RF: Switch from DerivativesDataSinks to Prep/Save nodes

Author: effigies

fmriprep/interfaces/__init__.py

@@ -1,10 +0,0 @@
-# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft=python sts=4 ts=4 sw=4 et:
-from niworkflows.interfaces.bids import DerivativesDataSink as _DDSink
-
-
-class DerivativesDataSink(_DDSink):
-    out_path_base = ''
-
-
-__all__ = ('DerivativesDataSink',)

fmriprep/workflows/base.py

@@ -37,11 +37,11 @@
 import bids
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.interfaces.bids import PrepareDerivative, SaveDerivative
 from niworkflows.utils.connections import listify
 from packaging.version import Version
 
 from .. import config
-from ..interfaces import DerivativesDataSink
 from ..interfaces.reports import AboutSummary, SubjectSummary
 from ..utils.bids import dismiss_echo
 
@@ -287,24 +287,34 @@ def init_single_subject_wf(subject_id: str):
         run_without_submitting=True,
     )
 
-    ds_report_summary = pe.Node(
-        DerivativesDataSink(
-            base_directory=config.execution.fmriprep_dir,
+    prep_report_summary = pe.Node(
+        PrepareDerivative(
             desc='summary',
             datatype='figures',
             dismiss_entities=dismiss_echo(),
         ),
+        name='prep_report_summary',
+        run_without_submitting=True,
+    )
+
+    ds_report_summary = pe.Node(
+        SaveDerivative(base_directory=config.execution.fmriprep_dir),
         name='ds_report_summary',
         run_without_submitting=True,
     )
 
-    ds_report_about = pe.Node(
-        DerivativesDataSink(
-            base_directory=config.execution.fmriprep_dir,
+    prep_report_about = pe.Node(
+        PrepareDerivative(
             desc='about',
             datatype='figures',
             dismiss_entities=dismiss_echo(),
         ),
+        name='prep_report_about',
+        run_without_submitting=True,
+    )
+
+    ds_report_about = pe.Node(
+        SaveDerivative(base_directory=config.execution.fmriprep_dir),
         name='ds_report_about',
         run_without_submitting=True,
     )
@@ -339,15 +349,15 @@ def init_single_subject_wf(subject_id: str):
         workflow.connect([
             (bidssrc, bids_info, [(('bold', fix_multi_T1w_source_name), 'in_file')]),
             (anat_fit_wf, summary, [('outputnode.t1w_preproc', 't1w')]),
-            (anat_fit_wf, ds_report_summary, [('outputnode.t1w_preproc', 'source_file')]),
-            (anat_fit_wf, ds_report_about, [('outputnode.t1w_preproc', 'source_file')]),
+            (anat_fit_wf, prep_report_summary, [('outputnode.t1w_preproc', 'source_file')]),
+            (anat_fit_wf, prep_report_about, [('outputnode.t1w_preproc', 'source_file')]),
         ])  # fmt:skip
     else:
         workflow.connect([
             (bidssrc, bids_info, [(('t1w', fix_multi_T1w_source_name), 'in_file')]),
             (bidssrc, summary, [('t1w', 't1w')]),
-            (bidssrc, ds_report_summary, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
-            (bidssrc, ds_report_about, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
+            (bidssrc, prep_report_summary, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
+            (bidssrc, prep_report_about, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
         ])  # fmt:skip
 
     workflow.connect([
@@ -363,8 +373,16 @@ def init_single_subject_wf(subject_id: str):
         (inputnode, summary, [('subjects_dir', 'subjects_dir')]),
         (bidssrc, summary, [('t2w', 't2w'), ('bold', 'bold')]),
         (bids_info, summary, [('subject', 'subject_id')]),
-        (summary, ds_report_summary, [('out_report', 'in_file')]),
-        (about, ds_report_about, [('out_report', 'in_file')]),
+        (summary, prep_report_summary, [('out_report', 'in_file')]),
+        (about, prep_report_about, [('out_report', 'in_file')]),
+        (prep_report_summary, ds_report_summary, [
+            ('out_file', 'in_file'),
+            ('out_path', 'relative_path'),
+        ]),
+        (prep_report_about, ds_report_about, [
+            ('out_file', 'in_file'),
+            ('out_path', 'relative_path'),
+        ]),
     ])  # fmt:skip
 
     # Set up the template iterator once, if used

fmriprep/workflows/bold/base.py

@@ -32,10 +32,10 @@
 
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.interfaces.bids import PrepareDerivative, SaveDerivative
 from niworkflows.utils.connections import listify
 
 from ... import config
-from ...interfaces import DerivativesDataSink
 from ...utils.bids import dismiss_echo
 from ...utils.misc import estimate_bold_mem_usage
 
@@ -336,22 +336,34 @@ def init_bold_wf(
     if multiecho:
         t2s_reporting_wf = init_t2s_reporting_wf()
 
-        ds_report_t2scomp = pe.Node(
-            DerivativesDataSink(
+        prep_report_t2scomp = pe.Node(
+            PrepareDerivative(
                 desc='t2scomp',
                 datatype='figures',
                 dismiss_entities=dismiss_echo(),
             ),
+            name='prep_report_t2scomp',
+            run_without_submitting=True,
+        )
+
+        ds_report_t2scomp = pe.Node(
+            SaveDerivative(),
             name='ds_report_t2scomp',
             run_without_submitting=True,
         )
 
-        ds_report_t2star_hist = pe.Node(
-            DerivativesDataSink(
+        prep_report_t2star_hist = pe.Node(
+            PrepareDerivative(
                 desc='t2starhist',
                 datatype='figures',
                 dismiss_entities=dismiss_echo(),
             ),
+            name='prep_report_t2star_hist',
+            run_without_submitting=True,
+        )
+
+        ds_report_t2star_hist = pe.Node(
+            SaveDerivative(),
             name='ds_report_t2star_hist',
             run_without_submitting=True,
         )
@@ -365,15 +377,24 @@ def init_bold_wf(
             (bold_native_wf, t2s_reporting_wf, [
                 ('outputnode.t2star_map', 'inputnode.t2star_file'),
             ]),
-            (t2s_reporting_wf, ds_report_t2scomp, [('outputnode.t2s_comp_report', 'in_file')]),
-            (t2s_reporting_wf, ds_report_t2star_hist, [('outputnode.t2star_hist', 'in_file')]),
+            (t2s_reporting_wf, prep_report_t2scomp, [('outputnode.t2s_comp_report', 'in_file')]),
+            (t2s_reporting_wf, prep_report_t2star_hist, [('outputnode.t2star_hist', 'in_file')]),
+            (prep_report_t2scomp, ds_report_t2scomp, [
+                ('out_file', 'in_file'),
+                ('out_path', 'relative_path'),
+            ]),
+            (prep_report_t2star_hist, ds_report_t2star_hist, [
+                ('out_file', 'in_file'),
+                ('out_path', 'relative_path'),
+            ]),
         ])  # fmt:skip
 
     if config.workflow.level == 'resampling':
         # Fill-in datasinks of reportlets seen so far
         for node in workflow.list_node_names():
             if node.split('.')[-1].startswith('ds_report'):
                 workflow.get_node(node).inputs.base_directory = fmriprep_dir
+            if node.split('.')[-1].startswith('prep_report'):
                 workflow.get_node(node).inputs.source_file = bold_file
         return workflow
 
@@ -584,9 +605,8 @@ def init_bold_wf(
             repetition_time=all_metadata[0]['RepetitionTime'],
         )
 
-        ds_bold_cifti = pe.Node(
-            DerivativesDataSink(
-                base_directory=fmriprep_dir,
+        prep_bold_cifti = pe.Node(
+            PrepareDerivative(
                 dismiss_entities=dismiss_echo(),
                 space='fsLR',
                 density=config.workflow.cifti_output,
@@ -595,10 +615,15 @@ def init_bold_wf(
                 TaskName=all_metadata[0].get('TaskName'),
                 **prepare_timing_parameters(all_metadata[0]),
             ),
+            name='prep_bold_cifti',
+        )
+        prep_bold_cifti.inputs.source_file = bold_file
+
+        ds_bold_cifti = pe.Node(
+            SaveDerivative(base_directory=fmriprep_dir),
             name='ds_bold_cifti',
             run_without_submitting=True,
         )
-        ds_bold_cifti.inputs.source_file = bold_file
 
         workflow.connect([
             # Resample BOLD to MNI152NLin6Asym, may duplicate bold_std_wf above
@@ -637,9 +662,14 @@ def init_bold_wf(
             (bold_fsLR_resampling_wf, bold_grayords_wf, [
                 ('outputnode.bold_fsLR', 'inputnode.bold_fsLR'),
             ]),
-            (bold_grayords_wf, ds_bold_cifti, [
+            (bold_grayords_wf, prep_bold_cifti, [
                 ('outputnode.cifti_bold', 'in_file'),
-                (('outputnode.cifti_metadata', _read_json), 'meta_dict'),
+                ('outputnode.cifti_metadata', 'meta_dict'),
+            ]),
+            (prep_bold_cifti, ds_bold_cifti, [
+                ('out_file', 'in_file'),
+                ('out_path', 'relative_path'),
+                ('out_meta', 'metadata'),
             ]),
         ])  # fmt:skip
 
@@ -653,18 +683,21 @@ def init_bold_wf(
         name='bold_confounds_wf',
     )
 
-    ds_confounds = pe.Node(
-        DerivativesDataSink(
-            base_directory=fmriprep_dir,
+    prepare_confounds = pe.Node(
+        PrepareDerivative(
             desc='confounds',
             suffix='timeseries',
             dismiss_entities=dismiss_echo(),
         ),
+        name='prepare_confounds',
+        run_without_submitting=True,
+    )
+    ds_confounds = pe.Node(
+        SaveDerivative(base_directory=fmriprep_dir),
         name='ds_confounds',
         run_without_submitting=True,
-        mem_gb=config.DEFAULT_MEMORY_MIN_GB,
     )
-    ds_confounds.inputs.source_file = bold_file
+    prepare_confounds.inputs.source_file = bold_file
 
     workflow.connect([
         (inputnode, bold_confounds_wf, [
@@ -681,10 +714,15 @@ def init_bold_wf(
         (bold_native_wf, bold_confounds_wf, [
             ('outputnode.bold_native', 'inputnode.bold'),
         ]),
-        (bold_confounds_wf, ds_confounds, [
+        (bold_confounds_wf, prepare_confounds, [
             ('outputnode.confounds_file', 'in_file'),
             ('outputnode.confounds_metadata', 'meta_dict'),
         ]),
+        (prepare_confounds, ds_confounds, [
+            ('out_file', 'in_file'),
+            ('out_path', 'relative_path'),
+            ('out_meta', 'metadata'),
+        ]),
     ])  # fmt:skip
 
     if spaces.get_spaces(nonstandard=False, dim=(3,)):
@@ -726,6 +764,7 @@ def _last(inlist):
     for node in workflow.list_node_names():
         if node.split('.')[-1].startswith('ds_report'):
             workflow.get_node(node).inputs.base_directory = fmriprep_dir
+        if node.split('.')[-1].startswith('prep_report'):
             workflow.get_node(node).inputs.source_file = bold_file
 
     return workflow