ants.LaplacianThickness with a set of tests which demonstrate the pro…

…blem of positional args

see e.g. nipy/nipype#2848

gears/nipype/ants/segmentation/LaplacianThickness/Dockerfile

@@ -1,26 +1,27 @@
-FROM neurodebian:stretch
+FROM neurodebian:stretch-non-free
 MAINTAINER Yaroslav O. Halchenko <[email protected]>
 
-# TODO: use snapshots for reproducible image!
-# Install additional APT mirror for NeuroDebian for better availability/resilience
-RUN echo deb http://neurodeb.pirsquared.org data main contrib non-free >> /etc/apt/sources.list.d/neurodebian.sources.list
-RUN echo deb http://neurodeb.pirsquared.org stretch main contrib non-free >> /etc/apt/sources.list.d/neurodebian.sources.list
+# Make image reproducible based on the date/state of things in Debian/NeuroDebian
+# land.
+# Time format yyyymmdd 
+RUN nd_freeze 20181221
 
 # To prevent interactive debconf during installations
 ARG DEBIAN_FRONTEND=noninteractive
-RUN apt-get update && \
-    apt-get install -y eatmydata
 
 # Make directory for flywheel spec (v0)
 # TODO:  gearificator prepare-docker recipename_or_url
 # cons: would somewhat loose cached steps (pre-installation, etc)
 # For now -- entire manual template
-RUN eatmydata apt-get update && echo "count 1" && \
-    eatmydata apt-get install -y --no-install-recommends python-pip python-nipype
+RUN apt-get update && echo "count 1" \
+    && apt-get install -y --no-install-recommends python-pip python-nipype \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Download/Install gearificator suite
 # TODO  install git if we do via git
-RUN eatmydata apt-get install -y git python-setuptools
+RUN apt-get update \ 
+    && apt-get install -y git python-setuptools \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 # TEMPMOVE RUN git clone git://github.com/yarikoptic/gearificator /srv/gearificator && echo 7
 # TEMPMOVE RUN pip install -e /srv/gearificator
 
@@ -32,12 +33,15 @@ RUN mkdir -p ${FLYWHEEL}
 ENV LC_ALL C.UTF-8
 
 # Now we do this particular Gear specific installations
-RUN eatmydata apt-get install -y --no-install-recommends python-nipype ants
-RUN apt-get clean
 
+RUN apt-get update \ 
+    && apt-get install -y --no-install-recommends python-nipype ants \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+RUN pip install  && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 RUN git clone git://github.com/yarikoptic/gearificator /srv/gearificator && echo 7
-RUN pip install -e /srv/gearificator
+RUN pip install -e /srv/gearificator && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 COPY run ${FLYWHEEL}/run
 COPY manifest.json ${FLYWHEEL}/manifest.json

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

@@ -4,7 +4,7 @@
   "author": "Yaroslav O. Halchenko",
   "maintainer": "Yaroslav O. Halchenko <[email protected]>",
   "license": "BSD-3-Clause",
-  "version": "0.1.dev.nipype.1.0.3.3",
+  "version": "0.2.dev1.nipype.1.1.8.g597c03f64",
   "config": {
     "num_threads": {
       "type": "integer",
@@ -18,27 +18,27 @@
     },
     "dT": {
       "type": "number",
-      "description": "Dt",
-      "optional": true
-    },
-    "opt_tolerance": {
-      "type": "number",
-      "description": "Opt tolerance",
+      "description": "Time delta used during integration (defaults to 0.01)",
       "optional": true
     },
     "prior_thickness": {
       "type": "number",
-      "description": "Prior thickness",
+      "description": "Prior thickness (defaults to 500)",
       "optional": true
     },
     "smooth_param": {
       "type": "number",
-      "description": "Smooth param",
+      "description": "Sigma of the Laplacian Recursive Image Filter (defaults to 1)",
       "optional": true
     },
     "sulcus_prior": {
-      "type": "boolean",
-      "description": "Sulcus prior",
+      "type": "number",
+      "description": "Positive floating point number for sulcus prior. Authors said that 0.15 might be a reasonable value",
+      "optional": true
+    },
+    "tolerance": {
+      "type": "number",
+      "description": "Tolerance to reach during optimization (defaults to 0.001)",
       "optional": true
     }
   },
@@ -57,7 +57,7 @@
       "base": "file"
     }
   },
-  "url": "http://nipype.readthedocs.io/en/1.0.3/interfaces/generated/interfaces.ants/registration.html",
+  "url": "http://nipype.readthedocs.io/en/1.1.8-dev+g597c03f64/interfaces/generated/interfaces.ants/registration.html",
   "source": "https://github.com/yarikoptic/gearificator",
   "custom": {
     "gearificator": {
@@ -73,9 +73,9 @@
       "suite": "ANTS 2"
     },
     "gear-builder": {
-      "image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.1.dev.nipype.1.0.3.3"
+      "image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.2.dev1.nipype.1.1.8.g597c03f64"
     },
-    "docker-image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.1.dev.nipype.1.0.3.3"
+    "docker-image": "gearificator/nipype-interfaces-ants-segmentation-laplacianthickness:0.2.dev1.nipype.1.1.8.g597c03f64"
   },
   "label": "LaplacianThickness"
 }

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

@@ -0,0 +1,11 @@
+inputs:
+ input_gm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors2.nii.gz
+ input_wm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors3.nii.gz
+config:
+ smooth_param: 1
+ prior_thickness: 500
+ dT: 0.01
+ # sulcus prior by default is not "engaged"
+ sulcus_prior: 0
+ tolerance: 0.001
+ # This one should produce results identical to simple1, just different output filename

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

@@ -0,0 +1 @@
+../simple1/gfoutput.nii.gz

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

@@ -0,0 +1,6 @@
+inputs:
+ input_gm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors2.nii.gz
+ input_wm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors3.nii.gz
+config:
+ # this one to verify that it doesn't stick it into smooth_param which is positional before it
+ prior_thickness: 3

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

@@ -0,0 +1,6 @@
+inputs:
+ input_gm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors2.nii.gz
+ input_wm: antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors3.nii.gz
+config:
+ # this and defaults test should wait for ... to be released
+ smooth_param: 3

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

@@ -0,0 +1 @@
+../../../../../../../.git/annex/objects/Zg/WW/MD5E-s24108--e48f2324c36819b02b5215420b798667.nii.gz/MD5E-s24108--e48f2324c36819b02b5215420b798667.nii.gz