How to export DICOM data and sample export formats.
You can use the Python SDK to export DICOM annotations.
This page shows how to declare different annotation types (as Python dictionaries and NDJSON objects) and demonstrates the export process.
A Python notebook demonstrates these steps and can be run directly with Google CoLab.
Export V1 is deprecated
Starting April 2024, Export V1 begins sunsetting on a rolling basis. For details, see Export v1 migration guide.
Export JSON annotations
# Set the export params to include/exclude certain fields. Make sure each of these fields are correctly grabbed
export_params= {
"attachments": True,
"metadata_fields": True,
"data_row_details": True,
"project_details": True,
"label_details": True,
"performance_details": True
}
# You can set the range for last_activity_at and label_created_at.
# For context, last_activity_at captures the creation and modification of labels, metadata, status, comments and reviews.
# Note: This is an AND logic between the filters, so usually using one filter is sufficient.
filters= {
"last_activity_at": ["2000-01-01 00:00:00", "2050-01-01 00:00:00"],
"workflow_status": "Done"
}
export_task = project.export_v2(params=export_params, filters=filters)
export_task.wait_till_done()
if export_task.errors:
print(export_task.errors)
export_json = export_task.result
print("results: ", export_json)
# Set the export params to include/exclude certain fields.
export_params= {
"attachments": True,
"metadata_fields": True,
"data_row_details": True,
"project_details": True,
"label_details": True,
"performance_details": True,
"interpolated_frames": True
}
# Note: Filters follow AND logic, so typically using one filter is sufficient.
filters= {
"last_activity_at": ["2000-01-01 00:00:00", "2050-01-01 00:00:00"],
"workflow_status": "<wkf-status>"
}
client.enable_experimental = True
export_task = project.export(params=export_params, filters=filters)
export_task.wait_till_done()
# Return JSON output strings from export task results/errors, one by one:
# Callback used for JSON Converter
def json_stream_handler(output: lb.JsonConverterOutput):
print(output.json_str)
if export_task.has_errors():
export_task.get_stream(
converter=lb.JsonConverter(),
stream_type=lb.StreamType.ERRORS
).start(stream_handler=lambda error: print(error))
if export_task.has_result():
export_json = export_task.get_stream(
converter=lb.JsonConverter(),
stream_type=lb.StreamType.RESULT
).start(stream_handler=json_stream_handler)
print("file size: ", export_task.get_total_file_size(stream_type=lb.StreamType.RESULT))
print("line count: ", export_task.get_total_lines(stream_type=lb.StreamType.RESULT))
Annotation export formats
Polyline
{
"feature_id": "clftr46h2002014wq1lvtntzi",
"feature_schema_id": "clftr3ueu061407xe3eam5gfh",
"name": "line_dicom",
"value": "line_dicom",
"annotation_kind": "DICOMPolyline",
"classifications": [],
"line": [
{
"x": 10.0,
"y": 10.0
},
{
"x": 200.0,
"y": 10.0
},
{
"x": 300.0,
"y": 300.0
}
]
}
Mask
{
"feature_id": "clftr46h2001z14wqod253zyk",
"feature_schema_id": "clftr3ueu061207xeeezscu35",
"name": "segmentation_mask_dicom",
"value": "segmentation_mask_dicom",
"annotation_kind": "DICOMSegmentationMask",
"classifications": [],
"mask": {
"url": "https://api.labelbox.com/api/v1/projects/clftr3und00cd07tzalqk2z8b/annotations/clftr46h2001z14wqod253zyk/index/1/mask"
},
"composite_mask": {
"url": "https://api.labelbox.com/api/v1/tasks/cluu2f9wn02m907wc9n9thld2/masks/clftr45oa001x14wqj2jqd42l/index/1",
"color_rgb": [
255,
255,
255
]
}
}
Sample project export
{
"data_row": {
"id": "clftqkks0004g075we24j7za1",
"global_key": "sample-dicom-1.dcm",
"row_data": "https://storage.googleapis.com/labelbox-datasets/dicom-sample-data/sample-dicom-1.dcm",
"details": {
"dataset_id": "clftqkjaz1f1g07y3519udly1",
"dataset_name": "dicom_demo_dataset",
"created_at": "2023-03-29T13:42:10.000+00:00",
"updated_at": "2023-03-29T13:42:10.000+00:00",
"last_activity_at": "2023-03-29T13:57:25.000+00:00",
"created_by": "[email protected]"
}
},
"media_attributes": {
"mime_type": "application/dicom"
},
"attachments": [],
"metadata_fields": [],
"projects": {
"clftr3und00cd07tzalqk2z8b": {
"name": "dicom_project_demo",
"labels": [
{
"label_kind": "DICOM",
"version": "1.0.0",
"id": "clftr46hg002114wq5dfz8nj4",
"label_details": {
"created_at": "2023-03-29T13:57:25.000+00:00",
"updated_at": "2023-03-29T13:57:25.000+00:00",
"created_by": "[email protected]",
"content_last_updated_at": "2023-03-29T13:57:24.947+00:00",
"reviews": []
},
"performance_details": {
"seconds_to_create": 0,
"seconds_to_review": 0,
"skipped": false
},
"annotations": {
"groups": {
"Axial": {
"name": "Axial",
"classifications": [],
"frames": {
"1": {
"objects": {
"clftr46h2001z14wqod253zyk": {
"feature_id": "clftr46h2001z14wqod253zyk",
"feature_schema_id": "clftr3ueu061207xeeezscu35",
"name": "segmentation_mask_dicom",
"value": "segmentation_mask_dicom",
"annotation_kind": "DICOMSegmentationMask",
"classifications": [],
"mask": {
"url": "https://api.labelbox.com/api/v1/projects/clftr3und00cd07tzalqk2z8b/annotations/clftr46h2001z14wqod253zyk/index/1/mask"
},
"composite_mask": {
"url": "https://api.labelbox.com/api/v1/tasks/cluu2f9wn02m907wc9n9thld2/masks/clftr45oa001x14wqj2jqd42l/index/1",
"color_rgb": [
255,
255,
255
]
}
},
"clftr46h2002014wq1lvtntzi": {
"feature_id": "clftr46h2002014wq1lvtntzi",
"feature_schema_id": "clftr3ueu061407xe3eam5gfh",
"name": "line_dicom",
"value": "line_dicom",
"annotation_kind": "DICOMPolyline",
"classifications": [],
"line": [
{
"x": 10.0,
"y": 10.0
},
{
"x": 200.0,
"y": 20.0
},
{
"x": 250.0,
"y": 250.0
}
]
}
},
"classifications": []
},
"5": {
"objects": {
"clftr46h2001z14wqod253zyk": {
"feature_id": "clftr46h2001z14wqod253zyk",
"feature_schema_id": "clftr3ueu061207xeeezscu35",
"name": "segmentation_mask_dicom",
"value": "segmentation_mask_dicom",
"annotation_kind": "DICOMSegmentationMask",
"classifications": [],
"mask": {
"url": "https://api.labelbox.com/api/v1/projects/clftr3und00cd07tzalqk2z8b/annotations/clftr46h2001z14wqod253zyk/index/5/mask"
},
"composite_mask": {
"url": "https://api.labelbox.com/api/v1/tasks/cluu2f9wn02m907wc9n9thld2/masks/clftr45oa001x14wqj2jqd42l/index/5",
"color_rgb": [
255,
255,
255
]
}
}
},
"classifications": []
},
"20": {
"objects": {
"clftr46h2002014wq1lvtntzi": {
"feature_id": "clftr46h2002014wq1lvtntzi",
"feature_schema_id": "clftr3ueu061407xe3eam5gfh",
"name": "line_dicom",
"value": "line_dicom",
"annotation_kind": "DICOMPolyline",
"classifications": [],
"line": [
{
"x": 10.0,
"y": 10.0
},
{
"x": 200.0,
"y": 10.0
},
{
"x": 300.0,
"y": 300.0
}
]
}
},
"classifications": []
}
}
},
"Sagittal": {
"name": "Sagittal",
"classifications": [],
"frames": {}
},
"Coronal": {
"name": "Coronal",
"classifications": [],
"frames": {}
}
},
"segments": {
"Axial": {
"clftr46h2001z14wqod253zyk": [
[
1,
1
],
[
5,
5
]
],
"clftr46h2002014wq1lvtntzi": [
[
1,
1
],
[
20,
20
]
]
},
"Sagittal": {},
"Coronal": {}
},
"classifications": [],
"key_frame_feature_map": {
"clftr46h2001z14wqod253zyk": {
"Axial": {
"1": true,
"5": true
},
"Coronal": {},
"Sagittal": {}
},
"clftr46h2002014wq1lvtntzi": {
"Axial": {
"1": true,
"20": true
},
"Coronal": {},
"Sagittal": {}
}
}
}
}
],
"project_details": {
"ontology_id": "clftr3ue6061107xee0xp3v6l",
"task_name": "Done",
"batch_id": "9a35aca0-ce39-11ed-bcf8-d178e6a2361d",
"batch_name": "first-batch-dicom-demo",
"workflow_status": "DONE",
"priority": 5,
"consensus_expected_label_count": 1,
"workflow_history": []
}
}
}
}
Sample model run export
Not supported.