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

[Michka Popoff]

To get the label, I suppose you may want to use the GetLabelFromTag method. (I never used Dicom before, so I suppose it's what you want).

GetLabelFromTag and GetValueFromTag have the same problem ... they fail with the same error message.
It's because in C++ you pass the argument as a string by reference, which you can't in Python.
I don't know how Swig is wrapping this, so I'll have to investigate a little bit.

I'll look at this soon and I'll keep you updated.


Le 25 juin 2014 à 14:22, Mathew Guilfoyle a écrit :

> Fantastic!  
> 
> Is there a way of getting the label as well as the value of the entry? It would be useful for checking that the dictionary entry is the one expected from the tag.
> 
> Out of interest, do you know the correct way of using the dicomIO.GetValueFromTag() method?
> 
> Thanks again
> Mat
> 
> 
> On 25 June 2014 13:12, Michka Popoff <michkapopoff at gmail.com> wrote:
> Hi
> 
> I think you can directly access it "python style":
> 
> tilt = metad['0018|1120']
> 
> In fact, the itlMetaDataDictionnary class has a __getitem__ method, which downcasts directly the value [1].
> 
> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/Python/PyBase/pyBase.i#L173
> 
> Le 25 juin 2014 à 13:35, Mathew Guilfoyle a écrit :
> 
> > 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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