Installation

  • If you install from a Debian package you can skip the following points, install it , and then go directly to the code invocation section

  • Using Git, sources can be retrived with the following commands: * public access

    git clone  https://gitlab.esrf.fr/mirone/tds2el.git

    • private access

      git clone git@gitlab.esrf.fr:mirone/tds2el.git

  • Branch version_1 is meant to work with the paper examples

and being usable. For a more updated branch use master branch. To retrieve such version sources, after cloning, go to tds2el directory and

git checkout version_1

But master will follow better the more recent developments. in particular TDS2EL2 the new version with the workgflow integrated in a unique GUI.

  • The installation process install both tds2el ( the original program of the prl paper ) and tds2el2.

  • The recomended installation is through the virtual environment environment. Alternatively a local installation may work

    virtualenv --python=python3 ~/software/VE_python3

for a python3 environment, or

virtualenv --python=python2 ~/software/VE_python2

So far the tds2el2 ( the new code) works on both 2 and 3. The old code works instead only on python2. Be sure that you unset spurious environment variables

unset LD_LIBRARY_PATH
unset LDFLAGS
unset CPPFLAGS
unset PYTHONPATH

you will need to load external packages, therefore manage the firewall variables, at esrf

export http_proxy=http://XXX.YYY.ZZZ:1234
export https_proxy=https://XXX.YYY.ZZZ:1234
(At ESRF ask to the TID for the exact location of the proxy)
export no_proxy="localhost,.esrf.fr"

Activate the virtualEnv

source ~/software/VE_python(2,3)/bin/activate # choose between 2 or 3 and remove ()

Upgrade your pip

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

Now you need to install a number of dependencies. If you plan to use only the new tds2el2 code

pip install git+https://github.com/silx-kit/silx   # get latest version of silx

# for python3 install pyqt5
   pip install pyqt5
# or install this on python2
   pip  install pySide2

pip install cython
pip install h5py
pip install scipy
pip install fabio
pip install PyOpenGL
pip install pyyaml
pip install pyfftw

Extra Packages

  • ab2tds

This is all for tds2el2. If you also need to use the old tds2el code

pip install pyopencl    # necessary if you plan to use the old version. not used in tds2el2
pip install matplotlib  # for the old version
pip install pymca5      # for the old version
pip install mpi4py      # for the old version

Still for the old version, 3D rendering of spots in reciprocal space is based on pymol. You may not need it if you dont want to perform such visualisation. On many linux distribution pymol is already available as a package and you can use it if you do a local installation of tds2el. We are here documenting the virtualEnv installation so, If you want it, you have to install it in your virtual environment. To do so

sudo apt-get install libglew-dev       # for the old version. Install libs needed to compile pymol
sudo apt-get install libglm-dev        # for the old version. Install libs needed to compile pymol
sudo apt-get install freeglut3-dev     # for the old version. Install libs needed to compile pymol
cd ~/software                                                     # for the old version. To install pymol
git clone https://github.com/schrodinger/pymol-open-source.git    # for the old version. To install pymol
cd pymol-open-source                                              # for the old version. To install pymol
python setup.py build install                                     # for the old version. To install pymol

Now go into the tds2el directory and run the installation command

python setup.py install

Then you are ready to run the code. If you have sourced

source ~/software/VE_python(2,3)/bin/activate  # choose 2 or 3 and remove ()

you have the executable in the path.

  • For the documentation go, from the source root directory, to doc subdirectory and

    make html

it will create the html pages into _build/html subdirectory.