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RF: Switch from DerivativesDataSinks to Prep/Save nodes #3352

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RF: Switch from DerivativesDataSinks to Prep/Save nodes #3352

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10 changes: 0 additions & 10 deletions fmriprep/interfaces/__init__.py
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Original file line number Diff line number Diff line change
@@ -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',)
44 changes: 31 additions & 13 deletions fmriprep/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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,
)
Expand Down Expand Up @@ -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([
Expand All @@ -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
Expand Down
77 changes: 58 additions & 19 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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,
)
Expand All @@ -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

Expand Down Expand Up @@ -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,
Expand All @@ -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
Expand Down Expand Up @@ -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

Expand All @@ -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, [
Expand All @@ -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,)):
Expand Down Expand Up @@ -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
Expand Down
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