[vmtk-users] Script doesn't work

[Berkowitz, Benjamin M]

Hi, I've been trying to make a python script that takes in models of vessels 
with cerebral aneurysms and will eventually give the user an isolated aneurysm. 
 Basically, the script is pretty simple and does almost the same thing as 
typing these commands into pypepad, but asks the user for the number of the 
centerline tract to construct around instead of vmtkcenterlinelabeler:

vmtksurfacereader -ifile surface1.vtp --pipe vmtkcenterlines --pipe 
vmtkbranchextractor --pipe vmtkcenterlinelabeler --pipe vmtkbranchclipper 
-groupids 2 -ofile surface.vtp --pipe vmtkrenderer --pipe vmtksurfaceviewer 
--pipe vmtksurfaceviewer -ifile  
/var/tmp/bberkowi/BIOMOST/Coil_Compaction_Growth_Project/Ben_B_auto_aneurysm_cutting/Recur_pt2_pre1L.vtp
 -opacity 0.5

It doesn't work, though.  I've just started to learn how to program with Python 
and PypeS, so I was hoping someone could take a quick look at it and tell me if 
I'm on the right track and if you see any glaring errors. I've attached the 
file.

Thanks,
Ben Berkowitz

#! /usr/bin/env python

import vtk
import sys
import math
import string
from vmtk import vmtkcenterlines
from vmtk import vmtkcenterlineviewer
from vmtk import vmtkrenderer

from vmtk import pypes
from vmtk import vmtkscripts

isolateaneurysm = 'isolateAneurysm'

class isolateAneurysm(pypes.pypeScript):
  
    def __init__(self):
    
	pypes.pypeScript.__init__(self)   

	self.Surface = None
	self.SurfaceInputFileName
	self.AneurysmSurface = None

	self.SetScriptName('isolateaneurysm')
	self.SetScriptDoc('Slices the aneurysm using a distance threshold from the centerline')
	self.SetInputMembers([
	    ['Surface','i','vtkPolyData',1,'','the input surface','vmtksurfacereader'],
	    ['SurfaceInputFileName','ifile','string',1,'','the input surface filename'],
	    ['SurfaceOutputFileName','ofile','string',1,'','the output surface filename']
	    ])
	self.SetOutputMembers([
	    ['AneurysmSurface','o','vtkPolyData',1,'','the output surface','vmtksurfacewriter']
	    ])

    def BranchInput(self):
	
	branchString = int(self.InputText('Please input aneurysm centerline groupID: '))
	
	for i in self.ExtractedBranches.GroupIdsArrayName:
	    if branchString == self.ExtractedBranches.GroupIdsArrayName:
		branchString = None
	return branchString
	
    def Execute(self):
    
	if self.Surface == None:
	    self.PrintError('Error: No Surface.')
	
	# get centerlines
	self.Centerlines = vmtkscripts.vmtkCenterlines
	self.Centerlines.Surface = self.Surface
	self.Centerlines.Execute()
	
	#split up centerlines
	self.ExtractedBranches = vmtkscripts.vmtkBranchExtractor
	self.ExtractedBranches.Centerlines = self.Centerlines
	self.ExtractedBranches.Execute()
	
	#display centerlines with IDs
	groupIdsArray = self.ExtractedBranches.Centerlines.GetCellData().GetArray(self.ExtractedBranches.GroupIdsArrayName)
	groupIds = []
	for i in range(groupIdsArray.GetNumberOfTuples()):
	    groupIds.append(int(groupIdsArray.GetComponent(i,0)))
	groupIds.sort()
	uniqueGroupIds = []
	for groupId in groupIds:
	    if groupId not in uniqueGroupIds:
		uniqueGroupIds.append(groupId)
		
	labelMap = {}
	
	viewer = vmtkcenterlineviewer.vmtkCenterlineViewer()
	viewer.Centerlines = self.ExtractedBranches.Centerlines
	viewer.CellDataArrayName = self.ExtractedBranches.GroupIdsArrayName
	viewer.vmtkRenderer = vmtkrenderer.vmtkRenderer()
	viewer.Execute()
	
	#isolate surface
	self.BranchClipper = vmtkscripts.vmtkBranchClipper
	while self.BranchNumber == None:
	    self.BranchNumber = self.BranchInput(self)
	    if self.BranchNumber == None:
		self.OutputText('Please enter a valid branch ID.')
	self.BranchClipper.Centerlines = self.ExtractedBranches.Centerlines
	self.BranchClipper.GroupIds = self.BranchNumber
	self.BranchClipper.Execute()
	
	#display aneurysm
	self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer
	self.SurfaceViewer.Surface = self.BranchClipper.Surface
	self.SurfaceViewer.Execute()
	
	#save aneurysm surface
	self.WriteSurface = vmtkscripts.vmtkSurfaceWriter
	self.WriteSurface.Surface = self.BranchClipper.Surface
	self.WriteSurface.OutputFileName = self.AneurysmSurface
	self.WriteSurface.Execute()
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