fix: parcellationschemes path

fix: verify map

_ci/region_attr_compliance.py

@@ -4,7 +4,7 @@
 def main():
 
     is_json=re.compile(r'\.json$')
-    path_to_parc='./parcellations/'
+    path_to_parc='./parcellationschemes/'
     files = [f for f in os.listdir(path_to_parc)
         if isfile(f'{path_to_parc}{f}') and is_json.search(f) ]
     for f in files:

_ci/verify_maps.py

@@ -4,7 +4,11 @@
 
 path_to_maps = Path("maps")
 path_to_space = Path("spaces")
-path_to_parcellations = Path("parcellations")
+path_to_parcellations = Path("parcellationschemes")
+
+PARCELLATION_MAP_TYPE = "siibra/atlases/parcellationmap/v0.1"
+SPACE_TYPE = "siibra/atlases/space/v0.1"
+PARCELLATION_TYPE = "siibra/atlases/parcellationscheme/v0.1"
 
 REMOVE_FROM_NAME = [
     "hemisphere",
@@ -32,20 +36,19 @@ def clear_name(name):
 def get_parcellation_region_names(region_tree):
     region_names = []
     for region in region_tree:
-        for key in region.keys():
-            if key == "name":
-                region_names.append(region["name"])
-            if key == "children":
-                children_names = get_parcellation_region_names(region["children"])
-                region_names.extend(children_names)
+        region_names.append(get_name(region))
+        children_names = get_parcellation_region_names(region.get("children", []))
+        region_names.extend(children_names)
     return region_names
 
 def compare_regions_to_parcellation(map_json, parc_region_tree):
     unmatched_regions = []
     parc_regions = get_parcellation_region_names(parc_region_tree)
-    for region in map_json.get("indices").keys():
-        if not any(region == parc_region for parc_region in parc_regions):
-            unmatched_regions.append(region)
+    for image in find_images(map_json):
+        mapping: dict = image.get("mapping", {})
+        for region in mapping.keys():
+            if not any(region == parc_region for parc_region in parc_regions):
+                unmatched_regions.append(region)
     return unmatched_regions
 
 def get_json(path: Path):
@@ -57,24 +60,58 @@ def get_json(path: Path):
             with open(file, "r") as fp:
                 yield json.load(fp=fp), str(file)
 
+def get_by_type(dir: str|Path, _type: str):
+    for f in Path(dir).glob("*.json"):
+        json_obj = json.loads(f.read_bytes())
+        if json_obj.get("@type") != _type:
+            continue
+        yield json_obj
+
+def get_maps(dir: str|Path):
+    yield from get_by_type(dir, PARCELLATION_MAP_TYPE)
+
+def get_spaces(dir: str|Path):
+    yield from get_by_type(dir, SPACE_TYPE)
+
+def get_parcs(dir: str|Path):
+    yield from get_by_type(dir, PARCELLATION_TYPE)
+
+def get_id(obj: dict):
+    id_attrs = [attr for attr in obj.get("attributes", []) if attr.get("@type") == "siibra/attr/desc/id/v0.1"]
+    assert len(id_attrs) == 1, f"expected one and only one id attr"
+    return id_attrs[0]["value"]
+
+def get_name(obj: dict):
+
+    name_attrs = [attr for attr in obj.get("attributes", []) if attr.get("@type") == "siibra/attr/desc/name/v0.1"]
+    assert len(name_attrs) == 1, f"expected one and only one id attr"
+    return name_attrs[0]["value"]
+
+def find_images(obj: dict):
+    return [attr for attr in obj.get("attributes", []) if attr.get("@type") == "siibra/attr/data/image/v0.1"]
+
 def main():
     parcs = dict()
     space_ids = set()
+    fail_flag = False
     for json_obj, _ in get_json(path_to_parcellations):
-        parcs[json_obj.get("@id")] = json_obj.get("regions")
+        parcs[get_id(json_obj)] = json_obj.get("regions")
     for json_obj, _ in get_json(path_to_space):
-        space_ids.add(json_obj.get("@id"))
+        space_ids.add(get_id(json_obj))
     for json_obj, filepath in get_json(path_to_maps):
         errmsg = f"map with path {str(filepath)}"
-        space_id = json_obj.get("space", {}).get("@id")
-        parc_id = json_obj.get("parcellation", {}).get("@id")
+        space_id = json_obj.get("space_id")
+        parc_id = json_obj.get("parcellation_id")
         assert space_id, f"{errmsg}, space id not defined!"
         assert parc_id, f"{errmsg}, parc id not defined!"
         assert parc_id in parcs.keys(), f"{errmsg}, parc id for {parc_id} not found in parcellations"
         assert space_id in space_ids, f"{errmsg}, space id for {space_id} not found in spaces"
         unmatched_regions = compare_regions_to_parcellation(json_obj, parcs[parc_id])
         if len(unmatched_regions) > 0:
+            fail_flag = True
             print(f"Following regions in {filepath} have no correspondence in parcellation {parc_id}: {unmatched_regions}")
+    if fail_flag:
+        raise Exception
 
 if __name__ == "__main__":
     main()