[ITK-users] Accessing DICOM header/meta data with Python ITK

[Mathew Guilfoyle]

Hi,

I need some help with how to correctly access the DICOM meta data
dictionary using Python wrapped ITK (v.4.5).  My CT scans are scanned with
gantry tilt which I need to correct with a shear transform prior to
segmenting.  The gantry tilt angle is stored in the DICOM header under tag
(0018, 1120)

example:

import itk

imdir = '/path/to/images'
image_t = itk.Image[itk.F, 3]

#set up reader
reader = itk.ImageSeriesReader[image_t].New()
dicomIO = itk.GDCMImageIO.New()
dicomFN = itk.GDCMSeriesFileNames.New()
reader.SetImageIO(dicomIO)

#get file names
dicomFN.SetUseSeriesDetails(True)
dicomFN.SetDirectory(imdir)

#get the first image series
uids = dicomFN.GetSeriesUIDs()
fnames = dicomFN.GetFileNames(uids[0])

#read in the files
reader.SetFileNames(fnames)
reader.Update()
image = reader.GetOutput()

#getting the image works fine.  Now to access the meta data dictionary
metad = dicomIO.GetMetaDataDictionary()

#get the entry for gantry tilt using the relevant DICOM tag (0018, 1120)
tilt = metad.Get('0018|1120')

At this point I am stuck.  tilt is of type itkMetaDataObjectBase, rather
than one the derived classes specific to strings, floats etc..
itkMetaDataObjectBase does not contain the GetMetaDataObjectValue() method,
whereas the derived classes do.

In the ITK manual, the C++ example uses a dynamic_cast at the type the tag
is extracted so that 'tilt' would be of one the derived class types.  I
have tried the following:

sst = itk.MetaDataObject.SS
tilt.__class__ = sst
tilt.GetMetaDataObjectValue()

casting tilt does work, and the GetMetaDataObjectValue() method is now
present as one of tilt's attributes, but just returns an error if executed.

The other approach I have tried is to use the dicomIO.GetValueFromTag()
method.  From the source file the method signature is


GetValueFromTag(self, string tag, string value)


'value' is, I presume, meant to be the name of the variable created
containing the tilt angle.  However if I try:

dicomIO.GetValueFromTag('0018|1120', 't_angle')

I get the error
   in method 'itkGDCMImageIO_GetValueFromTag', argument 3 of type
'std::string &

I would be tremendously grateful for any pointers on how to access the tag
data - it must be a routine operation for people using Python/ITK on DICOM
images!

Many thanks
Mat
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