add 2d/3d plotting support to base

base/Dockerfile

@@ -1,4 +1,40 @@
-FROM continuumio/miniconda3:4.8.2
+FROM ubuntu:20.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+ARG MNE_USER="mne_user"
+ARG HOME_DIR="/home/${MNE_USER}"
+ENV MNE_USER=${MNE_USER}
+ENV HOME_DIR=${HOME_DIR}
+
+ARG CONDA_DIR="/opt/conda/"
+
+# install xvfb
+RUN apt-get update && \
+    apt-get install -y xvfb wget && \
+    apt-get install -y qt5-default && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# setup entry point
+COPY prepare.sh /usr/bin/prepare.sh
+RUN chmod a+x /usr/bin/prepare.sh
+
+RUN chmod 777 /opt
+
+# setup mne user
+RUN useradd -ms /bin/bash -d ${HOME_DIR} ${MNE_USER}
+USER $MNE_USER
+WORKDIR $HOME_DIR
+
+# setup conda
+ENV PATH="${CONDA_DIR}/bin:${PATH}"
+ARG PATH="${CONDA_DIR}/bin:${PATH}"
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    sh ./Miniconda3-latest-Linux-x86_64.sh -b -p ${CONDA_DIR} && \
+    rm -f ./Miniconda3-latest-Linux-x86_64.sh && \
+    conda init
+SHELL ["/bin/bash", "--login", "-c"]
 
 RUN conda install --yes \
     -c conda-forge \
@@ -19,11 +55,14 @@ RUN conda install --yes \
     && rm -rf /opt/conda/pkgs
 
 RUN pip install s3fs
-RUN pip install mne
 RUN pip install bokeh
+RUN pip install vtk pyvista pyvistaqt PyQt5 matplotlib nibabel joblib h5py mne
 
-COPY prepare.sh /usr/bin/prepare.sh
-
-RUN mkdir /opt/app
+# setup environment for mne
+# MNE_3D_OPTION_ANTIALIAS is needed to avoid blank screenshots.
+# PYVISTA_OFF_SCREEN=true is *NOT* needed
+ENV \
+    MNE_3D_BACKEND=pyvista \
+    MNE_3D_OPTION_ANTIALIAS=false
 
 ENTRYPOINT ["tini", "-g", "--", "/usr/bin/prepare.sh"]

base/examples/test_mne_report.py

@@ -0,0 +1,31 @@
+# modified from 70_report.py
+
+import os
+import matplotlib.pyplot as plt
+import mne
+import sys
+
+path = mne.datasets.sample.data_path(verbose=True)
+
+subjects_dir = os.path.join(path, 'subjects')
+report = mne.Report(subject='sample', subjects_dir=subjects_dir,
+                    raw_psd=True, projs=True, verbose=True)
+report.parse_folder(path, render_bem=True)
+
+fname_stc = os.path.join(path, 'MEG', 'sample', 'sample_audvis-meg')
+stc = mne.read_source_estimate(fname_stc, subject='sample')
+figs = list()
+kwargs = dict(subjects_dir=subjects_dir, initial_time=0.13,
+              clim=dict(kind='value', lims=[3, 6, 9]))
+for hemi in ('lh', 'rh'):
+    brain = stc.plot(hemi=hemi, **kwargs)
+    brain.toggle_interface(False)
+    figs.append(brain.screenshot(time_viewer=True))
+    brain.close()
+
+# add the stc plot to the report:
+report.add_slider_to_section(figs)
+
+if len(sys.argv) >= 2:
+    report.save(sys.argv[1], overwrite=True, open_browser=False)
+

base/prepare.sh

@@ -26,5 +26,9 @@ if [ "$EXTRA_PIP_PACKAGES" ]; then
     /opt/conda/bin/pip install $EXTRA_PIP_PACKAGES
 fi
 
+/sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset
+sleep 3
+export DISPLAY=:99
+
 # Run extra commands
 exec "$@"