CastConvertPhilips.py

 
 
"""
Usage:
 
 python --public /path/to/directory/
or
 python --private /path/to/directory/
 
 python --public --extension bak /path/to/directory/
 
rename -f 's/\.bak$//' *.bak
 
TODO:
http://docs.python.org/library/optparse.html#module-optparse
"""
 
import vtkgdcm
import vtk
import sys
import gdcm
 
def ProcessOneFilePublic(filename, outfilename, tmpfile):
  gdcm.ImageHelper.SetForceRescaleInterceptSlope(True)
  vtkreader = vtkgdcm.vtkGDCMImageReader()
  vtkreader.SetFileName( filename )
  vtkreader.Update()
 
  cast = vtk.vtkImageCast()
  cast.SetInput( vtkreader.GetOutput() )
  cast.SetOutputScalarTypeToUnsignedShort()
 
  # vtkGDCMImageWriter does not support Sequence, so let's write a tmp file first:
  # Some operation will actually be discarded (we simply need a temp storage)
  vtkwriter = vtkgdcm.vtkGDCMImageWriter()
  vtkwriter.SetFileName( tmpfile )
  vtkwriter.SetMedicalImageProperties( vtkreader.GetMedicalImageProperties() )
  vtkwriter.SetDirectionCosines( vtkreader.GetDirectionCosines() )
  print "Format:",vtkreader.GetImageFormat()
  vtkwriter.SetImageFormat( vtkreader.GetImageFormat() )
  vtkwriter.SetInput( cast.GetOutput() )
  #vtkwriter.Update()
  vtkwriter.Write()
 
  # ok now rewrite the exact same file as the original (keep all info)
  # but use the Pixel Data Element from the written file
  tmpreader = gdcm.ImageReader()
  tmpreader.SetFileName( tmpfile )
  if not tmpreader.Read():
    sys.exit(1)
 
  reader = gdcm.Reader()
  reader.SetFileName( filename )
  if not reader.Read():
    sys.exit(1)
 
  # Make sure to remove Slope/Rescale to avoid re-execution
  ds = reader.GetFile().GetDataSet()
  tags = [
    gdcm.Tag(0x0028,0x1052),
    gdcm.Tag(0x0028,0x1053),
    gdcm.Tag(0x0028,0x1053),
  ]
  for tag in tags:
    ds.Remove( tag )
 
  writer = gdcm.ImageWriter()
  writer.SetFileName( outfilename )
  # Pass image from vtk written file
  writer.SetImage( tmpreader.GetImage() )
  # pass dataset from initial 'reader'
  writer.SetFile( reader.GetFile() )
  if not writer.Write():
    sys.exit(1)
 
def ProcessOneFilePrivate(filename, outfilename, tmpfile):
  vtkreader = vtkgdcm.vtkGDCMImageReader()
  vtkreader.SetFileName( filename )
  vtkreader.Update()
 
 
  # (2005,1409)     DS      4       0.0
  # (2005,140a)     DS      16      1.52283272283272
 
  # (2005,0014)     LO      26      Philips MR Imaging DD 005
  tag1 = gdcm.PrivateTag(0x2005,0x09,"Philips MR Imaging DD 005")
  tag2 = gdcm.PrivateTag(0x2005,0x0a,"Philips MR Imaging DD 005")
 
 
 
  # Need to access some private tags, reread the file (for now):
  reader = gdcm.Reader()
  reader.SetFileName( filename )
  if not reader.Read():
    sys.exit(1)
 
  ds = reader.GetFile().GetDataSet()
 
  el1 = ds.GetDataElement( tag1 )
  el2 = ds.GetDataElement( tag2 )
 
 
  #pf = gdcm.PythonFilter()
  #pf.SetFile( reader.GetFile() )
  #print el1.GetTag()
 
  print el1.GetByteValue()
  v1 = eval(el1.GetByteValue().GetBuffer())
  print el2.GetByteValue()
  v2 = eval(el2.GetByteValue().GetBuffer())
 
  print v1
  shift = v1
  print v2
  scale = v2
 
  ss = vtk.vtkImageShiftScale()
  ss.SetInput( vtkreader.GetOutput() )
  # because VTK image shift / scale convention is inverted from DICOM make sure shift is 0
  assert shift == 0
  ss.SetShift( shift )
  ss.SetScale( scale )
  ss.SetOutputScalarTypeToUnsignedShort ()
  ss.Update()
 
  # vtkGDCMImageWriter does not support Sequence, so let's write a tmp file first:
  # Some operation will actually be discarded (we simply need a temp storage)
  vtkwriter = vtkgdcm.vtkGDCMImageWriter()
  vtkwriter.SetFileName( tmpfile )
  vtkwriter.SetMedicalImageProperties( vtkreader.GetMedicalImageProperties() )
  vtkwriter.SetDirectionCosines( vtkreader.GetDirectionCosines() )
  vtkwriter.SetImageFormat( reader.GetImageFormat() )
  # do not pass shift/scale again
  vtkwriter.SetInput( ss.GetOutput() )
  #vtkwriter.Update()
  vtkwriter.Write()
 
  # ok now rewrite the exact same file as the original (keep all info)
  # but use the Pixel Data Element from the written file
  tmpreader = gdcm.ImageReader()
  tmpreader.SetFileName( tmpfile )
  if not tmpreader.Read():
    sys.exit(1)
 
  writer = gdcm.ImageWriter()
  writer.SetFileName( outfilename )
  # Pass image from vtk written file
  writer.SetImage( tmpreader.GetImage() )
  # pass dataset from initial 'reader'
  writer.SetFile( reader.GetFile() )
  if not writer.Write():
    sys.exit(1)
 
if __name__ == "__main__":
 
  gdcm.Trace.DebugOff()
  gdcm.Trace.WarningOff()
  #filename = sys.argv[1]
  #outfilename = sys.argv[2]
  tmpfile = "/tmp/philips_rescaled.dcm"
  #ProcessOneFile( filename, outfilename, tmpfile )
  rescaletype = sys.argv[1]
  assert rescaletype == "--public" or rescaletype == "--private"
  dirname = sys.argv[2]
  d = gdcm.Directory()
  d.Load( dirname )
 
  for f in d.GetFilenames():
    #print f
    ProcessOneFilePublic( f, f + ".bak", tmpfile )
 
 
print "success"