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The Cytomine-Python-client and Cytomine-Python-DataMining packages are already installed together with other Cytomine components using our regular Docker installation. These algorithms can be executed from the Cytomine-WebUi (see user guide). Indeed, following the standard installation procedure, algorithms are installed locally in the software_router docker container and we use RabbitMQ to send messages from Cytomine-WebUi/Cytomine-Core to the corresponding docker container. You can have access to algorithm code and logs here:
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./Miniconda2-latest-Linux-x86_64.sh -b -p $HOME/miniconda2
export PATH="$HOME/miniconda2/bin:$PATH"
conda create -n cytomine python=2.7 shapely opencv scikit-learn pillow joblib
cython
source activate cytomine |
In order to avoid having to update you path everytime you come back on you machine, you might want to append the export command (line 2) at the end of the ~/.bashrc file and then run:
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2.3 Install pyxit (located in cytomine-datamining/algorithms/pyxit/)
Cythonize, compile and install Install pyxit:
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cd $HOME/Cytomine/Cytomine-python-datamining/cytomine-datamining/algorithms/pyxit/
cython _estimator.pyx
python setup.py build
python setup.py install |
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