HTTomo (High Throughput Tomography pipeline)

HTTomo is a user interface (UI) written in Python for fast big data processing using MPI protocols. It orchestrates I/O data operations and enables processing on a CPU and/or a GPU. HTTomo utilises other libraries, such as TomoPy and HTTomolibgpu as backends for data processing. The methods from the libraries are exposed through YAML templates to enable fast task programming.

Installation

See detailed instructions for installation .

Documentation

Please check the full documentation.

Running HTTomo:

• Install the module following any chosen installation path.

• For help with the command line interface, execute python -m httomo --help

• Choose the existing YAML pipeline or build a new one using ready-to-be-used templates.

• Optional: perform the validity check of the YAML pipeline file with the YAML checker.

• Run HTTomo with python -m httomo run [OPTIONS] IN_DATA_FILE YAML_CONFIG OUT_DIR, see more on that here.

Release Tagging Scheme

We use the setuptools-git-versioning package for automatically determining the version from the latest git tag. For this to work, release tags should start with a v followed by the actual version, e.g. v1.1.0a.

Introduction

• HTTomo concept
  • Detailed concepts
• What is a template?
• What is a process list?
• Frequently Asked Questions
  • Working from a workstation at Diamond Light Source

How To's

• Installation Guide
  • Virtual environment
  • Conda environment
  • Setup HTTomo development environment:
• How to run HTTomo
  • Quick Overview of Running HTTomo
  • In-depth Look at Running HTTomo
• Process Lists Guide
  • Editing process lists
  • Methods order
• HTTomo Features
  • Previewing
  • Centre of Rotation (CoR)
  • Parameter Sweeping
  • Padding
• Interpret Log File

Reference guides

• What is YAML?
  • Format examples
• HTTomo Loaders
  • Available Loaders
  • Basic Usage of the Standard Loader
  • Dealing with darks and flats
  • Providing/Overriding Angles Data
  • Previewing
  • Continuous Scan Subset Selection

Data processing

• Supported libraries
  • HTTomolibgpu library (GPU)
  • HTTomolib library (CPU)
  • TomoPy software (CPU)
• Methods YAML Templates
  • Archived Templates
  • Latest Templates

Ready-to-use pipelines

• Full YAML pipelines
  • Pipelines for released HTTomo versions
  • Pipelines using HTTomo libraries
  • DLS-specific pipelines
  • Pipelines with parameter sweeps
  • Pipelines using TomoPy library

Utilities

• YAML Checker - Why use it?
  • Usage
  • What else do we check with the YAML checker?

Developers

• How to contribute
• GPU memory calculations
  • Max Slices Tests
• API
  • httomo.cli_utils
  • httomo.darks_flats
  • httomo.data
  • httomo.globals
  • httomo.logger
  • httomo.monitors
  • httomo.preview
  • httomo.runner
  • httomo.sweep_runner