256:
frequencies.SetTuple1(j, output.GetValue(j))
j = j + 1
# Convert the array to vtkDataObject
dataObject = vtk.vtkDataObject()
dataObject.GetFieldData().AddArray(frequencies)
# Create a barChart to display the histogram
barChart = vtk.vtkBarChartActor()
barChart.SetInput(dataObject)
barChart.SetTitle("Histogram")
barChart.GetPositionCoordinate().SetValue(0.05, 0.05, 0.0)
barChart.GetPosition2Coordinate().SetValue(0.95, 0.85, 0.0)
barChart.GetProperty().SetColor(1, 1, 1)
barChart.GetLegendActor().SetNumberOfEntries(
dataObject.GetFieldData().GetArray(0).GetNumberOfTuples())
barChart.LegendVisibilityOff()
barChart.LabelVisibilityOff()
count = 0
while count < 256:
barChart.SetBarColor(count, red)
count += 1
# Visualize the histogram
ren3 = vtk.vtkRenderer()
ren3.SetViewport(0.5, 0, 1.0, 0.5)
ren3.AddActor(barChart)
renWin.AddRenderer(ren3)
def plotHistogram(self, renderer):
barChart = vtk.vtkBarChartActor()
dataObject = vtk.vtkDataObject()
dataObject.GetFieldData().AddArray(self.FreqArray)
for i in range(0, self.BinsCount):
barChart.SetBarLabel(i, "{0:.2f}".format(self.getBinCenter(i)))
barChart.SetInput(dataObject)
barChart.GetLegendActor().SetNumberOfEntries(dataObject.GetFieldData().GetArray(0).GetNumberOfTuples())
barChart.LegendVisibilityOff()
barChart.LabelVisibilityOn()
barChart.GetProperty().SetColor(1, 1, 1)
renderer.AddActor(barChart)
def plot(values):
# convert data from python list of tuples => vtkFieldData
xCoords = vtk.vtkFloatArray()
yCoords = vtk.vtkFloatArray()
xCoords.SetNumberOfTuples(len(values))
yCoords.SetNumberOfTuples(len(values))
for i, v in enumerate(values):
xCoords.SetTuple1(i, v[0])
yCoords.SetTuple1(i, v[1])
curve = vtk.vtkFieldData()
curve.AddArray(xCoords)
curve.AddArray(yCoords)
# create vtkDataObject
plot = vtk.vtkDataObject()
plot.SetFieldData(curve)
# build a vtkXYPlotActor
xyplot = vtk.vtkXYPlotActor()
xyplot.AddDataObjectInput(plot)
#xyplot.SetDataObjectPlotModeToRows()
xyplot.SetDataObjectXComponent(0, 0)
xyplot.SetDataObjectYComponent(0, 1)
xyplot.GetPositionCoordinate().SetValue(0, 0.0, 0)
xyplot.GetPosition2Coordinate().SetValue(1, 1, 0)
xyplot.PlotPointsOn()
xyplot.PlotLinesOn()
xyplot.GetProperty().SetPointSize(5)
#xyplot.SetXRange(0, 100)
#xyplot.SetYRange(0, 20)
xyplot.SetPlotColor(0, 1, 1, 0)
# setup renderer / window / interactor
ren = vtk.vtkRenderer()
ren.SetBackground(0.1, 0.2, 0.4)
ren.AddActor2D(xyplot)
renWin = vtk.vtkRenderWindow()
renWin.SetSize(1000, 800)
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
renWin.Render()
iren.Start()
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
# put the data into the data arrays
for i in range(len(x)):
_xData.SetTuple1(i,x[i])
_yData.SetTuple1(i,y[i])
# create a field data object
# (I think this is as a containter to hold the data arrays)
_fieldData = vtk.vtkFieldData()
_fieldData.AllocateArrays(2)
_fieldData.AddArray(_xData)
_fieldData.AddArray(_yData)
# now put the field data object into a data object so that can add it as
# input to the xyPlotActor
_dataObject = vtk.vtkDataObject()
_dataObject.SetFieldData(_fieldData)
# set up the actor
_plot = vtk.vtkXYPlotActor()
_plot.AddDataObjectInput(_dataObject)
# set the title and stuff
_plot.SetTitle("Example 2D plot")
_plot.SetXTitle("x")
_plot.SetYTitle("x^2")
_plot.SetXValuesToValue()
# set which parts of the data object are to be used for which axis
_plot.SetDataObjectXComponent(0,0)
_plot.SetDataObjectYComponent(0,1)
_fieldData4.AddArray(_xData) _fieldData4.AddArray(_yData4) _fieldData5 = vtk.vtkFieldData() _fieldData5.AllocateArrays(2) _fieldData5.AddArray(_xData) _fieldData5.AddArray(_yData5) _fieldData6 = vtk.vtkFieldData() _fieldData6.AllocateArrays(2) _fieldData6.AddArray(_xData) _fieldData6.AddArray(_yData6) # now put the field data object into a data object so that can add it as # input to the xyPlotActor _dataObject1 = vtk.vtkDataObject() _dataObject1.SetFieldData(_fieldData1) _dataObject2 = vtk.vtkDataObject() _dataObject2.SetFieldData(_fieldData2) _dataObject3 = vtk.vtkDataObject() _dataObject3.SetFieldData(_fieldData3) _dataObject4 = vtk.vtkDataObject() _dataObject4.SetFieldData(_fieldData4) _dataObject5 = vtk.vtkDataObject() _dataObject5.SetFieldData(_fieldData5) _dataObject6 = vtk.vtkDataObject()
_fieldData1.AddArray(_xData) _fieldData1.AddArray(_yData1) _fieldData2 = vtk.vtkFieldData() _fieldData2.AllocateArrays(2) _fieldData2.AddArray(_xData) _fieldData2.AddArray(_yData2) _fieldData3 = vtk.vtkFieldData() _fieldData3.AllocateArrays(2) _fieldData3.AddArray(_xData) _fieldData3.AddArray(_yData3) # now put the field data object into a data object so that can add it as # input to the xyPlotActor _dataObject1 = vtk.vtkDataObject() _dataObject1.SetFieldData(_fieldData1) _dataObject2 = vtk.vtkDataObject() _dataObject2.SetFieldData(_fieldData2) _dataObject3 = vtk.vtkDataObject() _dataObject3.SetFieldData(_fieldData3) # set up the actor _plot = vtk.vtkXYPlotActor() _plot.AddDataObjectInput(_dataObject1) _plot.AddDataObjectInput(_dataObject2) _plot.AddDataObjectInput(_dataObject3) # the size of the actor should be 80% of the render window
def main():
colors = vtk.vtkNamedColors()
numTuples = 12
bitter = vtk.vtkFloatArray()
bitter.SetNumberOfTuples(numTuples)
crispy = vtk.vtkFloatArray()
crispy.SetNumberOfTuples(numTuples)
crunchy = vtk.vtkFloatArray()
crunchy.SetNumberOfTuples(numTuples)
salty = vtk.vtkFloatArray()
salty.SetNumberOfTuples(numTuples)
oily = vtk.vtkFloatArray()
oily.SetNumberOfTuples(numTuples)
rand_seq = vtk.vtkMinimalStandardRandomSequence()
rand_seq.SetSeed(8775070)
for i in range(numTuples):
bitter.SetTuple1(i, rand_seq.GetRangeValue(1, 10))
rand_seq.Next()
crispy.SetTuple1(i, rand_seq.GetRangeValue(-1, 1))
rand_seq.Next()
crunchy.SetTuple1(i, rand_seq.GetRangeValue(1, 100))
rand_seq.Next()
salty.SetTuple1(i, rand_seq.GetRangeValue(0, 10))
rand_seq.Next()
oily.SetTuple1(i, rand_seq.GetRangeValue(5, 25))
rand_seq.Next()
dobj = vtk.vtkDataObject()
dobj.GetFieldData().AddArray(bitter)
dobj.GetFieldData().AddArray(crispy)
dobj.GetFieldData().AddArray(crunchy)
dobj.GetFieldData().AddArray(salty)
dobj.GetFieldData().AddArray(oily)
actor = vtk.vtkSpiderPlotActor()
actor.SetInputData(dobj)
actor.SetTitle("Spider Plot")
actor.SetIndependentVariablesToColumns()
actor.GetPositionCoordinate().SetValue(0.05, 0.1, 0.0)
actor.GetPosition2Coordinate().SetValue(0.95, 0.85, 0.0)
actor.GetProperty().SetColor(colors.GetColor3d('Red'))
actor.SetAxisLabel(0, "Bitter")
actor.SetAxisRange(0, 1, 10)
actor.SetAxisLabel(1, "Crispy")
actor.SetAxisRange(1, -1, 1)
actor.SetAxisLabel(2, "Crunchy")
actor.SetAxisRange(2, 1, 100)
actor.SetAxisLabel(3, "Salty")
actor.SetAxisRange(3, 0, 10)
actor.SetAxisLabel(4, "Oily")
actor.SetAxisRange(4, 5, 25)
actor.GetLegendActor().SetNumberOfEntries(numTuples)
for i in range(numTuples):
r = rand_seq.GetRangeValue(0.4, 1.0)
rand_seq.Next()
g = rand_seq.GetRangeValue(0.4, 1.0)
rand_seq.Next()
b = rand_seq.GetRangeValue(0.4, 1.0)
rand_seq.Next()
actor.SetPlotColor(i, r, g, b)
actor.LegendVisibilityOn()
actor.GetTitleTextProperty().SetColor(colors.GetColor3d('MistyRose'))
actor.GetLabelTextProperty().SetColor(colors.GetColor3d('MistyRose'))
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
ren1.AddActor(actor)
ren1.SetBackground(colors.GetColor3d('DarkSlateGray'))
renWin.SetSize(600, 500)
renWin.SetWindowName('SpiderPlot')
iren.Initialize()
renWin.Render()
iren.Start()
def cornerPlot(points, pos=1, s=0.2, title="", c="b", bg="k", lines=True):
"""
Return a ``vtkXYPlotActor`` that is a plot of `x` versus `y`,
where `points` is a list of `(x,y)` points.
:param int pos: assign position:
- 1, topleft,
- 2, topright,
- 3, bottomleft,
- 4, bottomright.
"""
if len(points) == 2: # passing [allx, ally]
#points = list(zip(points[0], points[1]))
points = np.stack((points[0], points[1]), axis=1)
c = colors.getColor(c) # allow different codings
array_x = vtk.vtkFloatArray()
array_y = vtk.vtkFloatArray()
array_x.SetNumberOfTuples(len(points))
array_y.SetNumberOfTuples(len(points))
for i, p in enumerate(points):
array_x.InsertValue(i, p[0])
array_y.InsertValue(i, p[1])
field = vtk.vtkFieldData()
field.AddArray(array_x)
field.AddArray(array_y)
data = vtk.vtkDataObject()
data.SetFieldData(field)
plot = vtk.vtkXYPlotActor()
plot.AddDataObjectInput(data)
plot.SetDataObjectXComponent(0, 0)
plot.SetDataObjectYComponent(0, 1)
plot.SetXValuesToValue()
plot.SetAdjustXLabels(0)
plot.SetAdjustYLabels(0)
plot.SetNumberOfXLabels(3)
plot.GetProperty().SetPointSize(5)
plot.GetProperty().SetLineWidth(2)
plot.GetProperty().SetColor(colors.getColor(bg))
plot.SetPlotColor(0, c[0], c[1], c[2])
plot.SetXTitle(title)
plot.SetYTitle("")
plot.ExchangeAxesOff()
plot.PlotPointsOn()
if not lines:
plot.PlotLinesOff()
if pos == 1:
plot.GetPositionCoordinate().SetValue(0.0, 0.8, 0)
elif pos == 2:
plot.GetPositionCoordinate().SetValue(0.76, 0.8, 0)
elif pos == 3:
plot.GetPositionCoordinate().SetValue(0.0, 0.0, 0)
elif pos == 4:
plot.GetPositionCoordinate().SetValue(0.76, 0.0, 0)
else:
plot.GetPositionCoordinate().SetValue(pos[0], pos[1], 0)
plot.GetPosition2Coordinate().SetValue(s, s, 0)
return plot
colors = [ 1, 4, 5, 8, 9, 10, 12, 1, 16, 16, 16,16 ,18]
colors_numpy_array = np.asarray(colors)
bitter = numpy_to_vtk(colors_numpy_array, deep=True, array_type=vtk.VTK_FLOAT)
#print vtk_data_array
#bitter = vtk.vtkFloatArray
#bitter.SetNumberOfTuples(numTuples);
#for i in range(0, numTuples):#(int i=0; i<numTuples; i++)
# bitter.SetTuple1(i, vtk.vtkMath::Random(7,100))
dobj = vtk.vtkDataObject()
dobj.GetFieldData().AddArray(bitter)
actor = vtk.vtkBarChartActor()
actor.SetInput(dobj);
actor.SetTitle("Bar Chart");
actor.GetPositionCoordinate().SetValue(0.05,0.05,0.0);
actor.GetPosition2Coordinate().SetValue(0.95,0.85,0.0);
actor.GetProperty().SetColor(1,1,1);
actor.GetLegendActor().SetNumberOfEntries(numTuples);
'''
for (int i=0; i<numTuples; i++)
{
double red=vtkMath::Random(0,1);
double green=vtkMath::Random(0,1);
crunchy.SetNumberOfTuples(numTuples)
salty = vtk.vtkFloatArray()
salty.SetNumberOfTuples(numTuples)
oily = vtk.vtkFloatArray()
oily.SetNumberOfTuples(numTuples)
for i in range(numTuples):
bitter.SetTuple1(i, random.randint(1, 10))
crispy.SetTuple1(i, random.randint(-1, 1))
crunchy.SetTuple1(i, random.randint(1, 100))
salty.SetTuple1(i, random.randint(0, 10))
oily.SetTuple1(i, random.randint(5, 25))
dobj = vtk.vtkDataObject()
dobj.GetFieldData().AddArray(bitter)
dobj.GetFieldData().AddArray(crispy)
dobj.GetFieldData().AddArray(crunchy)
dobj.GetFieldData().AddArray(salty)
dobj.GetFieldData().AddArray(oily)
actor = vtk.vtkSpiderPlotActor()
actor.SetInputData(dobj)
actor.SetTitle("spider plot")
actor.SetIndependentVariablesToColumns()
actor.GetPositionCoordinate().SetValue(0.05, 0.1, 0.0)
actor.GetPosition2Coordinate().SetValue(0.95, 0.85, 0.0)
actor.GetProperty().SetColor(1, 0, 0)
actor.SetAxisLabel(0, "Bitter")
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()
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()
