test latest commit in smriprep, use unique layout object, integrate new datasinks (close #965, close #955)

Author: oesteban

fmriprep/__about__.py

@@ -89,7 +89,7 @@
     'nilearn',
     'nipype>=1.1.6',
     'nitime',
-    'niworkflows',
+    'niworkflows>=0.7.0,<0.8.0a',
     'numpy',
     'pandas',
     'psutil>=5.4',
@@ -104,10 +104,8 @@
 
 
 LINKS_REQUIRES = [
-    'git+https://github.com/oesteban/niworkflows.git@'
-    '0208e37b8915d89720856ac76becbed7592437c5#niworkflows-0.6.1',
     'git+https://github.com/oesteban/smriprep.git@'
-    'e504ddaca62da545b75a7cbc629ff91b8b48f2ee#smriprep-0.0.4',
+    '2ad4639b308a5d13183819e13bcb3ca6d4d93eac#smriprep-0.0.4',
 ]
 
 TESTS_REQUIRES = [

fmriprep/cli/run.py

@@ -552,6 +552,7 @@ def build_workflow(opts, retval):
     from subprocess import check_call, CalledProcessError, TimeoutExpired
     from pkg_resources import resource_filename as pkgrf
     from shutil import copyfile
+    from bids import BIDSLayout
 
     from nipype import logging, config as ncfg
     from niworkflows.utils.bids import collect_participants
@@ -606,9 +607,9 @@ def build_workflow(opts, retval):
 
     # First check that bids_dir looks like a BIDS folder
     bids_dir = os.path.abspath(opts.bids_dir)
+    layout = BIDSLayout(bids_dir, validate=False)
     subject_list = collect_participants(
-        bids_dir, participant_label=opts.participant_label,
-        bids_validate=False)
+        layout, participant_label=opts.participant_label)
 
     # Load base plugin_settings from file if --use-plugin
     if opts.use_plugin is not None:
@@ -716,6 +717,7 @@ def build_workflow(opts, retval):
         logger.warning('Option --debug is deprecated and has no effect')
 
     retval['workflow'] = init_fmriprep_wf(
+        layout=layout,
         subject_list=subject_list,
         task_id=opts.task_id,
         echo_idx=opts.echo_idx,
@@ -731,7 +733,6 @@ def build_workflow(opts, retval):
         skull_strip_fixed_seed=opts.skull_strip_fixed_seed,
         work_dir=work_dir,
         output_dir=output_dir,
-        bids_dir=bids_dir,
         freesurfer=opts.run_reconall,
         output_spaces=output_spaces,
         template=opts.template,

fmriprep/workflows/base.py

@@ -33,7 +33,7 @@
 from .bold import init_func_preproc_wf
 
 
-def init_fmriprep_wf(subject_list, task_id, echo_idx, run_uuid, work_dir, output_dir, bids_dir,
+def init_fmriprep_wf(layout, subject_list, task_id, echo_idx, run_uuid, work_dir, output_dir,
                      ignore, debug, low_mem, anat_only, longitudinal, t2s_coreg,
                      omp_nthreads, skull_strip_template, skull_strip_fixed_seed,
                      freesurfer, output_spaces, template, medial_surface_nan, cifti_output, hires,
@@ -51,15 +51,16 @@ def init_fmriprep_wf(subject_list, task_id, echo_idx, run_uuid, work_dir, output
         :simple_form: yes
 
         import os
-        os.environ['FREESURFER_HOME'] = os.getcwd()
+        from pybids import BIDSLayout
         from fmriprep.workflows.base import init_fmriprep_wf
-        wf = init_fmriprep_wf(subject_list=['fmripreptest'],
+        os.environ['FREESURFER_HOME'] = os.getcwd()
+        wf = init_fmriprep_wf(layout=BIDSLayout('.', validate=False),
+                              subject_list=['fmripreptest'],
                               task_id='',
                               echo_idx=None,
                               run_uuid='X',
                               work_dir='.',
                               output_dir='.',
-                              bids_dir='.',
                               ignore=[],
                               debug=False,
                               low_mem=False,
@@ -90,6 +91,8 @@ def init_fmriprep_wf(subject_list, task_id, echo_idx, run_uuid, work_dir, output
 
     Parameters
 
+        layout : BIDSLayout object
+            BIDS dataset layout
         subject_list : list
             List of subject labels
         task_id : str or None
@@ -103,8 +106,6 @@ def init_fmriprep_wf(subject_list, task_id, echo_idx, run_uuid, work_dir, output
             Directory in which to store workflow execution state and temporary files
         output_dir : str
             Directory in which to save derivatives
-        bids_dir : str
-            Root directory of BIDS dataset
         ignore : list
             Preprocessing steps to skip (may include "slicetiming", "fieldmaps")
         debug : bool
@@ -182,13 +183,13 @@ def init_fmriprep_wf(subject_list, task_id, echo_idx, run_uuid, work_dir, output
     reportlets_dir = os.path.join(work_dir, 'reportlets')
     for subject_id in subject_list:
         single_subject_wf = init_single_subject_wf(
+            layout=layout,
             subject_id=subject_id,
             task_id=task_id,
             echo_idx=echo_idx,
             name="single_subject_" + subject_id + "_wf",
             reportlets_dir=reportlets_dir,
             output_dir=output_dir,
-            bids_dir=bids_dir,
             ignore=ignore,
             debug=debug,
             low_mem=low_mem,
@@ -230,8 +231,8 @@ def init_fmriprep_wf(subject_list, task_id, echo_idx, run_uuid, work_dir, output
     return fmriprep_wf
 
 
-def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir, output_dir,
-                           bids_dir, ignore, debug, low_mem, anat_only, longitudinal, t2s_coreg,
+def init_single_subject_wf(layout, subject_id, task_id, echo_idx, name, reportlets_dir,
+                           output_dir, ignore, debug, low_mem, anat_only, longitudinal, t2s_coreg,
                            omp_nthreads, skull_strip_template, skull_strip_fixed_seed,
                            freesurfer, output_spaces, template, medial_surface_nan,
                            cifti_output, hires, use_bbr, bold2t1w_dof, fmap_bspline, fmap_demean,
@@ -252,13 +253,14 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
         :simple_form: yes
 
         from fmriprep.workflows.base import init_single_subject_wf
-        wf = init_single_subject_wf(subject_id='test',
+        from bids import BIDSLayout
+        wf = init_single_subject_wf(layout=BIDSLayout('.', validate=False),
+                                    subject_id='test',
                                     task_id='',
                                     echo_idx=None,
                                     name='single_subject_wf',
                                     reportlets_dir='.',
                                     output_dir='.',
-                                    bids_dir='.',
                                     ignore=[],
                                     debug=False,
                                     low_mem=False,
@@ -288,6 +290,8 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
 
     Parameters
 
+        layout : BIDSLayout object
+            BIDS dataset layout
         subject_id : str
             List of subject labels
         task_id : str or None
@@ -321,8 +325,6 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
             Directory in which to save reportlets
         output_dir : str
             Directory in which to save derivatives
-        bids_dir : str
-            Root directory of BIDS dataset
         freesurfer : bool
             Enable FreeSurfer surface reconstruction (may increase runtime)
         output_spaces : list
@@ -379,8 +381,7 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
         }
         layout = None
     else:
-        subject_data, layout = collect_data(
-            bids_dir, subject_id, task_id, echo_idx, bids_validate=False)
+        subject_data = collect_data(layout, subject_id, task_id, echo_idx)[0]
 
     # Make sure we always go through these two checks
     if not anat_only and subject_data['bold'] == []:
@@ -423,7 +424,7 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
                       name='bidssrc')
 
     bids_info = pe.Node(BIDSInfo(
-        bids_dir=bids_dir, bids_validate=False),
+        bids_dir=layout.root, bids_validate=False),
         name='bids_info', run_without_submitting=True)
 
     summary = pe.Node(SubjectSummary(output_spaces=output_spaces, template=template),
@@ -541,4 +542,3 @@ def _prefix(subid):
     if subid.startswith('sub-'):
         return subid
     return '-'.join(('sub', subid))
-

requirements.txt

@@ -1,4 +1,4 @@
 pybids>=0.7.0,<0.8
-git+https://github.com/oesteban/niworkflows.git@0208e37b8915d89720856ac76becbed7592437c5#niworkflows-0.6.1
-git+https://github.com/oesteban/smriprep.git@e504ddaca62da545b75a7cbc629ff91b8b48f2ee#smriprep-0.0.4
+niworkflows>=0.7.0,<0.8.0a
+git+https://github.com/oesteban/smriprep.git@2ad4639b308a5d13183819e13bcb3ca6d4d93eac#smriprep-0.0.4
 templateflow>=0.0.4