opengate-gate-tree

opengate-gate-tree extracts trees from GATE output ROOT files and converts them into the format that suits the analysis which follows.

It works both as a command line tool and as a library.

Supported GATE Versions

The package targets the C++ line of GATE, version 9.4.2 and newer. GATE 10, the Python implementation, is not supported.

What It Is For

Files written by this package are not meant to be read back by GATE. A typical run takes the ROOT file produced by a simulation, keeps the branches that matter for the analysis, and writes them in one of three formats:

Format	Typical consumer
root	further analysis in C++ with the ROOT framework
hdf5	analysis in Python or MATLAB, large datasets, columnar access
csv	quick inspection, spreadsheets, plain pandas.read_csv

User guide

• Quickstart
  • Requirements
  • Installation
  • First Run From The Command Line
  • First Script
  • Where To Go Next
• Using The Package As A Library
  • Public API
  • Reading A Tree
  • Working With The Data
  • Writing A File
  • Handling Failures
  • Logging
  • Structures, Merging And Statistics
  • Filtering And Selecting
  • PositroniumSource Branches
• Loading Files
  • What The Package Reads
  • Inspecting A File
  • How A Tree Is Found
  • What Reading Checks
  • Which Branch Types Are Supported
  • Selecting Branches
  • Memory
• The “Hits” Tree
  • Supported Structures
  • How A Structure Is Recognised
  • System Identifier Branches
  • What Validation Checks
  • Structures That Are Recognised But Not Supported
  • Branch Lists
• Event Identifiers
  • An Event Is A Run And An Event Together
  • Why Identifiers Are Never Renumbered
  • Telling Rows Apart After A Merge
• PositroniumSource Data
  • The Three Classes
  • Comparing A Column Against A Member
  • Selecting By What A Gamma Was
  • Reading Values As Names
  • Which Rows Carry Decay Metadata
  • In A Report
  • In A Written File
• Merging Trees
  • Reading A Split File
  • What The Package Does On Its Own
  • Where A Row Came From
  • What Merging Does Not Do
• Data Representations
  • The NumPy View
  • Selecting Branches
  • Immutability And Memory
  • The Data Frame View
  • Building Data Yourself
  • Values That Stand For Something
  • Picking Out Rows
• Filtering And Selecting
  • What Is Added, And What Is Not
  • Every Filter Comes In Two
  • Ranges
  • Shapes
  • Runs And Events
  • What A Gamma Was
  • The Process That Made A Hit
  • The gate Namespace
  • Filtering And What Follows
• Statistics
  • From The Command Line
  • From Python
  • What A Report Holds
• Exporting Files
  • Choosing A Format
  • How An Output File Is Named
  • Branch Names A Format Cannot Carry
  • Reading Your Own Output Back
  • What Each Format Preserves
  • ROOT Output
  • HDF5 Output
  • CSV Output
• Command Line
  • Options
  • Examples
  • Exit Codes
  • What Is Checked
  • Behaviour Worth Knowing
  • Running Without Installing The Script
  • Working With Split And Unusual Files

API reference

• Input and output
  • Reader
  • ROOT files
  • Validation
  • File names
  • Statistics files
  • Output formats
  • Writers
• Trees
  • Tree names
  • Tree data
  • Branch selection
  • Hits tree structures
  • Filters and selectors
  • Merging
  • Statistics
• Command line and errors
  • Errors
  • Run configuration
  • Entry point
  • Logging

Project conventions

• ROADMAP
• Contributing Guide
• Coding Conventions
• Testing Conventions
• Commit Conventions
• Version Upgrade Conventions