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DICOM

For site-specific access setup, see DICOMweb authentication. Choose the method and permissions approved by your administrator.

fyron.dicom is the DICOM-native boundary for imaging projects: DICOMweb acquisition, generated synthetic image export, and standards-compliant DICOM SEG writing. Keep protocol-specific work here, then hand local files to Imaging for array/NIfTI/QC operations.

Requests-based FHIR, DICOMweb, document, and LLM clients follow redirects only within the same scheme, host, and port. Cross-origin redirects, HTTPS downgrades, and URLs containing user credentials are blocked before forwarding request bodies or custom authentication headers. Configure the approved final endpoint directly when a service redirects elsewhere. This guard is also installed on supplied sessions, while preserving existing response hooks.

DICOM Submodules

ChapterUse it for
DICOMDownloaderDownload DICOMweb studies or series and write manifests.
Synthetic DICOM/NIfTI exportWrite generated or GAN-derived volumes with synthetic identifiers.
DICOM SEG exportWrite segmentation masks as source-referenced DICOM SEG objects.

Choose The Right Path

NeedPrefer
Download one study or seriesDICOMDownloader
Batch-download imaging rows from a cohort tableDICOMDownloader
Export generated CT/MR-like volumesSynthetic Export
Export model/manual segmentation masks to DICOM viewersDICOM SEG
Read local headers, series, NIfTI, geometry, or mask QCImaging

Typical Workflow

  1. Configure DICOMweb endpoint credentials.
  2. Download one test series and inspect the result.
  3. Scale to a DataFrame-driven batch download.
  4. Store manifests beside the cohort.
  5. Run local imaging QC before segmentation, radiomics, or DICOM SEG export.

Imports

python
from fyron import DICOMDownloader
from fyron.dicom.synthetic import write_synthetic_dicom_series
from fyron.dicom.seg import write_dicom_seg

Minimal Acquisition Example

python
from fyron import DICOMDownloader

downloader = DICOMDownloader(
    dicom_web_url="https://pacs.example.org/dicomweb",
    output_format="dicom",
)

result = downloader.download_series(
    study_uid="1.2.3",
    series_uid="1.2.3.4",
    output_dir="dicom_out",
)

CLI Examples

bash
fyron dicom-download \
  --dicom-web-url https://pacs.example.org/dicomweb \
  --study-uid 1.2.3 \
  --series-uid 1.2.3.4 \
  --output-dir dicom_out \
  --output-format dicom
bash
fyron dicom-seg \
  --mask total.nii.gz \
  --source-dicom original_dicom/case_001 \
  --segments segments.json \
  --output segmentations/case_001.seg.dcm \
  --validate

Common Pitfalls

  • Use output_format="dicom" if later writing DICOM SEG; SEG needs original source images.
  • Keep download manifests with the study cohort for reproducibility.
  • Do not use synthetic DICOM export for segmentation masks; use DICOM SEG.
  • Confirm UID columns before large batch downloads.
  • Imaging for local DICOM/NIfTI I/O and QC.
  • BOA for body-composition extraction, radiomics, and visualization.
  • Audit & Provenance for reproducibility manifests.