Skip to main content

EM Quasi-Isotropic Prediction

Project description

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
eqip-0.5.0.tar.gz (27.9 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page