Merge pull request #803 from mgxd/fix/templateflow-default-res

FIX: Inspect if template has resolution instead of assuming

Author: effigies

niworkflows/anat/ants.py

@@ -196,7 +196,7 @@ def init_brain_extraction_wf(
     template_spec["suffix"] = template_spec.get("suffix", bids_suffix)
 
     tpl_target_path, common_spec = get_template_specs(
-        in_template, template_spec=template_spec
+        in_template, template_spec=template_spec, fallback=True,
     )
 
     # Get probabilistic brain mask if available

niworkflows/interfaces/norm.py

@@ -429,6 +429,7 @@ def _get_ants_args(self):
                 self.inputs.template,
                 template_spec=template_spec,
                 default_resolution=default_resolution,
+                fallback=True,
             )
 
             # Set reference image

niworkflows/utils/misc.py

@@ -22,6 +22,8 @@
 #
 """Miscellaneous utilities."""
 import os
+from typing import Optional
+import warnings
 
 
 __all__ = [
@@ -35,7 +37,12 @@
 ]
 
 
-def get_template_specs(in_template, template_spec=None, default_resolution=1):
+def get_template_specs(
+    in_template: str,
+    template_spec: Optional[dict] = None,
+    default_resolution: int = 1,
+    fallback: bool = False
+):
     """
     Parse template specifications
 
@@ -61,8 +68,17 @@ def get_template_specs(in_template, template_spec=None, default_resolution=1):
     RuntimeError:
     ...
 
+    >>> get_template_specs('UNCInfant',
+    ...                    {'suffix': 'T1w', 'res': 1})[1] # doctest: +IGNORE_EXCEPTION_DETAIL
+    Traceback (most recent call last):
+    RuntimeError:
+    ...
+
+    >>> get_template_specs('UNCInfant',
+    ...                    {'cohort': 1, 'suffix': 'T1w', 'res': 1}, fallback=True)[1]
+    {'resolution': None, 'cohort': 1}
     """
-    from templateflow.api import get as get_template
+    import templateflow.api as tf
 
     # Massage spec (start creating if None)
     template_spec = template_spec or {}
@@ -72,11 +88,31 @@ def get_template_specs(in_template, template_spec=None, default_resolution=1):
         "res", template_spec.get("resolution", default_resolution)
     )
 
+    # Verify resolution is valid
+    if fallback:
+        res = template_spec['resolution']
+        if not isinstance(res, list):
+            try:
+                res = [int(res)]
+            except Exception:
+                res = None
+        if res is None:
+            res = []
+
+        available_resolutions = tf.TF_LAYOUT.get_resolutions(template=in_template)
+        if not (set(res) & set(available_resolutions)):
+            fallback_res = available_resolutions[0] if available_resolutions else None
+            warnings.warn(
+                f"Template {in_template} does not have resolution: {res}."
+                f"Falling back to resolution: {fallback_res}."
+            )
+            template_spec["resolution"] = fallback_res
+
     common_spec = {"resolution": template_spec["resolution"]}
     if "cohort" in template_spec:
         common_spec["cohort"] = template_spec["cohort"]
 
-    tpl_target_path = get_template(in_template, **template_spec)
+    tpl_target_path = tf.get(in_template, **template_spec)
     if not tpl_target_path:
         raise RuntimeError(
             """\