feat: allow download of big brain voi

api/common/data_handlers/compounds/download.py

@@ -5,6 +5,11 @@
 from uuid import uuid4
 from pathlib import Path
 from datetime import datetime
+import json
+import math
+
+BIGBRAIN_ID = "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588"
+BIGBRAIN_SIZE_LIMIT = 2 * 1024 * 1024
 
 README = """# Packaged Atlas Data
 
@@ -40,7 +45,7 @@
 LICENSE = """Please check the respective citations regarding licenses to use these data."""
 
 @data_decorator(ROLE)
-def download_all(space_id: str, parcellation_id: str, region_id: str=None, feature_id: str=None) -> str:
+def download_all(space_id: str, parcellation_id: str, region_id: str=None, feature_id: str=None, bbox=None) -> str:
     """Create a download bundle (zip) for the provided specification
     
     Args:
@@ -101,7 +106,18 @@ def write_desc(filename, obj, **kwargs):
             space_filename = f"{space.key}.nii.gz"
 
             # this should fetch anything (surface, nifti, ng precomputed)
-            space_vol = space.get_template().fetch()
+            if space.id == BIGBRAIN_ID:
+                if bbox:
+                    bounding_box = space.get_bounding_box(*json.loads(bbox))
+                    value = BIGBRAIN_SIZE_LIMIT
+                    for dim in bounding_box.maxpoint - bounding_box.minpoint:
+                        value /= dim
+                    cube_rooted = math.pow(value, 1/3)
+                    space_vol = space.get_template().fetch(voi=bounding_box, resolution_mm=1/cube_rooted)
+                else:
+                    raise RuntimeError(f"For big brain, bbox must be defined.")
+            else:
+                space_vol = space.get_template().fetch()
             zipfile.writestr(space_filename, gzip.compress(space_vol.to_bytes()))
             write_desc(f'{space_filename}.info.md', space)
         except Exception as e:

api/server/compounds/download.py

@@ -25,9 +25,9 @@ def cleanup(filepath: Path):
 @router.get("")
 @version(*FASTAPI_VERSION)
 @router_decorator(ROLE, func=download_all, queue_as_async=(ROLE=="server"))
-def get_download_bundle(space_id: str, parcellation_id: str, region_id: str=None, feature_id: str=None, *, background: BackgroundTasks, func):
+def get_download_bundle(space_id: str, parcellation_id: str, bbox=None, region_id: str=None, feature_id: str=None, *, background: BackgroundTasks, func):
     """Prepare the bundle. Given a specification, prepare/bundle according to the specification."""
-    returnval = func(space_id=space_id, parcellation_id=parcellation_id, region_id=region_id, feature_id=feature_id)
+    returnval = func(space_id=space_id, parcellation_id=parcellation_id, bbox=bbox, region_id=region_id, feature_id=feature_id)
     try:
         path_to_file = Path(returnval)
     except Exception as e:

requirements/siibra.txt

@@ -1,2 +1,2 @@
-siibra==0.4a78
+siibra==0.4a80
 plotly