tomwer 0.4.0

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 :

git clone https://github.com/payno/orange3.git
cd orange3
pip install -r requirements.txt
pip install -r requirements-gui.txt
pip install .

Note

if you have an old PyQt version, you might need to have a look at https://pythonhosted.org/silx/virtualenv.html?highlight=virtualenv to avoid rebuild of sip… you might want to create a symbolic link:

If you want to use PyQt4 installed in /usr/lib/python2.7/dist-packages/:

ln -s /usr/lib/python2.7/dist-packages/PyQt4 silx_venv/lib/python2.7/site-packages/
ln -s /usr/lib/python2.7/dist-packages/sip.so silx_venv/lib/python2.7/site-packages/

Step 2 - tomwer

clone the tomwer project

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

then install it

cd tomwer
pip install -r requirements.txt
pip install -e .

Note

-e option will register the add-on into Orange, but you shouldn’t copy it into the Python’s site-packages directory. This is due to the Orange add-on installation procedure. That mean also that any modification into this source code will be apply during execution time.

Make sure the installation whent well, and that Orange is running correctly.

python run_tests.py

Unit test should be executed without any error.

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 Orange

you can simply execute the command:

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