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#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkbifurcationsections.py,v $
## Language: Python
## Date: $Date: 2006/10/17 15:16:16 $
## Version: $Revision: 1.1 $
## Copyright (c) Luca Antiga, David Steinman. All rights reserved.
## See LICENCE file for details.
## This software is distributed WITHOUT ANY WARRANTY; without even
## the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
## PURPOSE. See the above copyright notices for more information.
import vtk
import vtkvmtk
import sys
import pypes
vmtkbifurcationsections = 'vmtkBifurcationSections'
class vmtkBifurcationSections(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Surface = None
self.Centerlines = None
self.BifurcationSections = None
self.NumberOfDistanceSpheres = 1
self.RadiusArrayName = ''
self.GroupIdsArrayName = ''
self.CenterlineIdsArrayName = ''
self.TractIdsArrayName = ''
self.BlankingArrayName = ''
self.OutputSectionPointGroupId = None
self.OutputSectionPointBifurcationGroupId = None
self.OutputSectionPoint = []
self.OutputSectionNormal = []
self.OutputSectionArea = 0.0
self.BifurcationSectionGroupIdsArrayName = 'BifurcationSectionGroupIds'
self.BifurcationSectionBifurcationGroupIdsArrayName = 'BifurcationSectionBifurcationGroupIds'
self.BifurcationSectionPointArrayName = 'BifurcationSectionPoint'
self.BifurcationSectionNormalArrayName = 'BifurcationSectionNormal'
self.BifurcationSectionAreaArrayName = 'BifurcationSectionArea'
self.BifurcationSectionMinSizeArrayName = 'BifurcationSectionMinSize'
self.BifurcationSectionMaxSizeArrayName = 'BifurcationSectionMaxSize'
self.BifurcationSectionShapeArrayName = 'BifurcationSectionShape'
self.BifurcationSectionClosedArrayName = 'BifurcationSectionClosed'
self.BifurcationSectionOrientationArrayName = 'BifurcationSectionOrientation'
self.BifurcationSectionDistanceSpheresArrayName = 'BifurcationSectionDistanceSpheres'
self.SetScriptName('vmtkbifurcationsections')
self.SetScriptDoc('compute branch sections located a fixed number of spheres away from each bifurcation. The script takes in input the surface and the relative centerlines, both already split into branches.')
self.SetInputMembers([
['Surface','i','vtkPolyData',1,'','the input surface, already split into branches','vmtksurfacereader'],
['Centerlines','centerlines','vtkPolyData',1,'','the input centerlines, already split into branches','vmtksurfacereader'],
['NumberOfDistanceSpheres','distancespheres','int',1,'','distance from the bifurcation at which the sections have to be taken; the distance is expressed in number of inscribed spheres, where each sphere touches the center of the previous one'],
['RadiusArrayName','radiusarray','str',1,'','name of the array where centerline radius is stored'],
['GroupIdsArrayName','groupidsarray','str',1,'','name of the array where centerline group ids are stored'],
['CenterlineIdsArrayName','centerlineidsarray','str',1,'','name of the array where centerline ids are stored'],
['TractIdsArrayName','tractidsarray','str',1,'','name of the array where centerline tract ids are stored'],
['BlankingArrayName','blankingarray','str',1,'','name of the array where centerline blanking information about branches is stored'],
['BifurcationSectionGroupIdsArrayName','bifurcationsectiongroupids','str',1,'','name of the array where the group id to which each section belongs has to be stored'],
['BifurcationSectionBifurcationGroupIdsArrayName','bifurcationsectionbifurcationgroupids','str',1,'','name of the array where the bifurcation group id to which each section belongs has to be stored'],
['BifurcationSectionPointArrayName','bifurcationsectionpoint','str',1,'','name of the array where the point at which bifurcation sections are defined have to be stored'],
['BifurcationSectionNormalArrayName','bifurcationsectionnormal','str',1,'','name of the array where the bifurcation section normals have to be stored'],
['BifurcationSectionAreaArrayName','bifurcationsectionarea','str',1,'','name of the array where the area of bifurcation sections have to be stored'],
['BifurcationSectionMinSizeArrayName','bifurcationsectionminsize','str',1,'','name of the array where the minimum diameter of each section has to be stored'],
['BifurcationSectionMaxSizeArrayName','bifurcationsectionmaxsize','str',1,'','name of the array where the maximum diameter of each bifurcation sections has to be stored'],
['BifurcationSectionShapeArrayName','bifurcationsectionshape','str',1,'','name of the array where the shape index, i.e. the ratio between minimum and maximum diameter, of each bifurcation section has to be stored'],
['BifurcationSectionClosedArrayName','bifurcationsectionclosed','str',1,'','name of the array containing 1 if a section is closed and 0 otherwise'],
['BifurcationSectionOrientationArrayName','bifurcationsectionorientation','str',1,'','name of the array containing 0 if a section is upstream and 0 downstream its bifurcation'],
['BifurcationSectionDistanceSpheresArrayName','bifurcationsectiondistancespheres','str',1,'','name of the array containing the number of spheres away from the bifurcation the section is located at'],
['OutputSectionPointGroupId','sectionpointgroupid','int',1,'(0,)'],
['OutputSectionPointBifurcationGroupId','sectionpointbifurcationgroupid','int',1,'(0,)']
])
self.SetOutputMembers([
['BifurcationSections','o','vtkPolyData',1,'','the output sections','vmtksurfacewriter'],
['BifurcationSectionGroupIdsArrayName','bifurcationsectiongroupids','str',1,'','name of the array where the group id to which each section belongs are stored'],
['BifurcationSectionBifurcationGroupIdsArrayName','bifurcationsectionbifurcationgroupids','str',1,'','name of the array where the bifurcation group id to which each section belongs has to be stored'],
['BifurcationSectionPointArrayName','bifurcationsectionpoint','str',1,'','name of the array where the point at which bifurcation sections are defined are stored'],
['BifurcationSectionNormalArrayName','bifurcationsectionnormal','str',1,'','name of the array where bifurcation section normals are stored'],
['BifurcationSectionAreaArrayName','bifurcationsectionarea','str',1,'','name of the array where the area of bifurcation sections are stored'],
['BifurcationSectionMinSizeArrayName','bifurcationsectionminsize','str',1,'','name of the array where the minimum diameter of each section are stored'],
['BifurcationSectionMaxSizeArrayName','bifurcationsectionmaxsize','str',1,'','name of the array where the minimum diameter of each bifurcation sections has to be stored'],
['BifurcationSectionShapeArrayName','bifurcationsectionshape','str',1,'','name of the array where the shape index, i.e. the ratio between minimum and maximum diameter, of each bifurcation section are stored'],
['BifurcationSectionClosedArrayName','bifurcationsectionclosed','str',1,'','name of the array containing 1 if a section is closed and 0 otherwise'],
['BifurcationSectionOrientationArrayName','bifurcationsectionorientation','str',1,'','name of the array containing 0 if a section is upstream and 0 downstream its bifurcation'],
['BifurcationSectionDistanceSpheresArrayName','bifurcationsectiondistancespheres','str',1,'','name of the array containing the number of spheres away from the bifurcation the section is located at'],
['OutputSectionPoint','sectionpoint','float',3],
['OutputSectionNormal','sectionnormal','float',3],
['OutputSectionArea','sectionarea','float',1]
])
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No input surface.')
if self.Centerlines == None:
self.PrintError('Error: No input centerlines.')
bifurcationSections = vtkvmtk.vtkvmtkPolyDataBifurcationSections()
bifurcationSections.SetInput(self.Surface)
bifurcationSections.SetGroupIdsArrayName(self.GroupIdsArrayName)
bifurcationSections.SetCenterlines(self.Centerlines)
bifurcationSections.SetNumberOfDistanceSpheres(self.NumberOfDistanceSpheres)
bifurcationSections.SetCenterlineRadiusArrayName(self.RadiusArrayName)
bifurcationSections.SetCenterlineGroupIdsArrayName(self.GroupIdsArrayName)
bifurcationSections.SetCenterlineIdsArrayName(self.CenterlineIdsArrayName)
bifurcationSections.SetCenterlineTractIdsArrayName(self.TractIdsArrayName)
bifurcationSections.SetBlankingArrayName(self.BlankingArrayName)
bifurcationSections.SetBifurcationSectionGroupIdsArrayName(self.BifurcationSectionGroupIdsArrayName)
bifurcationSections.SetBifurcationSectionBifurcationGroupIdsArrayName(self.BifurcationSectionBifurcationGroupIdsArrayName)
bifurcationSections.SetBifurcationSectionPointArrayName(self.BifurcationSectionPointArrayName)
bifurcationSections.SetBifurcationSectionNormalArrayName(self.BifurcationSectionNormalArrayName)
bifurcationSections.SetBifurcationSectionAreaArrayName(self.BifurcationSectionAreaArrayName)
bifurcationSections.SetBifurcationSectionMinSizeArrayName(self.BifurcationSectionMinSizeArrayName)
bifurcationSections.SetBifurcationSectionMaxSizeArrayName(self.BifurcationSectionMaxSizeArrayName)
bifurcationSections.SetBifurcationSectionShapeArrayName(self.BifurcationSectionShapeArrayName)
bifurcationSections.SetBifurcationSectionClosedArrayName(self.BifurcationSectionClosedArrayName)
bifurcationSections.SetBifurcationSectionOrientationArrayName(self.BifurcationSectionOrientationArrayName)
bifurcationSections.SetBifurcationSectionDistanceSpheresArrayName(self.BifurcationSectionDistanceSpheresArrayName)
bifurcationSections.Update()
self.BifurcationSections = bifurcationSections.GetOutput()
if self.OutputSectionPointGroupId != None and self.OutputSectionPointBifurcationGroupId != None:
groupIds = self.BifurcationSections.GetCellData().GetArray(self.BifurcationSectionGroupIdsArrayName)
bifurcationGroupIds = self.BifurcationSections.GetCellData().GetArray(self.BifurcationSectionBifurcationGroupIdsArrayName)
for i in range(self.BifurcationSections.GetNumberOfCells()):
if int(groupIds.GetTuple1(i)) == self.OutputSectionPointGroupId and int(bifurcationGroupIds.GetTuple1(i)) == self.OutputSectionPointBifurcationGroupId:
self.OutputSectionPoint = self.BifurcationSections.GetCellData().GetArray(self.BifurcationSectionPointArrayName).GetTuple3(i)
self.OutputSectionNormal = self.BifurcationSections.GetCellData().GetArray(self.BifurcationSectionNormalArrayName).GetTuple3(i)
self.OutputSectionArea = self.BifurcationSections.GetCellData().GetArray(self.BifurcationSectionAreaArrayName).GetTuple1(i)
self.InputInfo('SectionPoint: '+str(self.OutputSectionPoint))
self.InputInfo('SectionNormal: '+str(self.OutputSectionNormal))
self.InputInfo('SectionArea: '+str(self.OutputSectionArea))
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()
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