Add inverse transforms.

Author: tsalo

src/fmripost_template/data/io_spec.json

@@ -148,6 +148,11 @@
                 "desc": null,
                 "suffix": "xfm",
                 "extension": ".h5"
+            },
+            "all_transforms": {
+                "mode": "image",
+                "suffix": "xfm",
+                "extension": [".h5", ".txt"]
             }
         }
     },

src/fmripost_template/utils/utils.py

@@ -132,37 +132,77 @@ def find_shortest_path(space_pairs, start, end):
 
 
 def get_transforms(source, target, local_transforms=None):
-    """Get the transforms required to go from source to target space."""
+    """Get the transforms required to go from source to target space.
+
+    Parameters
+    ----------
+    source : str
+        The source space.
+    target : str
+        The target space.
+    local_transforms : list of str, optional
+        List of local transforms to consider.
+
+    Returns
+    -------
+    selected_transforms : list of str
+        List of selected transforms to go from source to target space.
+    selected_inversions : list of bool
+        List of booleans indicating whether the corresponding transform should be inverted.
+
+    Raises
+    ------
+    ValueError
+        If no chain of transforms can link the source and target spaces.
+    """
     import templateflow.api as tflow
     from bids.layout import Entity, parse_file_entities
 
     query = [
-        Entity('template', 'tpl-([a-zA-Z0-9]+)'),
-        Entity('from', 'from-([a-zA-Z0-9]+)'),
+        Entity('template', 'tpl-([a-zA-Z0-9+]+)'),
+        Entity('from', 'from-([a-zA-Z0-9+]+)'),
+        Entity('to', 'to-([a-zA-Z0-9+]+)'),
     ]
 
     all_transforms = local_transforms or []
 
     templates = tflow.get_templates()
+    tfl_transforms = []
     for template in templates:
         template_transforms = tflow.get(template, suffix='xfm', extension='h5')
         if not isinstance(template_transforms, list):
             template_transforms = [template_transforms]
-        all_transforms += template_transforms
+        tfl_transforms += template_transforms
 
+    all_transforms += tfl_transforms
     links = []
     for transform in all_transforms:
         entities = parse_file_entities(transform, entities=query)
-        link = (entities['from'], entities['template'])
+        if 'template' in entities:
+            link = (entities['from'], entities['template'])
+        else:
+            link = (entities['from'], entities['to'])
         links.append(link)
 
+    inversions = [False] * len(all_transforms)
+
+    # Add inverses of all templateflow transforms (local transforms might not be invertible)
+    for transform in tfl_transforms:
+        entities = parse_file_entities(transform, entities=query)
+        if 'template' in entities:
+            links.append((entities['template'], entities['from']))
+        else:
+            links.append((entities['to'], entities['from']))
+        inversions.append(True)
+
     path = None
     try:
         path = find_shortest_path(links, source, target)
         print('Shortest path:', path)
     except ValueError as e:
-        print(e)
+        raise ValueError(f'Failed to find a path from {source} to {target}') from e
 
     selected_transforms = [all_transforms[i] for i in path]
+    selected_inversions = [inversions[i] for i in path]
 
-    return selected_transforms
+    return selected_transforms, selected_inversions