Installation

Windows

Python

Install a Python 3 environment, e.g.

and make sure the following packages are installed:

  • numpy, matplotlib, pandas, sphinx

For the case of missing packages you can either use conda (provided the Anaconda stack was installed)

conda install numpy matplotlib scipy pandas sphinx

or pip

pip install numpy matplotlib scipy pandas sphinx

Setup a working directory

Create the directory: C:\crtomo and the following subdirectories:

* C:\\crtomo\\bin
* C:\\crtomo\\git

The directory C:\crtomo\bin will contain executables whereas C:\crtomo\git is intended for the different git repositories of the CRTomo-ecosystem. For further information about git and the maintenance of the repositories please refer to the upcoming section.

Git

Install git https://git-scm.com/download/win and get yourself familiar with the following git commands:

  • git clone
  • git pull / git push
  • git add
  • git commit
  • git branch
  • git checkout
  • git merge

Simply clone the following repositories

git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_doc.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_test.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_tools.git

into the corresponding folder C:\crtomo\git.

GMSH

Install gmsh: http://gmsh.info/ and copy the associated executable gmsh.exe to C:\crtomo\bin.

Compiling CRTomo, CRMod and CutMcK

For the compilation on Windows machines it is necessary to install MSYS2: https://www.msys2.org/. After the installation open the MSYS2 MinGW 64-bit console and install the following packages:

pacman -Syu
pacman -Sy pacman
pacman -S git
pacman -S automake
pacman -S autoconf
pacman -S mingw-w64-x86_64-gcc
pacman -S mingw-w64-x86_64-toolchain
pacman -S make

Still in the console, clone the repository

git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo.git

into the home folder of the MSYS2 install (e.g. C:\msys64\home). Then change to the cloned directory and run

./autogen.sh

Please make sure that line 25 in the file configure.ac writes:

  • AM_FC_FLAGS=”-static-libgcc -static”

and then compile the files with:

./configure --host=x86_64-w64-mingw32
./make

The CRTomo and CRMod executables can then be found in the subdirectory src. The executable for CutMcK is located in the subdirectory cutmckee. Please rename the files in the following manner crtomo.exe, crtmod.exe, cutmck.exe and copy them to the corresponding directory C:\crtomo\bin.

Linux

Todo

jg: add installation description for common linux distributions (debian, arch, suse, ?)

Python

Install a Python 3 environment and make sure the following packages are installed:

  • numpy, matplotlib, pandas, sphinx

For the case of missing packages you can either use conda (provided the Anaconda stack was installed)

conda install numpy matplotlib scipy pandas sphinx

or pip

pip install numpy matplotlib scipy pandas sphinx

Virtualenv

virtualenv is a tool to create isolated Python environments. Edit: How to install Virtualenv

Creat a virtual environment

mkvirtualenv --python /usr/bin/python3 NAME

with NAME as the name of your virtual environment. For e.g. CRTomo tool you can set NAME to crtomo or for EDF to edf. Open your virtual environment with

workon *NAME*

Setup a working directory

Create the directory: /home/USERNAME/crtomo and subdirectories for the different git repositiries.

Git

Install git and get yourself familiar with the following git commands:

  • git clone
  • git pull / git push
  • git add
  • git commit
  • git branch
  • git checkout
  • git merge

Simply clone the following repositories

git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_doc.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_test.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_tools.git

into the corresponding folder /home/USERNAME/crtomo.

For EDF/P4 clone the following repository (private from M. Weigand):

git clone ssh://git@ssh.geo.uni-bonn.de:4422/mweigand/EDF.git

For SIP-models clone the following repository (private from M. Weigand):

git clone ssh://git@ssh.geo.uni-bonn.de:4422/mweigand/sip_models.git

Example: Installation of EDF plus CRTomo tools and SIP-models

First, install Python and mkvirtualenv as described above. Second, install git and clone the following repositories

git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_doc.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/crtomo/crtomo_tools.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/mweigand/EDF.git
git clone ssh://git@ssh.geo.uni-bonn.de:4422/mweigand/sip_models.git

Go to the EDF directory …crtomoEDF and create the work environment (named edf) using the following commands:

mkvirtualenv --python /usr/bin/python3 edf
pip install --upgrade pip
workon edf
pip install -r requirements.txt
pip install ipython

In addition, install CRTomo tools in your environment. Got to the CRTomo tools directory …crtomocrtomo_tools and use the following commands:

pip install -r requirements.txt
python setup.py install

You should also install SIP-models tools in your environment. Got to the SIP-models directory …crtomosip_models and use the following commands:

pip install -U pip
pip install -U numpy matplotlib scipy pandas shapely
pip install -r requirements.txt
python setup.py install