#!/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()