eqip 0.5.0

EM Quasi-Isotropic Prediction

eqip

Electron-microscopy Quasi Isotropic Prediction scripts

Dependencies are specified as install_requires in setup.py. On top of that, you need the CNNectome quasi-isotropic branch on your PYTHONPATH. It is likely, yet untested, that the master branch works as well.

Install in conda enviornment on GPU cluster:

conda create -n eqip -c conda-forge -c cpape python=3.6 tensorflow-gpu=1.3
conda activate eqip
conda install -c conda-forge -c cpape pip z5py
conda install -c conda-forge scikit-image numpy scipy
conda install -c conda-forge h5py requests urllib3 idna
conda install -c conda-forge cython
conda install -c conda-forge pymongo
pip install malis==1.0
pip install git+https://github.com/hanslovsky/eqip

High Memory Usage/Unexpectedly Many Threads/Processes

Set environment, as needed:

export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export VECLIB_MAXIMUM_THREADS=1
export NUMEXPR_NUM_THREADS=1

numpy/nump#11826