Read a DICOMDIR dataset

This example shows how to read a DICOM :File-set’s DICOMDIR dataset.

Note

The FileSet class is a much better way of working with DICOM File-sets and allows creation and modification of DICOMDIR files. See the DICOM File-set example or the File-set tutorial.

Root directory: /root/project/pydicom/data/test_files/dicomdirtests

PATIENT: PatientID=77654033, PatientName=Doe^Archibald
  STUDY: StudyID=2, StudyDate=20010101, StudyDescription=XR C Spine Comp Min 4 Views
    SERIES: SeriesNumber=1, Modality=CR, SeriesDescription=(no value available) - 1 SOP Instance
      IMAGE: Path=77654033/CR1/6154
    SERIES: SeriesNumber=2, Modality=CR, SeriesDescription=(no value available) - 1 SOP Instance
      IMAGE: Path=77654033/CR2/6247
    SERIES: SeriesNumber=3, Modality=CR, SeriesDescription=(no value available) - 1 SOP Instance
      IMAGE: Path=77654033/CR3/6278
  STUDY: StudyID=2, StudyDate=19950903, StudyDescription=CT, HEAD/BRAIN WO CONTRAST
    SERIES: SeriesNumber=2, Modality=CT, SeriesDescription=(no value available) - 4 SOP Instances
      IMAGE: Path=77654033/CT2/17106
      IMAGE: Path=77654033/CT2/17136
      IMAGE: Path=77654033/CT2/17166
      IMAGE: Path=77654033/CT2/17196
PATIENT: PatientID=98890234, PatientName=Doe^Peter
  STUDY: StudyID=2, StudyDate=20010101, StudyDescription=(no value available)
    SERIES: SeriesNumber=4, Modality=CT, SeriesDescription=(no value available) - 2 SOP Instances
      IMAGE: Path=98892001/CT2N/6293
      IMAGE: Path=98892001/CT2N/6924
    SERIES: SeriesNumber=5, Modality=CT, SeriesDescription=(no value available) - 5 SOP Instances
      IMAGE: Path=98892001/CT5N/2062
      IMAGE: Path=98892001/CT5N/2392
      IMAGE: Path=98892001/CT5N/2693
      IMAGE: Path=98892001/CT5N/3023
      IMAGE: Path=98892001/CT5N/3353
  STUDY: StudyID=428, StudyDate=20030505, StudyDescription=Carotids
    SERIES: SeriesNumber=1, Modality=MR, SeriesDescription=(no value available) - 1 SOP Instance
      IMAGE: Path=98892003/MR1/15820
    SERIES: SeriesNumber=2, Modality=MR, SeriesDescription=(no value available) - 1 SOP Instance
      IMAGE: Path=98892003/MR2/15970
  STUDY: StudyID=134, StudyDate=20030505, StudyDescription=Brain
    SERIES: SeriesNumber=1, Modality=MR, SeriesDescription=(no value available) - 1 SOP Instance
      IMAGE: Path=98892003/MR1/4919
    SERIES: SeriesNumber=2, Modality=MR, SeriesDescription=(no value available) - 3 SOP Instances
      IMAGE: Path=98892003/MR2/4950
      IMAGE: Path=98892003/MR2/5011
      IMAGE: Path=98892003/MR2/4981
  STUDY: StudyID=2, StudyDate=20030505, StudyDescription=Brain-MRA
    SERIES: SeriesNumber=1, Modality=MR, SeriesDescription=(no value available) - 1 SOP Instance
      IMAGE: Path=98892003/MR1/5641
    SERIES: SeriesNumber=2, Modality=MR, SeriesDescription=(no value available) - 3 SOP Instances
      IMAGE: Path=98892003/MR2/6935
      IMAGE: Path=98892003/MR2/6605
      IMAGE: Path=98892003/MR2/6273
    SERIES: SeriesNumber=700, Modality=MR, SeriesDescription=(no value available) - 7 SOP Instances
      IMAGE: Path=98892003/MR700/4558
      IMAGE: Path=98892003/MR700/4528
      IMAGE: Path=98892003/MR700/4588
      IMAGE: Path=98892003/MR700/4467
      IMAGE: Path=98892003/MR700/4618
      IMAGE: Path=98892003/MR700/4678
      IMAGE: Path=98892003/MR700/4648

import os
from pathlib import Path

from pydicom import dcmread
from pydicom.data import get_testdata_file

# fetch the path to the test data
path = get_testdata_file('DICOMDIR')
ds = dcmread(path)
root_dir = Path(ds.filename).resolve().parent
print(f'Root directory: {root_dir}\n')

# Iterate through the PATIENT records
for patient in ds.patient_records:
    print(
        f"PATIENT: PatientID={patient.PatientID}, "
        f"PatientName={patient.PatientName}"
    )

    # Find all the STUDY records for the patient
    studies = [
        ii for ii in patient.children if ii.DirectoryRecordType == "STUDY"
    ]
    for study in studies:
        descr = study.StudyDescription or "(no value available)"
        print(
            f"{'  ' * 1}STUDY: StudyID={study.StudyID}, "
            f"StudyDate={study.StudyDate}, StudyDescription={descr}"
        )

        # Find all the SERIES records in the study
        all_series = [
            ii for ii in study.children if ii.DirectoryRecordType == "SERIES"
        ]
        for series in all_series:
            # Find all the IMAGE records in the series
            images = [
                ii for ii in series.children
                if ii.DirectoryRecordType == "IMAGE"
            ]
            plural = ('', 's')[len(images) > 1]

            descr = getattr(
                series, "SeriesDescription", "(no value available)"
            )
            print(
                f"{'  ' * 2}SERIES: SeriesNumber={series.SeriesNumber}, "
                f"Modality={series.Modality}, SeriesDescription={descr} - "
                f"{len(images)} SOP Instance{plural}"
            )

            # Get the absolute file path to each instance
            #   Each IMAGE contains a relative file path to the root directory
            elems = [ii["ReferencedFileID"] for ii in images]
            # Make sure the relative file path is always a list of str
            paths = [[ee.value] if ee.VM == 1 else ee.value for ee in elems]
            paths = [Path(*p) for p in paths]

            # List the instance file paths
            for p in paths:
                print(f"{'  ' * 3}IMAGE: Path={os.fspath(p)}")

                # Optionally read the corresponding SOP Instance
                # instance = dcmread(Path(root_dir) / p)
                # print(instance.PatientName)