Merge pull request #286 from oesteban/enh/pyBIDS

[ENH] Use pybids

circle.yml

@@ -19,20 +19,17 @@ dependencies:
   override:
     - 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 .
     - docker save mriqc:py35 > ~/docker/image.tar
 
 test:
   override:
     # Test mriqcp
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ${CIRCLE_TEST_REPORTS}:/scratch -w /root/src/mriqc --entrypoint="/usr/bin/run_tests" mriqc:py35 :
         timeout: 2600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH/func:/scratch -w /scratch mriqc:py27 /data/ds003_downsampled out/ participant -d func -w work/ --n_procs 12 --testing --verbose-reports :
-        timeout: 2600
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH:/scratch -w /scratch mriqc:py35 /data/ds003_downsampled out/ participant -w work/ --testing --verbose-reports :
+        timeout: 3200
     - 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 ~/data:/data:ro -v $SCRATCH/anat:/scratch -w /scratch mriqc:py35 /data/ds003_downsampled out/ participant -d anat -w work/ --testing --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/
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH/anat:/scratch -w /scratch mriqc:py35 /data/ds003_downsampled out/ group -d anat -w work/
 
 general:
   artifacts:

mriqc/bin/__init__.py

@@ -0,0 +1,6 @@
+#!/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:
+""" mriqc's executables """
+

mriqc/utils/mriqc_run.py → mriqc/bin/mriqc_run.py

@@ -17,16 +17,18 @@
 from argparse import ArgumentParser
 from argparse import RawTextHelpFormatter
 
-from mriqc.workflows import core as mwc
 from mriqc import __version__, MRIQC_LOG
 from mriqc.utils.misc import check_folder
 
 DEFAULT_MEM_GB = 8
 
 def main():
+    """Entry point"""
     from nipype import config as ncfg
+    from nipype.pipeline.engine import Workflow
+    from mriqc.utils.bids import collect_bids_data
+    from mriqc.workflows.core import build_workflow
 
-    """Entry point"""
     parser = ArgumentParser(description='MRI Quality Control',
                             formatter_class=RawTextHelpFormatter)
 
@@ -204,26 +206,35 @@ def main():
         'Running MRIQC-%s (analysis_level=%s, participant_label=%s)\n\tSettings=%s',
         __version__, opts.analysis_level, opts.participant_label, settings)
 
+    # Process data types
     qc_types = []
-    for qcdt in opts.data_type:
+    modalities = []
+    for qcdt in sorted(list(set([qcdt[:4] for qcdt in opts.data_type]))):
         if qcdt.startswith('anat'):
             qc_types.append('anatomical')
+            modalities.append('t1w')
         if qcdt.startswith('func'):
             qc_types.append('functional')
-    qc_types = sorted(list(set(qc_types)))
+            modalities.append('func')
+
+    dataset = collect_bids_data(settings['bids_dir'],
+                                participant_label=opts.participant_label)
+
     # Set up participant level
     if opts.analysis_level == 'participant':
-        for qctype in qc_types:
-            ms_func = getattr(mwc, 'ms_' + qctype[:4])
-            workflow = ms_func(subject_id=opts.participant_label, session_id=opts.session_id,
-                               run_id=opts.run_id, settings=settings)
-            if workflow is None:
-                MRIQC_LOG.warn('No scans were found for the given inputs')
+        workflow = Workflow(name='workflow_enumerator')
+        workflow.base_dir = settings['work_dir']
+
+        wf_list = []
+        for qctype, mod in zip(qc_types, modalities):
+            if not dataset[mod]:
+                MRIQC_LOG.warn('No %s scans were found in %s', qctype, settings['bids_dir'])
                 continue
 
-            workflow.base_dir = settings['work_dir']
-            if settings.get('write_graph', False):
-                workflow.write_graph()
+            wf_list.append(build_workflow(dataset[mod], qctype, settings=settings))
+
+        if wf_list:
+            workflow.add_nodes(wf_list)
 
             if not opts.dry_run:
                 workflow.run(**plugin_settings)

mriqc/info.py

@@ -61,11 +61,13 @@
     'svgutils',
     'nipype',
     'nipy',
-    'statsmodels'
+    'statsmodels',
+    'pybids'
 ]
 
 LINKS_REQUIRES = [
     'git+https://github.com/nipy/nipype.git#egg=nipype',
+    'git+https://github.com/incf/pybids.git@master#egg=pybids',
 ]
 
 TESTS_REQUIRES = [

mriqc/interfaces/__init__.py

@@ -9,7 +9,7 @@
 from __future__ import unicode_literals
 
 from mriqc.interfaces.anatomical import StructuralQC, ArtifactMask, ComputeQI2
-from mriqc.interfaces.functional import FunctionalQC
+from mriqc.interfaces.functional import FunctionalQC, Spikes
 from mriqc.interfaces.bids import ReadSidecarJSON
 from mriqc.interfaces.viz import PlotMosaic, PlotContours, PlotSpikes
 from mriqc.interfaces.common import ConformImage

mriqc/interfaces/bids.py

@@ -5,52 +5,54 @@
 #
 # @Author: oesteban
 # @Date:   2016-06-03 09:35:13
-# @Last Modified by:   oesteban
-# @Last Modified time: 2016-06-03 10:06:55
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-from __future__ import unicode_literals
+from __future__ import print_function, division, absolute_import, unicode_literals
 import os.path as op
+import re
 import simplejson as json
-from nipype.interfaces.base import (traits, isdefined, TraitedSpec, BaseInterface,
-                                    BaseInterfaceInputSpec, File)
-
+from nipype.interfaces.base import (traits, isdefined, TraitedSpec, BaseInterfaceInputSpec, File)
+from mriqc.interfaces.base import MRIQCBaseInterface
 
 class ReadSidecarJSONInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='the input nifti file')
     fields = traits.List(traits.Str, desc='get only certain fields')
 
 class ReadSidecarJSONOutputSpec(TraitedSpec):
+    subject_id = traits.Str()
+    session_id = traits.Str()
+    task_id = traits.Str()
+    acq_id = traits.Str()
+    rec_id = traits.Str()
+    run_id = traits.Str()
     out_dict = traits.Dict()
 
-class ReadSidecarJSON(BaseInterface):
+class ReadSidecarJSON(MRIQCBaseInterface):
     """
     An utility to find and read JSON sidecar files of a BIDS tree
     """
-
+    expr = re.compile('^(?P<subject_id>sub-[a-zA-Z0-9]+)(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
+                      '(_(?P<task_id>task-[a-zA-Z0-9]+))?(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
+                      '(_(?P<rec_id>rec-[a-zA-Z0-9]+))?(_(?P<run_id>run-[a-zA-Z0-9]+))?')
     input_spec = ReadSidecarJSONInputSpec
     output_spec = ReadSidecarJSONOutputSpec
 
-    def __init__(self, **inputs):
-        self._results = {}
-        super(ReadSidecarJSON, self).__init__(**inputs)
-
     def _run_interface(self, runtime):
         metadata = get_metadata_for_nifti(self.inputs.in_file)
+        output_keys = [key for key in list(self.output_spec().get().keys()) if key.endswith('_id')]
+        outputs = self.expr.search(op.basename(self.inputs.in_file)).groupdict()
+
+        for key in output_keys:
+            if outputs.get(key) is not None:
+                self._results[key] = outputs.get(key)
+            else:
+                self._results[key] = 'default_' + key.split('_')[0]
 
         if isdefined(self.inputs.fields) and self.inputs.fields:
             for fname in self.inputs.fields:
                 self._results[fname] = metadata[fname]
         else:
-            self._results = metadata
-
+            self._results['out_dict'] = metadata
         return runtime
 
-    def _list_outputs(self):
-        out = self.output_spec().get()
-        out['out_dict'] = self._results
-        return out
 
 def get_metadata_for_nifti(in_file):
     """Fetchs metadata for a given nifi file"""

mriqc/interfaces/viz.py

@@ -72,6 +72,7 @@ class PlotMosaicInputSpec(BaseInterfaceInputSpec):
                    desc='File to be plotted')
     subject_id = traits.Str(mandatory=True, desc='subject id')
     session_id = traits.Str(mandatory=True, desc='session id')
+    task_id = traits.Str(desc='task id')
     run_id = traits.Str(mandatory=True, desc='run id')
     task_id = traits.Str(desc='task id')
     title = traits.Str('Volume', usedefault=True,
@@ -107,9 +108,10 @@ def _run_interface(self, runtime):
         plot_mosaic_helper(
             self.inputs.in_file,
             self.inputs.subject_id,
-            self.inputs.session_id,
-            self.inputs.run_id,
-            self.inputs.out_file,
+            session_id=self.inputs.session_id,
+            task_id=self.inputs.task_id,
+            run_id=self.inputs.run_id,
+            out_file=self.inputs.out_file,
             title=self.inputs.title,
             only_plot_noise=self.inputs.only_noise,
             bbox_mask_file=mask,

mriqc/interfaces/viz_utils.py

@@ -490,19 +490,20 @@ def plot_bg_dist(in_file):
     return out_file
 
 
-def plot_mosaic_helper(in_file, subject_id, session_id,
-                       run_id, out_name, bbox_mask_file=None,
+def plot_mosaic_helper(in_file, subject_id, session_id=None,
+                       task_id=None, run_id=None, out_file=None, bbox_mask_file=None,
                        title=None, plot_sagittal=True, labels=None,
                        only_plot_noise=False, cmap=cm.Greys_r):
     if title is not None:
         title = title.format(**{"session_id": session_id,
-                              "run_id": run_id})
+                                "task_id": task_id,
+                                "run_id": run_id})
     fig = plot_mosaic(in_file, bbox_mask_file=bbox_mask_file, title=title, labels=labels,
                       only_plot_noise=only_plot_noise, cmap=cmap, plot_sagittal=plot_sagittal)
-    fig.savefig(out_name, format=out_name.split('.')[-1], dpi=300)
+    fig.savefig(out_file, format=out_file.split('.')[-1], dpi=300)
     fig.clf()
     fig = None
-    return op.abspath(out_name)
+    return op.abspath(out_file)
 
 def combine_svg_verbose(
         in_brainmask,

mriqc/utils/__init__.py

@@ -3,8 +3,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """ Module utils.misc contains utilities """
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-from __future__ import unicode_literals
-from mriqc.utils.misc import gather_bids_data, reorder_csv
+from __future__ import print_function, division, absolute_import, unicode_literals
+from mriqc.utils.misc import reorder_csv
+from mriqc.utils.bids import collect_bids_data