opengate-gate-tree
opengate-gate-tree is a utility for processing GATE 9 output ROOT file with trees (Hits, Singles,Coincidences)
Quick Start
Install From PyPI
pip3 install opengate-gate-tree
Install From Source
make init
make install
Command-Line Options
The CLI accepts the following options:
| Option | Type | Required | Allowed values | Description |
|---|---|---|---|---|
--input-gate-root-file |
path | yes | file with .root extension |
Path to the GATE ROOT input file. |
--output-dir |
path | yes | existing directory or new path | Directory where output file will be saved. If it does not exist, it is created automatically. |
--output-file-title |
string | yes | non-empty string | Base name of the output file (without extension). |
--gate-tree |
enum-like string | yes | Hits, Singles, Coincidences |
Name of the tree to process from the input ROOT file. |
--output-file-format |
enum-like string | yes | root, hdf5, csv |
Output file format. |
--branches-to-extract |
list of strings | no | branch names valid for selected tree | Space-separated list of branches to extract. |
Validation behavior:
- the input file must exist and end with
.root - the output path must resolve to a directory
- all required options above must be provided
- branch names are validated against the selected tree
Examples:
opengate-gate-tree \
--input-gate-root-file ./data/simulation.root \
--output-dir ./out \
--output-file-title patient_01 \
--gate-tree Hits \
--output-file-format csv
opengate-gate-tree \
--input-gate-root-file ./data/simulation.root \
--output-dir ./out \
--output-file-title patient_01 \
--gate-tree Singles \
--output-file-format hdf5 \
--branches-to-extract eventID trackID edep posX
Available Package Capabilities (Cumulative)
This section is append-only.
Add a capability entry only when its roadmap stage status changes from planned to completed.
Current development stage: version-0.1.1
Available capabilities:
- 0.1.0: project structure initialized and minimal buildable package code added.
Development
Common development commands:
make lint
make format
make typecheck
make test
make check
Pre-commit setup
You can install and activate pre-commit in two supported ways.
Option A (recommended): use uv in this repository
uv add --dev pre-commit
uv sync
uv run pre-commit install --hook-type pre-commit
Optional one-time verification on all files:
uv run pre-commit run --all-files
Option B: install pre-commit from Debian packages
sudo apt update
sudo apt install -y pre-commit
pre-commit --version
pre-commit install --hook-type pre-commit
Optional one-time verification on all files:
pre-commit run --all-files
The configured hook runs make check before each commit and blocks the commit if validation fails.
Project conventions and contribution standards:
License
MIT License
Contact: GitHub
Author
The project was designed and implemented by Mateusz Jakub Bała.
Contact: GitHub
Contribution
To contribute new functionality:
- create a branch from
develop - follow the commit conventions
- open a PR using the PR template
- follow the contribution guide
1 maintainer
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