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Convert DICOM data to GIFs.
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| # 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() |
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