pyCERR documentation

pyCERR (Python-based Computational Environment for Radiological Research) stores all data for a patient in a single PlanC container — scans, structures (segmentations), dose, treatment plans (beams) and deformations — defined in cerr.plan_container.

Features

Data import / export

• DICOM import of CT/MR/PT/US/NM scans plus RTSTRUCT, RTDOSE and RTPLAN (cerr.plan_container.loadDcmDir)

• NIfTI import/export of scans, segmentations and dose

• Full-PlanC HDF5 serialization (saveToH5 / loadFromH5)

• DICOM RTSTRUCT export (cerr.dcm_export.rtstruct_iod)

Segmentation & contours

• Lazy polygon → binary-mask rasterization (cerr.contour.rasterseg.getStrMask)

• Import label maps / binary masks as structures (cerr.dataclasses.structure.importStructureMask)

Radiomics (IBSI-compliant)

• Scalar features: morphology, first-order, GLCM / GLRLM / GLSZM / GLDZM / NGTDM / NGLDM (IBSI-1)

• Convolutional texture / filter-response maps: mean, LoG, Laws, Gabor, wavelet (IBSI-2)

• cerr.radiomics.ibsi1.computeScalarFeatures

Dosimetry & outcomes

• Dose–volume histograms and metrics — Dx, Vx, MOHx, MOCx, mean dose (cerr.dvh)

• Radiotherapy outcome models — NTCP/TCP: LKB, logistic, Cox, Appelt (cerr.roe)

• IMRT planning / beamlet dose calculation (cerr.imrtp)

Image processing

• Deformable image registration via plastimatch / ANTs (cerr.registration)

• Resampling, intensity preprocessing and masking (cerr.utils)

• Semi-quantitative DCE-MRI features (cerr.mri_metrics)

• Helpers for AI model training / inference (cerr.utils.ai_pipeline)

Visualization — three interchangeable viewers driven by the same planC (cerr.viewer):

• pycerr_napari — napari 2D/3D viewer

• pycerr_gui — PyQt5 CERR-style desktop viewer

• pycerr_nbviewer — Jupyter / Colab notebook viewer

cerr and its sub-packages

• cerr package
  • Subpackages
  • Submodules
  • cerr.dvh module
  • cerr.multiViewHelper module
  • cerr.plan_container module
  • Module contents
• cerr.dataclasses package
  • Submodules
  • cerr.dataclasses.beams module
  • cerr.dataclasses.deform module
  • cerr.dataclasses.dose module
  • cerr.dataclasses.header module
  • cerr.dataclasses.imrt module
  • cerr.dataclasses.scan module
  • cerr.dataclasses.scan_info module
  • cerr.dataclasses.structure module
  • Module contents
• cerr.radiomics package
  • Submodules
  • cerr.radiomics.first_order module
  • cerr.radiomics.gray_level_cooccurence module
  • cerr.radiomics.ibsi1 module
  • cerr.radiomics.neighbor_gray_level_dependence module
  • cerr.radiomics.neighbor_gray_tone module
  • cerr.radiomics.preprocess module
  • cerr.radiomics.run_length module
  • cerr.radiomics.shape module
  • cerr.radiomics.size_zone module
  • cerr.radiomics.texture_filters module
  • cerr.radiomics.texture_utils module
  • cerr.radiomics.vector_elasticity module
  • Module contents
• cerr.registration package
  • Submodules
  • cerr.registration.register module
  • Module contents
• cerr.utils package
  • Submodules
  • cerr.utils.ai_pipeline module
  • cerr.utils.custom_colormaps module
  • cerr.utils.image_proc module
  • cerr.utils.interp module
  • cerr.utils.mask module
  • cerr.utils.statistics module
  • cerr.utils.uid module
  • Module contents
• cerr.viewer package
  • Submodules
  • cerr.viewer.pycerr_napari module
  • cerr.viewer.pycerr_gui module
  • cerr.viewer.pycerr_nbviewer module
  • cerr.viewer.cerr_colormaps module
  • Module contents
• cerr.imrtp package
  • Subpackages
  • Submodules
  • cerr.imrtp.imrtp module
  • cerr.imrtp.imrtp_gui module
  • cerr.imrtp.imrtp_problem module
  • Module contents
• tests package
  • Submodules
  • tests.test_ibsi1_features module
  • tests.test_ibsi2_features module
  • tests.test_ibsi2_filters module
  • tests.test_nii_export_import module
  • Module contents

Indices and tables

• Index

• Module Index

• Search Page