Merge pull request #486 from nipreps/rf/tf-xfms

rf: retrieve transforms with templateflow

Author: mgxd

.circleci/config.yml

@@ -214,8 +214,6 @@ jobs:
     - run:
         name: Get intermediate transforms
         command: |
-          mkdir -p /tmp/pooch
-          cd /tmp/pooch
           # Caching intermediate templates so no need to constantly fetch
           XFM="from-MNI152NLin6Asym_to-MNIInfant+1_xfm.h5"
           echo "Downloading $XFM"
@@ -229,7 +227,6 @@ jobs:
         paths:
         - fslicense
         - bcp/nipype.cfg
-        - pooch/*
 
   test_pytest:
     !!merge <<: *machine_defaults
@@ -348,8 +345,7 @@ jobs:
               --nthreads 4 -vv --age-months 2 --sloppy \
               --surface-recon-method infantfs \
               --derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \
-              --output-layout bids --anat-only \
-              --pooch-cache-dir /tmp/pooch
+              --output-layout bids --anat-only
     - run:
         name: Checking outputs of anatomical nibabies run
         command: |
@@ -378,8 +374,7 @@ jobs:
               --nthreads 4 -vv --age-months 2 \
               --surface-recon-method infantfs \
               --derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \
-              --output-layout bids \
-              --pooch-cache-dir /tmp/pooch
+              --output-layout bids
     - run:
         name: Checking outputs of full nibabies run
         command: |
@@ -425,8 +420,7 @@ jobs:
               --nthreads 4 -vv --age-months 2 \
               --surface-recon-method infantfs \
               --derivatives precomputed=/tmp/data/${DATASET}-t2only/derivatives/bibsnet \
-              --output-layout bids --anat-only --cifti-output \
-              --pooch-cache-dir /tmp/pooch
+              --output-layout bids --anat-only --cifti-output
     - run:
         name: Checking outputs of T2-only nibabies anat
         command: |

nibabies/interfaces/download.py

@@ -345,7 +345,6 @@ def init_concat_registrations_wf(
         further use in downstream nodes.
 
     """
-    from nibabies.interfaces.download import RetrievePoochFiles
     from nibabies.interfaces.patches import CompositeTransformUtil
 
     ntpls = len(templates)
@@ -405,9 +404,9 @@ def init_concat_registrations_wf(
     ]
     outputnode = pe.Node(niu.IdentityInterface(fields=out_fields), name='outputnode')
 
-    intermed_xfms = pe.MapNode(
-        RetrievePoochFiles(),
-        name='retrieve_xfms',
+    fetch_tf_xfms = pe.MapNode(
+        niu.Function(function=_get_intermediate_xfms, output_names=['int2tgt_xfm', 'tgt2int_xfm']),
+        name='fetch_tf_xfms',
         iterfield=['target'],
         run_without_submitting=True,
     )
@@ -460,10 +459,10 @@ def init_concat_registrations_wf(
         # Transform concatenation
         (inputnode, dis_anat2int, [('anat2int_xfm', 'in_file')]),
         (inputnode, dis_int2anat, [('int2anat_xfm', 'in_file')]),
-        (inputnode, intermed_xfms, [('intermediate', 'intermediate'),
+        (inputnode, fetch_tf_xfms, [('intermediate', 'intermediate'),
                                     ('template', 'target')]),
-        (intermed_xfms, dis_int2std, [('int2tgt_xfm', 'in_file')]),
-        (intermed_xfms, dis_std2int, [('tgt2int_xfm', 'in_file')]),
+        (fetch_tf_xfms, dis_int2std, [('int2tgt_xfm', 'in_file')]),
+        (fetch_tf_xfms, dis_std2int, [('tgt2int_xfm', 'in_file')]),
         (dis_anat2int, order_anat2std, [
             ('affine_transform', 'in1'),
             ('displacement_field', 'in2'),
@@ -499,3 +498,28 @@ def init_concat_registrations_wf(
     ])  # fmt:skip
 
     return workflow
+
+
+def _get_intermediate_xfms(intermediate, target):
+    import templateflow.api as tf
+
+    # Native -> MNIInfant:cohort-X (int) -> Target (std)
+    ispace, _, icohort = intermediate.partition(':cohort-')
+    ispaceid = f'{ispace}+{icohort}' if icohort else ispace
+
+    int2std = tf.get(
+        target,
+        suffix='xfm',
+        **{'from': ispaceid},
+        raise_empty=True,
+    )
+
+    std2int = tf.get(
+        ispace,
+        cohort=icohort or None,
+        suffix='xfm',
+        **{'from': target},
+        raise_empty=True,
+    )
+
+    return int2std, std2int

nibabies/interfaces/tests/test_download.py

@@ -29,7 +29,6 @@ dependencies = [
     "numpy >= 1.21.0",
     "packaging",
     "pandas < 3",
-    "pooch",
     "psutil >= 5.4",
     "pybids >= 0.15.0",
     "requests",

nibabies/workflows/anatomical/registration.py

@@ -476,12 +476,6 @@ def _is_file(path, parser):
         type=os.path.abspath,
         help='Filter file',
     )
-    g_wrap.add_argument(
-        '--pooch-cache-dir',
-        metavar='DIR',
-        type=os.path.abspath,
-        help='Directory to serve as cache for pooch files'
-    )
 
     # Developer patch/shell options
     g_dev = parser.add_argument_group(
@@ -649,9 +643,6 @@ def main():
     if opts.deriv_filter_file:
         container.add_mount(opts.deriv_filter_file, '/opt/derivative_filters.json')
         unknown_args.extend(['--deriv-filter-file', '/opt/derivative_filters.json'])
-    if opts.pooch_cache_dir:
-        container.add_mount(opts.pooch_cache_dir, '/tmp/pooch_cache', read_only=False)
-        container.add_envvar(('NIBABIES_POOCH_DIR', '/tmp/pooch_cache'))
     # Patch derivatives for searching
     if opts.derivatives:
         deriv_args = ['--derivatives']