Note
Go to the end to download the full example code.
Read a DICOM File-setΒΆ
This example shows how to read and interact with a DICOM File-set.
DICOM File-set
Root directory: /root/project/src/pydicom/data/test_files/dicomdirtests
File-set ID: PYDICOM_TEST
File-set UID: 1.2.276.0.7230010.3.1.4.0.31906.1359940846.78187
Descriptor file ID: (no value available)
Descriptor file character set: (no value available)
Changes staged for write(): DICOMDIR update, directory structure update
Managed instances:
PATIENT: PatientID='77654033', PatientName='Doe^Archibald'
STUDY: StudyDate=20010101, StudyTime=000000, StudyDescription='XR C Spine Comp Min 4 Views'
SERIES: Modality=CR, SeriesNumber=1
IMAGE: 1 SOP Instance
SERIES: Modality=CR, SeriesNumber=2
IMAGE: 1 SOP Instance
SERIES: Modality=CR, SeriesNumber=3
IMAGE: 1 SOP Instance
STUDY: StudyDate=19950903, StudyTime=173032, StudyDescription='CT, HEAD/BRAIN WO CONTRAST'
SERIES: Modality=CT, SeriesNumber=2
IMAGE: 4 SOP Instances
PATIENT: PatientID='98890234', PatientName='Doe^Peter'
STUDY: StudyDate=20010101, StudyTime=000000
SERIES: Modality=CT, SeriesNumber=4
IMAGE: 2 SOP Instances
SERIES: Modality=CT, SeriesNumber=5
IMAGE: 5 SOP Instances
STUDY: StudyDate=20030505, StudyTime=050743, StudyDescription='Carotids'
SERIES: Modality=MR, SeriesNumber=1
IMAGE: 1 SOP Instance
SERIES: Modality=MR, SeriesNumber=2
IMAGE: 1 SOP Instance
STUDY: StudyDate=20030505, StudyTime=025109, StudyDescription='Brain'
SERIES: Modality=MR, SeriesNumber=1
IMAGE: 1 SOP Instance
SERIES: Modality=MR, SeriesNumber=2
IMAGE: 3 SOP Instances
STUDY: StudyDate=20030505, StudyTime=045357, StudyDescription='Brain-MRA'
SERIES: Modality=MR, SeriesNumber=1
IMAGE: 1 SOP Instance
SERIES: Modality=MR, SeriesNumber=2
IMAGE: 3 SOP Instances
SERIES: Modality=MR, SeriesNumber=700
IMAGE: 7 SOP Instances
PatientName=Doe^Archibald, PatientID=77654033
StudyDescription='XR C Spine Comp Min 4 Views', StudyDate=20010101
Modality=CR - 1 SOP Instance
Modality=CR - 1 SOP Instance
Modality=CR - 1 SOP Instance
StudyDescription='CT, HEAD/BRAIN WO CONTRAST', StudyDate=19950903
Modality=CT - 4 SOP Instances
PatientName=Doe^Peter, PatientID=98890234
StudyDescription='', StudyDate=20010101
Modality=CT - 2 SOP Instances
Modality=CT - 5 SOP Instances
StudyDescription='Carotids', StudyDate=20030505
Modality=MR - 1 SOP Instance
Modality=MR - 1 SOP Instance
StudyDescription='Brain', StudyDate=20030505
Modality=MR - 1 SOP Instance
Modality=MR - 3 SOP Instances
StudyDescription='Brain-MRA', StudyDate=20030505
Modality=MR - 1 SOP Instance
Modality=MR - 3 SOP Instances
Modality=MR - 7 SOP Instances
Found 7 instances for SeriesInstanceUID=1.3.6.1.4.1.5962.1.1.0.0.0.1196533885.18148.0.118
/root/project/src/pydicom/fileset.py:1476: UserWarning: None of the records in the DICOMDIR dataset contain all the query elements, consider using the 'load' parameter to expand the search to the corresponding SOP instances
warn_and_log(
Found 0 instances with PhotometricInterpretation='MONOCHROME1' without loading the stored instances and 3 instances with loading
Original File-set still at /root/project/src/pydicom/data/test_files/dicomdirtests
File-set copied to /tmp/tmpbh5n11k2 and contains the following files:
DICOMDIR
PT000000/ST000000/SE000000/IM000000
PT000000/ST000000/SE000001/IM000000
PT000000/ST000000/SE000002/IM000000
PT000000/ST000001/SE000000/IM000000
PT000000/ST000001/SE000000/IM000001
PT000000/ST000001/SE000000/IM000002
PT000000/ST000001/SE000000/IM000003
PT000001/ST000000/SE000000/IM000000
PT000001/ST000000/SE000000/IM000001
PT000001/ST000000/SE000001/IM000000
PT000001/ST000000/SE000001/IM000001
PT000001/ST000000/SE000001/IM000002
PT000001/ST000000/SE000001/IM000003
PT000001/ST000000/SE000001/IM000004
PT000001/ST000001/SE000000/IM000000
PT000001/ST000001/SE000001/IM000000
PT000001/ST000002/SE000000/IM000000
PT000001/ST000002/SE000001/IM000000
PT000001/ST000002/SE000001/IM000001
PT000001/ST000002/SE000001/IM000002
PT000001/ST000003/SE000000/IM000000
PT000001/ST000003/SE000001/IM000000
PT000001/ST000003/SE000001/IM000001
PT000001/ST000003/SE000001/IM000002
PT000001/ST000003/SE000002/IM000000
PT000001/ST000003/SE000002/IM000001
PT000001/ST000003/SE000002/IM000002
PT000001/ST000003/SE000002/IM000003
PT000001/ST000003/SE000002/IM000004
PT000001/ST000003/SE000002/IM000005
PT000001/ST000003/SE000002/IM000006
PT000002/ST000000/SE000000/IM000000
PT000003/ST000000/SE000000/IM000000
from pathlib import Path
from tempfile import TemporaryDirectory
from pydicom import examples
from pydicom.data import get_testdata_file
from pydicom.fileset import FileSet
from pydicom.uid import generate_uid
path = get_testdata_file("DICOMDIR")
# A File-set can be loaded from the path to its DICOMDIR dataset or the
# dataset itself
fs = FileSet(path) # or fs = FileSet(dcmread(path))
# A summary of the File-set's contents can be seen when printing
print(fs)
print()
# Iterating over the FileSet yields FileInstance objects
for instance in fs:
# Load the corresponding SOP Instance dataset
ds = instance.load()
# Do something with each dataset
# We can search the File-set
patient_ids = fs.find_values("PatientID")
for patient_id in patient_ids:
# Returns a list of FileInstance, where each one represents an available
# SOP Instance with a matching *Patient ID*
result = fs.find(PatientID=patient_id)
print(f"PatientName={result[0].PatientName}, " f"PatientID={result[0].PatientID}")
# Search available studies
study_uids = fs.find_values("StudyInstanceUID", instances=result)
for study_uid in study_uids:
result = fs.find(PatientID=patient_id, StudyInstanceUID=study_uid)
print(
f" StudyDescription='{result[0].StudyDescription}', "
f"StudyDate={result[0].StudyDate}"
)
# Search available series
series_uids = fs.find_values("SeriesInstanceUID", instances=result)
for series_uid in series_uids:
result = fs.find(
PatientID=patient_id,
StudyInstanceUID=study_uid,
SeriesInstanceUID=series_uid,
)
plural = ["", "s"][len(result) > 1]
print(
f" Modality={result[0].Modality} - "
f"{len(result)} SOP Instance{plural}"
)
# Of course you can just get the instances directly if you know what you want
series_uid = "1.3.6.1.4.1.5962.1.1.0.0.0.1196533885.18148.0.118"
result = fs.find(SeriesInstanceUID=series_uid)
print(f"\nFound {len(result)} instances for SeriesInstanceUID={series_uid}")
# We can search the actual stored SOP Instances by using `load=True`
# This can be useful as the DICOMDIR's directory records only contain a
# limited subset of the available elements, however its less efficient
result = fs.find(load=False, PhotometricInterpretation="MONOCHROME1")
result_load = fs.find(load=True, PhotometricInterpretation="MONOCHROME1")
print(
f"Found {len(result)} instances with "
f"PhotometricInterpretation='MONOCHROME1' without loading the stored "
f"instances and {len(result_load)} instances with loading"
)
# We can remove and add instances to the File-set
fs.add(examples.ct)
fs.add(examples.mr)
result = fs.find(StudyDescription="'XR C Spine Comp Min 4 Views'")
fs.remove(result)
# To edit the elements in the DICOMDIR's File-set Identification Module
# (Part 3, Annex F.3.2.1) use the following properties:
# (0004,1130) File-set ID
fs.ID = "MY FILESET"
# Change the File-set's UID
fs.UID = generate_uid()
# (0004,1141) File-set Descriptor File ID
fs.descriptor_file_id = "README"
# (0004,1142) Specific Character Set of File-set Descriptor File
fs.descriptor_character_set = "ISO_IR 100"
# Changes to the File-set are staged until write() is called
# Calling write() will update the File-set's directory structure to meet the
# semantics used by pydicom File-sets (if required), add/remove instances and
# and re-write the DICOMDIR file
# We don't do it here because it would overwrite your example data
# fs.write()
# Alternatively, the File-set can be copied to a new root directory
# This will apply any staged changes while leaving the original FileSet
# object unchanged
tdir = TemporaryDirectory()
new_fileset = fs.copy(tdir.name)
print(f"\nOriginal File-set still at {fs.path}")
root = Path(new_fileset.path)
print(f"File-set copied to {root} and contains the following files:")
# Note how the original File-set directory layout has been changed to
# the structure used by pydicom
for p in sorted(root.glob("**/*")):
if p.is_file():
print(f" {p.relative_to(root)}")
Total running time of the script: (0 minutes 0.234 seconds)