enh(bids): use ReadSidecarJSON from niworkflows

mriqc/interfaces/__init__.py

@@ -7,7 +7,25 @@
 from .anatomical import \
     StructuralQC, ArtifactMask, ComputeQI2, Harmonize, RotationMask
 from .functional import FunctionalQC, Spikes
-from .bids import ReadSidecarJSON, IQMFileSink
+from .bids import IQMFileSink
 from .viz import PlotMosaic, PlotContours, PlotSpikes
 from .common import ConformImage, EnsureSize
 from .webapi import UploadIQMs
+
+
+__all__ = [
+    'ArtifactMask',
+    'ComputeQI2',
+    'ConformImage',
+    'EnsureSize',
+    'FunctionalQC',
+    'Harmonize',
+    'IQMFileSink',
+    'PlotContours',
+    'PlotMosaic',
+    'PlotSpikes',
+    'RotationMask',
+    'Spikes',
+    'StructuralQC',
+    'UploadIQMs',
+]

mriqc/interfaces/bids.py

@@ -1,6 +1,5 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-import os.path as op
 from pathlib import Path
 import re
 import simplejson as json
@@ -9,64 +8,13 @@
     traits, isdefined, TraitedSpec, DynamicTraitedSpec, BaseInterfaceInputSpec,
     File, Undefined, Str, SimpleInterface
 )
-from ..utils.misc import BIDS_COMP, BIDS_EXPR
+from ..utils.misc import BIDS_COMP
 
 IFLOGGER = logging.getLogger('nipype.interface')
 
 
-class ReadSidecarJSONInputSpec(BaseInterfaceInputSpec):
-    in_file = File(exists=True, mandatory=True, desc='the input nifti file')
-    fields = traits.List(Str, desc='get only certain fields')
-
-
-class ReadSidecarJSONOutputSpec(TraitedSpec):
-    subject_id = Str()
-    session_id = Str()
-    task_id = Str()
-    acq_id = Str()
-    rec_id = Str()
-    run_id = Str()
-    out_dict = traits.Dict()
-    relative_path = Str()
-
-
-class ReadSidecarJSON(SimpleInterface):
-    """
-    An utility to find and read JSON sidecar files of a BIDS tree
-    """
-    expr = re.compile(BIDS_EXPR)
-    input_spec = ReadSidecarJSONInputSpec
-    output_spec = ReadSidecarJSONOutputSpec
-
-    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:
-            id_value = outputs.get(key)
-            if id_value is not None:
-                self._results[key] = outputs.get(key)
-
-        if isdefined(self.inputs.fields) and self.inputs.fields:
-            for fname in self.inputs.fields:
-                self._results[fname] = metadata[fname]
-        else:
-            self._results['out_dict'] = metadata
-
-        # Crawl back to the BIDS root
-        path = Path(self.inputs.in_file)
-        for i in range(1, 4):
-            if str(path.parents[i].name).startswith('sub-'):
-                bids_root = path.parents[i + 1]
-                break
-
-        self._results['relative_path'] = str(path.relative_to(bids_root))
-        return runtime
-
-
 class IQMFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
-    in_file = Str(mandatory=True, desc='path of input file relative to BIDS root')
+    in_file = Str(mandatory=True, desc='path of input file')
     subject_id = Str(mandatory=True, desc='the subject id')
     modality = Str(mandatory=True, desc='the qc type')
     session_id = traits.Either(None, Str, usedefault=True)
@@ -129,8 +77,15 @@ def _gen_outfile(self):
         if isdefined(self.inputs.out_dir):
             out_dir = Path(self.inputs.out_dir)
 
+        # Crawl back to the BIDS root
+        path = Path(self.inputs.in_file)
+        for i in range(1, 4):
+            if str(path.parents[i].name).startswith('sub-'):
+                bids_root = path.parents[i + 1]
+                break
+        in_file = str(path.relative_to(bids_root))
+
         # Build path and ensure directory exists
-        in_file = self.inputs.in_file
         bids_path = out_dir / in_file.replace(
             ''.join(Path(in_file).suffixes), '.json')
         bids_path.parent.mkdir(parents=True, exist_ok=True)
@@ -199,63 +154,6 @@ def _run_interface(self, runtime):
         return runtime
 
 
-def get_metadata_for_nifti(in_file):
-    """Fetchs metadata for a given nifi file"""
-    in_file = op.abspath(in_file)
-
-    fname, ext = op.splitext(in_file)
-    if ext == '.gz':
-        fname, ext2 = op.splitext(fname)
-        ext = ext2 + ext
-
-    side_json = fname + '.json'
-    fname_comps = op.basename(side_json).split("_")
-
-    session_comp_list = []
-    subject_comp_list = []
-    top_comp_list = []
-    ses = None
-    sub = None
-
-    for comp in fname_comps:
-        if comp[:3] != "run":
-            session_comp_list.append(comp)
-            if comp[:3] == "ses":
-                ses = comp
-            else:
-                subject_comp_list.append(comp)
-                if comp[:3] == "sub":
-                    sub = comp
-                else:
-                    top_comp_list.append(comp)
-
-    if any([comp.startswith('ses') for comp in fname_comps]):
-        bids_dir = '/'.join(op.dirname(in_file).split('/')[:-3])
-    else:
-        bids_dir = '/'.join(op.dirname(in_file).split('/')[:-2])
-
-    top_json = op.join(bids_dir, "_".join(top_comp_list))
-    potential_json = [top_json]
-
-    subject_json = op.join(bids_dir, sub, "_".join(subject_comp_list))
-    potential_json.append(subject_json)
-
-    if ses:
-        session_json = op.join(bids_dir, sub, ses, "_".join(session_comp_list))
-        potential_json.append(session_json)
-
-    potential_json.append(side_json)
-
-    merged_param_dict = {}
-    for json_file_path in potential_json:
-        if op.isfile(json_file_path):
-            with open(json_file_path, 'r') as jsonfile:
-                param_dict = json.load(jsonfile)
-                merged_param_dict.update(param_dict)
-
-    return merged_param_dict
-
-
 def _process_name(name, val):
     if '.' in name:
         newkeys = name.split('.')

mriqc/workflows/anatomical.py

@@ -37,12 +37,13 @@
 from nipype.interfaces import utility as niu
 from nipype.interfaces import fsl, ants
 from templateflow.api import get as get_template
-from niworkflows.anat.skullstrip import afni_wf as skullstrip_wf
+from niworkflows.interfaces.bids import ReadSidecarJSON
 from niworkflows.interfaces.registration import RobustMNINormalizationRPT as RobustMNINormalization
+from niworkflows.anat.skullstrip import afni_wf as skullstrip_wf
 
 from .. import DEFAULTS, logging
-from ..interfaces import (StructuralQC, ArtifactMask, ReadSidecarJSON,
-                          ConformImage, ComputeQI2, IQMFileSink, RotationMask)
+from ..interfaces import (StructuralQC, ArtifactMask, ConformImage,
+                          ComputeQI2, IQMFileSink, RotationMask)
 from .utils import get_fwhmx
 
 
@@ -265,8 +266,8 @@ def _getwm(inlist):
 
     workflow.connect([
         (inputnode, meta, [('in_file', 'in_file')]),
-        (meta, datasink, [('relative_path', 'in_file'),
-                          ('subject_id', 'subject_id'),
+        (inputnode, datasink, [('in_file', 'in_file')]),
+        (meta, datasink, [('subject_id', 'subject_id'),
                           ('session_id', 'session_id'),
                           ('acq_id', 'acq_id'),
                           ('rec_id', 'rec_id'),

mriqc/workflows/functional.py

@@ -31,14 +31,15 @@
 from nipype.interfaces import utility as niu
 from nipype.interfaces import afni, ants, fsl
 
+from niworkflows.interfaces.bids import ReadSidecarJSON
 from niworkflows.interfaces import segmentation as nws
 from niworkflows.interfaces import registration as nwr
 from niworkflows.interfaces import utils as niutils
 from niworkflows.interfaces.plotting import FMRISummary
 
 from .utils import get_fwhmx
 from .. import DEFAULTS, logging
-from ..interfaces import ReadSidecarJSON, FunctionalQC, Spikes, IQMFileSink
+from ..interfaces import FunctionalQC, Spikes, IQMFileSink
 
 
 DEFAULT_FD_RADIUS = 50.
@@ -269,11 +270,11 @@ def compute_iqms(settings, name='ComputeIQMs'):
         name='datasink', run_without_submitting=True)
 
     workflow.connect([
-        (inputnode, datasink, [('exclude_index', 'dummy_trs')]),
+        (inputnode, datasink, [('in_file', 'in_file'),
+                               ('exclude_index', 'dummy_trs')]),
         (inputnode, meta, [('in_file', 'in_file')]),
         (inputnode, addprov, [('in_file', 'in_file')]),
-        (meta, datasink, [('relative_path', 'in_file'),
-                          ('subject_id', 'subject_id'),
+        (meta, datasink, [('subject_id', 'subject_id'),
                           ('session_id', 'session_id'),
                           ('task_id', 'task_id'),
                           ('acq_id', 'acq_id'),