finish multiproc and dwi scan grouping

Author: josephmje

dmriprep/cli.py

@@ -98,6 +98,14 @@
     type=click.FloatRange(min=0, max=1)
 )
 # specific options for eddy
+@click.option(
+    '--acqp_file',
+    default=None,
+    help='If you want to pass in an acqp file for topup/eddy instead of'
+    'generating it from the json by default.',
+    type=click.Path(exists=True, dir_okay=False)
+)
+# workflow configuration
 @click.option(
     '--nthreads',
     default=1,
@@ -112,14 +120,6 @@
     help='Maximum number of threads per process',
     type=int
 )
-@click.option(
-    '--acqp_file',
-    default=None,
-    help='If you want to pass in an acqp file for topup/eddy instead of'
-    'generating it from the json by default.',
-    type=click.Path(exists=True, dir_okay=False)
-)
-# workflow configuration
 @click.option(
     '--ignore',
     '-i',
@@ -141,8 +141,10 @@
 )
 @click.option(
     '--write_graph',
+    is_flag=True,
     default=False,
-    help='Write out nipype workflow graph.'
+    help='Write out nipype workflow graph.',
+    type=bool
 )
 def main(
     bids_dir,
@@ -156,9 +158,9 @@ def main(
     output_resolution,
     bet_dwi,
     bet_mag,
+    acqp_file,
     nthreads,
     omp_nthreads,
-    acqp_file,
     ignore,
     work_dir,
     synb0_dir,
@@ -183,13 +185,13 @@ def main(
         )
 
     layout = BIDSLayout(bids_dir, validate=True)
-    all_subjects, subject_list = collect_participants(
+    subject_list = collect_participants(
         layout, participant_label=participant_label
     )
 
     if not skip_bids_validation:
         from .utils.bids import validate_input_dir
-        validate_input_dir(bids_dir, all_subjects, subject_list)
+        validate_input_dir(bids_dir, subject_list)
 
     if not work_dir:
         work_dir = os.path.join(output_dir, 'scratch')
@@ -241,8 +243,8 @@ def main(
         output_resolution=output_resolution,
         bet_dwi=bet_dwi,
         bet_mag=bet_mag,
-        omp_nthreads=omp_nthreads,
         acqp_file=acqp_file,
+        omp_nthreads=omp_nthreads,
         ignore=list(ignore),
         work_dir=work_dir,
         synb0_dir=synb0_dir

dmriprep/utils/bids.py

@@ -6,6 +6,7 @@
 import warnings
 import json
 import sys
+from pathlib import Path
 
 from bids.layout import BIDSLayout
 
@@ -111,7 +112,7 @@ def collect_participants(
             raise exc
         warnings.warn(exc.msg, BIDSWarning)
 
-    return all_participants, found_label
+    return found_label
 
 
 def collect_data(bids_dir, participant_label, concat_dwis, session_label=None):
@@ -142,7 +143,7 @@ def collect_data(bids_dir, participant_label, concat_dwis, session_label=None):
 
     subj_data['dwi'] = group_dwi(subj_data['dwi'], session_label, concat_dwis)
 
-    return subj_data, layout
+    return subj_data
 
 
 def group_dwi(dwi_files, session_list, concat_dwis):
@@ -158,20 +159,22 @@ def group_dwi(dwi_files, session_list, concat_dwis):
                     session_groups.append(f)
                 else:
                     all_dwis.append(f)
-            all_dwis.append(session_groups)
+            if not session_groups == []:
+                all_dwis.append(session_groups)
     else:
         session_groups = []
         for f in dwi_files:
             if any(acq in f for acq in concat_dwis):
                 session_groups.append(f)
             else:
                 all_dwis.append(f)
-        all_dwis.append(session_groups)
+        if not session_groups == []:
+            all_dwis.append(session_groups)
 
     return all_dwis
 
 
-def validate_input_dir(bids_dir, all_subjects, subject_list):
+def validate_input_dir(bids_dir, subject_list):
     # Ignore issues and warnings that should not influence DMRIPREP
     import tempfile
     import subprocess
@@ -217,7 +220,18 @@ def validate_input_dir(bids_dir, all_subjects, subject_list):
         "ignoredFiles": ["/dataset_description.json", "/participants.tsv"],
     }
     # Limit validation only to data from requested participants
-    ignored_subjects = all_subjects.difference(subject_list)
+    if subject_list:
+        bids_dir = Path(bids_dir)
+        all_subs = set([s.name[4:] for s in bids_dir.glob('sub-*')])
+        selected_subs = set([s[4:] if s.startswith('sub-') else s
+                             for s in subject_list])
+        bad_labels = selected_subs.difference(all_subs)
+        if bad_labels:
+            error_msg = 'Data for requested participant(s) label(s) not found. Could ' \
+                        'not find data for participant(s): %s. Please verify the requested ' \
+                        'participant labels.'
+            raise RuntimeError(error_msg % ','.join(bad_labels))
+    ignored_subjects = all_subs.difference(selected_subs)
     if ignored_subjects:
         for subject in ignored_subjects:
             validator_config_dict["ignoredFiles"].append("/sub-%s/**" % subject)

dmriprep/workflows/base.py

@@ -28,8 +28,8 @@ def init_dmriprep_wf(
     output_resolution,
     bet_dwi,
     bet_mag,
-    omp_nthreads,
     acqp_file,
+    omp_nthreads,
     ignore,
     work_dir,
     synb0_dir
@@ -55,8 +55,8 @@ def init_dmriprep_wf(
         output_resolution=(1, 1, 1),
         bet_dwi=0.3,
         bet_mag=0.3,
-        omp_nthreads=1,
         acqp_file='',
+        omp_nthreads=1,
         ignore=[],
         work_dir='.',
         synb0_dir=''
@@ -87,13 +87,14 @@ def init_dmriprep_wf(
         acqp_file: str
             Optionally supply eddy acquisition parameters file
         ignore: list
-            Preprocessing steps to skip (may include 'denoise', 'unring', 'fieldmaps'
+            Preprocessing steps to skip (may include 'denoise', 'unring', 'fieldmaps')
         work_dir: str
             Directory in which to store workflow execution state and temporary files
         synb0_dir: str
             Direction in which synb0 derivatives are saved
 
     """
+
     dmriprep_wf = pe.Workflow(name='dmriprep_wf')
     dmriprep_wf.base_dir = work_dir
 
@@ -231,47 +232,100 @@ def init_single_subject_wf(
     subject_wf = pe.Workflow(name=name)
 
     for dwi_file in subject_data['dwi']:
+        multiple_dwis = isinstance(dwi_file, list)
+
+        if multiple_dwis:
+            print(dwi_file)
+            ref_file = dwi_file[0]
+
+            from .dwi import init_dwi_concat_wf
+
+            dwi_concat_wf = init_dwi_concat_wf(ref_file, dwi_file)
+
+            concat_spec = dwi_concat_wf.get_node('inputnode')
+            concat_spec.inputs.ref_file = ref_file
+            concat_spec.inputs.dwi_list = dwi_file
+            concat_spec.inputs.bvec_list = [layout.get_bvec(bvec) for bvec in dwi_file]
+            concat_spec.inputs.bval_list = [layout.get_bval(bval) for bval in dwi_file]
+
+            metadata = layout.get_metadata(ref_file)
+
+            dwi_preproc_wf = init_dwi_preproc_wf(
+                layout=layout,
+                output_dir=output_dir,
+                subject_id=subject_id,
+                dwi_file=dwi_file,
+                metadata=metadata,
+                b0_thresh=b0_thresh,
+                output_resolution=output_resolution,
+                bet_dwi=bet_dwi,
+                bet_mag=bet_mag,
+                omp_nthreads=omp_nthreads,
+                acqp_file=acqp_file,
+                ignore=ignore,
+                synb0_dir=synb0_dir
+            )
+
+            dwi_preproc_wf.base_dir = os.path.join(
+                os.path.abspath(work_dir), subject_id
+            )
+
+            inputspec = dwi_preproc_wf.get_node('inputnode')
+            inputspec.inputs.subject_id = subject_id
+            inputspec.inputs.dwi_meta = metadata
+            inputspec.inputs.out_dir = os.path.abspath(output_dir)
+
+            subject_wf.connect([
+                (dwi_concat_wf, dwi_preproc_wf, [('outputnode.dwi_file', 'inputnode.dwi_file'),
+                                                 ('outputnode.bvec_file', 'inputnode.bvec_file'),
+                                                 ('outputnode.bval_file', 'inputnode.bval_file')])
+            ])
+
+        else:
+            ref_file = dwi_file
+
+            metadata = layout.get_metadata(ref_file)
+
+            dwi_preproc_wf = init_dwi_preproc_wf(
+                layout=layout,
+                output_dir=output_dir,
+                subject_id=subject_id,
+                dwi_file=dwi_file,
+                metadata=metadata,
+                b0_thresh=b0_thresh,
+                output_resolution=output_resolution,
+                bet_dwi=bet_dwi,
+                bet_mag=bet_mag,
+                omp_nthreads=omp_nthreads,
+                acqp_file=acqp_file,
+                ignore=ignore,
+                synb0_dir=synb0_dir
+            )
+
+            dwi_preproc_wf.base_dir = os.path.join(
+                os.path.abspath(work_dir), subject_id
+            )
+
+            inputspec = dwi_preproc_wf.get_node('inputnode')
+            inputspec.inputs.subject_id = subject_id
+            inputspec.inputs.dwi_file = dwi_file
+            inputspec.inputs.dwi_meta = metadata
+            inputspec.inputs.bvec_file = layout.get_bvec(dwi_file)
+            inputspec.inputs.bval_file = layout.get_bval(dwi_file)
+            inputspec.inputs.out_dir = os.path.abspath(output_dir)
+
         entities = layout.parse_file_entities(dwi_file)
         if 'session' in entities:
             session_id = entities['session']
         else:
             session_id = None
-        metadata = layout.get_metadata(dwi_file)
-
-        dwi_preproc_wf = init_dwi_preproc_wf(
-            layout=layout,
-            output_dir=output_dir,
-            subject_id=subject_id,
-            dwi_file=dwi_file,
-            metadata=metadata,
-            b0_thresh=b0_thresh,
-            output_resolution=output_resolution,
-            bet_dwi=bet_dwi,
-            bet_mag=bet_mag,
-            omp_nthreads=omp_nthreads,
-            acqp_file=acqp_file,
-            ignore=ignore,
-            synb0_dir=synb0_dir
-        )
 
         datasink_wf = init_dwi_derivatives_wf(
             subject_id=subject_id,
             session_id=session_id,
             output_folder=output_dir
         )
 
-        dwi_preproc_wf.base_dir = os.path.join(
-            os.path.abspath(work_dir), subject_id
-        )
-
-        inputspec = dwi_preproc_wf.get_node('inputnode')
-        inputspec.inputs.subject_id = subject_id
-        inputspec.inputs.dwi_file = dwi_file
-        inputspec.inputs.dwi_meta = metadata
-        inputspec.inputs.bvec_file = layout.get_bvec(dwi_file)
-        inputspec.inputs.bval_file = layout.get_bval(dwi_file)
-        inputspec.inputs.out_dir = os.path.abspath(output_dir)
-
         ds_inputspec = datasink_wf.get_node('inputnode')
         ds_inputspec.inputs.subject_id = subject_id
         ds_inputspec.inputs.session_id = session_id
@@ -312,23 +366,3 @@ def init_single_subject_wf(
         subject_wf.add_nodes([full_wf])
 
     return subject_wf
-
-
-def group_dwis(dwi_files, sessions, concat_dwis):
-
-    all_dwis = []
-
-    if sessions:
-        session_dwi_groups = []
-        for session in sessions:
-            session_dwi_files = [img for img in dwi_files if 'ses-{}'.format(session) in img]
-            for f in session_dwi_files:
-                if any(acq in f for acq in concat_dwis):
-                    session_dwi_groups.append(f)
-                else:
-                    all_dwis.append(f)
-        all_dwis.append(session_dwi_groups)
-    else:
-        all_dwis.append(f)
-
-    return all_dwis

dmriprep/workflows/dwi/__init__.py

@@ -6,6 +6,7 @@
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. automodule:: dmriprep.workflows.dwi.base
+.. automodule:: dmriprep.workflows.dwi.util
 .. automodule:: dmriprep.workflows.dwi.artifacts
 .. automodule:: dmriprep.workflows.dwi.eddy
 .. automodule:: dmriprep.workflows.dwi.tensor
@@ -14,13 +15,15 @@
 """
 
 from .base import init_dwi_preproc_wf
+from .util import init_dwi_concat_wf
 from .artifacts import init_dwi_artifacts_wf
 from .eddy import init_dwi_eddy_wf
 from .tensor import init_dwi_tensor_wf
 from .outputs import init_dwi_derivatives_wf
 
 __all__ = [
     'init_dwi_preproc_wf',
+    'init_dwi_concat_wf',
     'init_dwi_artifacts_wf',
     'init_dwi_eddy_wf',
     'init_dwi_tensor_wf',