FHIR Imaging Measurement Bundle

This example packages imaging-derived measurements as FHIR JSON. It is useful when BOA, radiomics, segmentation, or model outputs should remain linked to the source imaging study and series.

Build The Bundle

python

from fyron.fhir.builder import (
    build_imaging_measurement_bundle,
    codeable_concept,
    summarize_fhir_bundle,
    validate_fhir_bundle,
    validate_fhir_references,
    write_fhir_json,
)

bundle = build_imaging_measurement_bundle(
    subject="Patient/123",
    study_instance_uid="1.2.840.113619.2.55.3.604688654.123",
    series_instance_uid="1.2.840.113619.2.55.3.604688654.123.4",
    series_description="CT abdomen portal venous",
    measurements=[
        {
            "id": "l3-sma",
            "code": codeable_concept(text="L3 skeletal muscle area"),
            "value": 123.4,
            "unit": "cm2",
            "body_site": codeable_concept(text="L3"),
            "method": codeable_concept(text="Fyron BOA segmentation"),
        },
        {
            "id": "vat-volume",
            "code": codeable_concept(text="Visceral adipose tissue volume"),
            "value": 820.5,
            "unit": "ml",
            "body_site": codeable_concept(text="Abdomen"),
            "method": codeable_concept(text="Fyron body-composition extraction"),
        },
        {
            "id": "vat-sat-ratio",
            "code": codeable_concept(text="VAT/SAT ratio"),
            "value": 0.74,
            "unit": "ratio",
            "body_site": codeable_concept(text="Abdomen"),
            "method": codeable_concept(text="Fyron body-composition extraction"),
        },
    ],
    model_name="Fyron imaging feature extractor",
    model_endpoint_url="https://models.example.org/fyron/imaging",
    id_prefix="study-001",
    bundle_type="collection",
)

reference_report = validate_fhir_references(bundle)
summary = summarize_fhir_bundle(bundle)
validate_fhir_bundle(bundle)
write_fhir_json(bundle, "outputs/fhir/case_001_imaging_measurements.json")

print(reference_report["valid"])
print(summary["resource_types"])

What The Bundle Contains

ImagingStudy with study UID and optional series UID.
Observation resources for each measurement.
A DiagnosticReport grouping the measurements.
Optional Device and Endpoint resources for the model system.
Provenance linking measurements to source imaging and model metadata.

Server Upload

For server write-back, rebuild the same resources as a transaction bundle:

python

from fyron import FHIRRestClient
from fyron.fhir.builder import build_bundle

client = FHIRRestClient("https://fhir.example.org/fhir")

transaction = build_bundle(
    [entry["resource"] for entry in bundle["entry"]],
    bundle_type="transaction",
)

result = client.submit_bundle(transaction)
print(result.status_code)

Confirm the target server accepts your local codes, extensions, and profiles before production upload.