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#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkimagewriter.py,v $
## Language: Python
## Date: $Date: 2006/07/27 08:27:40 $
## Version: $Revision: 1.18 $
## 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
vmtkimagewriter = 'vmtkImageWriter'
class vmtkImageWriter(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Format = ''
self.GuessFormat = 1
self.UseITKIO = 1
self.ApplyTransform = 0
self.OutputFileName = ''
self.OutputRawFileName = ''
self.OutputDirectoryName = ''
self.PixelRepresentation = ''
self.Image = None
self.Input = None
self.WindowLevel = [1.0, 0.0]
self.RasToIjkMatrixCoefficients = [1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1]
self.SetScriptName('vmtkimagewriter')
self.SetScriptDoc('write an image to disk')
self.SetInputMembers([
['Image','i','vtkImageData',1,'','the input image','vmtkimagereader'],
['Format','f','str',1,'["vtkxml","vtk","meta","tiff","png","pointdata"]','file format'],
['GuessFormat','guessformat','bool',1,'','guess file format from extension'],
['UseITKIO','useitk','bool',1,'','use ITKIO mechanism'],
['ApplyTransform','transform','bool',1,'','apply transform on writing - ITKIO only'],
['OutputFileName','ofile','str',1,'','output file name'],
['OutputFileName','o','str',1,'','output file name (deprecated: use -ofile)'],
['OutputRawFileName','rawfile','str',1,'','name of the output raw file - meta image only'],
['OutputDirectoryName','d','str',1,'','output directory name - png, tiff'],
['PixelRepresentation','r','str',1,'["double","float","short"]','output scalar type'],
['WindowLevel','windowlevel','float',2,'','window and level for mapping graylevels to 0-255 before writing - png, tiff'],
['RasToIjkMatrixCoefficients','matrix','float',16]
])
self.SetOutputMembers([])
def WriteVTKImageFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing VTK image file.')
writer = vtk.vtkStructuredPointsWriter()
writer.SetInput(self.Image)
writer.SetFileName(self.OutputFileName)
writer.Write()
def WriteVTKXMLImageFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing VTK XML image file.')
writer = vtk.vtkXMLImageDataWriter()
writer.SetInput(self.Image)
writer.SetFileName(self.OutputFileName)
writer.Write()
def WriteMetaImageFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing meta image file.')
writer = vtk.vtkMetaImageWriter()
writer.SetInput(self.Image)
writer.SetFileName(self.OutputFileName)
if (self.OutputRawFileName != ''):
writer.SetRAWFileName(self.OutputRawFileName)
writer.Write()
def WritePNGImageFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing PNG image file.')
outputImage = self.Image
if self.Image.GetScalarTypeAsString() != 'unsigned char':
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInput(self.Image)
if self.WindowLevel[0] == 0.0:
scalarRange = self.Image.GetScalarRange()
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(255.0/(scalarRange[1]-scalarRange[0]))
else:
shiftScale.SetShift(-(self.WindowLevel[1]-self.WindowLevel[0]/2.0))
shiftScale.SetScale(255.0/self.WindowLevel[0])
shiftScale.SetOutputScalarTypeToUnsignedChar()
shiftScale.ClampOverflowOn()
shiftScale.Update()
outputImage = shiftScale.GetOutput()
writer = vtk.vtkPNGWriter()
writer.SetInput(outputImage)
if self.Image.GetDimensions()[2] == 1:
writer.SetFileName(self.OutputFileName)
else:
writer.SetFilePrefix(self.OutputFileName)
writer.SetFilePattern("%s%04d.png")
writer.Write()
def WriteTIFFImageFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing TIFF image file.')
outputImage = self.Image
if self.Image.GetScalarTypeAsString() != 'unsigned char':
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInput(self.Image)
if self.WindowLevel[0] == 0.0:
scalarRange = self.Image.GetScalarRange()
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(255.0/(scalarRange[1]-scalarRange[0]))
else:
shiftScale.SetShift(-(self.WindowLevel[1]-self.WindowLevel[0]/2.0))
shiftScale.SetScale(255.0/self.WindowLevel[0])
shiftScale.SetOutputScalarTypeToUnsignedChar()
shiftScale.ClampOverflowOn()
shiftScale.Update()
outputImage = shiftScale.GetOutput()
writer = vtk.vtkTIFFWriter()
writer.SetInput(outputImage)
if self.Image.GetDimensions()[2] == 1:
writer.SetFileName(self.OutputFileName)
else:
writer.SetFilePrefix(self.OutputFileName)
writer.SetFilePattern("%s%04d.tif")
writer.Write()
def WritePointDataImageFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing PointData file.')
f=open(self.OutputFileName, 'w')
line = "X Y Z"
arrayNames = []
if self.Image.GetPointData().GetScalars().GetName() == None:
self.Image.GetPointData().GetScalars().SetName('__Scalars')
for i in range(self.Image.GetPointData().GetNumberOfArrays()):
array = self.Image.GetPointData().GetArray(i)
arrayName = array.GetName()
if arrayName == None:
continue
if arrayName[-1]=='_':
continue
arrayNames.append(arrayName)
if array.GetNumberOfComponents() == 1:
line = line + ' ' + arrayName
else:
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + arrayName + str(j)
line = line + '\n'
f.write(line)
for i in range(self.Image.GetNumberOfPoints()):
point = self.Image.GetPoint(i)
line = str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2])
for arrayName in arrayNames:
array = self.Image.GetPointData().GetArray(arrayName)
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + str(array.GetComponent(i,j))
line = line + '\n'
f.write(line)
def WriteITKIO(self):
if self.OutputFileName == '':
self.PrintError('Error: no OutputFileName.')
writer = vtkvmtk.vtkvmtkITKImageWriter()
writer.SetInput(self.Image)
writer.SetFileName(self.OutputFileName)
writer.SetUseCompression(1)
if self.ApplyTransform and self.RasToIjkMatrixCoefficients:
matrix = vtk.vtkMatrix4x4()
matrix.DeepCopy(self.RasToIjkMatrixCoefficients)
writer.SetRasToIJKMatrix(matrix)
writer.Write()
def Execute(self):
if self.Image == None:
if self.Input == None:
self.PrintError('Error: no Image.')
self.Image = self.Input
extensionFormats = {'vti':'vtkxml',
'vtkxml':'vtkxml',
'vtk':'vtk',
'mhd':'meta',
'mha':'meta',
'tif':'tiff',
'png':'png',
'dat':'pointdata'}
if self.OutputFileName == 'BROWSER':
import tkFileDialog
import os.path
initialDir = pypes.pypeScript.lastVisitedPath
self.OutputFileName = tkFileDialog.asksaveasfilename(title="Output image",initialdir=initialDir)
pypes.pypeScript.lastVisitedPath = os.path.dirname(self.OutputFileName)
if not self.OutputFileName:
self.PrintError('Error: no OutputFileName.')
if self.OutputDirectoryName == 'BROWSER':
import tkFileDialog
initialDir = pypes.pypeScript.lastVisitedPath
self.OutputDirectoryName = tkFileDialog.askdirectory(title="Output directory",initialdir=initialDir)
pypes.pypeScript.lastVisitedPath = self.OutputDirectoryName
if not self.OutputDirectoryName:
self.PrintError('Error: no OutputDirectoryName.')
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.PixelRepresentation != '':
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
if self.PixelRepresentation == 'double':
cast.SetOutputScalarTypeToDouble()
elif self.PixelRepresentation == 'float':
cast.SetOutputScalarTypeToFloat()
elif self.PixelRepresentation == 'short':
cast.SetOutputScalarTypeToShort()
else:
self.PrintError('Error: unsupported pixel representation '+ self.PixelRepresentation + '.')
cast.Update()
self.Image = cast.GetOutput()
if self.UseITKIO and self.Format not in ['vtkxml','vtk','tiff','png','dat']:
self.WriteITKIO()
else:
if (self.Format == 'vtkxml'):
self.WriteVTKXMLImageFile()
elif (self.Format == 'vtk'):
self.WriteVTKImageFile()
elif (self.Format == 'meta'):
self.WriteMetaImageFile()
elif (self.Format == 'png'):
self.WritePNGImageFile()
elif (self.Format == 'tiff'):
self.WriteTIFFImageFile()
elif (self.Format == 'pointdata'):
self.WritePointDataImageFile()
else:
self.PrintError('Error: unsupported format '+ self.Format + '.')
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()
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