8000 ENH: Add naive isotropic smoothing by effigies · Pull Request #104 · poldracklab/fitlins · GitHub
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ENH: Add naive isotropic smoothing #104

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Merged
merged 5 commits into from
Feb 4, 2019
Merged

ENH: Add naive isotropic smoothing #104

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240a994
ENH: Add naive isotropic smoothing
effigies Feb 1, 2019
362d8c2
MNT: Regenerate Dockerfile, save neurodocker config
effigies Feb 4, 2019
3d64266
MNT: Drop PYTHON_VERSION args
effigies Feb 4, 2019
572c1ef
ENH: Install traits from conda, activate conda env
effigies Feb 4, 2019
5fa5560
FIX: Make -s return a string
effigies Feb 4, 2019
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1 change: 1 addition & 0 deletions .neurodocker.json
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{"pkg_manager": "apt", "instructions": [["base", "neurodebian@sha256:5fbbad8c68525b588a459092254094436aae9dc1f3920f8d871a03053b10377c"], ["label", {"maintainer": "Christopher J. Markiewicz"}], ["env", {"MKL_NUM_THREADS": "1", "OMP_NUM_THREADS": "1"}], ["fsl", {"version": "5.0.11"}], ["user", "neuro"], ["miniconda", {"create_env": "neuro", "conda_install": ["python=3.6", "icu=58.1", "mkl=2018.0.1", "mkl-service", "git=2.9.3"]}], ["miniconda", {"use_env": "neuro", "conda_install": ["numpy=1.16.1", "scipy=1.2.0", "scikit-learn=0.19.1", "matplotlib=3.0.2", "seaborn=0.9.0", "pytables=3.4.4", "pandas=0.24.1", "patsy", "traits"]}], ["copy", [".", "/src/fitlins"]], ["user", "root"], ["arg", {"VERSION": ""}], ["run", "echo \"$VERSION\" > /src/fitlins/fitlins/VERSION"], ["run", "mkdir /work && chown -R neuro /src /work && chmod a+w /work"], ["user", "neuro"], ["miniconda", {"use_env": "neuro", "pip_opts": "-r", "pip_install": ["/src/fitlins/requirements.txt"]}], ["miniconda", {"use_env": "neuro", "pip_opts": "-e", "pip_install": ["/src/fitlins[all]"], "activate": true}], ["workdir", "/work"], ["entrypoint", "/neurodocker/startup.sh fitlins"], ["arg", {"BUILD_DATE": "", "VCS_REF": ""}], ["label", {"org.label-schema.build-date": "$BUILD_DATE", "org.label-schema.name": "FitLins", "org.label-schema.description": "FitLins - Fit Linear Models to BIDS datasets", "org.label-schema.url": "http://github.com/poldracklab/fitlins", "org.label-schema.vcs-ref": "$VCS_REF", "org.label-schema.vcs-url": "https://github.com/poldracklab/fitlins", "org.label-schema.version": "$VERSION", "org.label-schema.schema-version": "1.0"}]]}
240 changes: 144 additions & 96 deletions Dockerfile
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# Generated by Neurodocker v0.3.2.
#
# Generated by Neurodocker version 0.4.3-6-g12a2b6f
# Timestamp: 2019-02-04 19:47:24 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/kaczmarj/neurodocker
#
# Timestamp: 2018-05-23 00:49:26

FROM neurodebian@sha256:5fbbad8c68525b588a459092254094436aae9dc1f3920f8d871a03053b10377c

ARG DEBIAN_FRONTEND=noninteractive
ARG DEBIAN_FRONTEND="noninteractive"

#----------------------------------------------------------
# Install common dependencies and create default entrypoint
#----------------------------------------------------------
ENV LANG="en_US.UTF-8" \
LC_ALL="C.UTF-8" \
LC_ALL="en_US.UTF-8" \
ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
apt-utils bzip2 ca-certificates curl locales unzip \
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& localedef --force --inputfile=en_US --charmap=UTF-8 C.UTF-8 \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
&& update-locale LANG="en_US.UTF-8" \
&& chmod 777 /opt && chmod a+s /opt \
&& mkdir -p /neurodocker \
&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
&& echo 'set +x' >> $ND_ENTRYPOINT \
&& echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
fi \
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
&& echo 'set -e' >> "$ND_ENTRYPOINT" \
&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

LABEL maintainer="Christopher J. Markiewicz"

ARG PYTHON_VERSION_MAJOR="3"
ARG PYTHON_VERSION_MINOR="6"

ENV MKL_NUM_THREADS="1" \
OMP_NUM_THREADS="1"

# Create new user: neuro
RUN useradd --no-user-group --create-home --shell /bin/bash neuro
ENV FSLDIR="/opt/fsl-5.0.11" \
PATH="/opt/fsl-5.0.11/bin:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
wget \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-5.0.11 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-5.0.11 --strip-components 1 \
&& sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
&& sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
&& sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
&& sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-5.0.11/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.11

RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro

#------------------
# 8000 Install Miniconda
#------------------
ENV CONDA_DIR=/opt/conda \
PATH=/opt/conda/bin:$PATH
RUN echo "Downloading Miniconda installer ..." \
&& miniconda_installer=/tmp/miniconda.sh \
&& curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& /bin/bash $miniconda_installer -b -p $CONDA_DIR \
&& rm -f $miniconda_installer \
ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
&& echo "Downloading Miniconda installer ..." \
&& conda_installer="/tmp/miniconda.sh" \
&& curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash "$conda_installer" -b -p /opt/miniconda-latest \
&& rm -f "$conda_installer" \
&& conda update -yq -nbase conda \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& conda update -n base conda \
&& conda clean -tipsy && sync

#-------------------------
# Create conda environment
#-------------------------
RUN conda create -y -q --name neuro python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} \
icu=58.1 \
mkl=2018.0.1 \
mkl-service \
git=2.9.3 \
&& sync && conda clean -tipsy && sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
&& conda create -y -q --name neuro \
&& conda install -y -q --name neuro \
'python=3.6' \
'icu=58.1' \
'mkl=2018.0.1' \
'mkl-service' \
'git=2.9.3' \
&& sync && conda clean -tipsy && sync

#-------------------------
# Update conda environment
#-------------------------
RUN conda install -y -q --name neuro numpy=1.14.1 \
scipy=1.0.0 \
scikit-learn=0.19.1 \
matplotlib=2.1.2 \
seaborn=0.8.1 \
pytables=3.4.2 \
pandas=0.22.0 \
nipype=1.1.1 \
patsy \
RUN conda install -y -q --name neuro \
'numpy=1.16.1' \
'scipy=1.2.0' \
'scikit-learn=0.19.1' \
'matplotlib=3.0.2' \
'seaborn=0.9.0' \
'pytables=3.4.4' \
'pandas=0.24.1' \
'patsy' \
'traits' \
&& sync && conda clean -tipsy && sync

COPY [".", "/src/fitlins"]
Expand All @@ -91,28 +120,24 @@ USER root

ARG VERSION

# User-defined instruction
RUN echo "$VERSION" > /src/fitlins/fitlins/VERSION

# User-defined instruction
RUN mkdir /work && chown -R neuro /src /work
RUN mkdir /work && chown -R neuro /src /work && chmod a+w /work

USER neuro

#-------------------------
# Update conda environment
#-------------------------
RUN /bin/bash -c "source activate neuro \
&& pip install --no-cache-dir --upgrade pip \
&& pip install -q --no-cache-dir --upgrade -r /src/fitlins/requirements.txt" \
RUN bash -c "source activate neuro \
&& pip install --no-cache-dir -r \
'/src/fitlins/requirements.txt'" \
&& rm -rf ~/.cache/pip/* \
&& sync

#-------------------------
# Update conda environment
#-------------------------
RUN /bin/bash -c "source activate neuro \
&& pip install -q --no-cache-dir -e /src/fitlins[all]" \
&& sync
RUN bash -c "source activate neuro \
&& pip install --no-cache-dir -e \
'/src/fitlins[all]'" \
&& rm -rf ~/.cache/pip/* \
&& sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT

WORKDIR /work

Expand All @@ -130,12 +155,8 @@ LABEL org.label-schema.build-date="$BUILD_DATE" \
org.label-schema.version="$VERSION" \
org.label-schema.schema-version="1.0"

#--------------------------------------
# Save container specifications to JSON
#--------------------------------------
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "check_urls": false, \
\n "instructions": [ \
\n [ \
\n "base", \
Expand All @@ -148,20 +169,16 @@ RUN echo '{ \
\n } \
\n ], \
\n [ \
\n "arg", \
\n "env", \
\n { \
\n "PYTHON_VERSION_MAJOR": "3", \
\n "PYTHON_VERSION_MINOR": "6", \
\n "BUILD_DATE": "", \
\n "VCS_REF": "", \
\n "VERSION": "" \
\n "MKL_NUM_THREADS": "1", \
\n "OMP_NUM_THREADS": "1" \
\n } \
\n ], \
\n [ \
\n "env", \
\n "fsl", \
\n { \
\n "MKL_NUM_THREADS": "1", \
\n "OMP_NUM_THREADS": "1" \
\n "version": "5.0.11" \
\n } \
\n ], \
\n [ \
Expand All @@ -171,16 +188,31 @@ RUN echo '{ \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "activate": true, \
\n "conda_install": "python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} icu=58.1 mkl=2018.0.1 mkl-service git=2.9.3" \
\n "create_env": "neuro", \
\n "conda_install": [ \
\n "python=3.6", \
\n "icu=58.1", \
\n "mkl=2018.0.1", \
\n "mkl-service", \
\n "git=2.9.3" \
\n ] \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "conda_install": "numpy=1.14.1 scipy=1.0.0 scikit-learn=0.19.1 matplotlib=2.1.2 seaborn=0.8.1 pytables=3.4.2 pandas=0.22.0 nipype=1.0.3 patsy" \
\n "use_env": "neuro", \
\n "conda_install": [ \
\n "numpy=1.16.1", \
\n "scipy=1.2.0", \
\n "scikit-learn=0.19.1", \
\n "matplotlib=3.0.2", \
\n "seaborn=0.9.0", \
\n "pytables=3.4.4", \
\n "pandas=0.24.1", \
\n "patsy", \
\n "traits" \
\n ] \
\n } \
\n ], \
\n [ \
Expand All @@ -195,12 +227,18 @@ RUN echo '{ \
\n "root" \
\n ], \
\n [ \
\n "arg", \
\n { \
\n "VERSION": "" \
\n } \
\n ], \
\n [ \
\n "run", \
\n "echo \"$VERSION\" > /src/fitlins/fitlins/VERSION" \
\n ], \
\n [ \
\n "run", 9E88 \
\n "mkdir /work && chown -R neuro /src /work" \
\n "mkdir /work && chown -R neuro /src /work && chmod a+w /work" \
\n ], \
\n [ \
\n "user", \
Expand All @@ -209,17 +247,22 @@ RUN echo '{ \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "use_env": "neuro", \
\n "pip_opts": "-r", \
\n "pip_install": "/src/fitlins/requirements.txt" \
\n "pip_install": [ \
\n "/src/fitlins/requirements.txt" \
\n ] \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "use_env": "neuro", \
\n "pip_opts": "-e", \
\n "pip_install": "/src/fitlins[all]" \
\n "pip_install": [ \
\n "/src/fitlins[all]" \
\n ], \
\n "activate": true \
\n } \
\n ], \
\n [ \
Expand All @@ -231,6 +274,13 @@ RUN echo '{ \
\n "/neurodocker/startup.sh fitlins" \
\n ], \
\n [ \
\n "arg", \
\n { \
\n "BUILD_DATE": "", \
\n "VCS_REF": "" \
\n } \
\n ], \
\n [ \
\n "label", \
\n { \
\n "org.label-schema.build-date": "$BUILD_DATE", \
Expand All @@ -243,7 +293,5 @@ RUN echo '{ \
\n "org.label-schema.schema-version": "1.0" \
\n } \
\n ] \
\n ], \
\n "generation_timestamp": "2018-05-23 00:49:26", \
\n "neurodocker_version": "0.3.2" \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
9 changes: 8 additions & 1 deletion fitlins/cli/run.py
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Expand Up @@ -95,6 +95,12 @@ def get_parser():
g_bids.add_argument('--desc-label', action='store', default='preproc',
help="use BOLD files with the provided description label")

g_prep = parser.add_argument_group('Options for preprocessing BOLD series')
g_prep.add_argument('-s', '--smoothing', action='store', metavar="TYPE:FWHM",
help="Smooth BOLD series with FWHM mm kernel prior to fitting. "
"Valid types: iso (isotropic); "
"e.g. `--smothing iso:5` will use an isotropic 5mm FWHM kernel")

g_perfm = parser.add_argument_group('Options to handle performance')
g_perfm.add_argument('--n-cpus', action='store', default=0, type=int,
help='maximum number of threads across all processes')
Expand Down Expand Up @@ -168,7 +174,8 @@ def run_fitlins(argv=None):
desc=opts.desc_label,
model=model,
participants=subject_list, base_dir=work_dir,
include_pattern=opts.include, exclude_pattern=opts.exclude
include_pattern=opts.include, exclude_pattern=opts.exclude,
smoothing=opts.smoothing,
)

retcode = 0
Expand Down
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