tomwer 0.7.1

Library for tomography workflow

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 0 - Create a virtual env

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

Note

To quit the virtual environment

deactivate

Step 1 - Orange3 installation

You will need a fork of the original Orange project in order to run the tomwer project. This is needed because small modification have been made in order to get the behavio we wanted (has looping workflows).

The fork is accessible here : https://github.com/payno/orange3.git

So install this fork :

pip install git+https://github.com/payno/orange3.git

Note

Orange will try to access ‘/var/log/orange’ to store logs of the last ten execusion. So if you want to keep those log make sure the directory exists.

Step 2 - tomwer

From wheel

To install it with the ‘minimal’ features:

pip install tomwer

To install it with all the potential ‘feature’:

pip install tomwer[full]

From source

clone the tomwer project

git clone [e-mail]:payno/tomwer.git

then install it

cd tomwer
pip install .

or for the ‘full’ version

pip install .[full]

Step 3 - web log

the workflow tool can send some log into graylog in order to get view of the status of the workflow execution. If this is active (by default) then you will be able to see important log from a web interface.

To get more information see https://www.graylog.org/

Launching applications

After the installation tomwer is embedding several applications.

Those applications can be launched by calling:

tomwer appName {options}

Note

if you only call tomwer then the man page will be displayed.

Note

You can access each application help using ``

tomwer appName --help

tomwer canvas - orange canvas

You can launch the canvas to create workflows from the different ‘bricks’

tomwer canvas

Note

you can also use orange-canvas

Note

if your installed a virtual environment do not forget to active it :

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

Note

the build of the documentation need sphinx to be installed. This is not an hard dependacy. So you might need to install it.

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

cd doc
make htmlhelp