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############################################################################
#
# Program: GDCM (Grassroots DICOM). A DICOM library
#
# Copyright (c) 2006-2011 Mathieu Malaterre
# All rights reserved.
# See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html 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 notice for more information.
#
############################################################################
"""
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"
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