Merge pull request #336 from mgxd/fix/templateflow-select

FIX: Query templateflow files to see if resolution is available

Author: mgxd

.circleci/config.yml

@@ -272,7 +272,7 @@ jobs:
           name: Pull TemplateFlow down, pre-cache some templates
           command: |
             export TEMPLATEFLOW_HOME=/tmp/templateflow
-            pip install -U --user --no-cache-dir "$( grep templateflow /tmp/src/smriprep/setup.cfg | xargs )"
+            pip install -U --user --no-cache-dir templateflow
             python -c "from templateflow import api as tfapi; \
                        tfapi.get(['MNI152Lin', 'MNI152NLin2009cAsym', 'OASIS30ANTs'], suffix='T1w'); \
                        tfapi.get(['MNI152Lin', 'MNI152NLin2009cAsym', 'OASIS30ANTs'], desc='brain', suffix='mask'); \

setup.cfg

@@ -25,7 +25,7 @@ install_requires =
     matplotlib >= 2.2.0
     nibabel >= 4.0.1
     nipype >= 1.7.0
-    niworkflows >= 1.7.0
+    niworkflows @ git+https://github.com/nipreps/niworkflows.git@master
     numpy
     packaging
     pybids >= 0.11.1

smriprep/interfaces/templateflow.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Interfaces to get templates from TemplateFlow."""
+import logging
 from templateflow import api as tf
 from nipype.interfaces.base import (
     SimpleInterface,
@@ -32,6 +33,8 @@
     InputMultiObject,
 )
 
+LOGGER = logging.getLogger("nipype.interface")
+
 
 class _TemplateFlowSelectInputSpec(BaseInterfaceInputSpec):
     template = traits.Str("MNI152NLin2009cAsym", mandatory=True, desc="Template ID")
@@ -87,8 +90,11 @@ class TemplateFlowSelect(SimpleInterface):
     '.../tpl-MNIPediatricAsym_cohort-5_res-1_T1w.nii.gz'
 
     >>> select = TemplateFlowSelect()
-    >>> select.inputs.template = 'UNCInfant:cohort-1'
-    >>> result = select.run()  # doctest: +SKIP
+    >>> select.inputs.template = 'MNI305'
+    >>> select.inputs.template_spec = {'resolution': 1}
+    >>> result = select.run()
+    >>> result.outputs.t1w_file  # doctest: +ELLIPSIS
+    '.../tpl-MNI305_T1w.nii.gz'
 
     """
 
@@ -115,6 +121,18 @@ def _run_interface(self, runtime):
                 }
             )
 
+        if specs['resolution'] and not isinstance(specs['resolution'], list):
+            specs['resolution'] = [specs['resolution']]
+
+        available_resolutions = tf.TF_LAYOUT.get_resolutions(template=name[0])
+        if specs['resolution'] and not set(specs["resolution"]) & set(available_resolutions):
+            fallback_res = available_resolutions[0] if available_resolutions else None
+            LOGGER.warning(
+                f"Template {name[0]} does not have resolution(s): {specs['resolution']}."
+                f"Falling back to resolution: {fallback_res}."
+            )
+            specs["resolution"] = fallback_res
+
         self._results["t1w_file"] = tf.get(name[0], desc=None, suffix="T1w", **specs)
 
         self._results["brain_mask"] = (