Downsample DICOM images and write out as DICOM or fall back to NIfTI

dicom_downsampling.py

import os, time, traceback, pathlib
import SimpleITK as sitk


def downsample_dicom(
    dicom_path: str, output_path: str, downsample_factor: int = 0.5
) -> None:
    """
    Downsample DICOM images and save them to the output path.

    Args:
        dicom_path (str): The path to the DICOM images.
        output_path (str): The path to save the downsampled DICOM images.
        downsample_factor (int, optional): The downsample factor. Defaults to 0.5.
    """
    if not output_path.endswith(".nii.gz"):
        pathlib.Path(output_path).mkdir(parents=True, exist_ok=True)

    dicom_detected = False
    if os.path.isdir(dicom_path):
        # Read DICOM images
        reader = sitk.ImageSeriesReader()
        dicom_names = reader.GetGDCMSeriesFileNames(dicom_path)
        reader.SetFileNames(dicom_names)
        reader.MetaDataDictionaryArrayUpdateOn()
        image = reader.Execute()
        dicom_detected = True
    else:
        # Read image using generic SimpleITK reader
        image = sitk.ReadImage(dicom_path)

    # Downsample DICOM images
    downsampled_image = sitk.Resample(
        image,
        [
            int(image.GetWidth() * downsample_factor),
            int(image.GetHeight() * downsample_factor),
            int(image.GetDepth() * downsample_factor),
        ],
        sitk.Transform(),
        sitk.sitkLinear,
        image.GetOrigin(),
        image.GetSpacing(),
        image.GetDirection(),
        0,
        image.GetPixelID(),
    )

    if dicom_detected:
        # Save downsampled DICOM images
        writer = sitk.ImageFileWriter()

        tags_to_copy = [
            # "0010|0010",  # Patient Name
            "0010|0020",  # Patient ID
            "0010|0030",  # Patient Birth Date
            "0020|000D",  # Study Instance UID, for machine consumption
            "0020|0010",  # Study ID, for human consumption
            "0008|0020",  # Study Date
            "0008|0030",  # Study Time
            "0008|0050",  # Accession Number
            "0008|0060",  # Modality
        ]

        # Use the study/series/frame of reference information given in the meta-data
        # dictionary and not the automatically generated information from the file IO
        writer.KeepOriginalImageUIDOn()
        modification_time = time.strftime("%H%M%S")
        modification_date = time.strftime("%Y%m%d")

        direction = downsampled_image.GetDirection()
        series_tag_values = [
            (k, reader.GetMetaData(0, k.lower()))
            for k in tags_to_copy
            if reader.HasMetaDataKey(0, k.lower())
        ] + [
            ("0008|0031", modification_time),  # Series Time
            ("0008|0021", modification_date),  # Series Date
            ("0008|0008", "DERIVED\\SECONDARY"),  # Image Type
            (
                "0020|000e",
                "1.2.826.0.1.3680043.2.1125."
                + modification_date
                + ".1"
                + modification_time,
            ),
            # Series Instance UID
            (
                "0020|0037",
                "\\".join(
                    map(
                        str,
                        (
                            direction[0],
                            direction[3],
                            direction[6],
                            direction[1],
                            direction[4],
                            direction[7],
                        ),  # Image Orientation (Patient)
                    )
                ),
            ),
            (
                "0008|103e",
                reader.GetMetaData(0, "0008|103e")
                if reader.HasMetaDataKey(0, "0008|103e")
                else "" + " Processed-SimpleITK",
            ),  # Series Description is an optional tag, so may not exist
        ]

        try:
            for i in range(downsampled_image.GetDepth()):
                image_slice = downsampled_image[:, :, i]
                # Tags shared by the series.
                for tag, value in series_tag_values:
                    image_slice.SetMetaData(tag, value)
                # Slice specific tags.
                #   Instance Creation Date
                image_slice.SetMetaData("0008|0012", time.strftime("%Y%m%d"))
                #   Instance Creation Time
                image_slice.SetMetaData("0008|0013", time.strftime("%H%M%S"))
                #   Image Position (Patient)
                image_slice.SetMetaData(
                    "0020|0032",
                    "\\".join(
                        map(str, downsampled_image.TransformIndexToPhysicalPoint((0, 0, i)))
                    ),
                )
                #   Instance Number
                image_slice.SetMetaData("0020|0013", str(i))

                # Write to the output directory and add the extension dcm, to force writing
                # in DICOM format.
                writer.SetFileName(os.path.join(output_path, str(i) + ".dcm"))
                writer.Execute(image_slice)
        except Exception:
            print("ERROR: Could not write DICOM image, falling back to NIfTI")
            print("Traceback:", traceback.format_exc())

            sitk.WriteImage(
                downsampled_image,
                os.path.join(output_path, f"downsampled_{downsample_factor}.nii.gz"),
            )
    else:
        # Save downsampled image
        if not output_path.endswith(".nii.gz"):
            output_path = os.path.join(output_path, f"downsampled_{downsample_factor}.nii.gz")
        sitk.WriteImage(
            downsampled_image,
            os.path.join(output_path),
        )