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ants.LaplacianThickness with a set of tests which demonstrate the problem of positional args
see e.g. nipy/nipype#2848
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‎gears/nipype/ants/segmentation/LaplacianThickness/Dockerfile

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FROM neurodebian:stretch
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FROM neurodebian:stretch-non-free
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MAINTAINER Yaroslav O. Halchenko <debian@onerussian.com>
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# TODO: use snapshots for reproducible image!
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# Install additional APT mirror for NeuroDebian for better availability/resilience
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RUN echo deb http://neurodeb.pirsquared.org data main contrib non-free >> /etc/apt/sources.list.d/neurodebian.sources.list
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RUN echo deb http://neurodeb.pirsquared.org stretch main contrib non-free >> /etc/apt/sources.list.d/neurodebian.sources.list
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# Make image reproducible based on the date/state of things in Debian/NeuroDebian
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# land.
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# Time format yyyymmdd
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RUN nd_freeze 20181221
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# To prevent interactive debconf during installations
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update && \
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apt-get install -y eatmydata
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# Make directory for flywheel spec (v0)
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# TODO: gearificator prepare-docker recipename_or_url
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# cons: would somewhat loose cached steps (pre-installation, etc)
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# For now -- entire manual template
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RUN eatmydata apt-get update && echo "count 1" && \
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eatmydata apt-get install -y --no-install-recommends python-pip python-nipype
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RUN apt-get update && echo "count 1" \
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&& apt-get install -y --no-install-recommends python-pip python-nipype \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Download/Install gearificator suite
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# TODO install git if we do via git
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RUN eatmydata apt-get install -y git python-setuptools
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RUN apt-get update \
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&& apt-get install -y git python-setuptools \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# TEMPMOVE RUN git clone git://github.com/yarikoptic/gearificator /srv/gearificator && echo 7
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# TEMPMOVE RUN pip install -e /srv/gearificator
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ENV LC_ALL C.UTF-8
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# Now we do this particular Gear specific installations
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RUN eatmydata apt-get install -y --no-install-recommends python-nipype ants
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RUN apt-get clean
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends python-nipype ants \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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RUN pip install && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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RUN git clone git://github.com/yarikoptic/gearificator /srv/gearificator && echo 7
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RUN pip install -e /srv/gearificator
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RUN pip install -e /srv/gearificator && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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COPY run ${FLYWHEEL}/run
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COPY manifest.json ${FLYWHEEL}/manifest.json

‎gears/nipype/ants/segmentation/LaplacianThickness/manifest.json

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"author": "Yaroslav O. Halchenko",
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"maintainer": "Yaroslav O. Halchenko <debian@onerussian.com>",
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"license": "BSD-3-Clause",
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"version": "0.1.dev.nipype.1.0.3.3",
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"version": "0.2.dev1.nipype.1.1.8.g597c03f64",
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"config": {
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"num_threads": {
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"type": "integer",
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},
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"dT": {
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"type": "number",
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"description": "Dt",
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"optional": true
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},
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"opt_tolerance": {
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"type": "number",
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"description": "Opt tolerance",
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"description": "Time delta used during integration (defaults to 0.01)",
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"optional": true
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},
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"prior_thickness": {
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"type": "number",
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"description": "Prior thickness",
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"description": "Prior thickness (defaults to 500)",
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"optional": true
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},
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"smooth_param": {
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"type": "number",
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"description": "Smooth param",
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"description": "Sigma of the Laplacian Recursive Image Filter (defaults to 1)",
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"optional": true
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},
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"sulcus_prior": {
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"type": "boolean",
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"description": "Sulcus prior",
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"type": "number",
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"description": "Positive floating point number for sulcus prior. Authors said that 0.15 might be a reasonable value",
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"optional": true
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},
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"tolerance": {
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"type": "number",
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"description": "Tolerance to reach during optimization (defaults to 0.001)",
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"optional": true
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}
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},
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"base": "file"
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}
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},
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"url": "http://nipype.readthedocs.io/en/1.0.3/interfaces/generated/interfaces.ants/registration.html",
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"url": "http://nipype.readthedocs.io/en/1.1.8-dev+g597c03f64/interfaces/generated/interfaces.ants/registration.html",
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"source": "https://github.com/yarikoptic/gearificator",
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"custom": {
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"gearificator": {
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"suite": "ANTS 2"
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},
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"gear-builder": {
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"image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.1.dev.nipype.1.0.3.3"
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"image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.2.dev1.nipype.1.1.8.g597c03f64"
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},
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"docker-image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.1.dev.nipype.1.0.3.3"
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"docker-image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.2.dev1.nipype.1.1.8.g597c03f64"
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},
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"label": "LaplacianThickness"
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}

‎gears/nipype/ants/segmentation/LaplacianThickness/tests/defaults.yaml

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inputs:
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input_gm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors2.nii.gz
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input_wm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors3.nii.gz
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config:
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smooth_param: 1
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prior_thickness: 500
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dT: 0.01
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# sulcus prior by default is not "engaged"
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sulcus_prior: 0
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tolerance: 0.001
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# This one should produce results identical to simple1, just different output filename

‎gears/nipype/ants/segmentation/LaplacianThickness/tests/defaults/exampleBrainSegmentationPosteriors3_thickness.nii.gz

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../simple1/gfoutput.nii.gz

‎gears/nipype/ants/segmentation/LaplacianThickness/tests/prior_thickness.yaml

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inputs:
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input_gm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors2.nii.gz
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input_wm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors3.nii.gz
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config:
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# this one to verify that it doesn't stick it into smooth_param which is positional before it
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prior_thickness: 3

‎gears/nipype/ants/segmentation/LaplacianThickness/tests/smooth_param.yaml

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inputs:
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input_gm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors2.nii.gz
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input_wm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors3.nii.gz
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config:
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# this and defaults test should wait for ... to be released
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smooth_param: 3

‎gears/nipype/ants/segmentation/LaplacianThickness/tests/smooth_param/exampleBrainSegmentationPosteriors3_thickness.nii.gz

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../../../../../../../.git/annex/objects/Zg/WW/MD5E-s24108--e48f2324c36819b02b5215420b798667.nii.gz/MD5E-s24108--e48f2324c36819b02b5215420b798667.nii.gz

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