https://github.com/Radiomics/pyradiomics
Revision 214b848e37c72c6fa1d67495d2bff61c09f0a571 authored by Andrey Fedorov on 01 August 2017, 22:53:09 UTC, committed by Andrey Fedorov on 01 August 2017, 23:02:10 UTC
It appears that the presence of this attribute in settings causes feature calculation failure in https://github.com/Radiomics/SlicerRadiomics/pull/26
1 parent c1eb7ec
Tip revision: 214b848e37c72c6fa1d67495d2bff61c09f0a571 authored by Andrey Fedorov on 01 August 2017, 22:53:09 UTC
BUG: remove inputImage from settings
BUG: remove inputImage from settings
Tip revision: 214b848
Dockerfile
# Build Pyradiomics inside the Jupyter Datascience Notebook
FROM jupyter/datascience-notebook
MAINTAINER Radiomics Project (http://github.com/radiomics)
# Build information
ARG BUILD_DATE
ARG GIT_REF
LABEL org.label-schema.build-data=$BUILD_DATE \
org.label-schema.vcs-url="https://github.com/radiomics/pyradiomics.git" \
org.label-schema.vcs-ref=$GIT_REF \
org.label-schema.schema-version="1.0.0-rc1"
USER root
ADD . /root/pyradiomics
# Install in Python 3
RUN /bin/bash -c "source activate root \
&& cd /root/pyradiomics \
&& python -m pip install --no-cache-dir -r requirements.txt \
&& python setup.py install"
# Python 2
RUN /bin/bash -c "source activate python2 \
&& cd /root/pyradiomics \
&& python -m pip install --no-cache-dir -r requirements.txt \
&& python setup.py install"
# Install sample data and notebooks
ADD data/ /home/jovyan/work/example_data/
ADD notebooks/RadiomicsExample.ipynb /home/jovyan/work/
ADD notebooks/FeatureVisualization.ipynb /home/jovyan/work/
ADD notebooks/FeatureVisualizationWithClustering.ipynb /home/jovyan/work/
ADD notebooks/FilteringEffects.ipynb /home/jovyan/work/
ADD examples/exampleSettings/Params.yaml /home/jovyan/work/
# Make a global directory and link it to the work directory
RUN mkdir /data
RUN ln -s /data /home/jovyan/work/data
RUN chown -R jovyan:users /home/jovyan/work
# Trust the notebooks that we've installed
USER jovyan
RUN jupyter trust /home/jovyan/work/*.ipynb
# Run the notebooks
RUN jupyter nbconvert --ExecutePreprocessor.kernel_name=python2 --ExecutePreprocessor.timeout=-1 --to notebook --execute /home/jovyan/work/*.ipynb
RUN jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --execute /home/jovyan/work/*.ipynb
# The user's data will show up as /data
VOLUME /data
![swh spinner](/static/img/swh-spinner.gif)
Computing file changes ...