def decimation_pro(data,ratio):
sim = vtk.vtkDecimatePro();
sim.SetTargetReduction(ratio);
sim.SetInputData(data);
sim.PreserveTopologyOn();
sim.SplittingOff();
sim.BoundaryVertexDeletionOff();
sim.Update()
return sim.GetOutput();0
def get_actor(vtk_source, color=color_diffuse, opacity=1.0,
has_scalar_visibility=False, has_decimator=False):
"""
Set `scalar_visibility` be `True` makes `color` unavailable.
:return: a vtkActor
"""
if has_decimator:
# Reduce the number of triangles
decimator = vtk.vtkDecimatePro()
decimator.SetInputConnection(vtk_source.GetOutputPort())
# decimator.SetInputData(vtk_source)
decimator.SetFeatureAngle(60)
decimator.MaximumIterations = 1
decimator.PreserveTopologyOn()
decimator.SetMaximumError(0.0002)
decimator.SetTargetReduction(1)
decimator.SetErrorIsAbsolute(1)
decimator.SetAbsoluteError(0.0002)
decimator.ReleaseDataFlagOn()
# Generate Normals
normals = vtk.vtkPolyDataNormals()
if has_decimator:
normals.SetInputConnection(decimator.GetOutputPort())
else:
normals.SetInputConnection(vtk_source.GetOutputPort())
normals.SetFeatureAngle(60.0)
normals.ReleaseDataFlagOn()
stripper = vtk.vtkStripper()
stripper.SetInputConnection(normals.GetOutputPort())
stripper.ReleaseDataFlagOn()
mapper = vtk.vtkPolyDataMapper()
# mapper.SetInputConnection(vtk_source.GetOutputPort())
mapper.SetInputConnection(stripper.GetOutputPort())
mapper.SetScalarVisibility(has_scalar_visibility)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetDiffuseColor(color)
actor.GetProperty().SetSpecular(0.3)
actor.GetProperty().SetSpecularPower(20)
actor.GetProperty().SetInterpolation(2)
# actor.GetProperty().SetRepresentation(2)
# actor.GetProperty().SetEdgeVisibility(True)
# actor.GetProperty().SetOpacity(opacity)
if opacity < 1.0:
if is_depth_peeling_supported(render_window, renderer, True):
setup_evn_for_depth_peeling(render_window, renderer, max_peels, occlusion)
actor.GetProperty().SetOpacity(opacity)
else:
print "Depth Peeling is not supported."
return actor
def applyFilters(self, state):
surface = None
surface = state.inputModelNode.GetPolyDataConnection()
if state.decimation:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputConnection(surface)
decimation = vtk.vtkDecimatePro()
decimation.SetTargetReduction(state.reduction)
decimation.SetBoundaryVertexDeletion(state.boundaryDeletion)
decimation.PreserveTopologyOn()
decimation.SetInputConnection(triangle.GetOutputPort())
surface = decimation.GetOutputPort()
if state.smoothing:
if state.smoothingMethod == "Laplace":
smoothing = vtk.vtkSmoothPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.laplaceIterations)
smoothing.SetRelaxationFactor(state.laplaceRelaxation)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
elif state.smoothingMethod == "Taubin":
smoothing = vtk.vtkWindowedSincPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.taubinIterations)
smoothing.SetPassBand(state.taubinPassBand)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
if state.normals:
normals = vtk.vtkPolyDataNormals()
normals.AutoOrientNormalsOn()
normals.SetFlipNormals(state.flipNormals)
normals.SetSplitting(state.splitting)
normals.SetFeatureAngle(state.featureAngle)
normals.ConsistencyOn()
normals.SetInputConnection(surface)
surface = normals.GetOutputPort()
if state.cleaner:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(surface)
surface = cleaner.GetOutputPort()
if state.connectivity:
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetExtractionModeToLargestRegion()
connectivity.SetInputConnection(surface)
surface = connectivity.GetOutputPort()
state.outputModelNode.SetPolyDataConnection(surface)
return True
def decimatePolygon(polyObject,reduceFactor=0.5):
'''
'''
deci = vtk.vtkDecimatePro()
deci.SetInputData(polyObject)
deci.SetTargetReduction(reduceFactor)
deci.BoundaryVertexDeletionOff()
deci.PreserveTopologyOn()
deci.SetSplitting(0)
deci.Update()
return deci.GetOutput()
def __init__(self, inputs = (1,1)):
"""
Initialization
"""
self.defaultLower = 0
self.defaultUpper = 255
lib.ProcessingFilter.ProcessingFilter.__init__(self,(1,1))
self.contour = vtk.vtkMarchingCubes()
self.decimate = vtk.vtkDecimatePro()
self.descs = {"Simplify": "Simplify surface", "IsoValue":"Iso-surface value",
"PreserveTopology":"PreserveTopology"}
self.filterDesc = "Creates iso-surface as polygons\nInput: Binary image (Grayscale image)\nOutput: Surface mesh";
def vtk_smooth(iso, iter=20, relax=0.5, decimate=0.0):
isoSmooth = vtk.vtkSmoothPolyDataFilter()
if decimate>0:
deci = vtk.vtkDecimatePro()
deci.SetInput(iso.GetOutput())
deci.SetTargetReduction(decimate)
deci.PreserveTopologyOn()
isoSmooth.SetInputConnection(deci.GetOutputPort())
else:
isoSmooth.SetInputConnection(iso.GetOutputPort())
isoSmooth.SetNumberOfIterations(100)
isoSmooth.BoundarySmoothingOn()
isoSmooth.FeatureEdgeSmoothingOff()
isoSmooth.SetFeatureAngle(45)
isoSmooth.SetEdgeAngle(15)
isoSmooth.SetRelaxationFactor(relax)
return isoSmooth
def __init__(self, parent, visualizer, **kws):
"""
Initialization
"""
self.init = False
VisualizationModule.__init__(self, parent, visualizer, numberOfInputs=(2, 2), **kws)
# self.name = "Surface Rendering"
self.normals = vtk.vtkPolyDataNormals()
self.smooth = None
self.volumeModule = None
self.scalarRange = (0, 255)
for i in range(1, 3):
self.setInputChannel(i, i)
self.eventDesc = "Rendering iso-surface"
self.decimate = vtk.vtkDecimatePro()
self.mapper = vtk.vtkPolyDataMapper()
self.mapper2 = vtk.vtkPolyDataMapper()
self.contour = vtk.vtkMarchingCubes()
self.contour2 = vtk.vtkDiscreteMarchingCubes()
self.descs = {
"Normals": "Smooth surface with normals",
"FeatureAngle": "Feature angle of normals\n",
"Simplify": "Simplify surface",
"PreserveTopology": "Preserve topology",
"Transparency": "Surface transparency",
"Distance": "Distance to consider inside",
"MarkColor": "Mark in/outside objects with colors",
}
self.actor = self.lodActor = vtk.vtkLODActor()
self.lodActor.SetMapper(self.mapper)
self.lodActor.SetNumberOfCloudPoints(10000)
self.actor2 = vtk.vtkLODActor()
self.actor2.SetMapper(self.mapper2)
self.actor2.SetNumberOfCloudPoints(10000)
self.renderer = self.parent.getRenderer()
self.renderer.AddActor(self.lodActor)
self.renderer.AddActor(self.actor2)
lib.messenger.connect(None, "highlight_object", self.onHighlightObject)
def GeneratePolyData(self):
if self._imagemask:
contour_filter = vtk.vtkMarchingCubes()
contour_filter.ReleaseDataFlagOn()
contour_filter.SetNumberOfContours(1)
contour_filter.SetComputeScalars(0)
contour_filter.SetComputeNormals(0)
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
contour_filter.SetInputData(self._imagemask)
else:
contour_filter.SetInput(self._imagemask)
contour_filter.SetValue(0, 128.0)
try:
contour_filter.Update()
except:
print sys.exc_type, sys.exc_value
return False
decimate = vtk.vtkDecimatePro()
decimate.ReleaseDataFlagOn()
decimate.SetInputConnection(contour_filter.GetOutputPort())
decimate.PreserveTopologyOn()
decimate.SetTargetReduction(0)
try:
decimate.Update()
except:
print sys.exc_type, sys.exc_value
return False
if self._polydata is None:
self._polydata = GeometryObject(
self._name, self._name, decimate.GetOutputPort())
else:
self._polydata.SetInputConnection(decimate.GetOutputPort())
if self._wireframe:
self._polydata.SetWireFrameOn()
else:
self._polydata.SetWireFrameOff()
self._polydata.SetVisibilityOff()
def __init__(self, parent, visualizer, **kws):
"""
Initialization
"""
VisualizationModule.__init__(self, parent, visualizer, **kws)
# self.name = "Surface Rendering"
# for i in range(1, 3):
# self.setInputChannel(i, i)
self.normals = vtk.vtkPolyDataNormals()
self.smooth = None
self.volumeModule = None
self.scalarRange = (0, 255)
self.eventDesc = "Rendering iso-surface"
self.decimate = vtk.vtkDecimatePro()
self.setMethod(1)
self.init = 0
self.mapper = vtk.vtkPolyDataMapper()
self.descs = {
"Method": "Surface rendering method",
"Gaussian": "Smooth surface with gaussian smoothing",
"Normals": "Smooth surface with normals",
"FeatureAngle": "Feature angle of normals\n",
"Simplify": "Simplify surface",
"PreserveTopology": "Preserve topology",
"IsoValue": "Iso value",
"SurfaceRangeBegin": "Generate surfaces in range:\n",
"SurfaceAmnt": "Number of surfaces",
"Transparency": "Surface transparency",
"MultipleSurfaces": "Visualize multiple surfaces",
"SolidColor": "Color surface with max. intensity",
}
self.actor = self.lodActor = vtk.vtkLODActor()
self.lodActor.SetMapper(self.mapper)
self.lodActor.SetNumberOfCloudPoints(10000)
self.renderer = self.parent.getRenderer()
self.renderer.AddActor(self.lodActor)
# self.updateRendering()
self.filterDesc = "Create and visualize iso-surface"
def decimateSurface(self, polyData):
'''
'''
decimationFilter = vtk.vtkDecimatePro()
decimationFilter.SetInputData(polyData)
decimationFilter.SetTargetReduction(0.99)
decimationFilter.SetBoundaryVertexDeletion(0)
decimationFilter.PreserveTopologyOn()
decimationFilter.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(decimationFilter.GetOutput())
cleaner.Update()
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(cleaner.GetOutput())
triangleFilter.Update()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy(triangleFilter.GetOutput())
return outPolyData
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
# the decimator only works on triangle data, so we make sure
# that it only gets triangle data
self._triFilter = vtk.vtkTriangleFilter()
self._decimate = vtk.vtkDecimatePro()
self._decimate.PreserveTopologyOn()
self._decimate.SetInput(self._triFilter.GetOutput())
module_utils.setup_vtk_object_progress(self, self._triFilter, "Converting to triangles")
module_utils.setup_vtk_object_progress(self, self._decimate, "Decimating mesh")
# now setup some defaults before our sync
self._config.target_reduction = self._decimate.GetTargetReduction() * 100.0
config_list = [
(
"Target reduction (%):",
"target_reduction",
"base:float",
"text",
"Decimate algorithm will attempt to reduce by this much.",
)
]
ScriptedConfigModuleMixin.__init__(
self,
config_list,
{"Module (self)": self, "vtkDecimatePro": self._decimate, "vtkTriangleFilter": self._triFilter},
)
self.sync_module_logic_with_config()
def applyFilters(self, state):
surface = None
surface = state.inputModelNode.GetPolyDataConnection()
if state.decimation:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputConnection(surface)
decimation = vtk.vtkDecimatePro()
decimation.SetTargetReduction(state.reduction)
decimation.SetBoundaryVertexDeletion(state.boundaryDeletion)
decimation.PreserveTopologyOn()
decimation.SetInputConnection(triangle.GetOutputPort())
surface = decimation.GetOutputPort()
if state.smoothing:
if state.smoothingMethod == "Laplace":
smoothing = vtk.vtkSmoothPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.laplaceIterations)
smoothing.SetRelaxationFactor(state.laplaceRelaxation)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
elif state.smoothingMethod == "Taubin":
smoothing = vtk.vtkWindowedSincPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.taubinIterations)
smoothing.SetPassBand(state.taubinPassBand)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
if state.normals:
normals = vtk.vtkPolyDataNormals()
normals.SetAutoOrientNormals(state.autoOrientNormals)
normals.SetFlipNormals(state.flipNormals)
normals.SetSplitting(state.splitting)
normals.SetFeatureAngle(state.featureAngle)
normals.ConsistencyOn()
normals.SetInputConnection(surface)
surface = normals.GetOutputPort()
if state.mirror:
mirrorTransformMatrix = vtk.vtkMatrix4x4()
mirrorTransformMatrix.SetElement(0, 0, -1 if state.mirrorX else 1)
mirrorTransformMatrix.SetElement(1, 1, -1 if state.mirrorY else 1)
mirrorTransformMatrix.SetElement(2, 2, -1 if state.mirrorZ else 1)
mirrorTransform = vtk.vtkTransform()
mirrorTransform.SetMatrix(mirrorTransformMatrix)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputConnection(surface)
transformFilter.SetTransform(mirrorTransform)
surface = transformFilter.GetOutputPort()
if mirrorTransformMatrix.Determinant()<0:
reverse = vtk.vtkReverseSense()
reverse.SetInputConnection(surface)
surface = reverse.GetOutputPort()
if state.cleaner:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(surface)
surface = cleaner.GetOutputPort()
if state.fillHoles:
fillHoles = vtk.vtkFillHolesFilter()
fillHoles.SetHoleSize(state.fillHolesSize)
fillHoles.SetInputConnection(surface)
# Need to auto-orient normals, otherwise holes
# could appear to be unfilled when only front-facing elements
# are chosen to be visible.
normals = vtk.vtkPolyDataNormals()
normals.AutoOrientNormalsOn()
normals.ConsistencyOn()
normals.SetInputConnection(fillHoles.GetOutputPort())
surface = normals.GetOutputPort()
if state.connectivity:
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetExtractionModeToLargestRegion()
connectivity.SetInputConnection(surface)
surface = connectivity.GetOutputPort()
state.outputModelNode.SetPolyDataConnection(surface)
return True
def create_polygon_reducer(extractor):
reducer = vtk.vtkDecimatePro()
reducer.SetInputConnection(extractor.GetOutputPort())
reducer.SetTargetReduction(0.5)
reducer.PreserveTopologyOn()
return reducer
def load_map(gfx,mapfile,root,status,scale,rendtype,isov,opct,cropentry,nfv,vardeci,varsmooth,color,caller):
if caller != 'fit':
root.configure(cursor='watch')
status.set('Map loading ... please wait')
if mapfile =='' or mapfile == None or mapfile ==() :
MB.showwarning('Info','Select map file')
status.clear()
root.configure(cursor='arrow')
return
try:
gfx.renderer.RemoveActor(gfx.map[0].acteur)
gfx.renderer.RemoveActor(gfx.map[0].box)
except:
pass
if mapfile == 0:
mapfile = gfx.map[0].fn
if gfx.map == []:
gfx.map = [Map()]
gfx.map[0].id=0
if 'map' in caller :
clean_map(gfx) #supression des fichiers sort.s xudi et iudi
if '.vtk' in mapfile:
chdir(gfx.tmpdir)
v2v_out='info_map'
if caller != 'crop':
gfx.map[0].sigma,gfx.map[0].avg = map_sigma_avg(v2v_out)
if scale != gfx.map[0].scale:
spc = None
o = None
f = open(mapfile,'r')
for l in f:
if l.startswith('SPACING'):
spc = l.split()[1:4]
if l.startswith('ORIGIN'):
o = l.split()[1:4]
if spc != None and o != None:
break
f.close()
gfx.map[0].ratio = scale/gfx.map[0].scale
if spc != None and o != None:
system("sed -i -e /^SPACING/s/.*/'SPACING %f %f %f'/ %s"%(float(spc[0])*gfx.map[0].ratio,float(spc[1])*gfx.map[0].ratio,float(spc[2])*gfx.map[0].ratio,mapfile))
system("sed -i -e /^ORIGIN/s/.*/'ORIGIN %f %f %f'/ %s"%(float(o[0])*gfx.map[0].ratio,float(o[1])*gfx.map[0].ratio,float(o[2])*gfx.map[0].ratio,mapfile))
chdir(gfx.workdir)
if '.ezd' in mapfile:
chdir(gfx.tmpdir)
mapfileout = extract_file_from_path(mapfile)[:-4]+'.vtk'
e2v_out='info_map'
system(gfx.vedabin+'/e2v.exe >> %s <<ENDOF\n%s \n%f \n%s \nENDOF'%(e2v_out,mapfile,scale,mapfileout))
mapfile = gfx.tmpdir + '/' + mapfileout
gfx.map[0].sigma,gfx.map[0].avg = map_sigma_avg(e2v_out)
chdir(gfx.workdir)
gfx.map[0].fn = mapfile
gfx.map[0].id = set_map_id(gfx)
gfx.map[0].color = color
gfx.map[0].oldscale = gfx.map[0].scale
gfx.map[0].scale = scale
if nfv !=None:
nfv.set(extract_file_from_path(gfx.map[0].fn))
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(mapfile)
reader.Update() #by calling Update() we read the file
gfx.map[0].reader=reader
iso = vtk.vtkMarchingContourFilter()
iso.UseScalarTreeOn()
iso.ComputeNormalsOn()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0,isov*gfx.map[0].sigma+gfx.map[0].avg)
gfx.map[0].iso=iso
gfx.map[0].isov=isov
if varsmooth == '1':
#generate vectors
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(iso.GetOutputPort())
clean.ConvertStripsToPolysOn()
smooth = vtk.vtkWindowedSincPolyDataFilter()
smooth.SetInputConnection(clean.GetOutputPort())
smooth.BoundarySmoothingOn()
smooth.GenerateErrorVectorsOn()
smooth.GenerateErrorScalarsOn()
smooth.NormalizeCoordinatesOn()
smooth.NonManifoldSmoothingOn()
smooth.FeatureEdgeSmoothingOn()
smooth.SetEdgeAngle(90)
smooth.SetFeatureAngle(90)
smooth.Update()
if vardeci=='1':
deci = vtk.vtkDecimatePro()
if varsmooth == '0':
deci.SetInput(iso.GetOutput())
else :
deci.SetInput(smooth.GetOutput())
deci.PreserveTopologyOn()
deci.BoundaryVertexDeletionOn()
deci.SplittingOn()
deci.PreSplitMeshOn()
deci.SetTargetReduction(0.97)
gfx.map[0].isdeci='1'
mapper = vtk.vtkOpenGLPolyDataMapper()
mapper.SetInputConnection(deci.GetOutputPort())
else :
mapper = vtk.vtkOpenGLPolyDataMapper()
if varsmooth == '1':
mapper.SetInputConnection(smooth.GetOutputPort()) ### <- connection here
else :
mapper.SetInputConnection(iso.GetOutputPort())
#mapper.SetInput(newpd) ### <- newpd connect there
gfx.map[0].isdeci='0'
mapper.ScalarVisibilityOff()
mapper.Update()
gfx.map[0].mapper=mapper
actor = vtk.vtkOpenGLActor()
actor.SetMapper(mapper)
gfx.map[0].acteur=actor
#actor.SetScale(scale,scale,scale) gerer differament
actor.GetProperty().SetColor(gfx.map[0].color)
actor.PickableOff()
#definition de la box
outline = vtk.vtkOutlineFilter()
outline.SetInput(reader.GetOutput())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInput(outline.GetOutput())
box=vtk.vtkActor()
box.SetMapper( outlineMapper )
box.GetProperty().SetColor((invcolor(gfx.map[0].color)))
box.PickableOff()
#box.SetScale(scale,scale,scale)
gfx.map[0].box = box
#get boxwidget bounds and set axes lenth
(xmin,xmax,ymin,ymax,zmin,zmax)=box.GetBounds()
x=abs(xmin-xmax)/2.0
y=abs(ymin-ymax)/2.0
z=abs(zmin-zmax)/2.0
gfx.axes.SetTotalLength( x, y , z ) #defini la longeurs des axe
init_cam_slab(gfx,(xmin,xmax,ymin,ymax,zmin,zmax)) #defini le slab correct
gfx.map[0].rendtype=rendtype
if rendtype=='Wireframe':
actor.GetProperty().SetRepresentationToWireframe()
elif rendtype=='Surface':
actor.GetProperty().SetRepresentationToSurface()
elif rendtype=='Points':
actor.GetProperty().SetRepresentationToPoints()
actor.GetProperty().SetPointSize(5)
else :
actor.GetProperty().SetRepresentationToWireframe()
gfx.map[0].opct=opct
actor.GetProperty().SetOpacity(opct)
actor.GetProperty().SetInterpolationToGouraud()
actor.GetProperty().SetSpecular(.4)
actor.GetProperty().SetSpecularPower(10)
if cropentry!=None:
if gfx.crop==None:
gfx.crop=Crop(gfx,iso,cropentry,None) #here entryval = None
rendermap(gfx)
#ajustement pour la symetry helicoidale
if gfx.map[0].scale != gfx.map[0].oldscale:#changement de scale
gfx.itf.propagate_scale(gfx,scale,caller)
if gfx.ps != None:
if gfx.ps.solidtype == 'Helicoidal':
gfx.ps.display_tube(gfx,caller)
elif gfx.ps.solidtype == 'Icosahedral' or gfx.ps.solidtype =='Octahedral' or gfx.ps.solidtype == 'Tetrahedral':
gfx.ps.display_platonic(gfx,gfx.ps.ori)
elif gfx.ps.solidtype =='Cn' or gfx.ps.solidtype == 'Dn':
gfx.ps.display_Xn(gfx)
if caller == 'crop':#crop uniquement helicoidal
if gfx.ps != None:
if gfx.ps.solidtype == 'Helicoidal':
gfx.ps.display_tube(gfx,caller)
if caller != 'fit':
status.clear()
root.configure(cursor='arrow')
polydata = contour.GetOutput() #export the 3D image as a polygon data file algordata = contour.GetOutputPort() #export the 3D image as an algorithm file """ """ #VOXEL CONTOURING ALGORITHM (doesnt work yet) vcsf = vtk.vtkVoxelContoursToSurfaceFilter() vcsf.SetInputConnection(imgThreshold) vcsf.Update() polydata = vcsf.GetOutput() #export the 3D image as a polygon data file algordata = vcsf.GetOutputPort() #export the 3D image as an algorithm file """ ############################# #Reduce Number of Triangles decimator = vtk.vtkDecimatePro() decimator.SetInputConnection(algordata) decimator.SetTargetReduction(0.5) decimator.SetPreserveTopology(1) decimator.Update() reducetri = decimator.GetOutputPort() # #Smooth smooth = vtk.vtkSmoothPolyDataFilter() smooth.SetInputConnection(filhol) smooth.SetNumberOfIterations(15) smooth.SetFeatureAngle(10) smooth.SetRelaxationFactor(0.05) smooth.FeatureEdgeSmoothingOn()
def procData(self):
# double negative so that the name doesn't collide with the same option that is off by default in dpLoadh5
#if not self.no_legacy_transpose: cube = self.data_cube.transpose((1,0,2))
# changed this to off by default and use same flag from dpLoadh5
if self.legacy_transpose: cube = self.data_cube.transpose((1,0,2))
else: cube = self.data_cube
# for easy saving of scale as attribute in hdf5 output
self.scale = self.data_attrs['scale']
# Pad data with zeros so that meshes are closed on the edges
sizes = np.array(cube.shape); r = self.RAD; sz = sizes + 2*r;
dataPad = np.zeros(sz, dtype=self.data_type); dataPad[r:sz[0]-r, r:sz[1]-r, r:sz[2]-r] = cube
# old method
# # get all unique seeds in the cube
# self.seeds = np.unique(cube)
# # remove the background label (label 0)
# if self.seeds.size > 0 and self.seeds[0] == 0: self.seeds = self.seeds[1:]
# get sizes first with hist (prevents sums in meshing loop)
#self.nVoxels = emLabels.getSizes(cube)[1:]
self.nVoxels = emLabels.getSizesMax(cube, sum(self.data_attrs['types_nlabels']))[1:]
self.seeds = np.arange(1, self.nVoxels.size+1, dtype=np.int64); self.seeds = self.seeds[self.nVoxels>0]
#print(np.argmax(self.nVoxels))
assert( self.seeds.size > 0 ) # error, no labels
n = self.seeds.size; #self.nVoxels = np.zeros((n,), dtype=np.int64)
assert( n == self.seeds[-1] or not self.mesh_outfile_stl ) # for consistency with stl file, no empty labels
# intended for debug, only process a subset of the seeds
if self.seed_range[0] < 1 or self.seed_range[0] > n: self.seed_range[0] = 0
if self.seed_range[1] < 1 or self.seed_range[1] < 0: self.seed_range[1] = n
# threw me off in debug twice, if the supervoxels are contiguous then have the seed_range mean actual seed
if n == self.seeds[-1] and self.seed_range[0] > 0: self.seed_range[0] -= 1
# other inits
if self.do_smooth: W = np.ones(self.smooth, dtype=self.PDTYPE) / self.smooth.prod()
# allocate outputs
self.faces = n * [None]; self.vertices = n * [None]; self.mins = n * [None]; self.rngs = n * [None]
self.bounds_beg = n * [None]; self.bounds_end = n * [None]
self.nFaces = np.zeros((n,), dtype=np.uint64); self.nVertices = np.zeros((n,), dtype=np.uint64);
if self.doplots or self.mesh_outfile_stl: self.allPolyData = vtk.vtkAppendPolyData()
# get bounding boxes for each supervoxel
svox_bnd = nd.measurements.find_objects(dataPad, n)
if self.dpLabelMesher_verbose:
tloop = time.time(); t = time.time()
for i in range(self.seed_range[0], self.seed_range[1]):
if self.dpLabelMesher_verbose and i % self.print_every == 0:
print('seed : %d is %d / %d' % (self.seeds[i],i+1,self.seed_range[1]))
# old method
# # select the labels
# #bwdpls = (dataPad == self.seeds[i]);
# #self.nVoxels[i] = bwdpls.sum();
# if self.dpLabelMesher_verbose: print('\tnVoxels = %d' % self.nVoxels[i])
#
# # get the voxel coordinates relative to padded and non-padded cube
# idpls = np.argwhere(bwdpls)
# # bounding box within zero padded cube
# imin = idpls.min(axis=0); imax = idpls.max(axis=0)
cur_bnd = svox_bnd[self.seeds[i]-1]
imin = np.array([x.start for x in cur_bnd]); imax = np.array([x.stop-1 for x in cur_bnd])
# min and max coordinates of this seed within zero padded cube
pmin = imin - r; pmax = imax + r;
# min coordinates of this seed relative to original (non-padded cube)
self.mins[i] = pmin - r; self.rngs[i] = pmax - pmin + 1
# old method
# crop out the bounding box plus the padding, then optionally smooth
#crpdpls = bwdpls[pmin[0]:pmax[0]+1,pmin[1]:pmax[1]+1,pmin[2]:pmax[2]+1].astype(self.PDTYPE)
# crop out the bounding box then binarize this seed within bounding box
crpdpls = (dataPad[pmin[0]:pmax[0]+1,pmin[1]:pmax[1]+1,
pmin[2]:pmax[2]+1] == self.seeds[i]).astype(self.PDTYPE)
if self.do_smooth:
crpdplsSm = filters.convolve(crpdpls, W, mode='reflect', cval=0.0, origin=0)
# if smoothing results in nothing above contour level, use original without smoothing
if (crpdplsSm > self.contour_lvl).any():
del crpdpls; crpdpls = crpdplsSm; del crpdplsSm
if self.doplots: showImgData(np.squeeze(crpdpls[:,:,crpdpls.shape[2]/2]),'slice')
# vtkImageImport is used to create image data from memory in vtk
# http://wiki.scipy.org/Cookbook/vtkVolumeRendering
dataImporter = vtk.vtkImageImport()
# The preaviusly created array is converted to a byte string (not string, see np docs) and imported.
data_string = crpdpls.transpose((2,1,0)).tostring();
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
# Set the type of the newly imported data
#dataImporter.SetDataScalarTypeToUnsignedChar()
#dataImporter.SetDataScalarTypeToUnsignedShort()
dataImporter.SetDataScalarTypeToDouble()
# Because the data that is imported only contains an intensity value (i.e. not RGB), the importer
# must be told this is the case.
dataImporter.SetNumberOfScalarComponents(1)
if self.set_voxel_scale:
# Have to set the voxel anisotropy here, as there does not seem an easy way once the poly is created.
dataImporter.SetDataSpacing(self.data_attrs['scale'])
# Data extent is the extent of the actual buffer, whole extent is ???
# Use extents that are relative to non-padded cube
beg = self.mins[i]; end = self.mins[i] + self.rngs[i] - 1
dataImporter.SetDataExtent(beg[0], end[0], beg[1], end[1], beg[2], end[2])
dataImporter.SetWholeExtent(beg[0], end[0], beg[1], end[1], beg[2], end[2])
# save bounds relative to entire dataset
self.bounds_beg[i] = beg + self.dataset_index; self.bounds_end[i] = end + self.dataset_index;
# use vtk for isosurface contours and surface mesh reduction
iso = vtk.vtkContourFilter()
iso.SetInputConnection(dataImporter.GetOutputPort())
iso.SetComputeNormals(0)
iso.SetValue(0, self.contour_lvl)
if self.decimatePro:
deci = vtk.vtkDecimatePro()
rf = 1-self.reduce_frac; deci.SetTargetReduction(rf); df = 0.01
deci.SplittingOn(); deci.PreserveTopologyOff(); deci.BoundaryVertexDeletionOn()
if self.min_faces > 0: updates = range(100)
else: updates = ['deci.BoundaryVertexDeletionOff()','deci.PreserveTopologyOn()','0']
else:
deci = vtk.vtkQuadricClustering()
#deci.SetDivisionOrigin(0.0,0.0,0.0); deci.SetDivisionSpacing(self.reduce_spacing)
nb = self.reduce_nbins; deci.SetNumberOfDivisions(nb,nb,nb); deci.AutoAdjustNumberOfDivisionsOff()
updates = ['deci.AutoAdjustNumberOfDivisionsOn()','0']
# thought of adding checking for closed surfaces, http://comments.gmane.org/gmane.comp.lib.vtk.user/47957
# this did not work, for low reduce_frac, many open edges remain even for large objects
# not clear that triangle filter does anything, contour filter already makes triangulated meshes?
# send polygonal mesh from isosurface to triangle filter to convert to triangular mesh
#tri = vtk.vtkTriangleFilter(); tri.SetInputConnection(iso.GetOutputPort());
#deci.SetInputConnection(tri.GetOutputPort())
deci.SetInputConnection(iso.GetOutputPort())
# xxx - this is kindof a cheap trick, if we reduce down "too much", then rerun to preserve more
for update in updates:
deci.Update()
# http://forrestbao.blogspot.com/2012/06/vtk-polygons-and-other-cells-as.html
# http://stackoverflow.com/questions/6684306/how-can-i-read-a-vtk-file-into-a-python-datastructure
dOut = deci.GetOutput()
# xxx - points seem to be single instead of inputted type, probably depends on vtk version:
# http://public.kitware.com/pipermail/vtkusers/2010-April/059413.html
self.vertices[i] = nps.vtk_to_numpy(dOut.GetPoints().GetData())
if self.center_origin:
self.vertices[i][:,0] -= sizes[0]/2; self.vertices[i][:,1] -= sizes[1]/2
self.vertices[i][:,2] = sizes[2]/2 - self.vertices[i][:,2]
self.faces[i] = nps.vtk_to_numpy(dOut.GetPolys().GetData()).reshape((-1,4))[:,1:]
if self.flip_faces: self.faces[i] = self.faces[i][:,::-1]
self.nVertices[i] = self.vertices[i].shape[0]
self.nFaces[i] = self.faces[i].shape[0]
if self.dpLabelMesher_verbose and i % self.print_every == 0:
print('\t%d vertices, %d faces' % (self.nVertices[i], self.nFaces[i]))
if self.min_faces > 0:
if self.nFaces[i] >= self.min_faces: break
rf -= df; deci.SetTargetReduction(rf)
else:
if self.nVertices[i] > 2 and self.nFaces[i] > 0: break
eval(update)
assert( self.nVertices[i] > 2 and self.nFaces[i] > 0 ) # there has to be at least one face
if self.doplots:
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(deci.GetOutputPort())
dpLabelMesher.vtkShow(mapper)
# append the current surface to vtk object with all the surfaces
if self.doplots or self.mesh_outfile_stl:
self.allPolyData.AddInputConnection(deci.GetOutputPort())
if self.doplots:
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputConnection(self.allPolyData.GetOutputPort())
connectivityFilter.SetExtractionModeToAllRegions()
connectivityFilter.ColorRegionsOn()
connectivityFilter.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(connectivityFilter.GetOutputPort())
mapper.SetScalarRange(connectivityFilter.GetOutput().GetPointData().GetArray("RegionId").GetRange())
dpLabelMesher.vtkShow(mapper)
if self.dpLabelMesher_verbose and i % self.print_every == 0:
print('\tdone in %.3f s' % (time.time() - t,)); t = time.time()
if self.dpLabelMesher_verbose: print('Total ellapsed time meshing %.3f s' % (time.time() - tloop,))
def __init__ (self, interactor, renderer, mesh_filename, reg_filename):
self.interactor = interactor
self.renderer = renderer
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(mesh_filename)
cf = vtk.vtkContourFilter()
cf.SetInput(reader.GetOutput())
cf.SetValue(0, 1)
deci = vtk.vtkDecimatePro()
deci.SetInput(cf.GetOutput())
deci.SetTargetReduction(.1)
deci.PreserveTopologyOn()
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInput(deci.GetOutput())
smoother.SetNumberOfIterations(100)
normals = vtk.vtkPolyDataNormals()
normals.SetInput(smoother.GetOutput())
normals.FlipNormalsOn()
normals.SetFeatureAngle(60.0)
stripper = vtk.vtkStripper()
stripper.SetInputConnection(normals.GetOutputPort())
lut = vtk.vtkLookupTable()
lut.SetHueRange(0, 0)
lut.SetSaturationRange(0, 0)
lut.SetValueRange(0.2, 0.55)
contourMapper = vtk.vtkPolyDataMapper()
#contourMapper.SetInput(normals.GetOutput())
contourMapper.SetInput(stripper.GetOutput())
contourMapper.SetLookupTable(lut)
self.contours = vtk.vtkActor()
self.contours.SetMapper(contourMapper)
#self.contours.GetProperty().SetRepresentationToWireframe()
self.contours.GetProperty().SetRepresentationToSurface()
#self.contours.GetProperty().SetInterpolationToGouraud()
#self.contours.GetProperty().SetOpacity(1.0)
#self.contours.GetProperty().SetAmbient(0.1)
self.contours.GetProperty().SetDiffuse(0.1)
#self.contours.GetProperty().SetSpecular(0.1)
#self.contours.GetProperty().SetSpecularPower(0.1)
# now setmatrix() on the actor from the reg file !
def array_to_vtkmatrix4x4(scipy_array):
vtkmat = vtk.vtkMatrix4x4()
for i in range(0,4):
for j in range(0,4):
vtkmat.SetElement(i,j, scipy_array[i,j])
return vtkmat
mat = pickle.load(file(reg_filename, 'r'))
vtkmat = array_to_vtkmatrix4x4(mat)
self.contours.SetUserMatrix(vtkmat)
#self.contours.GetProperty().SetOpacity(.38) #adjustable in the grid manager now
# XXX YAH somehow get a callback when actor is moved...
self.renderer.AddActor(self.contours)
def _BuildPipeline(self):
"""_BuildPipeline - Builds the visualization pipeline"""
image = component.getUtility(ICurrentImage)
# update image (VTK-6 compatible)
image.Update()
# image reslice object
reslice = vtk.vtkImageReslice()
reslice.SetInterpolationModeToCubic()
reslice.ReleaseDataFlagOn()
reslice.SetInputConnection(image.GetOutputPort())
if self._transform:
reslice.SetTransform(self._transform)
# get extents, spacings, etc
in_extent = image.GetExtent()
in_spacing = image.GetSpacing()
in_origin = image.GetOrigin()
# get stencil data
stencil_data = image.GetStencilData()
# Set image resample factor
f = self.gui.m_sliderSurfaceQuality.GetValue() / 100.0
if f == 0.0:
f = 0.001
# Set surface decimation factor
decf = self.gui.m_sliderDecimationFactor.GetValue() / 100.0
# Enable/Disable stencil usage
if self.gui.m_checkBoxClipping.GetValue() is True and stencil_data:
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
reslice.SetStencilData(stencil_data)
else:
reslice.SetStencil(stencil_data)
reslice.SetBackgroundLevel(image.GetScalarRange()[0])
ext = stencil_data.GetExtent()
else:
ext = in_extent
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
reslice.SetStencilData(None)
else:
reslice.SetStencil(None)
# expand extent slightly - account for downsampling later too
fudge = int(math.ceil(1.0 / f))
ext = [ext[0] - fudge, ext[1] + fudge, ext[2] - fudge, ext[3] + fudge, ext[4] - fudge, ext[5] + fudge]
reslice.SetOutputExtent(ext)
# set default origin/spacing -- these two lines work...
reslice.SetOutputSpacing(in_spacing)
reslice.SetOutputOrigin(in_origin)
# do we need to downsample the image?
if f < 1.0:
resample = vtk.vtkImageResample()
resample.SetInputConnection(reslice.GetOutputPort())
resample.ReleaseDataFlagOn()
for i in range(3):
resample.SetAxisMagnificationFactor(i, f)
obj = resample
else:
obj = reslice
# do we need to smooth the image?
if self.gui.m_checkBoxImageSmoothing.GetValue() == True:
smooth = vtk.vtkImageGaussianSmooth()
smooth.SetStandardDeviation(1.0)
smooth.ReleaseDataFlagOn()
smooth.SetInputConnection(obj.GetOutputPort())
obj = smooth
clip = vtk.vtkImageClip()
clip.SetInputConnection(obj.GetOutputPort())
# setup contour filter
cf = vtk.vtkMarchingCubes()
cf.SetNumberOfContours(1)
val = float(self.gui.m_textCtrlImageThreshold.GetValue())
cf.SetValue(0, val)
cf.SetComputeScalars(0)
cf.SetComputeNormals(0)
cf.SetInputConnection(clip.GetOutputPort())
# decimate surface
decimate = vtk.vtkDecimatePro()
decimate.SetInputConnection(cf.GetOutputPort())
decimate.PreserveTopologyOn()
decimate.SetTargetReduction(decf)
# To cut down on memory consumption, we use the clip object
# to process the image a chunk at a time. By default we
# use 20 chunks -- but if the chunks are too small, we'll adjust this
# number
clip.UpdateInformation()
ext = clip.GetInput().GetExtent()
# main processing loop
with wx.BusyCursor():
event.notify(ProgressEvent("Generating surface...", 0.0))
clip.SetOutputWholeExtent(ext[0], ext[1], ext[2], ext[3], ext[4], ext[5])
decimate.Update()
event.notify(ProgressEvent("Generating surface...", 1.0))
# Create the rendered Geometry
if not self._app_states[self._current_image_index].GetFactory():
self._app_states[self._current_image_index].SetFactory(
vtkAtamai.SurfaceObjectFactory.SurfaceObjectFactory()
)
self._app_states[self._current_image_index].GetFactory().SetInputConnection(decimate.GetOutputPort())
self._app_states[self._current_image_index].GetFactory().SetBackfaceProperty(
self._app_states[self._current_image_index].GetFactory().GetProperty()
)
self._app_states[self._current_image_index].GetFactory().NormalGenerationOn()
self.SetSurfaceColor()
self.GetMicroView().pane3D.ConnectActorFactory(self._app_states[self._current_image_index].GetFactory())
self._app_states[self._current_image_index]._disconnected = False
# Update math values
self.UpdateMathValues()
def contours(img,spacing=[1.0,1.0,1.0],contours=[]):
importer = numpy2VTK(img,spacing)
if len(contours) == 0:
contours = [[img.max(),1.0,1.0,1.0,1.0]]
actors = []
for c in contours:
contourExtractor = vtk.vtkContourFilter()
contourExtractor.SetInputConnection(importer.GetOutputPort())
contourExtractor.SetValue(0, c[0])
# contourNormals = vtk.vtkPolyDataNormals()
# contourNormals.SetInputConnection(contourExtractor.GetOutputPort())
# contourNormals.SetFeatureAngle(60.0)
# contourStripper = vtk.vtkStripper()
# contourStripper.SetInputConnection(contourNormals.GetOutputPort())
deci = vtk.vtkDecimatePro()
deci.SetInputConnection(contourExtractor.GetOutputPort())
deci.SetTargetReduction(0.99)
deci.PreserveTopologyOn ()
# smoother = vtk.vtkSmoothPolyDataFilter()
# smoother.SetInputConnection(deci.GetOutputPort())
# smoother.SetNumberOfIterations(50)
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(deci.GetOutputPort())
normals.FlipNormalsOn()
# smoothFilter = vtk.vtkSmoothPolyDataFilter()
# smoothFilter.SetInputConnection(contourStripper.GetOutputPort())
# smoothFilter.SetNumberOfIterations(50)
# smoothFilter.Update()
contourMapper = vtk.vtkPolyDataMapper()
# contourMapper.SetInputConnection(contourStripper.GetOutputPort())
contourMapper.SetInputConnection(normals.GetOutputPort())
contourMapper.ScalarVisibilityOff()
actor = vtk.vtkActor()
actor.SetMapper( contourMapper)
actor.GetProperty().SetColor(c[1],c[2],c[3])
actor.GetProperty().SetOpacity(c[4])
actor.GetProperty().SetRepresentationToSurface()
# # An outline provides context around the data.
# outlineData = vtk.vtkOutlineFilter()
# outlineData.SetInputConnection(v16.GetOutputPort())
# mapOutline = vtk.vtkPolyDataMapper()
# mapOutline.SetInputConnection(outlineData.GetOutputPort())
# outline = vtk.vtkActor()
# outline.SetMapper(mapOutline)
# outline.GetProperty().SetColor(0, 0, 0)
actors.append(actor)
return actors
def decimate(points, faces, reduction=0.5, smooth_steps=100,
scalars=[], save_vtk=False, output_vtk=''):
"""
Decimate vtk triangular mesh with vtk.vtkDecimatePro.
Parameters
----------
points : list of lists of floats
each element is a list of 3-D coordinates of a vertex on a surface mesh
faces : list of lists of integers
each element is list of 3 indices of vertices that form a face
on a surface mesh
reduction : float
fraction of mesh faces to remove
smooth_steps : integer
number of smoothing steps
scalars : list of integers or floats
optional scalars for output VTK file
save_vtk : Boolean
output decimated vtk file?
output_vtk : string
output decimated vtk file name
Returns
-------
points : list of lists of floats
decimated points
faces : list of lists of integers
decimated faces
scalars : list of integers or floats
scalars for output VTK file
output_vtk : string
output decimated vtk file
Examples
--------
>>> import os
>>> from mindboggle.utils.io_vtk import read_vtk, write_vtk
>>> from mindboggle.utils.mesh import decimate
>>> from mindboggle.utils.plots import plot_vtk
>>> path = os.environ['MINDBOGGLE_DATA']
>>> input_vtk = os.path.join(path, 'arno', 'labels', 'label22.vtk')
>>> reduction = 0.5
>>> smooth_steps = 100
>>> save_vtk = False
>>> output_vtk = ''
>>> faces, lines, indices, points, npoints, scalars, scalar_names,
... o2 = read_vtk(input_vtk)
>>> points, faces, scalars, output_vtk = decimate(points, faces, reduction,
>>> smooth_steps, scalars,
>>> save_vtk, output_vtk)
>>> len(points) == 2679
True
>>> len(points)
2679
>>> # View:
>>> output_vtk = 'decimated.vtk'
>>> write_vtk(output_vtk, points, indices, lines, faces, scalars,
>>> scalar_names) # doctest: +SKIP
>>> plot_vtk(output_vtk) # doctest: +SKIP
"""
import os
import vtk
#-------------------------------------------------------------------------
# vtk points:
#-------------------------------------------------------------------------
vtk_points = vtk.vtkPoints()
[vtk_points.InsertPoint(i, x[0], x[1], x[2]) for i,x in enumerate(points)]
#-------------------------------------------------------------------------
# vtk faces:
#-------------------------------------------------------------------------
vtk_faces = vtk.vtkCellArray()
for face in faces:
vtk_face = vtk.vtkPolygon()
vtk_face.GetPointIds().SetNumberOfIds(3)
vtk_face.GetPointIds().SetId(0, face[0])
vtk_face.GetPointIds().SetId(1, face[1])
vtk_face.GetPointIds().SetId(2, face[2])
vtk_faces.InsertNextCell(vtk_face)
#-------------------------------------------------------------------------
# vtk scalars:
#-------------------------------------------------------------------------
if scalars:
vtk_scalars = vtk.vtkFloatArray()
vtk_scalars.SetName("scalars")
for scalar in scalars:
vtk_scalars.InsertNextValue(scalar)
#-------------------------------------------------------------------------
# vtkPolyData:
#-------------------------------------------------------------------------
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.SetPolys(vtk_faces)
if scalars:
polydata.GetPointData().SetScalars(vtk_scalars)
#-------------------------------------------------------------------------
# Decimate:
#-------------------------------------------------------------------------
# We want to preserve topology (not let any cracks form).
# This may limit the total reduction possible.
decimate = vtk.vtkDecimatePro()
decimate.SetInput(polydata)
decimate.SetTargetReduction(reduction)
decimate.PreserveTopologyOn()
#-------------------------------------------------------------------------
# Smooth:
#-------------------------------------------------------------------------
if save_vtk:
if not output_vtk:
output_vtk = os.path.join(os.getcwd(), 'decimated.vtk')
exporter = vtk.vtkPolyDataWriter()
if smooth_steps > 0:
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInput(decimate.GetOutput())
smoother.SetNumberOfIterations(smooth_steps)
smoother.Update()
out = smoother.GetOutput()
if save_vtk:
exporter.SetInput(smoother.GetOutput())
else:
decimate.Update()
out = decimate.GetOutput()
if save_vtk:
exporter.SetInput(decimate.GetOutput())
#-------------------------------------------------------------------------
# Export output:
#-------------------------------------------------------------------------
if save_vtk:
exporter.SetFileName(output_vtk)
exporter.Write()
if not os.path.exists(output_vtk):
raise(IOError(output_vtk + " not found"))
#-------------------------------------------------------------------------
# Extract decimated points, faces, and scalars:
#-------------------------------------------------------------------------
points = [list(out.GetPoint(point_id))
for point_id in range(out.GetNumberOfPoints())]
if out.GetNumberOfPolys() > 0:
polys = out.GetPolys()
pt_data = out.GetPointData()
faces = [[int(polys.GetData().GetValue(j))
for j in range(i*4 + 1, i*4 + 4)]
for i in range(polys.GetNumberOfCells())]
if scalars:
scalars = [pt_data.GetScalars().GetValue(i)
for i in range(len(points))]
else:
faces = []
scalars = []
return points, faces, scalars, output_vtk
def applyFilters(self, state):
surface = None
if vtk.VTK_MAJOR_VERSION <= 5:
surface = state.inputModelNode.GetPolyData()
else:
surface = state.inputModelNode.GetPolyDataConnection()
if state.decimation:
triangle = vtk.vtkTriangleFilter()
if vtk.VTK_MAJOR_VERSION <= 5:
triangle.SetInput(surface)
else:
triangle.SetInputConnection(surface)
decimation = vtk.vtkDecimatePro()
decimation.SetTargetReduction(state.reduction)
decimation.SetBoundaryVertexDeletion(state.boundaryDeletion)
decimation.PreserveTopologyOn()
if vtk.VTK_MAJOR_VERSION <= 5:
decimation.SetInput(triangle.GetOutput())
decimation.Update()
surface = decimation.GetOutput()
else:
decimation.SetInputConnection(triangle.GetOutputPort())
surface = decimation.GetOutputPort()
if state.smoothing:
if state.smoothingMethod == "Laplace":
smoothing = vtk.vtkSmoothPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.laplaceIterations)
smoothing.SetRelaxationFactor(state.laplaceRelaxation)
if vtk.VTK_MAJOR_VERSION <= 5:
smoothing.SetInput(surface)
smoothing.Update()
else:
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
elif state.smoothingMethod == "Taubin":
smoothing = vtk.vtkWindowedSincPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.taubinIterations)
smoothing.SetPassBand(state.taubinPassBand)
if vtk.VTK_MAJOR_VERSION <= 5:
smoothing.SetInput(surface)
smoothing.Update()
surface = smoothing.GetOutput()
else:
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
if state.normals:
normals = vtk.vtkPolyDataNormals()
normals.AutoOrientNormalsOn()
normals.SetFlipNormals(state.flipNormals)
normals.SetSplitting(state.splitting)
normals.SetFeatureAngle(state.featureAngle)
normals.ConsistencyOn()
if vtk.VTK_MAJOR_VERSION <= 5:
normals.SetInput(surface)
normals.Update()
surface = normals.GetOutput()
else:
normals.SetInputConnection(surface)
surface = normals.GetOutputPort()
if state.cleaner:
cleaner = vtk.vtkCleanPolyData()
if vtk.VTK_MAJOR_VERSION <= 5:
cleaner.SetInput(surface)
cleaner.Update()
surface = cleaner.GetOutput()
else:
cleaner.SetInputConnection(surface)
surface = cleaner.GetOutputPort()
if state.connectivity:
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetExtractionModeToLargestRegion()
if vtk.VTK_MAJOR_VERSION <= 5:
connectivity.SetInput(surface)
connectivity.Update()
surface = connectivity.GetOutput()
else:
connectivity.SetInputConnection(surface)
surface = connectivity.GetOutputPort()
if vtk.VTK_MAJOR_VERSION <= 5:
state.outputModelNode.SetAndObservePolyData(surface)
else:
state.outputModelNode.SetPolyDataConnection(surface)
return True
def testDeciFranFace(self):
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
ren2 = vtk.vtkRenderer()
ren3 = vtk.vtkRenderer()
ren4 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.AddRenderer(ren2)
renWin.AddRenderer(ren3)
renWin.AddRenderer(ren4)
pnm1 = vtk.vtkPNGReader()
pnm1.SetFileName(VTK_DATA_ROOT + "/Data/fran_cut.png")
atext = vtk.vtkTexture()
atext.SetInputConnection(pnm1.GetOutputPort())
atext.InterpolateOn()
# create a cyberware source
#
fran = vtk.vtkPolyDataReader()
fran.SetFileName(VTK_DATA_ROOT + "/Data/fran_cut.vtk")
# Create a table of decimation conditions
#
boundaryVertexDeletion = ["On", "Off"]
accumulates = ["On", "Off"]
deci = dict()
mapper = dict()
actor = dict()
for topology in boundaryVertexDeletion:
for accumulate in accumulates:
idx = topology + accumulate
deci.update({idx: vtk.vtkDecimatePro()})
deci[idx].SetInputConnection(fran.GetOutputPort())
deci[idx].SetTargetReduction(.95)
if topology == "On":
deci[idx].PreserveTopologyOn()
elif topology == "Off":
deci[idx].PreserveTopologyOff()
if accumulate == "On":
deci[idx].AccumulateErrorOn()
elif accumulate == "Off":
deci[idx].AccumulateErrorOff()
mapper.update({idx: vtk.vtkPolyDataMapper()})
mapper[idx].SetInputConnection(deci[idx].GetOutputPort())
actor.update({idx: vtk.vtkActor()})
actor[idx].SetMapper(mapper[idx])
actor[idx].SetTexture(atext)
# Add the actors to the renderer, set the background and size
#
ren1.SetViewport(0, .5, .5, 1)
ren2.SetViewport(.5, .5, 1, 1)
ren3.SetViewport(0, 0, .5, .5)
ren4.SetViewport(.5, 0, 1, .5)
ren1.AddActor(actor["OnOn"])
ren2.AddActor(actor["OnOff"])
ren3.AddActor(actor["OffOn"])
ren4.AddActor(actor["OffOff"])
camera = vtk.vtkCamera()
ren1.SetActiveCamera(camera)
ren2.SetActiveCamera(camera)
ren3.SetActiveCamera(camera)
ren4.SetActiveCamera(camera)
ren1.GetActiveCamera().SetPosition(0.314753, -0.0699988, -0.264225)
ren1.GetActiveCamera().SetFocalPoint(0.00188636, -0.136847, -5.84226e-09)
ren1.GetActiveCamera().SetViewAngle(30)
ren1.GetActiveCamera().SetViewUp(0, 1, 0)
ren1.ResetCameraClippingRange()
ren2.ResetCameraClippingRange()
ren3.ResetCameraClippingRange()
ren4.ResetCameraClippingRange()
ren1.SetBackground(1, 1, 1)
ren2.SetBackground(1, 1, 1)
ren3.SetBackground(1, 1, 1)
ren4.SetBackground(1, 1, 1)
renWin.SetSize(500, 500)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin);
renWin.Render()
img_file = "deciFranFace.png"
vtk.test.Testing.compareImage(iRen.GetRenderWindow(), vtk.test.Testing.getAbsImagePath(img_file), threshold=25)
vtk.test.Testing.interact()
def loadafmasmesh(path, flatten=True, gaussianblursize=5):
# load the image
img = misc.imread(path)
if flatten: #if we want to remove the parabolic/spherical background from AFM image
#make a kernal to scan with; This should be tested with more images to choose the best shape and size;
#Current kernel is a 20x20 square
kernel = np.ones((20, 20), np.uint8)
#Remove background artifact
img = img - np.minimum(img, cv2.morphologyEx(img, cv2.MORPH_OPEN, kernel))
#Add optional gaussian blur to denoise
if gaussianblursize>0:
img = cv2.GaussianBlur(img, (0, 0), gaussianblursize)
#img = cv2.bilateralFilter(img,9,80,80)
if img.shape.__len__()>2:
if img.shape[2] == 3: #if the image is a 3 channel rgb average the channels
img = np.sum(img, axis=2) / 3.0
#make a grid array for x and y
xx, yy = np.mgrid[0:img.shape[0], 0:img.shape[1]]
#make the array of points, then reshape it to an Nx3 array
points = np.array([xx, yy, img])
points = points.reshape((3, img.shape[0] * img.shape[1])).T
pointsforvtk = vtk.vtkPoints()
polygondata=vtk.vtkPolyData()
cellarray=vtk.vtkCellArray()
delaunay=vtk.vtkDelaunay2D()
boundary=vtk.vtkPolyData()
pointsarray = numpytovtk(points)
#print type(pointsarray)
pointsforvtk.SetData(pointsarray)
polygondata.SetPoints(pointsforvtk)
boundary.SetPoints(polygondata.GetPoints())
boundary.SetPolys(cellarray)
delaunay.SetInputData(polygondata)
delaunay.SetSourceData(boundary)
#print(delaunay.GetOutput())
#meshpoly=delaunay.GetOutput()
decimator = vtk.vtkDecimatePro()
decimator.SetInputConnection(delaunay.GetOutputPort())
decimator.SetTargetReduction(0.999)
decimator.PreserveTopologyOn()
#decimator.BoundaryVertexDeletionOff()
decimator.Update()
plotvtk(decimator,boundary)
print "mesh finished"
points,triangles=polytopointstriangles(decimator.GetOutput())
print(triangles.__len__())
return points, triangles
def __init__(self, filename, renderer):
self.renderer = renderer
reader = vtk.vtkStructuredPointsReader()
#reader.SetFileName('/home/mcc/src/devel/extract_mri_slices/braintest2.vtk')
reader.SetFileName(filename)
# we want to move this from its (.87 .92 .43) esque position to something more like 'the center'
# how to do this?!?
# ALTERNATIVELY: we want to use vtkInteractorStyleTrackballActor
# somewhere instead of the interactor controlling the main window and 3 planes
imagedata = reader.GetOutput()
#reader.SetFileName(filename)
cf = vtk.vtkContourFilter()
cf.SetInput(imagedata)
# ???
cf.SetValue(0, 1)
deci = vtk.vtkDecimatePro()
deci.SetInput(cf.GetOutput())
deci.SetTargetReduction(.1)
deci.PreserveTopologyOn()
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInput(deci.GetOutput())
smoother.SetNumberOfIterations(100)
# XXX try to call SetScale directly on actor..
#self.scaleTransform = vtk.vtkTransform()
#self.scaleTransform.Identity()
#self.scaleTransform.Scale(.1, .1, .1)
#transformFilter = vtk.vtkTransformPolyDataFilter()
#transformFilter.SetTransform(self.scaleTransform)
#transformFilter.SetInput(smoother.GetOutput())
#cf.SetValue(1, 2)
#cf.SetValue(2, 3)
#cf.GenerateValues(0, -1.0, 1.0)
#deci = vtk.vtkDecimatePro()
#deci.SetInput(cf.GetOutput())
#deci.SetTargetReduction(0.8) # decimate_value
normals = vtk.vtkPolyDataNormals()
#normals.SetInput(transformFilter.GetOutput())
normals.SetInput(smoother.GetOutput())
normals.FlipNormalsOn()
"""
tags = vtk.vtkFloatArray()
tags.InsertNextValue(1.0)
tags.InsertNextValue(0.5)
tags.InsertNextValue(0.7)
tags.SetName("tag")
"""
lut = vtk.vtkLookupTable()
lut.SetHueRange(0, 0)
lut.SetSaturationRange(0, 0)
lut.SetValueRange(0.2, 0.55)
contourMapper = vtk.vtkPolyDataMapper()
contourMapper.SetInput(normals.GetOutput())
contourMapper.SetLookupTable(lut)
###contourMapper.SetColorModeToMapScalars()
###contourMapper.SelectColorArray("tag")
self.contours = vtk.vtkActor()
self.contours.SetMapper(contourMapper)
#if (do_wireframe):
#self.contours.GetProperty().SetRepresentationToWireframe()
#elif (do_surface):
self.contours.GetProperty().SetRepresentationToSurface()
self.contours.GetProperty().SetInterpolationToGouraud()
self.contours.GetProperty().SetOpacity(1.0)
self.contours.GetProperty().SetAmbient(0.1)
self.contours.GetProperty().SetDiffuse(0.1)
self.contours.GetProperty().SetSpecular(0.1)
self.contours.GetProperty().SetSpecularPower(0.1)
# XXX arbitrarily setting scale to this
#self.contours.SetScale(.1, .1,.1)
renderer.AddActor(self.contours)
# XXX: mcc will this work?!?
print "PlaneWidgetsXYZ.set_image_data: setting EventHandler.set_vtkactor(self.contours)!"
EventHandler().set_vtkactor(self.contours)
def execute(self, inputs, update = 0, last = 0):
"""
Execute the filter with given inputs and return the output
"""
if not lib.ProcessingFilter.ProcessingFilter.execute(self, inputs):
return None
self.progressObj.setProgress(0.0)
self.updateProgress(None, "ProgressEvent")
rightDataType = True
labelImage = self.getInput(1)
labelImage.Update()
if "vtkImageData" in str(labelImage.__class__):
rightDataType = (labelImage.GetScalarType() == 9)
elif not "itkImageUL" in str(labelImage.__class__):
rightDataType = False
if not rightDataType:
Logging.error("Incompatible data type", "Please convert the input to label data of type unsigned long. Segmented data can be labeled with 'Connected component labeling' or 'Object separation' in 'Segmentation -> Object Processing'.")
origImage = self.getInput(2)
origImage.Update()
origRange = origImage.GetScalarRange()
print "Input for label shape=",self.getInputDataUnit(1)
print "Orig. dataunit = ",self.getInputDataUnit(2)
diritk = dir(itk)
if "LabelImageToStatisticsLabelMapFilter" in diritk and "LabelMap" in diritk and "StatisticsLabelObject" and "LabelGeometryImageFilter" in diritk:
newITKStatistics = 1
else:
newITKStatistics = 0
# Do necessary conversions of datatype
origVTK = origImage
if self.parameters["AvgInt"] or self.parameters["NonZero"] or newITKStatistics:
origITK = self.convertVTKtoITK(origVTK)
# Cannot have two convertVTKtoITK in same filter
if self.parameters["AvgInt"] or self.parameters["Area"]:
labelVTK = self.convertITKtoVTK(labelImage)
if "itkImage" not in str(labelImage.__class__):
extent = labelImage.GetWholeExtent()
if extent[5] - extent[4] == 0:
dim = 2
else:
dim = 3
scalarType = labelImage.GetScalarType()
if scalarType != 9: # Convert to unsigned long
castVTK = vtk.vtkImageCast()
castVTK.SetOutputScalarTypeToUnsignedLong()
castVTK.SetInput(labelImage)
labelImage = castVTK.GetOutput()
labelImage.Update()
vtkItk = eval("itk.VTKImageToImageFilter.IUL%d.New()"%dim)
vtkItk.SetInput(labelImage)
labelITK = vtkItk.GetOutput()
labelITK.Update()
else:
labelITK = labelImage
dim = labelITK.GetLargestPossibleRegion().GetSize().GetSizeDimension()
# Initializations
spacing = self.dataUnit.getSpacing()
x, y, z = self.dataUnit.getVoxelSize()
x *= 1000000
y *= 1000000
z *= 1000000
if z == 0: z = 1.0
vol = x * y * z
voxelSizes = [x, y, z]
values = []
centersofmass = []
umcentersofmass = []
avgints = []
avgintsstderrs = []
objIntSums = []
avgDists = []
avgDistsStdErrs = []
objAreasUm = []
objRoundness = []
objMinorLength = []
objMajorLength = []
objElongation = []
objAngleMinX = []
objAngleMinY = []
objAngleMinZ = []
objAngleMajX = []
objAngleMajY = []
objAngleMajZ = []
objSmoothness = []
ignoreLargest = 1
currFilter = self
while currFilter:
if currFilter.ignoreObjects > ignoreLargest:
ignoreLargest = currFilter.ignoreObjects
currFilter = currFilter.prevFilter
startIntensity = ignoreLargest
print "Ignoring",startIntensity,"first objects"
if newITKStatistics: # Change spacing for correct results, or not
#changeInfoLabel = itk.ChangeInformationImageFilter[labelITK].New()
#changeInfoLabel.SetInput(labelITK)
#changeInfoLabel.ChangeSpacingOn()
#changeInfoOrig = itk.ChangeInformationImageFilter[origITK].New()
#changeInfoOrig.SetInput(origITK)
#changeInfoOrig.ChangeSpacingOn()
if dim == 3:
lm = itk.LabelMap._3.New()
#changeInfoLabel.SetOutputSpacing(voxelSizes)
#changeInfoOrig.SetOutputSpacing(voxelSizes)
else:
lm = itk.LabelMap._2.New()
#changeInfoLabel.SetOutputSpacing(voxelSizes[:2])
#changeInfoOrig.SetOutputSpacing(voxelSizes[:2])
labelStatistics = itk.LabelImageToStatisticsLabelMapFilter[labelITK,origITK,lm].New()
#labelStatistics.SetInput1(changeInfoLabel.GetOutput())
#labelStatistics.SetInput2(changeInfoOrig.GetOutput())
labelStatistics.SetInput1(labelITK)
labelStatistics.SetInput2(origITK)
if self.parameters["Area"]:
labelStatistics.ComputePerimeterOn()
labelStatistics.Update()
labelMap = labelStatistics.GetOutput()
numberOfLabels = labelMap.GetNumberOfLabelObjects()
else:
labelShape = itk.LabelShapeImageFilter[labelITK].New()
labelShape.SetInput(labelITK)
data = labelShape.GetOutput()
data.Update()
numberOfLabels = labelShape.GetNumberOfLabels()
if self.parameters["AvgInt"]:
avgintCalc = itk.LabelStatisticsImageFilter[origITK,labelITK].New()
avgintCalc.SetInput(origITK)
avgintCalc.SetLabelInput(labelITK)
avgintCalc.Update()
self.progressObj.setProgress(0.2)
self.updateProgress(None, "ProgressEvent")
# Area calculation pipeline
if self.parameters["Area"]:
voxelArea = x*y*2 + x*z*2 + y*z*2
largestSize = labelITK.GetLargestPossibleRegion().GetSize()
# if 2D image, calculate area using volume
if largestSize.GetSizeDimension() > 2 and largestSize.GetElement(2) > 1:
areaSpacing = labelVTK.GetSpacing()
objectThreshold = vtk.vtkImageThreshold()
objectThreshold.SetInput(labelVTK)
objectThreshold.SetOutputScalarTypeToUnsignedChar()
objectThreshold.SetInValue(255)
objectThreshold.SetOutValue(0)
marchingCubes = vtk.vtkMarchingCubes()
#marchingCubes.SetInput(labelVTK)
marchingCubes.SetInput(objectThreshold.GetOutput())
massProperties = vtk.vtkMassProperties()
massProperties.SetInput(marchingCubes.GetOutput())
areaDiv = (areaSpacing[0] / x)**2
if self.parameters["Smoothness"]:
smoothDecimate = vtk.vtkDecimatePro()
smoothProperties = vtk.vtkMassProperties()
smoothDecimate.SetTargetReduction(0.9)
smoothDecimate.PreserveTopologyOff()
smoothDecimate.SetInput(marchingCubes.GetOutput())
smoothProperties.SetInput(smoothDecimate.GetOutput())
# Filter needed for axes calculations
if self.parameters["Axes"] and newITKStatistics:
labelGeometry = itk.LabelGeometryImageFilter[labelITK,labelITK].New()
labelGeometry.SetCalculateOrientedBoundingBox(1)
labelGeometry.SetInput(labelITK)
labelGeometry.Update()
# Get results and do some calculations for each object
tott = 0
voxelSize = voxelSizes[0] * voxelSizes[1] * voxelSizes[2]
for i in range(startIntensity, numberOfLabels+1):
areaInUm = 0.0
avgInt = 0
avgIntStdErr = 0.0
roundness = 0.0
objIntSum = 0.0
minorLength = 0.0
majorLength = 0.0
elongation = 0.0
angleMinX = 0.0
angleMinY = 0.0
angleMinZ = 0.0
angleMajX = 0.0
angleMajY = 0.0
angleMajZ = 0.0
smoothness = 0.0
if newITKStatistics:
try:
labelObj = labelMap.GetLabelObject(i)
except:
continue
volume = labelObj.GetSize()
#com = labelObj.GetCenterOfGravity()
com = labelObj.GetCentroid()
c = []
c2 = []
for k in range(0,com.GetPointDimension()):
v = com[k]
v /= spacing[k]
c.append(v)
c2.append(v * voxelSizes[k])
if com.GetPointDimension() == 2:
c.append(0)
c2.append(0.0)
if self.parameters["AvgInt"]:
avgInt = labelObj.GetMean()
avgIntStdErr = math.sqrt(labelObj.GetVariance()) / math.sqrt(volume)
objIntSum = avgInt * volume
#if self.parameters["Area"]:
# areaInUm = labelObj.GetPerimeter()
# roundness = labelObj.GetRoundness()
# Get area of object, copied old way because roundness is not
# working
if self.parameters["Area"]:
if largestSize.GetSizeDimension() > 2 and largestSize.GetElement(2) > 1:
objectThreshold.ThresholdBetween(i,i)
marchingCubes.SetValue(0,255)
polydata = marchingCubes.GetOutput()
polydata.Update()
if polydata.GetNumberOfPolys() > 0:
massProperties.Update()
areaInUm = massProperties.GetSurfaceArea() / areaDiv
else:
areaInUm = voxelArea
# Calculate roundness
hypersphereR = ((3*volume*vol)/(4*math.pi))**(1/3.0)
hypersphereArea = 3 * volume * vol / hypersphereR
roundness = hypersphereArea / areaInUm
# Calculate surface smoothness
if self.parameters["Smoothness"]:
# Smooth surface with vtkDecimatePro.
polydata = smoothDecimate.GetOutput()
polydata.Update()
if polydata.GetNumberOfPolys() > 0:
smoothProperties.Update()
smoothArea = smoothProperties.GetSurfaceArea() / areaDiv
smoothness = smoothArea / areaInUm
else:
areaInUm = volume * x * y
if self.parameters["Axes"]:
vert = labelGeometry.GetOrientedBoundingBoxVertices(i)
vertices = []
for vNum in range(vert.size()):
vertices.append(vert.pop())
boxVect = []
if dim == 3:
vertNums = [1,2,4]
else:
vertNums = [1,2]
for vertNum in vertNums:
vertex1 = vertices[0]
vertex2 = vertices[vertNum]
boxVect.append([abs(vertex2[dimN]-vertex1[dimN]) * voxelSizes[dimN] for dimN in range(dim)])
boxVectLen = []
minAxNum = -1
majAxNum = -1
minorLength = -1
majorLength = -1
for num,vect in enumerate(boxVect):
length = 0.0
for vectComp in vect:
length += vectComp**2
length = math.sqrt(length)
boxVectLen.append(length)
if length > majorLength:
majorLength = length
majAxNum = num
if length < minorLength or minorLength < 0:
minorLength = length
minAxNum = num
elongation = majorLength / minorLength
# Calculate angle between major, minor axes and x,y,z axes
for dimN in range(dim):
boxVect[minAxNum][dimN] /= minorLength
boxVect[majAxNum][dimN] /= majorLength
vecX = (1.0, 0.0, 0.0)
vecY = (0.0, 1.0, 0.0)
vecZ = (0.0, 0.0, 1.0)
angleMinX = lib.Math.angle(boxVect[minAxNum], vecX)
angleMinY = lib.Math.angle(boxVect[minAxNum], vecY)
angleMinZ = lib.Math.angle(boxVect[minAxNum], vecZ)
angleMajX = lib.Math.angle(boxVect[majAxNum], vecX)
angleMajY = lib.Math.angle(boxVect[majAxNum], vecY)
angleMajZ = lib.Math.angle(boxVect[majAxNum], vecZ)
else:
if not labelShape.HasLabel(i):
continue
else:
volume = labelShape.GetVolume(i)
centerOfMass = labelShape.GetCenterOfGravity(i)
if self.parameters["AvgInt"]:
avgInt = avgintCalc.GetMean(i)
avgIntStdErr = math.sqrt(abs(avgintCalc.GetVariance(i))) / math.sqrt(volume)
objIntSum = avgintCalc.GetSum(i)
c = []
c2 = []
for k in range(0, dim):
v = centerOfMass.GetElement(k)
c.append(v)
c2.append(v * voxelSizes[k])
if dim == 2:
c.append(0)
c2.append(0.0)
# Get area of object
if self.parameters["Area"]:
if largestSize.GetSizeDimension() > 2 and largestSize.GetElement(2) > 1:
objectThreshold.ThresholdBetween(i,i)
marchingCubes.SetValue(0,255)
polydata = marchingCubes.GetOutput()
polydata.Update()
if polydata.GetNumberOfPolys() > 0:
massProperties.Update()
areaInUm = massProperties.GetSurfaceArea() / areaDiv
else:
areaInUm = voxelArea
# Calculate roundness
hypersphereR = ((3*volume*vol)/(4*math.pi))**(1/3.0)
hypersphereArea = 3 * volume * vol / hypersphereR
roundness = hypersphereArea / areaInUm
else:
areaInUm = volume * x * y
# Add object results to result arrays
centersofmass.append(tuple(c))
umcentersofmass.append(tuple(c2))
values.append((volume, volume * vol))
avgints.append(avgInt)
avgintsstderrs.append(avgIntStdErr)
objIntSums.append(objIntSum)
objAreasUm.append(areaInUm)
objRoundness.append(roundness)
objMinorLength.append(minorLength)
objMajorLength.append(majorLength)
objElongation.append(elongation)
objAngleMinX.append(angleMinX)
objAngleMinY.append(angleMinY)
objAngleMinZ.append(angleMinZ)
objAngleMajX.append(angleMajX)
objAngleMajY.append(angleMajY)
objAngleMajZ.append(angleMajZ)
objSmoothness.append(smoothness)
self.progressObj.setProgress(0.7)
self.updateProgress(None, "ProgressEvent")
# Do distance calculations
t0 = time.time()
for i, cm in enumerate(umcentersofmass):
distList = []
if self.parameters["AvgDist"]:
for j, cm2 in enumerate(umcentersofmass):
if i == j: continue
dx = cm[0] - cm2[0]
dy = cm[1] - cm2[1]
dz = cm[2] - cm2[2]
dist = math.sqrt(dx*dx+dy*dy+dz*dz)
distList.append(dist)
avgDist, avgDistStd, avgDistStdErr = lib.Math.meanstdeverr(distList)
avgDists.append(avgDist)
avgDistsStdErrs.append(avgDistStdErr)
print "Distance calculations took", time.time()-t0
self.progressObj.setProgress(0.8)
self.updateProgress(None, "ProgressEvent")
# Calculate average values and errors
n = len(values)
avgint, avgintstd, avgintstderr = lib.Math.meanstdeverr(avgints)
intSum = sum(objIntSums, 0.0)
ums = [x[1] for x in values]
avgums, avgumsstd, avgumsstderr = lib.Math.meanstdeverr(ums)
sumums = sum(ums, 0.0)
pxs = [x[0] for x in values]
avgpxs, avgpxsstd, avgpxsstderr = lib.Math.meanstdeverr(pxs)
distMean, distStd, distStdErr = lib.Math.meanstdeverr(avgDists)
avground, avgroundstd, avgroundstderr = lib.Math.meanstdeverr(objRoundness)
avgAreaUm, avgAreaUmStd, avgAreaUmStdErr = lib.Math.meanstdeverr(objAreasUm)
areaSumUm = sum(objAreasUm, 0.0)
avgminlen, avgminlenstd, avgminlenstderr = lib.Math.meanstdeverr(objMinorLength)
avgmajlen, avgmajlenstd, avgmajlenstderr = lib.Math.meanstdeverr(objMajorLength)
avgelon, avgelonstd, avgelonstderr = lib.Math.meanstdeverr(objElongation)
avgangminx, avgangminxstd, avgangminxstderr = lib.Math.meanstdeverr(objAngleMinX)
avgangminy, avgangminystd, avgangminystderr = lib.Math.meanstdeverr(objAngleMinY)
avgangminz, avgangminzstd, avgangminzstderr = lib.Math.meanstdeverr(objAngleMinZ)
avgangmajx, avgangmajxstd, avgangmajxstderr = lib.Math.meanstdeverr(objAngleMajX)
avgangmajy, avgangmajystd, avgangmajystderr = lib.Math.meanstdeverr(objAngleMajY)
avgangmajz, avgangmajzstd, avgangmajzstderr = lib.Math.meanstdeverr(objAngleMajZ)
avgsmooth, avgsmoothstd, avgsmoothstderr = lib.Math.meanstdeverr(objSmoothness)
# Calculate average intensity outside objects
avgIntOutsideObjs = 0.0
avgIntOutsideObjsStdErr = 0.0
avgIntOutsideObjsNonZero = 0.0
avgIntOutsideObjsNonZeroStdErr = 0.0
nonZeroVoxels = -1
if self.parameters["AvgInt"]:
variances = 0.0
allVoxels = 0
for i in range(0,startIntensity):
if newITKStatistics:
try:
labelObj = labelMap.GetLabelObject(i)
voxelAmount = labelObj.GetSize()
allVoxels += voxelAmount
avgIntOutsideObjs += labelObj.GetMean() * voxelAmount
variances += voxelAmount * abs(labelObj.GetVariance())
except:
pass
else:
if labelShape.HasLabel(i):
voxelAmount = labelShape.GetVolume(i)
allVoxels += voxelAmount
avgIntOutsideObjs += avgintCalc.GetMean(i) * voxelAmount
if voxelAmount > 1:
variances += voxelAmount * abs(avgintCalc.GetVariance(i))
if allVoxels > 0:
avgIntOutsideObjs /= allVoxels
avgIntOutsideObjsStdErr = math.sqrt(variances / allVoxels) / math.sqrt(allVoxels)
labelAverage = vtkbxd.vtkImageLabelAverage()
labelAverage.AddInput(origVTK)
labelAverage.AddInput(labelVTK)
labelAverage.SetBackgroundLevel(startIntensity)
labelAverage.Update()
avgIntOutsideObjsNonZero = labelAverage.GetAverageOutsideLabels()
if labelAverage.GetVoxelsOutsideLabels() == 0:
avgIntOutsideObjsNonZeroStdErr = 0.0
else:
avgIntOutsideObjsNonZeroStdErr = labelAverage.GetOutsideLabelsStdDev() / math.sqrt(labelAverage.GetVoxelsOutsideLabels())
# Get also non zero voxels here that there is no need to recalculate
nonZeroVoxels = labelAverage.GetNonZeroVoxels()
self.progressObj.setProgress(0.9)
self.updateProgress(None, "ProgressEvent")
# Calculate average intensity inside objects
avgIntInsideObjs = 0.0
avgIntInsideObjsStdErr = 0.0
if self.parameters["AvgInt"]:
variances = 0.0
allVoxels = 0
for i in range(startIntensity, numberOfLabels+1):
if newITKStatistics:
try:
labelObj = labelMap.GetLabelObject(i)
voxelAmount = labelObj.GetSize()
allVoxels += voxelAmount
avgIntInsideObjs += labelObj.GetMean() * voxelAmount
if voxelAmount > 1:
variances += voxelAmount * abs(labelObj.GetVariance())
except:
pass
else:
if labelShape.HasLabel(i):
voxelAmount = labelShape.GetVolume(i)
allVoxels += voxelAmount
avgIntInsideObjs += avgintCalc.GetMean(i) * voxelAmount
variances += voxelAmount * abs(avgintCalc.GetVariance(i))
if allVoxels > 0:
avgIntInsideObjs /= allVoxels
avgIntInsideObjsStdErr = math.sqrt(variances / allVoxels) / math.sqrt(allVoxels)
# Calculate non-zero voxels
if self.parameters["NonZero"] and nonZeroVoxels < 0:
labelShape = itk.LabelShapeImageFilter[origITK].New()
labelShape.SetInput(origITK)
labelShape.Update()
for i in range(1, int(origRange[1]) + 1):
if labelShape.HasLabel(i):
nonZeroVoxels += labelShape.GetVolume(i)
# Set results
self.values = values
self.centersofmass = centersofmass
self.umcentersofmass = umcentersofmass
self.avgIntList = avgints
self.avgIntStdErrList = avgintsstderrs
self.intSums = objIntSums
self.avgDistList = avgDists
self.avgDistStdErrList = avgDistsStdErrs
self.objAreasUm = objAreasUm
self.objRoundness = objRoundness
self.objMinorLength = objMinorLength
self.objMajorLength = objMajorLength
self.objElongation = objElongation
self.objAngleMinX = objAngleMinX
self.objAngleMinY = objAngleMinY
self.objAngleMinZ = objAngleMinZ
self.objAngleMajX = objAngleMajX
self.objAngleMajY = objAngleMajY
self.objAngleMajZ = objAngleMajZ
self.intSum = intSum
self.objSmoothness = objSmoothness
#self.distMean = distMean
#self.distStdErr = distStdErr
#self.avgRoundness = avground
#self.avgRoundnessStdErr = avgroundstderr
#self.avgIntInsideObjs = avgIntInsideObjs
#self.avgIntInsideObjsStdErr = avgIntInsideObjsStdErr
#self.avgIntOutsideObjs = avgIntOutsideObjs
#self.avgIntOutsideObjsStdErr = avgIntOutsideObjsStdErr
#self.avgIntOutsideObjsNonZero = avgIntOutsideObjsNonZero
#self.avgIntOutsideObjsNonZeroStdErr = avgIntOutsideObjsNonZeroStdErr
self.setResultVariable("NumberOfObjects",len(values))
self.setResultVariable("ObjAvgVolInVoxels",avgpxs)
self.setResultVariable("ObjAvgVolInUm",avgums)
self.setResultVariable("ObjVolSumInUm",sumums)
self.setResultVariable("ObjAvgAreaInUm",avgAreaUm)
self.setResultVariable("ObjAreaSumInUm",areaSumUm)
self.setResultVariable("ObjAvgIntensity",avgint)
self.setResultVariable("AvgIntOutsideObjs", avgIntOutsideObjs)
self.setResultVariable("AvgIntOutsideObjsNonZero", avgIntOutsideObjsNonZero)
self.setResultVariable("AvgIntInsideObjs", avgIntInsideObjs)
self.setResultVariable("NonZeroVoxels", nonZeroVoxels)
self.setResultVariable("AverageDistance", distMean)
self.setResultVariable("AvgDistanceStdErr", distStdErr)
self.setResultVariable("ObjAvgVolInVoxelsStdErr",avgpxsstderr)
self.setResultVariable("ObjAvgVolInUmStdErr",avgumsstderr)
self.setResultVariable("ObjAvgAreaInUmStdErr",avgAreaUmStdErr)
self.setResultVariable("ObjAvgIntensityStdErr",avgintstderr)
self.setResultVariable("AvgIntOutsideObjsStdErr",avgIntOutsideObjsStdErr)
self.setResultVariable("AvgIntOutsideObjsNonZeroStdErr",avgIntOutsideObjsNonZeroStdErr)
self.setResultVariable("AvgIntInsideObjsStdErr",avgIntInsideObjsStdErr)
self.setResultVariable("ObjIntensitySum", intSum)
self.setResultVariable("ObjAvgRoundness",avground)
self.setResultVariable("ObjAvgRoundnessStdErr",avgroundstderr)
self.setResultVariable("ObjAvgMajorAxisLen",avgmajlen)
self.setResultVariable("ObjAvgMajorAxisLenStdErr",avgmajlenstderr)
self.setResultVariable("ObjAvgMinorAxisLen",avgminlen)
self.setResultVariable("ObjAvgMinorAxisLenStdErr",avgminlenstderr)
self.setResultVariable("ObjAvgElongation",avgelon)
self.setResultVariable("ObjAvgElongationStdErr",avgelonstderr)
self.setResultVariable("ObjAvgAngleXMajorAxis",avgangmajx)
self.setResultVariable("ObjAvgAngleXMajorAxisStdErr",avgangmajxstderr)
self.setResultVariable("ObjAvgAngleYMajorAxis",avgangmajy)
self.setResultVariable("ObjAvgAngleYMajorAxisStdErr",avgangmajystderr)
self.setResultVariable("ObjAvgAngleZMajorAxis",avgangmajz)
self.setResultVariable("ObjAvgAngleZMajorAxisStdErr",avgangmajzstderr)
self.setResultVariable("ObjAvgAngleXMinorAxis",avgangminx)
self.setResultVariable("ObjAvgAngleXMinorAxisStdErr",avgangminxstderr)
self.setResultVariable("ObjAvgAngleYMinorAxis",avgangminy)
self.setResultVariable("ObjAvgAngleYMinorAxisStdErr",avgangminystderr)
self.setResultVariable("ObjAvgAngleZMinorAxis",avgangminz)
self.setResultVariable("ObjAvgAngleZMinorAxisStdErr",avgangminzstderr)
self.setResultVariable("ObjAvgSmoothness",avgsmooth)
self.setResultVariable("ObjAvgSmoothnessStdErr",avgsmoothstderr)
self.stats = [n, avgums, avgumsstderr, avgpxs, avgpxsstderr, avgAreaUm, avgAreaUmStdErr, avgint, avgintstderr, avgIntOutsideObjs, avgIntOutsideObjsStdErr, distMean, distStdErr, sumums, areaSumUm, avgIntOutsideObjsNonZero, avgIntOutsideObjsNonZeroStdErr, avgIntInsideObjs, avgIntInsideObjsStdErr, nonZeroVoxels, avground, avgroundstderr, intSum, avgmajlen, avgmajlenstderr, avgminlen, avgminlenstderr, avgelon, avgelonstderr, avgangmajx, avgangmajxstderr, avgangmajy, avgangmajystderr, avgangmajz, avgangmajzstderr, avgangminx, avgangminxstderr, avgangminy, avgangminystderr, avgangminz, avgangminzstderr, avgsmooth, avgsmoothstderr]
if self.reportGUI:
self.reportGUI.DeleteAllItems()
self.reportGUI.setVolumes(values)
self.reportGUI.setCentersOfMass(centersofmass)
self.reportGUI.setAverageIntensities(avgints, avgintsstderrs)
self.reportGUI.setIntensitySums(objIntSums)
self.reportGUI.setAverageDistances(avgDists, avgDistsStdErrs)
self.reportGUI.setAreasUm(objAreasUm)
self.reportGUI.setRoundness(objRoundness)
self.reportGUI.setMajorAxisLengths(objMajorLength)
self.reportGUI.setMinorAxisLengths(objMinorLength)
self.reportGUI.setElongations(objElongation)
self.reportGUI.setMajorAngles(objAngleMajX, objAngleMajY, objAngleMajZ)
self.reportGUI.setMinorAngles(objAngleMinX, objAngleMinY, objAngleMinZ)
self.reportGUI.setSmoothness(objSmoothness)
self.totalGUI.setStats(self.stats)
self.progressObj.setProgress(1.0)
self.updateProgress(None, "ProgressEvent")
return self.getInput(1)
def decimate(points, faces, reduction=0.5, smooth_steps=100, output_vtk=''):
"""
Decimate vtk triangular mesh with vtk.vtkDecimatePro.
Parameters
----------
points : list of lists of floats
each element is a list of 3-D coordinates of a vertex on a surface mesh
faces : list of lists of integers
each element is list of 3 indices of vertices that form a face
on a surface mesh
reduction : float
fraction of mesh faces to remove
smooth_steps : integer
number of smoothing steps
output_vtk : string
output decimated vtk file
Returns
-------
points : list of lists of floats
decimated points
faces : list of lists of integers
decimated faces
output_vtk : string
output decimated vtk file
Examples
--------
>>> import os
>>> from mindboggle.utils.io_vtk import read_vtk, write_vtk
>>> from mindboggle.utils.mesh import decimate
>>> path = os.environ['MINDBOGGLE_DATA']
>>> input_vtk = os.path.join(path, 'arno', 'labels', 'label22.vtk')
>>> reduction = 0.5
>>> smooth_steps = 100
>>> output_vtk = ''
>>> faces, lines, indices, points, npoints, scalars, scalar_names,
... o2 = read_vtk(input_vtk)
>>> points, faces, output_vtk = decimate(points, faces, reduction,
>>> smooth_steps, output_vtk)
>>> len(points) == 4567
True
>>> len(points)
4567
>>> # View:
>>> write_vtk('decimated.vtk', points, indices, lines, faces, scalars,
>>> scalar_names) # doctest: +SKIP
>>> os.system('mayavi2 -d decimated.vtk -m Surface &') # doctest: +SKIP
"""
import os
import vtk
from mindboggle.utils.io_vtk import read_vtk
# vtk points:
vtk_points = vtk.vtkPoints()
[vtk_points.InsertPoint(i, x[0], x[1], x[2]) for i,x in enumerate(points)]
# vtk faces:
vtk_faces = vtk.vtkCellArray()
for face in faces:
vtk_face = vtk.vtkPolygon()
vtk_face.GetPointIds().SetNumberOfIds(3)
vtk_face.GetPointIds().SetId(0, face[0])
vtk_face.GetPointIds().SetId(1, face[1])
vtk_face.GetPointIds().SetId(2, face[2])
vtk_faces.InsertNextCell(vtk_face)
# vtkPolyData:
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.SetPolys(vtk_faces)
# We want to preserve topology (not let any cracks form).
# This may limit the total reduction possible.
decimate = vtk.vtkDecimatePro()
decimate.SetInput(polydata)
decimate.SetTargetReduction(reduction)
decimate.PreserveTopologyOn()
# Export output:
if not output_vtk:
output_vtk = os.path.join(os.getcwd(), 'decimated_file.vtk')
#exporter = vtk.vtkPolyDataWriter()
if smooth_steps > 0:
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInput(decimate.GetOutput())
smoother.SetNumberOfIterations(smooth_steps)
smoother.Update()
out = smoother.GetOutput()
#exporter.SetInput(smoother.GetOutput())
else:
decimate.Update()
out = decimate.GetOutput()
#exporter.SetInput(decimate.GetOutput())
#exporter.SetFileName(output_vtk)
#exporter.Write()
## Extract points and faces:
#faces, u1, u2, points, u4, u5, u6, u7 = read_vtk(output_vtk)
points = [list(out.GetPoint(point_id))
for point_id in range(out.GetNumberOfPoints())]
if out.GetNumberOfPolys() > 0:
polys = out.GetPolys()
faces = [[int(polys.GetData().GetValue(j))
for j in range(i*4 + 1, i*4 + 4)]
for i in range(polys.GetNumberOfCells())]
else:
faces = []
return points, faces, output_vtk
def decimate_file(input_vtk, reduction=0.5, smooth_steps=100, output_vtk=''):
"""
Decimate vtk triangular mesh file with vtk.vtkDecimatePro.
Parameters
----------
input_vtk : string
input vtk file with triangular surface mesh
reduction : float
fraction of mesh faces to remove
do_smooth : Boolean
smooth after decimation?
output_vtk : string
output decimated vtk file
Returns
-------
output_vtk : string
output decimated vtk file
Examples
--------
>>> import os
>>> from mindboggle.utils.mesh import decimate_file
>>> path = os.environ['MINDBOGGLE_DATA']
>>> input_vtk = os.path.join(path, 'arno', 'labels', 'label22.vtk')
>>> output_vtk = 'decimated_file.vtk'
>>> reduction = 0.9
>>> smooth_steps = 0
>>> decimate_file(input_vtk, reduction=reduction,
>>> smooth_steps=smooth_steps, output_vtk=output_vtk)
>>> # View:
>>> os.system('mayavi2 -d ' + output_vtk + ' -m Surface &')
"""
import os
import vtk
from mindboggle.utils.io_vtk import read_vtk
# Read VTK surface mesh file:
faces, u1, u2, points, u4, labels, u5, u6 = read_vtk(input_vtk)
# vtk points:
vtk_points = vtk.vtkPoints()
[vtk_points.InsertPoint(i, x[0], x[1], x[2]) for i,x in enumerate(points)]
# vtk faces:
vtk_faces = vtk.vtkCellArray()
for face in faces:
vtk_face = vtk.vtkPolygon()
vtk_face.GetPointIds().SetNumberOfIds(3)
vtk_face.GetPointIds().SetId(0, face[0])
vtk_face.GetPointIds().SetId(1, face[1])
vtk_face.GetPointIds().SetId(2, face[2])
vtk_faces.InsertNextCell(vtk_face)
# vtkPolyData:
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.SetPolys(vtk_faces)
# We want to preserve topology (not let any cracks form).
# This may limit the total reduction possible.
decimate = vtk.vtkDecimatePro()
decimate.SetInput(polydata)
decimate.SetTargetReduction(reduction)
decimate.PreserveTopologyOn()
# Export output:
if not output_vtk:
output_vtk = os.path.join(os.getcwd(), 'decimated_file.vtk')
exporter = vtk.vtkPolyDataWriter()
if smooth_steps > 0:
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInputConnection(decimate.GetOutputPort())
smoother.SetNumberOfIterations(smooth_steps)
exporter.SetInput(smoother.GetOutput())
else:
exporter.SetInput(decimate.GetOutput())
exporter.SetFileName(output_vtk)
exporter.Write()
return output_vtk
# vtk faces:
vtk_faces = vtk.vtkCellArray()
for face in faces:
vtk_face = vtk.vtkPolygon()
vtk_face.GetPointIds().SetNumberOfIds(3)
vtk_face.GetPointIds().SetId(0, face[0])
vtk_face.GetPointIds().SetId(1, face[1])
vtk_face.GetPointIds().SetId(2, face[2])
vtk_faces.InsertNextCell(vtk_face)
# vtkPolyData:
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.SetPolys(vtk_faces)
# We want to preserve topology (not let any cracks form).
# This may limit the total reduction possible.
decimate = vtk.vtkDecimatePro()
decimate.SetInput(polydata)
decimate.SetTargetReduction(reduction)
decimate.PreserveTopologyOn()
if smooth_steps > 0:
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInputConnection(decimate.GetOutputPort())
smoother.SetNumberOfIterations(smooth_steps)
output = smoother.GetOutput()
else:
output = decimate.GetOutput()
def renderIBC(filePrefix, imgLow, imgHigh):
global picker, redCone, greenCone
#
# This example reads a volume dataset, extracts an isosurface that
# represents the skin and displays it.
#
# The following reader is used to read a series of 2D slices (images)
# that compose the volume. The slice dimensions are set, and the
# pixel spacing. The data Endianness must also be specified. The reader
# usese the FilePrefix in combination with the slice number to construct
# filenames using the format FilePrefix.%d. (In this case the FilePrefix
# is the root name of the file: quarter.)
#vtkVolume16Reader v13R
# v13R SetDataDimensions 1388 1040
# v13R SetDataByteOrderToBigEndian
# v13R SetFilePrefix "IBC146h.R_s"
# v13R SetImageRange 0 44
# v13R SetDataSpacing 1 1 2
# Image reader
v13G = vtk.vtkTIFFReader()
v13G.SetDataExtent(1, 1380, 1, 1030, imgLow, imgHigh)
v13G.SetDataByteOrderToLittleEndian()
v13G.SetFilePrefix(filePrefix)
v13G.SetDataSpacing(0.1, 0.1, 0.6)
# Gaussian Smoothing
gaus_v13G = vtk.vtkImageGaussianSmooth()
gaus_v13G.SetDimensionality(3)
gaus_v13G.SetStandardDeviation(1)
gaus_v13G.SetRadiusFactors(1, 1, 1)
gaus_v13G.SetInput(v13G.GetOutput())
# Set up the volume rendering
volumeMapper = vtk.vtkVolumeTextureMapper3D()
volumeMapper.SetInput(v13G.GetOutput())
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
# Surface rendering
bactExtractor = vtk.vtkMarchingCubes()
bactExtractor.SetInputConnection(gaus_v13G.GetOutputPort())
bactExtractor.SetValue(0,20000)
# bactNormals = vtk.vtkPolyDataNormals()
# bactNormals.SetInputConnection(bactExtractor.GetOutputPort())
# bactNormals.SetFeatureAngle(90.0)
#
# bactStripper = vtk.vtkStripper()
# bactStripper.SetInputConnection(bactNormals.GetOutputPort())
#
bactLocator = vtk.vtkCellLocator()
bactLocator.SetDataSet(bactExtractor.GetOutput())
bactLocator.LazyEvaluationOn()
#
# bactMapper = vtk.vtkPolyDataMapper()
# bactMapper.SetInputConnection(bactStripper.GetOutputPort())
# bactMapper.ScalarVisibilityOff()
# skinE_v13G = vtk.vtkContourFilter()
## skinE_v13G = vtk.vtkMarchingCubes()
# skinE_v13G.UseScalarTreeOn()
# skinE_v13G.SetInput(gaus_v13G.GetOutput())
# skinE_v13G.SetValue(0, 10000)
#
smooth_v13G = vtk.vtkSmoothPolyDataFilter()
smooth_v13G.SetInput(bactExtractor.GetOutput())
smooth_v13G.SetNumberOfIterations(50)
deci_v13G = vtk.vtkDecimatePro()
deci_v13G.SetInput(smooth_v13G.GetOutput())
deci_v13G.SetTargetReduction(0.5)
deci_v13G.PreserveTopologyOn()
smoother_v13G = vtk.vtkSmoothPolyDataFilter()
smoother_v13G.SetInput(deci_v13G.GetOutput())
smoother_v13G.SetNumberOfIterations(50)
skinNormals_v13G = vtk.vtkPolyDataNormals()
skinNormals_v13G.SetInput(deci_v13G.GetOutput())
skinNormals_v13G.SetFeatureAngle(60.0)
skinStripper_v13G = vtk.vtkStripper()
skinStripper_v13G.SetInput(skinNormals_v13G.GetOutput())
skinMapper_v13G = vtk.vtkPolyDataMapper()
skinMapper_v13G.SetInput(skinStripper_v13G.GetOutput())
skinMapper_v13G.ScalarVisibilityOff()
skin_v13G = vtk.vtkActor()
skin_v13G.SetMapper(skinMapper_v13G)
skin_v13G.GetProperty().SetDiffuseColor(0.2, 1, 0.2)
skin_v13G.GetProperty().SetSpecular(.1)
skin_v13G.GetProperty().SetSpecularPower(5)
skin_v13G.GetProperty().SetOpacity(0.9)
# It is convenient to create an initial view of the data. The FocalPoint
# and Position form a vector direction. Later on (ResetCamera() method)
# this vector is used to position the camera to look at the data in
# this direction.
aCamera = vtk.vtkCamera()
aCamera.SetViewUp(0, 0, -1)
aCamera.SetPosition(0, 1.1, 2)
aCamera.SetFocalPoint(0, -0.25, 0)
aCamera.ComputeViewPlaneNormal()
# Actors are added to the renderer. An initial camera view is created.
# The Dolly() method moves the camera towards the FocalPoint,
# thereby enlarging the image.
#aRenderer AddActor skin_v13R
ren.AddActor(skin_v13G)
ren.SetActiveCamera(aCamera)
ren.ResetCamera()
aCamera.Dolly(1.0)
# Note that when camera movement occurs (as it does in the Dolly()
# method), the clipping planes often need adjusting. Clipping planes
# consist of two planes: near and far along the view direction. The
# near plane clips out objects in front of the plane the far plane
# clips out objects behind the plane. This way only what is drawn
# between the planes is actually rendered.
ren.ResetCameraClippingRange()
# render
renWin.Render()
# CONE PICKER RENDER
#---------------------------------------------------------
# the cone points along the -x axis
coneSource = vtk.vtkConeSource()
coneSource.CappingOn()
coneSource.SetHeight(2)
coneSource.SetRadius(1)
coneSource.SetResolution(11)
coneSource.SetCenter(1,0,0)
coneSource.SetDirection(-1,0,0)
coneMapper = vtk.vtkDataSetMapper()
coneMapper.SetInputConnection(coneSource.GetOutputPort())
redCone = vtk.vtkActor()
redCone.PickableOff()
redCone.SetMapper(coneMapper)
redCone.GetProperty().SetColor(1,0,0)
greenCone = vtk.vtkActor()
greenCone.PickableOff()
greenCone.SetMapper(coneMapper)
greenCone.GetProperty().SetColor(0,1,0)
# Add the two cones (or just one, if you want)
ren.AddViewProp(redCone)
ren.AddViewProp(greenCone)
#---------------------------------------------------------
# the picker
picker = vtk.vtkVolumePicker()
picker.SetTolerance(1e-6)
picker.SetVolumeOpacityIsovalue(0.1)
# locator is optional, but improves performance for large polydata
picker.AddLocator(bactLocator)
#---------------------------------------------------------
# custom interaction
iren.AddObserver("MouseMoveEvent", MoveCursor)
# END CONE PICKER RENDER
# initialize and start the interactor
iren.Initialize()
iren.Start()
def surface(points, triangles, labels, ctab=None, opacity=1, set_lut=True,
decimation_ratio=1):
""" Create a colored triangular surface.
Parameters
----------
points: array (n_vertices, 3)
the surface vertices.
triangles: array
nfaces x 3 array defining mesh triangles.
labels: array (n_vertices)
Annotation id at each vertex.
If a vertex does not belong to any label its id must be negative.
ctab: ndarray (n_labels, 5) (optional, default None)
RGBA + label id color table array. If None a default blue to red
256 levels lookup table is used.
opacity: float (optional, default 1)
the actor global opacity.
set_lut: bool (optional, default True)
if True set a tuned lut.
decimation_ratio: float (optional, default 1)
how many triangles should reduced by specifying the percentage
([0,1]) of triangles to be removed.
Returns
-------
actor: vtkActor
one actor handling the surface.
"""
# First setup points, triangles and colors
vtk_points = vtk.vtkPoints()
vtk_triangles = vtk.vtkCellArray()
vtk_colors = vtk.vtkUnsignedCharArray()
vtk_colors.SetNumberOfComponents(1)
labels[numpy.where(labels < 0)] = 0
for index in range(len(points)):
vtk_points.InsertNextPoint(points[index])
vtk_colors.InsertNextTuple1(labels[index])
for cnt, triangle in enumerate(triangles):
vtk_triangle = vtk.vtkTriangle()
vtk_triangle.GetPointIds().SetId(0, triangle[0])
vtk_triangle.GetPointIds().SetId(1, triangle[1])
vtk_triangle.GetPointIds().SetId(2, triangle[2])
vtk_triangles.InsertNextCell(vtk_triangle)
# Make a lookup table using vtkColorSeries
lut = vtk.vtkLookupTable()
if ctab is not None:
nb_of_labels = len(ctab)
lut.SetNumberOfColors(nb_of_labels)
lut.Build()
for cnt, lut_element in enumerate(ctab):
lut.SetTableValue(
cnt, lut_element[0] / 255., lut_element[1] / 255.,
lut_element[2] / 255., lut_element[3] / 255.)
lut.SetNanColor(1, 0, 0, 1)
# This creates a blue to red lut.
else:
nb_of_labels = 255
lut.SetHueRange(0.667, 0.0)
lut.SetNumberOfColors(nb_of_labels)
lut.Build()
# Create (geometry and topology) the associated polydata
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.GetPointData().SetScalars(vtk_colors)
polydata.SetPolys(vtk_triangles)
# Decimate the mesh
decimate = vtk.vtkDecimatePro()
decimate.SetInputConnection(polydata.GetProducerPort())
decimate.SetTargetReduction(decimation_ratio)
# Create the mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(decimate.GetOutput())
if set_lut:
mapper.SetLookupTable(lut)
mapper.SetColorModeToMapScalars()
mapper.SetScalarRange(0, nb_of_labels)
mapper.SetScalarModeToUsePointData()
else:
mapper.ScalarVisibilityOff()
# Create the actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(opacity)
actor.GetProperty().SetColor(0.9, 0.9, 0.9)
return actor
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkDecimatePro(), 'Processing.',
('vtkPolyData',), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInput(self.Surface)
triangleFilter.Update()
decimationFilter = vtk.vtkDecimatePro()
decimationFilter.SetInput(triangleFilter.GetOutput())
decimationFilter.SetTargetReduction(self.TargetReduction)
decimationFilter.SetBoundaryVertexDeletion(self.BoundaryVertexDeletion)
decimationFilter.PreserveTopologyOn()
decimationFilter.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(decimationFilter.GetOutput())
cleaner.Update()
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInput(cleaner.GetOutput())
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
if self.Surface.GetSource():
self.Surface.GetSource().UnRegisterAllOutputs()