pycerr 2.0.0

A Computational Environment for Radiological Research

pyCERR - A Python-based Computational Environment for Radiological Research

pyCERR provides convenient data structure for imaging metadata and their associations. Utilities are provided to to extract, transform, organize metadata and visualize results of image processing for image and dosimetry features, image processing for AI model training and inference.

Features

All data for a patient lives in a single PlanC container — scans, structures (segmentations), dose, treatment plans (beams) and deformations — defined in cerr.plan_container. Around it, pyCERR provides:

Data import / export

• DICOM import of CT/MR/PT/US/NM scans plus RTSTRUCT, RTDOSE and RTPLAN — pc.loadDcmDir
• NIfTI import/export of scans, segmentations and dose — pc.loadNiiScan / loadNiiStructure / loadNiiDose, .saveNii
• Full-PlanC HDF5 serialization — pc.saveToH5 / pc.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, configured via JSON settings

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 (influence-matrix) 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 pipelines — cerr.utils.ai_pipeline

Visualization — three interchangeable viewers driven by the same planC (napari 2D/3D, a PyQt5 CERR-style desktop GUI, and a Jupyter/Colab notebook viewer); see visualize scan, dose and segmentation below.

Documentation

• Example notebooks (grouped by topic): https://github.com/cerr/pyCERR-Notebooks
• API reference — https://pycerr.readthedocs.io (built from docs/; build locally with cd docs && make html)
• Desktop GUI scripting API — cerr/viewer/API_pycerr_gui.md
• Test suite & coverage — tests/README.md

Install Miniconda and Git

It is recommended to install CERR in an isolated environment such as Anaconda or VENV from GitHub repository. Please refer to

1. https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html for installing Miniconda and
2. https://git-scm.com/downloads for installing Git on your system.

Install pyCERR

Launch Miniconda terminal, create a Conda environment with Python 3.8 and install CERR. Note that CERR requires Python version >= 3.8 to use Napari Viewer.

conda create -y --name pycerr python=3.11
conda activate pycerr
pip install "pyCERR[napari] @ git+https://github.com/cerr/pyCERR"

The above steps will install CERR under testcerr/Lib/site-packages.

Install Jupyter Lab or Notebook to try out example notebooks.

pip install jupyterlab

Example Notebooks

Example notebooks are hosted at https://github.com/cerr/pyCERR-Notebooks/ . Clone this repository to use notebooks as a starting point.

git clone https://github.com/cerr/pyCERR-Notebooks.git

Example snippets

Run python from the above Anaconda environment and try out the following code samples.

Import modules for planC and viewer

import numpy as np
from cerr import plan_container as pc
from cerr.viewer import pycerr_napari        # napari API (pycerr_napari.showNapari, ...)

Read DICOM directory contents to planC

dcmDir = r"\\path\to\Data\dicom\directory"
planC = pc.loadDcmDir(dcmDir)

Read NifTi scan to planC

scanNiiFileName = r"\\path\to\Data\scan.nii.gz"
planC = pc.loadNiiScan(scanNiiFileName, imageType = "CT SCAN")

Read NifTi scan in a specified orientation to planC

planC = pc.loadNiiScan(scanNiiFileName, imageType = "CT SCAN", direction='HFS')

Read NifTi scan and append to an existing planC

planC = pc.loadNiiScan(scanNiiFileName, imageType = "CT SCAN", direction='HFS', planC)

Read NifTi segmentation to planC

structNiiFileName = r"\\path\to\Data\structure.nii.gz"
assocScanNum = 0
labelDict = {1: 'GTV_P', 2: 'GTV_N'}
planC = pc.loadNiiStructure(niiFileName, assocScanNum, planC, labelDict)

Export Structures to DICOM

from cerr.dcm_export import rtstruct_iod

structDcmFileName = r"\\path\to\Data\structure.dcm"
structNums = [0,2,3]
exportOpts = {'seriesDescription': "Exported by pyCERR"}
rtstruct_iod.create(structNums,structDcmFileName,planC,exportOpts)

Export Scan, Structure and Dose to NifTi

scanNiiFileName = r"\\path\to\Data\scan.nii.gz"
scanNum = 0
planC.scan[scanNum].saveNii(scanNiiFileName)

structNiiFileName = r"\\path\to\Data\structure.nii.gz"
structNum = 0
planC.structure[structNum].saveNii(structNiiFileName, planC)    

doseNiiFileName = r"\\path\to\Data\dose.nii.gz"
doseNum = 0
planC.dose[doseNum].saveNii(doseNiiFileName)

visualize scan, dose and segmentation

pyCERR ships three interchangeable viewers under the cerr.viewer sub-package, all driven by the same planC:

Viewer	Module	Best for
napari 2D/3D	cerr.viewer.pycerr_napari (showNapari)	quick interactive review, 3D rendering
PyQt5 desktop	cerr.viewer.pycerr_gui (show)	CERR-style slice viewer: contouring, registration QA, IMRTP/ROE, scripting API
notebook	cerr.viewer.pycerr_nbviewer (showNB)	Jupyter / JupyterLab / VS Code / Google Colab

PyQt5 desktop viewer

from cerr.viewer import pycerr_gui
viewer = pycerr_gui.show(planC)            # opens the CERR-style desktop GUI
# ... or launch empty and drag-and-drop a DICOM directory / NIfTI file in.
# The viewer exposes a scripting API (set_scan/set_dose/goto_structure,
# registration-QA setup, DVH export, save_screenshot, ...); see
# cerr/viewer/API_pycerr_gui.md for the full reference.

Notebook viewer (Jupyter / Colab)

from cerr.viewer import pycerr_nbviewer
viewer = pycerr_nbviewer.showNB(planC, scan_nums=[0], struct_nums=strNumList,
                                 dose_nums=[0])

napari viewer

from cerr.viewer import pycerr_napari
scanNumList = [0]
doseNumList = [0]
numStructs = len(planC.structure)
strNumList = np.arange(numStructs)
displayMode = '2d' # '2d' or '3d'
vectDict = {}
viewer, scan_layer, struct_layer, dose_lyer, dvf_layer = \
               pycerr_napari.showNapari(planC, scan_nums=scanNumList, struct_nums=strNumList,\
	       dose_nums=doseNumList, vectors_dict=vectDict, displayMode = '2d')

Compute DVH-based metrics

from cerr import dvh
structNum = 0
doseNum = 0
dosesV, volsV, isErr = dvh.getDVH(structNum, doseNum, planC)
binWidth = 0.025
doseBinsV,volHistV = dvh.doseHist(dosesV, volsV, binWidth)
percent = 70
dvh.MOHx(doseBinsV,volHistV,percent)