CT_Scan (CBCT utilities)

Python tooling to inspect PreXion-style cone-beam CT exports: DICOM metadata, .pxv slice folders, and LUTTemplate XML presets. Optional viewers use matplotlib, PyVista, and VTK.

Repository: github.com/msherekar/CT_Scan

Important disclaimer

This code is for research, engineering, and offline inspection only. It is not a medical device and must not be used for clinical diagnosis or treatment decisions. Vendor viewer software and your institution’s policies govern any clinical use.

Requirements

• Python 3.10+ (uses from __future__ import annotations and modern typing)
• From the repo root, install what you need:

# Core: DICOM batch read + LUT XML parsing + PXV summaries
pip install pydicom

# 2D viewers / MPR / dental slice UI
pip install numpy matplotlib pydicom

# 3D volume + LUT presets (pyvista + vtk)
pip install numpy pydicom pyvista vtk

Repository layout

Path	Role
src/read_cbct_files.py	Single-file or batch .dcm / .pxv read; optional DICOM series browser
src/process_pxv_folders.py	Summarize .pxv trees under Data/ (sizes, empties, hashes)
src/process_lut_templates.py	Parse LUTTemplate/**/*.xml into JSON/CSV
src/run_all.py	Runs scan steps + LUT step; writes output/full_pipeline_summary.json
src/visualize_cbct.py, visualize_cbct_3d.py, mpr_viewer.py, dental_viewer.py	Visualization entry points
src/lut_parser.py	LUT XML → VTK transfer functions (used by 3D path)
scripts/	Git helpers and set_up_github_repo.sh

Large or proprietary trees (DICOM/, Data/, LUTTemplate/, output/, etc.) are typically gitignored; clone the repo and place your data beside src/ as your workflow requires.

Quick start

Run commands from the repository root (CBCT/).

Batch DICOM metadata (requires pydicom):

python3 src/read_cbct_files.py --batch-folder path/to/dicom/folder --kind dcm

Summarize .pxv folders (defaults point at ./Data/...; override with --folders):

python3 src/process_pxv_folders.py --folders ./Data/your/study

Export LUT presets:

python3 src/process_lut_templates.py

Full pipeline (edit src/run_all.py if your DICOM path differs from the baked-in example):

python3 src/run_all.py

Browse a DICOM series (matplotlib):

python3 src/read_cbct_files.py --browse-series path/to/dicom/folder

Windows viewer bundle

Startup.bat launches PrexViewer.exe next to it. That executable and related media are not part of this Python package; they come from the vendor distribution. Use only in line with PreXion’s license and disclaimer (see any included ReadMe.txt).

License

Add a LICENSE file if you intend to open-source this repo; until then, all rights reserved unless you state otherwise.