Keep all tags

[ryder-cobean-nih]

#49

This pull request should cover a small change to rap_sitkCore that enables the user to retain tag values and tags themselves as seen when the file is loaded. rap_sitkCore's functions for converting color spaces and safely opening a file for use in processing pipelines are vital, but other tools perform the necessary anonymization. This enables the image to be opened with less tampering by the observer, if desired.

keep_all_tags defaults to FALSE so if omitted (as it would be in existing uses in other scripts), existing behavior remains the same.

usage:

from pathlib import Path
from rap_sitkCore import read_dcm

img = read_dcm(Path(path_to_dicom), keep_all_tags=TRUE)

[blowekamp]

The lower level _read_dcm_pydicom function also only copies the white list tags, partly because support for converting all value representations (CR) to the SITK string representation was not implemented.

Please let me know if you would like to continue to work on the PR, or if I should address it.

[blowekamp]

After srgb2gray is run the output image img contains none of the original DICOM tags.

When `keep_all_tags' is true, all the tags need to be copies.

[ryder-cobean-nih]

@blowekamp made the requested changes - please review? I think this should cover it in the lower level function.

[blowekamp]

When keep_all_tags is true, the tags still need to be copied from img to out.

[blowekamp]

These two blocks are very similar but have different behavior. Is this intentional? Were there files that has issues that needed to be addressed?

[ryder-cobean-nih]

Check out these changes, in latest commit:

def _get_string_representation(de: pydicom.dataelem.DataElement) -> str:
        """
        Get the string representation of the DICOM tag.
        
        Parameters:
        de (pydicom.dataelem.DataElement): The DICOM date element (a particular tag and its metadata).

        Returns:
        str: The string representation of the DICOM tag.
        """
        try:
            if de.value in [None, ""]:
                return ""
            elif de.VR == "DS":
                if de.VM > 1:
                    return convert_float_list_to_mv_ds(de.value)
                else:
                    return str(float(de.value))
            elif de.VR == "US":
                return str(int(de.value))
            else:
                return de.value
        except (TypeError, ValueError) as e:
            raise RuntimeError(
                f'"Error parsing data element "{de.name}" with value "{de.value}" '
                f'and value representation "{de.VR}". Error: {e}'
            )


def _read_dcm_pydicom(filename: Path, keep_all_tags: bool = False) -> sitk.Image:
    """
    Reading implementation with pydicom for DICOM
    """
    ds = pydicom.dcmread(filename)

    arr = ds.pixel_array

    if ds.PhotometricInterpretation == "MONOCHROME2":
        img = sitk.GetImageFromArray(arr, isVector=False)
    elif ds.PhotometricInterpretation == "MONOCHROME1":
        # only works with unsigned
        assert ds.PixelRepresentation == 0
        # use complement to invert the pixel intensity.
        img = sitk.GetImageFromArray(~arr, isVector=False)
    elif ds.PhotometricInterpretation in ["YBR_FULL_422", "YBR_FULL", "RGB"]:
        if ds.PhotometricInterpretation != "RGB":
            from pydicom.pixel_data_handlers.util import convert_color_space
            arr = convert_color_space(ds.pixel_array, ds.PhotometricInterpretation, "RGB")

        img = sitk.GetImageFromArray(arr, isVector=True)
    else:
        raise RuntimeError(f'Unsupported PhotometricInterpretation: "{ds.PhotometricInterpretation}"')

    # keep_all_tags is either all tags other than PixelData or the tags specified in 
    # _keyword_to_copy, provided they are present in the dataset
    if keep_all_tags:
        _keyword_to_copy = [elem.keyword for elem in ds if elem.keyword != "PixelData"]
    else:
        _keyword_to_copy = [keyword for keyword in _keyword_to_copy if keyword in ds]
    

    # iterate through all tags and copy the ones specified in _keyword_to_copy
    # to the SimpleITK image
    for tag in _keyword_to_copy:
        de = ds.data_element(tag)
        key = f"{de.tag.group:04x}|{de.tag.elem:04x}"
        img[key] = _get_string_representation(de)

    return img

[blowekamp]

There is also a need for testing. The cases when I have seen the tags not being copied should be triggering some test failures.

[blowekamp]

Isn't this going to overwrite the file local _keyword_to_copy? Please use a different variable name.

[blowekamp]

When keep_all_tags is true, the tags still need to be copied from img to out.

[blowekamp]

Updated work here: #53