DICOM

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.

DICOM Submodules

Choose The Right Path

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

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

Minimal Acquisition Example

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

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

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.

Related Modules

• Imaging for local DICOM/NIfTI I/O and QC.
• BOA for body-composition extraction, radiomics, and visualization.
• Audit & Provenance for reproducibility manifests.