Python

Only for courageous people that really love python. Guide to setup python to run/develop SET-pipeline without singularity image

Requirements

See Setup for basic requirements

or Setup Dev for full requirements

Annaconda

Always use environments with anaconda.

wget https://repo.anaconda.com/archive/Anaconda3-2020.07-Linux-x86_64.sh
bash Anaconda3-2020.07-Linux-x86_64.sh

source ~/.bashrc
# Remove the default install
conda config --set auto_activate_base false

Python 3.7 (for scilpy DEV)

conda create -n set37 python=3.7
conda activate set37

cd ~
mkdir src/
cd src/
git clone https://github.com/scilus/scilpy.git scilpy
cd scilpy
pip install -e .

conda install matplotlib ipython jupyter

Python 2.7 (for set DEV)

conda create -n set27 python=2.7
conda activate set27

conda install numpy scipy matplotlib ipython jupyter cython

pip install h5py==2.9.0
pip install imageio==2.4.1
pip install moviepy==0.2.3.5
pip install openpyxl==2.4.8
pip install pandas==0.20.3
pip install Pillow==5.2.0
pip install requests==2.19.1
pip install scikit-learn==0.19.0
pip install vtk==8.1.2
pip install PyMCubes==0.0.9
pip install nibabel==2.4.0
pip install git+https://github.com/MarcCote/tractconverter@master#tractconverter
pip install fury==0.4.0
pip install dipy==0.16.0
pip install trimeshpy==0.0.2

cd ~
mkdir src/
cd src/
git clone ${SCILPYB} scilpy_b
cd scilpy_b

python setup.py build_all
pip install -e .

Python 2.7 (for set-nf)

set_dipy.tar.bz2 & set_scilpy.tar.bz2

conda create -n set27 python=2.7
conda activate set27

conda install numpy scipy matplotlib ipython jupyter cython

pip install h5py==2.9.0
pip install imageio==2.4.1
pip install moviepy==0.2.3.5
pip install openpyxl==2.4.8
pip install pandas==0.20.3
pip install Pillow==5.2.0
pip install requests==2.19.1
pip install scikit-learn==0.19.0
pip install vtk==8.1.2
pip install PyMCubes==0.0.9
pip install nibabel==2.4.0
pip install git+https://github.com/MarcCote/tractconverter@master#tractconverter
pip install fury==0.4.0
pip install dipy==0.16.0
pip install cythongsl==0.2.2
pip install trimeshpy==0.0.2

# unzip packages
mkdir ~/src_set
mkdir ~/src_set/dipy
tar -jxf set_dipy.tar.bz2 -C ~/src_set/dipy

mkdir ~/src_set/scilpy
tar -jxf set_scilpy.tar.bz2 -C ~/src_set/scilpy


# Install dipy
cd  ~/src_set/dipy
pip install .

# Install scilpy (SET)
cd /src_set/scilpy
python setup.py build_all
#sed -i '38s/.*/backend : Agg/' /usr/local/lib/python2.7/dist-packages/matplotlib/mpl-data/matplotlibrc
pip install -e .