Reading DICOM metadata

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Note

DICOM metadata is distinct from clientMetadata, which is the metadata associated with individual data units. See our tutorial on clientMetadata for more information.

DICOM related metadata is accessed by specifying the dataset using the <project_hash>. It contains the patient ID, series ID, and study ID that link the unlabeled DICOM data to the labeled data that is exported from Encord.

Reading series metadata

The following code reads and prints the patient ID (patient_id), series ID (series_uid) and study ID (study_uid) of all label rows in the specified project.

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Note


#Import dependencies
from encord import EncordUserClient

# Authenticate with Encord using the path to your private key
client = EncordUserClient.create_with_ssh_private_key(
    ssh_private_key_path="<private_key_path>"
)

# Specify the project for which you want to read the patient and series IDs
project = client.get_project("<project_hash>")

# Fetch the label and frame information for this project
label_rows = project.list_label_rows_v2()

for label_row in label_rows:
    # Initialize labels
    label_row.initialise_labels()
    # Print Patient ID, Series ID, and Study ID
    print (label_row.metadata)


patient_id='example_fmri_140207' study_uid='1.2.840.113619.6.283.47340.8065.13236498290.27' series_uid='1.2.840.113619.2.28.3100000.21673.1390073.97'

Reading frame metadata

The following code reads and prints frame specific DICOM metadata including the DICOM instance ID (dicom_instance_uid), the multiframe frame number (multiframe_frame_number), the file URI (file_uri) and the height as well as width of the frame, as can be seen in the sample output provided. 


#Import dependencies
from encord import EncordUserClient

# Authenticate with Encord using the path to your private key
client = EncordUserClient.create_with_ssh_private_key(
    ssh_private_key_path="<private_key_path>"
)

# Specify the project for which you want to read the patient and series IDs
project = client.get_project("<project_hash>")

# Fetch the label and frame information for this project
label_rows = project.list_label_rows_v2()

for label_row in label_rows:
    # Initialize labels
    label_row.initialise_labels()
    
    # Print Frame specific DICOM metadata
    for v in label_row.get_frame_views():
        print(v.metadata)



dicom_instance_uid='1.5.740.183619.283.6905.311000.16119.13000477777.716' multiframe_frame_number=None file_uri='my-storage-location/iaDJxNNrMubabutFPcP9oszw2shmeHm2/5e8880c2-9177-4cf6-b298-ebd3d1d31eb8' width=256 height=256

Reading frame dimensions

Use the script below to obtain the dimensions for a given slice or frame.

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Caution

Width and height fields other than those printed by this script may be present in the metadata. These refer to the DICOM series' dimensions (the maximum width and height of the series) and will not be applicable to all slices or frames.


#Import dependencies
from encord import EncordUserClient

# Authenticate with Encord using the path to your private key
client = EncordUserClient.create_with_ssh_private_key(
    ssh_private_key_path="<private_key_path>"
)

# Specify the project for which you want to read the patient and series IDs
project = client.get_project("<project_hash>")

# Fetch the label and frame information for this project
label_rows = project.list_label_rows_v2()

for label_row in label_rows:
    # Initialize labels
    label_row.initialise_labels()

    for v in label_row.get_frame_views():
        print(f"frame width: {v.metadata.width}, height: {v.metadata.height}")


series width: 1381, height: 1982
frame width: 1381, height: 1982
frame metadata width: 934, height: 1982
frame width: 1381, height: 1982
frame metadata width: 1381, height: 1632