tomwer

tomwer is offering tools to automate acquisition and reconstruction processes for Tomography. It contains:

• a library to access each acquisition process individually
• gui and applications to control main processes (reconstruction, data transfert...) and execute them as a stand alone application.
• an orange add-on to help users defining their own workflow (http://orange.biolab.si)

Documentation

Documentation of latest release is available at http://www.edna-site.org/pub/doc/tomwer/latest

Installation

Step 1 - Create a virtual env (recommended)

It is recommended to create a python virtual environment to run the workflow tool. Virtual environment might avoid some conflict between python packages. But you can also install it on your 'current' python environment and move to step 1.

virtualenv --python=python3 --system-site-packages myvirtualenv

Then activate the virtual environment

source myvirtualenv/bin/activate

First update pip and setuptools to avoid some potential errors

pip install --upgrade pip
pip install setuptools --upgrade

deactivate

Step 2 - tomwer (madatory)

To install it with all 'features':

pip install tomwer[full]

alternatively you can install the master branch from

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

Step 3 - update orange-canvas-core and orange-widget-base (recommended)

To access 'processing' wheels you might want to install forks of update orange-canvas-core and orange-widget-base

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

Launching applications

After the installation tomwer is embedding several applications.

Those applications can be launched by calling:

tomwer appName {options}

tomwer appName --help

tomwer canvas - orange canvas

You can launch the canvas to create workflows from the different 'bricks'

tomwer canvas

source myvirtualenv/bin/activate

Documentation

cd doc
make html

The documentation is build in doc/build/html and the entry point is index.html

firefox build/html/index.html

You also should generate documentation to be accessible from Orange GUI (pressing the F1 key).

cd doc
make htmlhelp