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#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtknetworkwriter.py,v $
## Language: Python
## Date: $Date: 2006/07/27 08:27:40 $
## Version: $Revision: 1.13 $
## 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.
## Developed with support from the EC FP7/2007-2013: ARCH, Project n. 224390
import vtk
import sys
import pypes
vmtknetworkwriter = 'vmtkNetworkWriter'
class vmtkNetworkWriter(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Format = ''
self.GuessFormat = 1
self.OutputFileName = ''
self.Network = None
self.Input = None
self.InputUnits = 'mm'
self.RadiusArrayName = 'Radius'
self.LabelsArrayName = 'Labels'
self.SetScriptName('vmtknetworkwriter')
self.SetScriptDoc('write network to disk')
self.SetInputMembers([
['Network','i','vtkPolyData',1,'','the input network','vmtksurfacereader'],
['Format','f','str',1,'["vtkxml","vtk","arch"]','file format'],
['InputUnits','u','str',1,'["mm","cm","m"]','units in which the input network is represented'],
['GuessFormat','guessformat','bool',1,'','guess file format from extension'],
['RadiusArrayName','radiusarray','str',1,'','name of the point data array where radius is stored (arch format)'],
['LabelsArrayName','labelsarray','str',1,'','name of the cell data array where labels are stored (arch format)'],
['OutputFileName','ofile','str',1,'','output file name'],
['OutputFileName','o','str',1,'','output file name (deprecated: use -ofile)']
])
self.SetOutputMembers([])
def WriteVTKNetworkFile(self):
if self.OutputFileName == '':
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing VTK network file.')
writer = vtk.vtkPolyDataWriter()
writer.SetInput(self.Network)
writer.SetFileName(self.OutputFileName)
writer.Write()
def WriteVTKXMLNetworkFile(self):
if self.OutputFileName == '':
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing VTK XML network file.')
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInput(self.Network)
writer.SetFileName(self.OutputFileName)
#writer.SetDataModeToAscii()
writer.Write()
def WriteARCHNetworkFile(self):
if self.OutputFileName == '':
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing ARCH network file.')
factor = 1.0
if self.InputUnits == 'cm':
factor = 0.01
elif self.InputUnits == 'mm':
factor = 0.001
radiusArray = None
if self.RadiusArrayName:
radiusArray = self.Network.GetPointData().GetArray(self.RadiusArrayName)
labelsArray = None
if self.LabelsArrayName != '':
labelsArray = vtk.vtkStringArray.SafeDownCast(self.Network.GetCellData().GetAbstractArray(self.LabelsArrayName))
from xml.dom import minidom
xmlDocument = minidom.Document()
xmlNetworkGraph = xmlDocument.appendChild(xmlDocument.createElement('NetworkGraph'))
xmlNetworkGraph.setAttribute('id','1')
xmlNetworkGraph.setAttribute('version','3.0')
xmlNetworkGraph.setAttribute('xmlns:xsi','http://www.w3.org/2001/XMLSchema-instance')
xmlNetworkGraph.setAttribute('xsi:noNamespaceSchemaLocation','vascular_network_v2.3.xsd')
xmlCase = xmlNetworkGraph.appendChild(xmlDocument.createElement('case'))
xmlPatientId = xmlCase.appendChild(xmlDocument.createElement('patient_id'))
xmlPatientId.appendChild(xmlDocument.createTextNode('00000'))
xmlVisit = xmlCase.appendChild(xmlDocument.createElement('visit'))
xmlVisit.appendChild(xmlDocument.createTextNode('other'))
nodeMap = {}
edgeCellIds = []
edges = []
for i in range(self.Network.GetNumberOfCells()):
cell = self.Network.GetCell(i)
if not (cell.GetCellType() in (3,4)):
continue
pointId0 = cell.GetPointId(0)
pointId1 = cell.GetPointId(cell.GetNumberOfPoints()-1)
if not nodeMap.has_key(pointId0):
nodeId = len(nodeMap)
nodeMap[pointId0] = nodeId
if not nodeMap.has_key(pointId1):
nodeId = len(nodeMap)
nodeMap[pointId1] = nodeId
edgeId = len(edges)
edgeCellIds.append(edgeId)
edges.append((nodeMap[pointId0],nodeMap[pointId1]))
nodes = nodeMap.values()[:]
nodes.sort()
xmlNodes = xmlNetworkGraph.appendChild(xmlDocument.createElement('nodes'))
for node in nodes:
xmlNode = xmlNodes.appendChild(xmlDocument.createElement('node'))
xmlNode.setAttribute('id','%d' % node)
#xmlNodeClassification = xmlNode.appendChild(xmlDocument.createElement('node_classification'))
xmlEdges = xmlNetworkGraph.appendChild(xmlDocument.createElement('edges'))
for i in range(len(edges)):
edge = edges[i]
xmlEdge = xmlEdges.appendChild(xmlDocument.createElement('edge'))
xmlEdge.setAttribute('id','%d' % i)
xmlEdge.setAttribute('node1_id','%d' % edge[0])
xmlEdge.setAttribute('node2_id','%d' % edge[1])
if labelsArray:
label = labelsArray.GetValue(edgeCellIds[i])
if 'aorta' in label or 'artery' in label or 'art' in label or 'a.' in label:
xmlEdge.setAttribute('side','arterial')
if 'vena' in label or 'vein' in label or 'v.' in label:
xmlEdge.setAttribute('side','venous')
xmlEdge.setAttribute('name',label)
else:
xmlEdge.setAttribute('side','arterial')
xmlEdge.setAttribute('name','edge%d' % i)
#xmlEdgeClassification = xmlEdge.appendChild(xmlDocument.createElement('edge_classification'))
#if labelsArray:
# label = labelsArray.GetValue(edgeCellIds[i])
# if 'aorta' in label or 'artery' in label or 'art' in label or 'a.' in label:
# xmlEdgeClassification.setAttribute('side','arterial')
# if 'vena' in label or 'vein' in label or 'v.' in label:
# xmlEdgeClassification.setAttribute('side','venous')
# xmlEdgeClassification.appendChild(xmlDocument.createTextNode(label))
xmlGeometry = xmlEdge.appendChild(xmlDocument.createElement('geometry'))
length = 0.0
cell = self.Network.GetCell(edgeCellIds[i])
cellPoints = cell.GetPoints()
prevPoint = cellPoints.GetPoint(0)
abscissas = [0.0]
coordinates = [[factor*el for el in prevPoint]]
for j in range(1,cell.GetNumberOfPoints()):
point = cellPoints.GetPoint(j)
length += factor * vtk.vtkMath.Distance2BetweenPoints(prevPoint,point)**0.5
abscissas.append(length)
coordinates.append([factor*el for el in point])
prevPoint = point
xmlLength = xmlGeometry.appendChild(xmlDocument.createElement('length'))
xmlLength.setAttribute('unit','m')
xmlScalar = xmlLength.appendChild(xmlDocument.createElement('scalar'))
xmlScalar.appendChild(xmlDocument.createTextNode('%f' % length))
xmlCoordinatesArray = xmlGeometry.appendChild(xmlDocument.createElement('coordinates_array'))
for j in range(len(abscissas)):
xmlCoordinates = xmlCoordinatesArray.appendChild(xmlDocument.createElement('coordinates'))
#TODO: check for length == 0
xmlCoordinates.setAttribute('s','%f' % (abscissas[j]/length))
xmlCoordinates.setAttribute('x','%f' % coordinates[j][0])
xmlCoordinates.setAttribute('y','%f' % coordinates[j][1])
xmlCoordinates.setAttribute('z','%f' % coordinates[j][2])
xmlProperties = xmlEdge.appendChild(xmlDocument.createElement('properties'))
if radiusArray:
xmlRadiusArray = xmlProperties.appendChild(xmlDocument.createElement('radius_array'))
xmlRadiusArray.setAttribute('unit','m')
for j in range(cell.GetNumberOfPoints()):
pointId = cell.GetPointId(j)
radius = factor * radiusArray.GetTuple1(pointId)
xmlValue = xmlRadiusArray.appendChild(xmlDocument.createElement('value'))
xmlValue.setAttribute('s','%f' % (abscissas[j]/length))
xmlScalar = xmlValue.appendChild(xmlDocument.createElement('scalar'))
xmlScalar.appendChild(xmlDocument.createTextNode('%f' % radius))
#xmlTransformations = xmlNetworkGraph.appendChild(xmlDocument.createElement('transformations'))
xmlFile = open(self.OutputFileName,'w')
xmlFile.write(xmlDocument.toprettyxml())
xmlFile.close()
def Execute(self):
if self.Network == None:
if self.Input == None:
self.PrintError('Error: no Network.')
self.Network = self.Input
extensionFormats = {'vtp':'vtkxml',
'vtkxml':'vtkxml',
'xml':'arch'}
if self.OutputFileName == 'BROWSER':
import tkFileDialog
import os.path
initialDir = pypes.pypeScript.lastVisitedPath
self.OutputFileName = tkFileDialog.asksaveasfilename(title="Output network",initialdir=initialDir)
pypes.pypeScript.lastVisitedPath = os.path.dirname(self.OutputFileName)
if not self.OutputFileName:
self.PrintError('Error: no OutputFileName.')
if self.GuessFormat and self.OutputFileName and not self.Format:
import os.path
extension = os.path.splitext(self.OutputFileName)[1]
if extension:
extension = extension[1:]
if extension in extensionFormats.keys():
self.Format = extensionFormats[extension]
if (self.Format == 'vtk'):
self.WriteVTKNetworkFile()
elif (self.Format == 'vtkxml'):
self.WriteVTKXMLNetworkFile()
elif (self.Format == 'arch'):
self.WriteARCHNetworkFile()
else:
self.PrintError('Error: unsupported format '+ self.Format + '.')
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()
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