tomwer 1.6.20

Tomography workflow tools

Introduction

Tomwer provides tools to automate acquisition and reconstruction processes for tomography. The package includes:

• A library to individually access each acquisition process.

• Graphical User Interface (GUI) applications to control key processes such as reconstruction and data transfer, which can be executed as standalone applications.

• An Orange add-on to help users define custom workflows (Orange3).

Tomwer relies on Nabu for tomographic reconstruction.

Note: Currently, the software is only compatible with Linux.

Documentation

The latest version of the documentation is available here.

Installation

Step 1: Installing Tomwer

To install Tomwer with all features:

pip install tomwer[full]

Alternatively, you can install the latest development branch from the repository:

pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]

Step 2: (Optional) Update Orange-CANVAS-CORE and Orange-WIDGET-BASE

If you need access to additional ‘processing’ wheels and ‘reprocess action,’ you may want to update these Orange forks. This is optional, as the project works with the native Orange libraries.

pip install git+https://github.com/payno/orange-canvas-core --no-deps --upgrade
pip install git+https://github.com/payno/orange-widget-base --no-deps --upgrade

Launching Applications

After installation, Tomwer includes several applications. You can launch an application by running:

tomwer <appName> [options]

• If you run tomwer without arguments, a manual page will be displayed.

• For application-specific help, run:

tomwer <appName> --help

Tomwer Canvas - Orange Canvas

You can launch the Orange canvas to create workflows using the available building blocks:

tomwer canvas

• Alternatively, you can use orange-canvas.

• If you’re using a virtual environment, remember to activate it:

source myvirtualenv/bin/activate

Building Documentation

To build the documentation:

sphinx-build doc build/html

The documentation will be generated in doc/build/html, and the entry point is index.html. To view the documentation in a browser:

firefox build/html/index.html

Note: Building the documentation requires sphinx to be installed, which is not a hard dependency of Tomwer. If needed, install it separately.