Merge pull request #10 from josephmje/nipreps_tests

FIX: Remove count of dwi scans according to task_id

Author: oesteban

dmriprep/interfaces/reports.py

@@ -5,21 +5,18 @@
 import os
 import time
 
-from collections import Counter
 from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec,
     File, Directory, InputMultiObject, Str, isdefined,
     SimpleInterface)
 from nipype.interfaces import freesurfer as fs
-from niworkflows.utils.bids import BIDS_NAME
 
 
 SUBJECT_TEMPLATE = """\
 \t<ul class="elem-desc">
 \t\t<li>Subject ID: {subject_id}</li>
 \t\t<li>Structural images: {n_t1s:d} T1-weighted {t2w}</li>
 \t\t<li>Diffusion Weighted Images: {n_dwi:d}</li>
-{tasks}
 \t\t<li>Standard output spaces: {std_spaces}</li>
 \t\t<li>Non-standard output spaces: {nstd_spaces}</li>
 \t\t<li>FreeSurfer reconstruction: {freesurfer_status}</li>
@@ -105,28 +102,14 @@ def _generate_segment(self):
         if self.inputs.t2w:
             t2w_seg = '(+ {:d} T2-weighted)'.format(len(self.inputs.t2w))
 
-        # Add list of tasks with number of runs
         dwi_files = self.inputs.dwi if isdefined(self.inputs.dwi) else []
         dwi_files = [s[0] if isinstance(s, list) else s for s in dwi_files]
 
-        counts = Counter(BIDS_NAME.search(series).groupdict()['task_id'][5:]
-                         for series in dwi_files)
-
-        tasks = ''
-        if counts:
-            header = '\t\t<ul class="elem-desc">'
-            footer = '\t\t</ul>'
-            lines = ['\t\t\t<li>Task: {task_id} ({n_runs:d} run{s})</li>'.format(
-                     task_id=task_id, n_runs=n_runs, s='' if n_runs == 1 else 's')
-                     for task_id, n_runs in sorted(counts.items())]
-            tasks = '\n'.join([header] + lines + [footer])
-
         return SUBJECT_TEMPLATE.format(
             subject_id=self.inputs.subject_id,
             n_t1s=len(self.inputs.t1w),
             t2w=t2w_seg,
             n_dwi=len(dwi_files),
-            tasks=tasks,
             std_spaces=', '.join(self.inputs.std_spaces),
             nstd_spaces=', '.join(self.inputs.nstd_spaces),
             freesurfer_status=freesurfer_status)

dmriprep/utils/bids.py

@@ -8,8 +8,7 @@
 from bids import BIDSLayout
 
 
-def collect_data(bids_dir, participant_label, task=None, echo=None,
-                 bids_validate=True):
+def collect_data(bids_dir, participant_label, bids_validate=True):
     """Replacement for niworkflows' version."""
     if isinstance(bids_dir, BIDSLayout):
         layout = bids_dir
@@ -19,20 +18,12 @@ def collect_data(bids_dir, participant_label, task=None, echo=None,
     queries = {
         'fmap': {'datatype': 'fmap'},
         'dwi': {'datatype': 'dwi', 'suffix': 'dwi'},
-        'bold': {'datatype': 'func', 'suffix': 'bold'},
-        'sbref': {'datatype': 'func', 'suffix': 'sbref'},
         'flair': {'datatype': 'anat', 'suffix': 'FLAIR'},
         't2w': {'datatype': 'anat', 'suffix': 'T2w'},
         't1w': {'datatype': 'anat', 'suffix': 'T1w'},
         'roi': {'datatype': 'anat', 'suffix': 'roi'},
     }
 
-    if task:
-        queries['bold']['task'] = task
-
-    if echo:
-        queries['bold']['echo'] = echo
-
     subj_data = {
         dtype: sorted(layout.get(return_type='file', subject=participant_label,
                                  extension=['nii', 'nii.gz'], **query))
@@ -60,10 +51,10 @@ def write_derivative_description(bids_dir, deriv_dir):
     }
 
     # Keys that can only be set by environment
-    if 'FMRIPREP_DOCKER_TAG' in os.environ:
-        desc['DockerHubContainerTag'] = os.environ['FMRIPREP_DOCKER_TAG']
-    if 'FMRIPREP_SINGULARITY_URL' in os.environ:
-        singularity_url = os.environ['FMRIPREP_SINGULARITY_URL']
+    if 'DMRIPREP_DOCKER_TAG' in os.environ:
+        desc['DockerHubContainerTag'] = os.environ['DMRIPREP_DOCKER_TAG']
+    if 'DMRIPREP_SINGULARITY_URL' in os.environ:
+        singularity_url = os.environ['DMRIPREP_SINGULARITY_URL']
         desc['SingularityContainerURL'] = singularity_url
 
         singularity_md5 = _get_shub_version(singularity_url)
@@ -88,7 +79,7 @@ def write_derivative_description(bids_dir, deriv_dir):
 
 
 def validate_input_dir(exec_env, bids_dir, participant_label):
-    # Ignore issues and warnings that should not influence FMRIPREP
+    # Ignore issues and warnings that should not influence dMRIPrep
     import tempfile
     import subprocess
     validator_config_dict = {
@@ -98,25 +89,20 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
             "TSV_EQUAL_ROWS",
             "TSV_EMPTY_CELL",
             "TSV_IMPROPER_NA",
-            "VOLUME_COUNT_MISMATCH",
-            "BVAL_MULTIPLE_ROWS",
-            "BVEC_NUMBER_ROWS",
-            "DWI_MISSING_BVAL",
             "INCONSISTENT_SUBJECTS",
             "INCONSISTENT_PARAMETERS",
-            "BVEC_ROW_LENGTH",
-            "B_FILE",
             "PARTICIPANT_ID_COLUMN",
             "PARTICIPANT_ID_MISMATCH",
             "TASK_NAME_MUST_DEFINE",
             "PHENOTYPE_SUBJECTS_MISSING",
             "STIMULUS_FILE_MISSING",
-            "DWI_MISSING_BVEC",
+            "BOLD_NOT_4D",
             "EVENTS_TSV_MISSING",
             "TSV_IMPROPER_NA",
             "ACQTIME_FMT",
             "Participants age 89 or higher",
             "DATASET_DESCRIPTION_JSON_MISSING",
+            "TASK_NAME_CONTAIN_ILLEGAL_CHARACTER",
             "FILENAME_COLUMN",
             "WRONG_NEW_LINE",
             "MISSING_TSV_COLUMN_CHANNELS",
@@ -131,8 +117,6 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
             "ACQTIME_FMT",
             "SUSPICIOUSLY_LONG_EVENT_DESIGN",
             "SUSPICIOUSLY_SHORT_EVENT_DESIGN",
-            "MALFORMED_BVEC",
-            "MALFORMED_BVAL",
             "MISSING_TSV_COLUMN_EEG_ELECTRODES",
             "MISSING_SESSION"
         ],

dmriprep/workflows/base.py

@@ -314,7 +314,7 @@ def init_single_subject_wf(
         # for documentation purposes
         subject_data = {
             't1w': ['/completely/made/up/path/sub-01_T1w.nii.gz'],
-            'dwi': ['/completely/made/up/path/sub-01_task-nback_bold.nii.gz']
+            'dwi': ['/completely/made/up/path/sub-01_dwi.nii.gz']
         }
     else:
         subject_data = collect_data(layout, subject_id)[0]