# ReWriteSCAsMR.py

    ############################################################################
    #
    #  Program: GDCM (Grassroots DICOM). A DICOM library
    #  Module:  $URL$
    #
    #  Copyright (c) 2006-2010 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.
    #
    ############################################################################

    """
    GDCM 1.x would write out MR Image Storage as Secondary Capture Object while still setting Rescale Slope/Intercept
    and saving the Pixel Spacing in (0028,0030)
    """

    import gdcm
    import sys,os

    def CheckSecondaryCaptureObjectIsMRImageStorage(r):
      ds = r.GetFile().GetDataSet()
      # Check Source Image Sequence
      if ds.FindDataElement( gdcm.Tag(0x0008,0x2112) ):
        sis = ds.GetDataElement( gdcm.Tag(0x0008,0x2112) )
        sqsis = sis.GetSequenceOfItems()
        if sqsis.GetNumberOfItems():
          item1 = sqsis.GetItem(1)
          nestedds = item1.GetNestedDataSet()
          if nestedds.FindDataElement( gdcm.Tag(0x0008,0x1150) ):
            ReferencedSOPClassUID = nestedds.GetDataElement( gdcm.Tag(0x0008,0x1150) )
            raw = ReferencedSOPClassUID.GetByteValue().GetPointer()
            uids = gdcm.UIDs()
            # what is the actual object we are looking at ?
            ms = gdcm.MediaStorage()
            ms.SetFromDataSet(ds)
            msuid = ms.GetString()
            uids.SetFromUID( msuid )
            msuidname = uids.GetName() # real Media Storage Name
            uids.SetFromUID( raw )
            sqmsuidname = uids.GetName() # Source Image Sequence Media Storage Name
            # If object is SC and Source derivation is MRImageStorage then we can assume 'Pixel Spacing' is correct
            if( sqmsuidname == 'MR Image Storage' and msuidname == 'Secondary Capture Image Storage' ):
              return True
      # in all other case simply return the currentspacing:
      return False

    if __name__ == "__main__":
      r = gdcm.ImageReader()
      filename = sys.argv[1]
      r.SetFileName( filename )
      if not r.Read():
        sys.exit(1)
      f = r.GetFile()

      if( CheckSecondaryCaptureObjectIsMRImageStorage(r) ):
        # Special handling of the spacing:
        # GDCM 1.2.0 would not rewrite correcly DICOM Object and would always set them as 'Secondary Capture Image Storage'
        # while we would rather have 'MR Image Storage'
        gdcm.ImageHelper.SetForcePixelSpacing( True )
        mrspacing = gdcm.ImageHelper.GetSpacingValue( r.GetFile() )
        # TODO: I cannot do simply the following:
        #image.SetSpacing( mrspacing )
        image.SetSpacing(0, mrspacing[0] )
        image.SetSpacing(1, mrspacing[1] )
        image.SetSpacing(2, mrspacing[2] )
        gdcm.ImageHelper.SetForceRescaleInterceptSlope( True )
        ris = gdcm.ImageHelper.GetRescaleInterceptSlopeValue( r.GetFile() )
        image.SetIntercept( ris[0] )
        image.SetSlope( ris[1] )

      outfilename = sys.argv[2]
      w = gdcm.ImageWriter()
      w.SetFileName( outfilename )
      w.SetFile( r.GetFile() )
      w.SetImage( image )
      if not w.Write():
        sys.exit(1)

      sys.exit(0)