enh: update workflows to use config, add mock config system

Author: oesteban

MANIFEST.in

@@ -5,6 +5,3 @@ include LICENSE
 # versioneer
 include versioneer.py
 include dmriprep/_version.py
-
-# data
-include dmriprep/config/reports-spec.yml

dmriprep/cli/parser.py

@@ -245,7 +245,7 @@ def parse_args(args=None, namespace=None):
 
     # Initialize --output-spaces if not defined
     if config.execution.output_spaces is None:
-        config.execution.output_spaces = SpatialReferences([Reference(("run", {}))])
+        config.execution.output_spaces = SpatialReferences([Reference("run")])
 
     # Retrieve logging level
     build_log = config.loggers.cli

dmriprep/cli/workflow.py

@@ -63,7 +63,7 @@ def build_workflow(config_file, retval):
 
     # Build main workflow
     INIT_MSG = """
-    Running dMRIPREP version {version}:
+    Running dMRIPrep version {version}:
       * BIDS dataset path: {bids_dir}.
       * Participant list: {subject_list}.
       * Run identifier: {uuid}.

dmriprep/config/__init__.py

@@ -11,7 +11,7 @@
 The module has a :py:func:`~dmriprep.config.to_filename` function to allow writing out
 the settings to hard disk in *ToML* format, which looks like:
 
-.. literalinclude:: ../dmriprep/data/tests/config.toml
+.. literalinclude:: ../../dmriprep/data/tests/config.toml
    :language: toml
    :name: dmriprep.toml
    :caption: **Example file representation of dMRIPrep settings**.
@@ -532,11 +532,5 @@ def init_spaces(checkpoint=True):
     if checkpoint and not spaces.is_cached():
         spaces.checkpoint()
 
-    # Add the default standard space if not already present (required by several sub-workflows)
-    if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
-        spaces.add(
-            Reference("MNI152NLin2009cAsym", {})
-        )
-
     # Make the SpatialReferences object available
     workflow.spaces = spaces

dmriprep/config/testing.py

@@ -0,0 +1,35 @@
+"""Utilities and mocks for testing and documentation building."""
+import os
+from contextlib import contextmanager
+from pathlib import Path
+from pkg_resources import resource_filename as pkgrf
+from toml import loads
+from tempfile import mkdtemp
+
+
+@contextmanager
+def mock_config():
+    """Create a mock config for documentation and testing purposes."""
+    from .. import config
+    _old_fs = os.getenv('FREESURFER_HOME')
+    if not _old_fs:
+        os.environ['FREESURFER_HOME'] = mkdtemp()
+
+    filename = Path(pkgrf('dmriprep', 'data/tests/config.toml'))
+    settings = loads(filename.read_text())
+    for sectionname, configs in settings.items():
+        if sectionname != 'environment':
+            section = getattr(config, sectionname)
+            section.load(configs, init=False)
+    config.nipype.init()
+    config.loggers.init()
+    config.init_spaces()
+
+    config.execution.work_dir = Path(mkdtemp())
+    config.execution.bids_dir = Path(pkgrf('dmriprep', 'data/tests/THP')).absolute()
+    config.execution.init()
+
+    yield
+
+    if not _old_fs:
+        del os.environ["FREESURFER_HOME"]

dmriprep/data/tests/THP/CHANGES

@@ -0,0 +1,12 @@
+2.0.0	2018-04-09
+
+	- Renamed dataset name to same as OpenfMRI
+	- Entered authors
+
+1.0.0	2018-04-09
+
+	- Initial publish
+
+1.0.0 2016-08-31
+   
+  -  initial release

dmriprep/data/tests/THP/README

@@ -0,0 +1,53 @@
+
+This Datasets is from a Traveling Human Phantom (THP) dataset that was
+collected for a multi-site neuroimaging reliability study.  The THP dataset
+includes repeated multi-modal magnetic resonance (MR) images
+obtained for five healthy controls performed at eight imaging centers. The
+modalities include diffusion weighted images (DWI) and three-dimensional T1
+weighted MP-RAGE and T2 SPACE sequences.  Intra-subject and inter-site
+variability for MRI scans was and can be assessed as repeated images were taken
+across multiple imaging protocols.
+
+Another use for the THP dataset could be to evaluate and improve one's tool
+against multi-modal and multi-site data. In addition to the THP dataset, which
+is useful as it is, we share our processed results. DWI datasets were processed
+to produce common rotationally invariant scalar images and diffusion tensor
+images. Anatomical images, T1 and T2, were processed with the BRAINSTools suite
+to produce anatomical segmentations. 
+
+@article{magnotta2012multicenter,
+abstract = {A number of studies are now collecting diffusion tensor imaging
+(DTI) data across sites. While the reliability of anatomical images has been
+established by a number of groups, the reliability of DTI data has not been
+studied as extensively. In this study, five healthy controls were recruited and
+imaged at eight imaging centers. Repeated measures were obtained across two
+imaging protocols allowing intra-subject and inter-site variability to be
+assessed. Regional measures within white matter were obtained for standard
+rotationally invariant measures: fractional anisotropy, mean diffusivity,
+radial diffusivity, and axial diffusivity. Intra-subject coefficient of
+variation (CV) was typically {\textless}1{\%} for all scalars and regions.
+Inter-site CV increased to {\~{}}1{\%}-3{\%}. Inter-vendor variation was
+similar to inter-site variability. This variability includes differences in the
+actual implementation of the sequence.}, author = {Magnotta, Vincent a. and
+Matsui, Joy T. and Liu, Dawei and Johnson, Hans J. and Long, Jeffrey D. and
+Bolster, Bradley D. and Mueller, Bryon a. and Lim, Kelvin O. and Mori, Susumu
+and Helmer, Karl and Turner, Jessica a. and Lowe, Mark J. and Aylward,
+Elizabeth and Flashman, Laura a. and Bonett, Greg and Paulsen, Jane S.},
+doi = {10.1089/brain.2012.0112},
+isbn = {8605457767},
+issn = {2158-0014},
+journal = {Brain Connectivity},
+keywords = {diffusion tensor,fractional anisotropy,magnetic resonance,mean diffusivity,reliability,white matter},
+mendeley-groups = {ReginaThesis,BiosketchReferences,JoysThesis,JoyCrossSectionalDWI,TEMP{\_}HOWES{\_}RE},
+month = {jan},
+number = {6},
+pages = {121018043201009},
+pmid = {23075313},
+publisher = {Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA},
+title = {{Multi-Center Reliability of Diffusion Tensor Imaging}},
+url = {http://www.ncbi.nlm.nih.gov/pubmed/23075313 http://online.liebertpub.com/doi/abs/10.1089/brain.2012.0112 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3623569},
+volume = {2},
+year = {2012}
+}
+
+

dmriprep/data/tests/THP/dataset_description.json

@@ -0,0 +1 @@
+{"Name":"DWI Traveling Human Phantom Study","BIDSVersion":"1.0.0","License":"PDDL","Authors":["Vincent A. Magnotta","Joy T. Matsui","Dawei Liu","Hans J. Johnson","Jeffrey D. Long","Bradley D. Bolster Jr","Bryon A. Mueller","Kelvin Lim","Susumu Mori","Karl G. Helmer","Jessica A. Turner","Sarah Reading","Mark J. Lowe","Elizabeth Aylward","Laura A. Flashman","Greg Bonett","Jane S. Paulsen"],"HowToAcknowledge":"Please reference the following papers:  DOI: 10.1089/brain.2012.0112 V. a. Magnotta, J. T. Matsui, D. Liu, H. J. Johnson, J. D. Long, B. D. Bolster, B. a. Mueller, K. O. Lim, S. Mori, K. Helmer, J. a. Turner, M. J. Lowe, E. Aylward, L. a. Flashman, G. Bonett, and J. S. Paulsen, 'Multi-Center Reliability of Diffusion Tensor Imaging,' Brain Connect., vol. 2, no. 6, p. 121018043201009, Jan. 2012.","Funding":"This work was supported, in part, by awards from CHDI Foundation, Inc.; NIH R01NS050568; NINDS NS40068 Neu- robiological Predictors of Huntington's Disease; and NINDS R01 NS054893 Cognitive and Functional Brain Changes in Preclinical HD. Dr. Turner was supported by NCRR 1 U24 RR021992 from the Functional Imaging Biomedical Infor- matics Network (S.G. Potkin, PI) for her work on this project while at the University of California, Irvine. This publication was supported by the National Center for Research Resour- ces and the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant UL1RR024979. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.","ReferencesAndLinks":["http://online.liebertpub.com/doi/abs/10.1089/brain.2012.0112"],"DatasetDOI":"10.1089/brain.2012.0112"}

dmriprep/data/tests/THP/sub-THP0005/anat/sub-THP0005_T1w.json

@@ -0,0 +1,10 @@
+{
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "TrioTim",
+	"MagneticFieldStrength": 3,
+	"FlipAngle": 10,
+	"EchoTime": 0.00287,
+	"RepetitionTime": 2.3,
+	"PhaseEncodingDirection": "i-",
+	"PulseSequenceType": "MPRAGE"
+}