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Collect and apply field maps #79

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7 changes: 4 additions & 3 deletions src/fmripost_aroma/data/io_spec.json
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
{
"name": "aroma",
"queries": {
"raw": {
"bold_raw": {
Expand Down Expand Up @@ -151,8 +152,8 @@
},
"entities": [
{
"name": "datatype",
"pattern": "[/\\\\]+(anat|func)[/\\\\]+"
"name": "fmapid",
"pattern": "fmapid-([a-zA-Z0-9]+)"
},
{
"name": "cohort",
Expand All @@ -172,7 +173,7 @@
"pattern": "(?:^|_)thresh-([a-zA-Z0-9]+)"
}
],
"patterns": [
"default_path_patterns": [
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<tsv|json>|tsv}",
Expand Down
2 changes: 1 addition & 1 deletion src/fmripost_aroma/interfaces/bids.py
Original file line number Diff line number Diff line change
Expand Up @@ -31,4 +31,4 @@ class DerivativesDataSink(BaseDerivativesDataSink):
_allowed_entities = set(config_entities)
_config_entities = config_entities
_config_entities_dict = merged_entities
_file_patterns = fmripost_aroma_spec['patterns']
_file_patterns = fmripost_aroma_spec['default_path_patterns']
11 changes: 9 additions & 2 deletions src/fmripost_aroma/utils/bids.py
Original file line number Diff line number Diff line change
Expand Up @@ -98,14 +98,21 @@ def collect_derivatives(
if not entities:
entities = {}

_spec = None
if spec is None or patterns is None:
_spec = json.loads(load_data.readable('io_spec.json').read_text())

if spec is None:
spec = _spec['queries']

if patterns is None:
patterns = _spec['patterns']
patterns = _spec['default_path_patterns']

_spec.pop('queries')

config = ['bids', 'derivatives']
if _spec:
config = ['bids', 'derivatives', _spec]

# Search for derivatives data
derivs_cache = defaultdict(list, {})
Expand All @@ -114,7 +121,7 @@ def collect_derivatives(
if isinstance(layout, Path):
layout = BIDSLayout(
layout,
config=['bids', 'derivatives'],
config=config,
validate=False,
)

Expand Down
25 changes: 22 additions & 3 deletions src/fmripost_aroma/workflows/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,7 @@
if config.execution.derivatives:
# Raw dataset + derivatives dataset
config.loggers.workflow.info('Raw+derivatives workflow mode enabled')
# Just build a list of BOLD files right now
subject_data = collect_derivatives(
raw_dataset=config.execution.layout,
derivatives_dataset=None,
Expand All @@ -191,6 +192,7 @@
else:
# Derivatives dataset only
config.loggers.workflow.info('Derivatives-only workflow mode enabled')
# Just build a list of BOLD files right now
subject_data = collect_derivatives(
raw_dataset=None,
derivatives_dataset=config.execution.layout,
Expand Down Expand Up @@ -304,14 +306,31 @@

entities = extract_entities(bold_file)

# Attempt to extract the associated fmap ID
fmapid = None
all_fmapids = config.execution.layout.get_fmapids(

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subject=entities['subject'],
session=entities.get('session', None),
)
if all_fmapids:
fmap_file = config.execution.layout.get_nearest(

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bold_file,
to=all_fmapids,
suffix='xfm',
extension='.txt',
strict=False,
**{'from': 'boldref'},
)
fmapid = config.execution.layout.get_file(fmap_file).entities['to']

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functional_cache = defaultdict(list, {})
if config.execution.derivatives:
# Collect native-space derivatives and transforms
functional_cache = collect_derivatives(
raw_dataset=config.execution.layout,
derivatives_dataset=None,
entities=entities,
fieldmap_id=None,
fieldmap_id=fmapid,
allow_multiple=False,
spaces=None,
)
Expand All @@ -322,7 +341,7 @@
raw_dataset=None,
derivatives_dataset=deriv_dir,
entities=entities,
fieldmap_id=None,
fieldmap_id=fmapid,
allow_multiple=False,
spaces=spaces,
),
Expand All @@ -347,7 +366,7 @@
raw_dataset=None,
derivatives_dataset=config.execution.layout,
entities=entities,
fieldmap_id=None,
fieldmap_id=fmapid,
allow_multiple=False,
spaces=spaces,
),
Expand Down
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