Method _get_frame_data

monai/data/image_reader.py:773–827

yield frames and description from the segmentation image. This function is adapted from Highdicom: https://github.com/herrmannlab/highdicom/blob/v0.18.2/src/highdicom/seg/utils.py which has the following license... # ========================================

(self, img, filename, array_data)

        return affine

    def _get_frame_data(self, img, filename, array_data) -> Iterator:
        """
        yield frames and description from the segmentation image.
        This function is adapted from Highdicom:
        https://github.com/herrmannlab/highdicom/blob/v0.18.2/src/highdicom/seg/utils.py

        which has the following license...

        # =========================================================================
        # https://github.com/herrmannlab/highdicom/blob/v0.18.2/LICENSE
        #
        # Copyright 2020 MGH Computational Pathology
        # Permission is hereby granted, free of charge, to any person obtaining a
        # copy of this software and associated documentation files (the
        # "Software"), to deal in the Software without restriction, including
        # without limitation the rights to use, copy, modify, merge, publish,
        # distribute, sublicense, and/or sell copies of the Software, and to
        # permit persons to whom the Software is furnished to do so, subject to
        # the following conditions:
        # The above copyright notice and this permission notice shall be included
        # in all copies or substantial portions of the Software.
        # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
        # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
        # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
        # IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
        # CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
        # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
        # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
        # =========================================================================

        (https://github.com/herrmannlab/highdicom/issues/188)

        Args:
            img: a Pydicom dataset object that has attribute "SegmentSequence".

        """

        if not hasattr(img, "PerFrameFunctionalGroupsSequence"):
            raise NotImplementedError(f"To read dicom seg: {filename}, 'PerFrameFunctionalGroupsSequence' is required.")

        frame_seg_nums = []
        for f in img.PerFrameFunctionalGroupsSequence:
            if not hasattr(f, "SegmentIdentificationSequence"):
                raise NotImplementedError(
                    f"To read dicom seg: {filename}, 'SegmentIdentificationSequence' is required for each frame."
                )
            frame_seg_nums.append(int(f.SegmentIdentificationSequence[0].ReferencedSegmentNumber))

        frame_seg_nums_arr = cp.array(frame_seg_nums) if self.to_gpu else np.array(frame_seg_nums)

        seg_descriptions = {int(f.SegmentNumber): f for f in img.SegmentSequence}

        for i in np.unique(frame_seg_nums_arr) if not self.to_gpu else cp.unique(frame_seg_nums_arr):
            indices = np.where(frame_seg_nums_arr == i)[0] if not self.to_gpu else cp.where(frame_seg_nums_arr == i)[0]
            yield (array_data[indices, ...], seg_descriptions[i])

    def _get_seg_data(self, img, filename):
        """