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rf: retrieve xfms through templateflow, remove pooch
1 parent 27a69d6 commit 06cb6ea

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4 files changed

+31
-100
lines changed

4 files changed

+31
-100
lines changed

nibabies/interfaces/download.py

Lines changed: 0 additions & 73 deletions
This file was deleted.

nibabies/interfaces/tests/test_download.py

Lines changed: 0 additions & 19 deletions
This file was deleted.

nibabies/workflows/anatomical/registration.py

Lines changed: 31 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -345,7 +345,6 @@ def init_concat_registrations_wf(
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further use in downstream nodes.
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"""
348-
from nibabies.interfaces.download import RetrievePoochFiles
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from nibabies.interfaces.patches import CompositeTransformUtil
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ntpls = len(templates)
@@ -405,9 +404,9 @@ def init_concat_registrations_wf(
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]
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outputnode = pe.Node(niu.IdentityInterface(fields=out_fields), name='outputnode')
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intermed_xfms = pe.MapNode(
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RetrievePoochFiles(),
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name='retrieve_xfms',
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fetch_tf_xfms = pe.MapNode(
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niu.Function(function=_get_intermediate_xfms, output_names=['int2tgt_xfm', 'tgt2int_xfm']),
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name='fetch_tf_xfms',
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iterfield=['target'],
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run_without_submitting=True,
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)
@@ -460,10 +459,10 @@ def init_concat_registrations_wf(
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# Transform concatenation
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(inputnode, dis_anat2int, [('anat2int_xfm', 'in_file')]),
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(inputnode, dis_int2anat, [('int2anat_xfm', 'in_file')]),
463-
(inputnode, intermed_xfms, [('intermediate', 'intermediate'),
462+
(inputnode, fetch_tf_xfms, [('intermediate', 'intermediate'),
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('template', 'target')]),
465-
(intermed_xfms, dis_int2std, [('int2tgt_xfm', 'in_file')]),
466-
(intermed_xfms, dis_std2int, [('tgt2int_xfm', 'in_file')]),
464+
(fetch_tf_xfms, dis_int2std, [('int2tgt_xfm', 'in_file')]),
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(fetch_tf_xfms, dis_std2int, [('tgt2int_xfm', 'in_file')]),
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(dis_anat2int, order_anat2std, [
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('affine_transform', 'in1'),
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('displacement_field', 'in2'),
@@ -499,3 +498,28 @@ def init_concat_registrations_wf(
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]) # fmt:skip
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return workflow
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def _get_intermediate_xfms(intermediate, target):
504+
import templateflow.api as tf
505+
506+
# Native -> MNIInfant:cohort-X (int) -> Target (std)
507+
ispace, _, icohort = intermediate.partition(':cohort-')
508+
ispaceid = f'{ispace}+{icohort}' if icohort else ispace
509+
510+
int2std = tf.get(
511+
target,
512+
suffix='xfm',
513+
**{'from': ispaceid},
514+
raise_empty=True,
515+
)
516+
517+
std2int = tf.get(
518+
ispace,
519+
cohort=icohort or None,
520+
suffix='xfm',
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**{'from': target},
522+
raise_empty=True,
523+
)
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525+
return int2std, std2int

pyproject.toml

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,6 @@ dependencies = [
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"numpy >= 1.21.0",
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"packaging",
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"pandas < 3",
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"pooch",
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"psutil >= 5.4",
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"pybids >= 0.15.0",
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"requests",

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