Convert DICOM data to GIFs.

make_dicom_gifs.py

# Derived from: https://github.com/pydicom/pydicom/blob/master/examples/input_output/plot_read_dicom_directory.py.

import imageio
import matplotlib.pyplot as plt
import numpy as np
import pydicom

from os import mkdir
from os.path import join
from PIL import Image
from pydicom.filereader import read_dicomdir

dicom_dir = read_dicomdir("DICOMDIR")
out_names = {}
try:
    mkdir("gifs")
except FileExistsError:
    pass

for patient_record in dicom_dir.patient_records:
    if hasattr(patient_record, "PatientID") and hasattr(patient_record, "PatientName"):
        print(f"Patient: {patient_record.PatientID}: {patient_record.PatientName}")

    studies = patient_record.children
    for study in studies:
        indent = 4 * " "
        print(
            f"{indent}Study {study.StudyID}: {study.StudyDate}: {study.StudyDescription}"
        )
        all_series = study.children
        for series in all_series:
            image_count = len(series.children)
            plural = ("", "s")[image_count > 1]

            if "SeriesDescription" not in series:
                series.SeriesDescription = "N/A"

            indent = 8 * " "
            print(
                f"{indent}Series {series.SeriesNumber}: {series.Modality}: {series.SeriesDescription} ({image_count} image{plural})"
            )

            indent = 12 * " "
            print(f"{indent}Reading images...")
            image_records = series.children
            out_name = "".join(
                [x if x.isalnum() else "_" for x in series.SeriesDescription]
            )
            out_names[out_name] = out_names.get(out_name, 0) + 1
            out_name += "_" + str(out_names[out_name]).zfill(2)

            gif_f = f"gifs/{out_name}.gif"
            writer = imageio.get_writer(gif_f, mode="I")
            for image_rec in image_records:
                image_f = join(*image_rec.ReferencedFileID)
                ds = pydicom.dcmread(image_f)
                fig = plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
                plt.axis("off")
                fig.axes.get_xaxis().set_visible(False)
                fig.axes.get_yaxis().set_visible(False)
                plt.savefig("tmp.png", bbox_inches="tight", pad_inches=0)
                image = Image.open("tmp.png")
                writer.append_data(np.array(image))

            writer.close()