[UNKNOWN_PRINT_CHARACTERISTICS] when reading MINC headers

Confused · August 16, 2024, 1:49pm

Hello,

I am a beginner in using simpleitk. I have came across an issue with when reading specific header informatic from my MINC file resulting in [UNKNOWN_PRINT_CHARACTERISTICS]. However, when I view these information using external programs like ITKsnap, these information are present. Any suggestions on how I can fix this? See example below:

reader = sitk.ImageFileReader()
reader.SetImageIO("MINCImageIO")
reader.SetFileName(inputImageFileName)
image = reader.Execute()

metadata = {key: reader.GetMetaData(key) for key in reader.GetMetaDataKeys()}

age = metadata.get("patient:age", "")

This would then output:

[UNKNOWN_PRINT_CHARACTERISTICS]

As compared to when viewing this specific header information in ITKsnap

This specific information is viewable. Any suggestions on how this can be fixed?

dzenanz · August 16, 2024, 2:03pm

This is a general problem with printing entries of MetaDataDictionary values from Python. @blowekamp I guess we should fix this?

Confused · August 16, 2024, 2:12pm

Amazing! Please let me know when there is a fix or an alternative. This would definitely help stream line some of my work.

blowekamp · August 16, 2024, 2:30pm

What version of SimpleITK are you using? What binaries were installed etc.?

Also do you have a sample MINC file with this field that could be shared?

@gdevenyi Do you know where this field is added into the metadata dictionary in MINICIO?

Confused · August 16, 2024, 2:52pm

I am using 2.3.1, I can definitely share the environment I am using.

Unfortunately I can’t share the MINC file as it’s confidential. Thanks

gdevenyi · August 20, 2024, 3:53pm

The relevant lines which iterate over all of the header objects in the MINC file are here:

github.com

InsightSoftwareConsortium/ITK/blob/master/Modules/IO/MINC/src/itkMINCImageIO.cxx#L742-L858


      
          // iterate over all root level groups , and extract all underlying attributes
          // unfortunately more complicated attribute structure of MINC2 is not supported
          // at least it is not used anywhere
          milisthandle_t grplist;
          
          if ((milist_start(m_MINCPImpl->m_Volume, "", 0, &grplist)) == MI_NOERROR)
          {
            char           group_name[256];
            milisthandle_t attlist;
          
            while (milist_grp_next(grplist, group_name, sizeof(group_name)) == MI_NOERROR)
            {
              if ((milist_start(m_MINCPImpl->m_Volume, group_name, 1, &attlist)) == MI_NOERROR)
              {
                char attribute[256];
          
                while (milist_attr_next(
                         m_MINCPImpl->m_Volume, attlist, group_name, sizeof(group_name), attribute, sizeof(attribute)) ==
                       MI_NOERROR)
                {

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blowekamp · August 20, 2024, 5:08pm

@gdevenyi Thank you. Do you have a sample MINC files with one of these array fields that I could use to further investigate?

blowekamp · August 20, 2024, 5:46pm

After writing a quick implementation to call the value object’s Print method or operator<< if implemented I read the documentation for the MetaDataObject class:

github.com

InsightSoftwareConsortium/ITK/blob/52cfd0b6f7228e72837644d41efb3b20e829447a/Modules/Core/Common/include/itkMetaDataObject.h#L61-L69


      
          * The behavior of the MetaDataObject<Type>::Print() function has many plausible
          * application dependent implementations.  The default implementation prints the
          * string "[UNKNOWN PRINT CHARACTERISTICS]" that works for all possible
          * MetaDataObject types.
          *
          * The application developer may overload the default implementation to provide
          * a specialized Print() characteristics to produce results desirable for their application.
          * A set of very crude Macros {NATIVE_TYPE_METADATAPRINT, ITK_OBJECT_TYPE_METADATAPRINT_1COMMA,
          * ITK_IMAGE_TYPE_METADATAPRINT  } are provided to facilitate a very simple implementation, and as an example.

So it appear that this is a feature and not a bug? @hjmjohnson

It would appear that it is simpleITK’s responsibility to explicitly implement the Print method for these types, and avoid conflict of other libraries using ITK.

phcerdan · August 20, 2024, 11:15pm

I hit this some time ago, and had a stab on it.

github.com/InsightSoftwareConsortium/ITK

BUG: Fix printing of values in MetaDataObject

InsightSoftwareConsortium:master ← phcerdan:fix_metadataobject_print

opened 12:37AM - 14 Dec 23 UTC

phcerdan

+102 -72

Also removes dead code related to METADATAPRINT Fix #1454 ## PR Checklist … - [x] No [API changes](https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md#breaking-changes) were made (or the changes have been approved) - [x] No [major design changes](https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md#design-changes) were made (or the changes have been approved) - [x] Added test (or behavior not changed) - [x] Updated API documentation (or API not changed) - [NA] Added Python wrapping to new files (if any) as described in [ITK Software Guide](https://itk.org/ItkSoftwareGuide.pdf) Section 9.5

However, I didn’t have time to fight compilers to address reviewers comments to get to the finish line.
In case somebody wants to follow on.

gdevenyi · August 21, 2024, 7:36pm

Here’s a rich MINC2 file generated by dcm2mnc,

blowekamp · August 21, 2024, 8:41pm

@gdevenyi Thank you for the image

@phcerdan Thanks for the reference to the PR, and the open issue. Which includes @hjmjohnson comment that he is in favor of removing the old macros, and including support for printing for the MetaDataObjects directly in ITK.

I made a PR with the implementation I did before I saw yours.

github.com/InsightSoftwareConsortium/ITK

BUG: Fix printing of values in MetaDataObject

InsightSoftwareConsortium:master ← blowekamp:print_metadata_object

opened 03:12PM - 21 Aug 24 UTC

blowekamp

+43 -57

Also removes dead code related to METADATAPRINT Does not currently add printi…ng for std::vector. Fix #1454 Near duplicate of: #4368 Co-Author: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com>   ## PR Checklist - [ ] No [API changes](https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md#breaking-changes) were made (or the changes have been approved) - [ ] No [major design changes](https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md#design-changes) were made (or the changes have been approved) - [ ] Added test (or behavior not changed) - [ ] Updated API documentation (or API not changed) - [ ] Added [license](https://github.com/InsightSoftwareConsortium/ITK/blob/master/Utilities/KWStyle/ITKHeader.h) to new files (if any) - [ ] Added Python wrapping to new files (if any) as described in [ITK Software Guide](https://itk.org/ItkSoftwareGuide.pdf) Section 9.5 - [ ] Added [ITK examples](https://github.com/InsightSoftwareConsortium/ITKSphinxExamples) for all new major features (if any) Refer to the [ITK Software Guide](https://itk.org/ItkSoftwareGuide.pdf) for further development details if necessary.

It appears to work with the current infrastructure.