Merge pull request #219 from oesteban/enh/RefactorAnatomical

[ENH] Large refactoring of anatomical workflow

.pylintrc

@@ -1,2 +1,14 @@
 [pre-commit-hook]
 limit=8.1
+
+
+[MESSAGES CONTROL]
+# Disable the following PyLint messages:
+# W0621: Redefining name %r from outer scope (line %s)
+# W0622: Redefining built-in %r
+disable-msg=W0621,W0622
+
+
+[FORMAT]
+# Maximum number of characters on a single line.
+max-line-length=99

circle.yml

@@ -20,9 +20,9 @@ dependencies:
     # Create scratch folder and force group permissions
     - mkdir -p $SCRATCH && sudo setfacl -d -m group:ubuntu:rwx $SCRATCH && sudo setfacl -m group:ubuntu:rwx $SCRATCH
     - if [[ ! -d ~/data/ds003_downsampled ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O ds003_downsampled.tar.gz "${DS003_URL}" && tar xzf ds003_downsampled.tar.gz -C ~/data/; fi
-    - pip install "niworkflows>=0.0.3a11"
+    - pip install "niworkflows>=0.0.3a14"
   override:
-    - python -c "from niworkflows import data as nwd; nwd.get_mni_template(); nwd.get_ds003_downsampled(); nwd.get_brainweb_1mm_normal()"
+    - python -c "from niworkflows import data as nwd; nwd.get_mni_icbm152_nlin_asym_09c(); nwd.get_ds003_downsampled(); nwd.get_brainweb_1mm_normal()"
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/Dockerfile_py35 -t mriqc:py35 .
     - docker build -f docker/Dockerfile_py27 -t mriqc:py27 .
@@ -35,7 +35,7 @@ test:
         timeout: 2600
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/.cache/stanford-crn:/root/.cache/stanford-crn -v ~/data:/data:ro -v $SCRATCH/func:/scratch -w /scratch mriqc:py35 /data/ds003_downsampled out/ participant -d func -w work/ --nthreads ${FUNC_NPROCS} --testing
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH/func:/scratch -w /scratch mriqc:py35 /data/ds003_downsampled out/ group -d func -w work/
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/.cache/stanford-crn:/root/.cache/stanford-crn -v ~/data:/data:ro -v $SCRATCH/anat:/scratch -w /scratch mriqc:py35 /data/ds003_downsampled out/ participant -d anat -w work/ --nthreads ${ANAT_NPROCS} --testing --ants-nthreads ${ANTS_NTHREADS}:
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/.cache/stanford-crn:/root/.cache/stanford-crn -v ~/data:/data:ro -v $SCRATCH/anat:/scratch -w /scratch mriqc:py35 /data/ds003_downsampled out/ participant -d anat -w work/ --nthreads ${ANAT_NPROCS} --testing --ants-nthreads ${ANTS_NTHREADS} --verbose-reports :
         timeout: 2600
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH/anat:/scratch -w /scratch mriqc:py27 /data/ds003_downsampled out/ group -d anat -w work/
 

mriqc/data/__init__.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+from __future__ import absolute_import, division, print_function, unicode_literals
+
+from .config import Template, IndividualTemplate

mriqc/data/config.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Utilities: Jinja2 templates
+"""
+from __future__ import absolute_import, division, print_function, unicode_literals
+
+from io import open  # pylint: disable=W0622
+import jinja2
+from pkg_resources import resource_filename as pkgrf
+
+
+class Template(object):
+    """
+    Utility class for generating a config file from a jinja template.
+    https://github.com/oesteban/endofday/blob/f2e79c625d648ef45b08cc1f11fd0bd84342d604/endofday/core/template.py
+    """
+    def __init__(self, template_str):
+        self.template_str = template_str
+        self.env = jinja2.Environment(
+            loader=jinja2.FileSystemLoader(searchpath='/'),
+            trim_blocks=True, lstrip_blocks=True)
+
+    def compile(self, configs):
+        """Generates a string with the replacements"""
+        template = self.env.get_template(self.template_str)
+        return template.render(configs)
+
+    def generate_conf(self, configs, path):
+        """Saves the oucome after replacement on the template to file"""
+        output = self.compile(configs)
+        with open(path, 'w+') as output_file:
+            output_file.write(output)
+
+
+class IndividualTemplate(Template):
+    """Specific template for the individual report"""
+
+    def __init__(self):
+        super(IndividualTemplate, self).__init__(pkgrf('mriqc', 'data/reports/individual.html'))