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

[Michka Popoff]

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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