8000 WIP: Neuroscout related changes by adelavega · Pull Request #1 · effigies/fitlins · GitHub
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Merged
merged 4 commits into from
Dec 3, 2018
Merged

WIP: Neuroscout related changes #1

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45180ba
Extract model paths from BIDSFile objects
adelavega Nov 30, 2018
487b62a
Change preproc_dir to more generic derivatives which complies with BI…
adelavega Nov 30, 2018
cb17b01
Fix derivatives typos
adelavega Nov 30, 2018
8079d95
Store derivatives into a single list
effigies Dec 3, 2018
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16 changes: 5 additions & 11 deletions fitlins/cli/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,9 +79,9 @@ def get_parser():
'removed)')
g_bids.add_argument('-m', '--model', action='store', default='model.json',
help='location of BIDS model description (default bids_dir/model.json)')
g_bids.add_argument('-p', '--preproc-dir', action='store', default='fmriprep',
help='location of preprocessed data (if relative path, search '
'bids_dir/derivatives, followed by output_dir)')
g_bids.add_argument('-d', '--derivatives', action='store', nargs='+',
help='location of derivatives (including preprocessed images).'
'If none specified, indexes all derivatives under bids_dir/derivatives.')
g_bids.add_argument('--derivative-label', action='store', type=str,
help='execution label to append to derivative directory name')
g_bids.add_argument('--space', action='store',
Expand Down Expand Up @@ -139,13 +139,7 @@ def run_fitlins(argv=None):
if opts.model in (None, 'default') and not op.exists(model):
model = 'default'

preproc_dir = default_path(opts.preproc_dir,
op.join(opts.bids_dir, 'derivatives'),
'fmriprep')
if not op.exists(preproc_dir):
preproc_dir = default_path(opts.preproc_dir, opts.output_dir, 'fmriprep')
if not op.exists(preproc_dir):
raise RuntimeError("Preprocessed data could not be found")
derivatives = True if not opts.derivatives else opts.derivatives

pipeline_name = 'fitlins'
if opts.derivative_label:
Expand All @@ -158,7 +152,7 @@ def run_fitlins(argv=None):
work_dir = mkdtemp() if opts.work_dir is None else opts.work_dir

fitlins_wf = init_fitlins_wf(
opts.bids_dir, preproc_dir, deriv_dir, opts.space, model=model,
opts.bids_dir, derivatives, deriv_dir, opts.space, model=model,
participants=subject_list, base_dir=work_dir,
include_pattern=opts.include, exclude_pattern=opts.exclude
)
Expand Down
23 changes: 10 additions & 13 deletions fitlins/interfaces/bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,13 +103,13 @@ def _run_interface(self, runtime):
layout = bids.BIDSLayout(self.inputs.bids_dir, validate=False)

if not isdefined(models):
models = layout.get(suffix='smdl')
models = layout.get(suffix='smdl', return_type='file')
if not models:
raise ValueError("No models found")
elif models == 'default':
models = auto_model(layout)

models = [_ensure_model(m.path) for m in models]
models = [_ensure_model(m) for m in models]

if self.inputs.selectors:
# This is almost certainly incorrect
Expand All @@ -136,8 +136,8 @@ class LoadBIDSModelInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(exists=True,
mandatory=True,
desc='BIDS dataset root directory')
preproc_dir = Directory(exists=True,
desc='Optional preprocessed files directory')
derivatives = traits.Either(traits.Bool, InputMultiPath(Directory(exists=True)),
desc='Derivative folders')
model = traits.Dict(desc='Model specification', mandatory=True)
selectors = traits.Dict(desc='Limit collected sessions', usedefault=True)
include_pattern = InputMultiPath(
Expand All @@ -164,16 +164,16 @@ def _run_interface(self, runtime):
import bids
include = self.inputs.include_pattern
exclude = self.inputs.exclude_pattern
derivatives = self.inputs.preproc_dir
derivatives = self.inputs.derivatives
if not isdefined(include):
include = None
if not isdefined(exclude):
exclude = None
if not isdefined(derivatives):
exclude = False

layout = bids.BIDSLayout(self.inputs.bids_dir, include=include, exclude=exclude,
derivatives=derivatives)
layout = bids.BIDSLayout(self.inputs.bids_dir, include=include,
exclude=exclude, derivatives=derivatives)

selectors = self.inputs.selectors

Expand Down Expand Up @@ -364,8 +364,8 @@ class BIDSSelectInputSpec(BaseInterfaceInputSpec):
bids_dir = Directory(exists=True,
mandatory=True,
desc='BIDS dataset root directories')
preproc_dir = Directory(exists=True,
desc='Optional preprocessed files directory')
derivatives = traits.Either(True, InputMultiPath(Directory(exists=True)),
desc='Derivative folders')
entities = InputMultiPath(traits.Dict(), mandatory=True)
selectors = traits.Dict(desc='Additional selectors to be applied',
usedefault=True)
Expand All @@ -384,10 +384,7 @@ class BIDSSelect(SimpleInterface):
def _run_interface(self, runtime):
import bids

derivatives = self.inputs.preproc_dir
if not isdefined(derivatives):
exclude = False

derivatives = self.inputs.derivatives
layout = bids.BIDSLayout(self.inputs.bids_dir, derivatives=derivatives)

bold_files = []
Expand Down
11 changes: 3 additions & 8 deletions fitlins/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from ..interfaces.utils import MergeAll


def init_fitlins_wf(bids_dir, preproc_dir, out_dir, space, exclude_pattern=None,
def init_fitlins_wf(bids_dir, derivatives, out_dir, space, exclude_pattern=None,
include_pattern=None, model=None, participants=None,
base_dir=None, name='fitlins_wf'):
wf = pe.Workflow(name=name, base_dir=base_dir)
Expand All @@ -31,12 +31,10 @@ def init_fitlins_wf(bids_dir, preproc_dir, out_dir, space, exclude_pattern=None,

loader = pe.Node(
LoadBIDSModel(bids_dir=bids_dir,
preproc_dir=preproc_dir,
derivatives=derivatives,
selectors=selectors),
name='loader')

if preproc_dir is not None:
loader.inputs.preproc_dir = preproc_dir
if exclude_pattern is not None:
loader.inputs.exclude_pattern = exclude_pattern
if include_pattern is not None:
Expand All @@ -53,13 +51,10 @@ def init_fitlins_wf(bids_dir, preproc_dir, out_dir, space, exclude_pattern=None,

# Select preprocessed BOLD series to analyze
getter = pe.Node(
BIDSSelect(bids_dir=bids_dir,
BIDSSelect(bids_dir=bids_dir, derivatives=derivatives,
selectors={'type': 'preproc', 'space': space}),
name='getter')

if preproc_dir is not None:
getter.inputs.preproc_dir = preproc_dir

select_l1_contrasts = pe.Node(niu.Select(index=0), name='select_l1_contrasts')

# Run first level model
Expand Down
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