def ExtractGeometry(centerlines):
#centerlines=EquispacedSpline(centerlines.Centerlines,0.05) # every 0.5mm
centerlineResampling = vmtkscripts.vmtkCenterlineResampling()
centerlineResampling.Centerlines = centerlines.Centerlines
centerlineResampling.Length = 0.05
centerlineResampling.Execute()
centerlineGeometry = vmtkscripts.vmtkCenterlineGeometry()
centerlineGeometry.Centerlines = centerlineResampling.Centerlines
centerlineGeometry.SmoothingFactor = 0.4
centerlineGeometry.FrenetTangentArrayName = 'FrenetTangent'
centerlineGeometry.FrenetNormalArrayName = 'FrenetNormal'
centerlineGeometry.FrenetBinormalArrayName = 'FrenetBinormal'
centerlineGeometry.Execute()
centerlineAttributes = vmtkscripts.vmtkCenterlineAttributes()
centerlineAttributes.Centerlines = centerlineGeometry.Centerlines
centerlineAttributes.Execute()
branchExtractor = vmtkscripts.vmtkBranchExtractor()
branchExtractor.Centerlines = centerlineAttributes.Centerlines
branchExtractor.GroupIdsArrayName = 'GroupIds'
branchExtractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
branchExtractor.CenterlineIdsArrayName = 'CenterlineIds'
branchExtractor.BlankingArrayName = 'Blanking'
branchExtractor.Execute()
return branchExtractor
def extract_branches(self, params):
""" Split and group centerlines along branches.
"""
self.logger.info("Split and group centerlines along branches ...");
branch_extractor = vmtkscripts.vmtkBranchExtractor()
branch_extractor.Centerlines = self.geometry
branch_extractor.Execute()
self.branch_geometry = branch_extractor.Centerlines
#print(self.centerlines_branch_geometry)
self.logger.info("The centerlines branches have been calculated.");
def compute(infile, outfile):
"""
Calls VMTK routine for centerline extraction.
Parameters
----------
infile : string
Path to input mesh with open inlet/outlets (.stl format).
outfile : string
Path to output centerline (.vtp format).
Returns
-------
None
"""
# read surface
centerlineReader = vmtkscripts.vmtkSurfaceReader()
centerlineReader.InputFileName = infile
centerlineReader.Execute()
# centerline
centerline = vmtkscripts.vmtkCenterlines()
centerline.Surface = centerlineReader.Surface
centerline.SeedSelectorName = 'openprofiles'
centerline.AppendEndPoints = 1
centerline.Execute()
# extract branches
branchExtractor = vmtkscripts.vmtkBranchExtractor()
branchExtractor.Centerlines = centerline.Centerlines
branchExtractor.Execute()
# merge centerlines
centerlineMerge = vmtkscripts.vmtkCenterlineMerge()
centerlineMerge.Centerlines = branchExtractor.Centerlines
centerlineMerge.Execute()
# write surface
centerlineWriter = vmtkscripts.vmtkSurfaceWriter()
centerlineWriter.OutputFileName = outfile
centerlineWriter.Surface = centerlineMerge.Centerlines
centerlineWriter.Execute()
def vmtk_compute_branch_extractor(centerlines):
"""
Wrapper for vmtkBranchExtractor.
Split and group centerlines along branches:
Args:
centerlines (vtkPolyData): Line to split into branches.
Returns:
vtkPolyData: Split centerline.
"""
brancher = vmtkscripts.vmtkBranchExtractor()
brancher.Centerlines = centerlines
brancher.RadiusArrayName = radiusArrayName
brancher.Execute()
centerlines_branched = brancher.Centerlines
return centerlines_branched
def vmtkbranchextractor(centerlines):
"""Split centerlines into branches.
Args:
centerlines: Centerlines.
Returns:
Centerlines split into branches.
Celldata (selection):
CenterlineId: Cellid of centerline from which the tract was split.
TractId: Id identifying each tract along one centerline.
GroupId: Id of the group to which the tract belongs.
Blanking: Boolean indicating whether tract belongs to bifurcation.
"""
extractor = vmtkscripts.vmtkBranchExtractor()
extractor.Centerlines = centerlines
extractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
extractor.Execute()
return extractor.Centerlines
def vmtkbranchextractor(centerlines):
"""Split centerlines into branches.
Args:
centerlines: Centerlines.
Returns:
Centerlines split into branches.
Celldata (selection):
CenterlineId: Cellid of centerline from which the tract was split.
TractId: Id identifying each tract along one centerline.
GroupId: Id of the group to which the tract belongs.
Blanking: Boolean indicating whether tract belongs to bifurcation.
"""
extractor = vmtkscripts.vmtkBranchExtractor()
extractor.Centerlines = centerlines
extractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
extractor.Execute()
return extractor.Centerlines
def extract_center_lines(self):
""" Extract the centerlines of a surface.
The centerline geometry is returned as a vtkPolyData object.
"""
self.logger.info("---------- Extract Centerlines ---------- ")
mesh = self.mesh
surface = mesh.surface
surface_caps = mesh.surface_caps
source_centers = []
source_ids = []
target_centers = []
target_ids = []
## Get source and target face centers.
#
for faceID, face in surface_caps.items():
self.logger.info(" ")
self.logger.info("----- Face ID %d ----- " % int(faceID))
center = face.get_center()
ptID, id_center = face.get_id(center)
if face.source:
self.logger.info("Source")
source_centers.extend(center)
self.graphics.add_sphere(center, [1.0, 0.0, 0.0])
self.graphics.add_sphere(id_center, [1.0, 0.0, 0.0])
source_ids.append(ptID)
else:
self.logger.info("Target")
target_centers.extend(center)
self.graphics.add_sphere(center, [0.0, 1.0, 0.0])
self.graphics.add_sphere(id_center, [0.0, 1.0, 0.0])
target_ids.append(ptID)
self.logger.info("Center ID: %d" % ptID)
self.logger.info("Center: %s" % str(center))
self.logger.info("ID Center: %s" % str(id_center))
#__for faceID in face_ids
## Extract centerlines using vmtk.
#
self.logger.info(" ")
self.logger.info("Calculating surface centerlines ...")
centerlines = vmtkscripts.vmtkCenterlines()
centerlines.Surface = mesh.surface
centerlines.AppendEndPoints = 1
"""
source_ids = [67628]
target_ids = [67626, 67627 ,67628 ,67629 ,67630 ,67631 ,67632 ,67633]
surface.GetPoint(source_ids[0], id_center);
self.graphics.add_sphere(id_center, [1.0,0.0,0.0])
"""
use_id_list = True
if use_id_list:
self.logger.info("Use source and target IDs")
self.logger.info("Source IDs: %s" % str(source_ids))
self.logger.info("Target IDs: %s" % str(target_ids))
centerlines.SeedSelectorName = "idlist"
centerlines.SourceIds = source_ids
centerlines.TargetIds = target_ids
else:
centerlines.SeedSelectorName = "pointlist"
centerlines.SourcePoints = source_centers
centerlines.TargetPoints = target_centers
centerlines.Execute()
self.geometry = centerlines.Centerlines
self.logger.info("The surface centerlines have been calculated.")
self.graphics.add_graphics_geometry(self.geometry, [0.0, 0.0, 1.0])
self.logger.info("Split and group centerlines along branches ...")
branch_extractor = vmtkscripts.vmtkBranchExtractor()
branch_extractor.Centerlines = self.geometry
branch_extractor.Execute()
self.branch_geometry = branch_extractor.Centerlines
#print(self.centerlines_branch_geometry)
self.logger.info("The centerlines branches have been calculated.")
file_name = "branch_geometry.vtp"
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName(file_name)
writer.SetInputData(self.branch_geometry)
writer.Update()
writer.Write()
def Execute(self):
print("Compute VC orientation")
self.ctrliner = vmtkscripts.vmtkCenterlines()
self.ctrliner.Surface = self.Surface
self.ctrliner.Execute()
self.Centerlines = self.ctrliner.Centerlines
cc = self.Centerlines
ptCoord = []
for c in xrange(cc.GetNumberOfPoints()):
ptCoord.append(cc.GetPoints().GetPoint(c))
ptCoord = np.array(ptCoord)
datamean = ptCoord.mean(axis=0)
uu, dd, vv = np.linalg.svd(ptCoord - datamean)
# vector of the general direction of the VC
# print(vv[0], datamean, datamean+10*vv[0])
VCvect = vv[0]
if self.ComputeCenterlines:
# print(self.Surface)
self.ctrliner = vmtkscripts.vmtkCenterlines()
self.ctrliner.Surface = self.Surface
# self.ctrliner.SeedSelector = 'openprofiles'
self.ctrliner.Execute()
self.Centerlines = self.ctrliner.Centerlines
# self.Surface = self.Centerlines
else:
self.Centerlines = self.Surface
# if self.Centerlines == None:
# self.PrintError('DUMBASS')
self.vmtkReader = vmtkscripts.vmtkSurfaceReader()
self.vmtkRenderer = vmtkscripts.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
# self.Surface = self.Centerlines
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.Execute()
self.myattr = vmtkscripts.vmtkCenterlineAttributes()
self.myattr.Centerlines = self.Centerlines
self.myattr.Execute()
self.mybranchextractor = vmtkscripts.vmtkBranchExtractor()
self.mybranchextractor.Centerlines = self.myattr.Centerlines
self.mybranchextractor.RadiusArrayName = self.RadiusArrayName
self.mybranchextractor.Execute()
self.ctrl = self.mybranchextractor.Centerlines
self.mywriter = vmtkscripts.vmtkSurfaceWriter()
self.mywriter.Surface = self.mybranchextractor.Centerlines
self.mywriter.OutputFileName = '/home/florian/liverSim/morpho_analysis/test_surf_open_small_ctrlTESTbranc1.vtp'
self.mywriter.Execute()
self.mybifref = vmtkscripts.vmtkBifurcationReferenceSystems()
self.mybifref.Centerlines = self.ctrl
self.mybifref.RadiusArrayName = self.RadiusArrayName
self.mybifref.BlankingArrayName = self.BlankingArrayName
self.mybifref.GroupIdsArrayName = self.GroupIdsArrayName
self.mybifref.CenterlineIdsArrayName = self.CenterlineIdsArrayName
self.mybifref.TractIdsArrayName = self.TractIdsArrayName
self.mybifref.Execute()
self.myvect = vmtkscripts.vmtkBifurcationVectors()
self.myvect.Centerlines = self.ctrl
self.myvect.ReferenceSystems = self.mybifref.ReferenceSystems
self.myvect.RadiusArrayName = self.RadiusArrayName
self.myvect.BlankingArrayName = self.BlankingArrayName
self.myvect.GroupIdsArrayName = self.GroupIdsArrayName
self.myvect.TractIdsArrayName = self.TractIdsArrayName
self.myvect.CenterlineIdsArrayName = self.CenterlineIdsArrayName
self.myvect.ReferenceSystemsNormalArrayName = self.mybifref.ReferenceSystemsNormalArrayName
self.myvect.ReferenceSystemsUpNormalArrayName = self.mybifref.ReferenceSystemsUpNormalArrayName
self.myvect.Execute()
'''TEMP'''
self.mywriter = vmtkscripts.vmtkSurfaceWriter()
self.mywriter.Surface = self.myvect.BifurcationVectors
self.mywriter.OutputFileName = '/home/florian/liverSim/morpho_analysis/test_surf_open_small_bifvect.vtp'
self.mywriter.Execute()
self.mywriter.Surface = self.ctrl
self.mywriter.OutputFileName = '/home/florian/liverSim/morpho_analysis/test_surf_open_small_ctrl.vtp'
self.mywriter.Execute()
'''/TEMP'''
self.numpytator = vmtksurfacetonumpy.vmtkSurfaceToNumpy()
self.numpytator.Surface = self.myvect.BifurcationVectors
self.numpytator.Execute()
vectData = self.numpytator.ArrayDict.values()
cprint(figlet_format('Results!', font='bubble'))
print('\n InPlaneBifurcationVectors angle:')
print(np.degrees(self.angle_between(vectData[0]["InPlaneBifurcationVectors"][1, :],
vectData[0]["InPlaneBifurcationVectors"][2, :])))
# print('\n OutOfPlaneBifurcationVectors angle:')
# print(np.degrees(self.angle_between(vectData[0]["OutOfPlaneBifurcationVectors"][1, :],
# vectData[0]["OutOfPlaneBifurcationVectors"][2, :])))
print('\n bifurcation angle with the VC:')
print(np.degrees(self.angle_between(vectData[0]["OutOfPlaneBifurcationVectors"][0, :],
VCvect)))
'''
weighted average vector between the vectors pointing from the second
to the first reference point on each centerline
'''
print('\n global direction of the birfurcation:')
print(vectData[0]["BifurcationVectors"][0, :])
'''
the origin of the bifurcation is defined as the barycenter of the four reference points
weighted by the surface of the maximum inscribed sphere defined on the reference points.
The reason of the weighting is that small branches have less impact on the position of
the bifurcation origin
'''
print('\n Origin of the bifurcation:')
print(vectData[1][0])
pass
args = "vmtksurfacereader -ifile " + surfaceFile
myPype = pypes.PypeRun(args)
mySurface = myPype.GetScriptObject('vmtksurfacereader', '0').Surface
myctrl = vmtkscripts.vmtkCenterlines()
myctrl.Surface = mySurface
myctrl.SeedSelectorName = 'openprofiles'
# myctrl.Centerlines = centerlinesFile
myctrl.Execute()
myattr = vmtkscripts.vmtkCenterlineAttributes()
myattr.Centerlines = myctrl.Centerlines
myattr.Execute()
mybranchextractor = vmtkscripts.vmtkBranchExtractor()
mybranchextractor.Centerlines = myattr.Centerlines
mybranchextractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
mybranchextractor.Execute()
# mywriter = vmtkscripts.vmtkSurfaceWriter()
# mywriter.Surface = mybranchextractor.Centerlines
# mywriter.OutputFileName = centerlinesFileName
# mywriter.Execute()
mybifref = vmtkscripts.vmtkBoundaryReferenceSystems()
mybifref.Surface = mybranchextractor.Centerlines
mybifref.Execute()
# mywriter = vmtkscripts.vmtkSurfaceWriter()
# mywriter.Surface = mybifref.Centerlines
def vmtkbranchextractor(centerline):
extractor = vmtkscripts.vmtkBranchExtractor()
extractor.Centerlines = centerline
extractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
extractor.Execute()
return extractor.Centerlines
def vmtkbranchextractor(centerline):
extractor = vmtkscripts.vmtkBranchExtractor()
extractor.Centerlines = centerline
extractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
extractor.Execute()
return extractor.Centerlines