revert: use old worker for all but /assign endpoints

VERSION

@@ -1 +1 @@
-0.3.19
+0.3.20

api/common/data_handlers/core/__init__.py

@@ -2,3 +2,4 @@
 from . import space
 from . import region
 from . import parcellation
+from . import misc

api/common/data_handlers/core/misc.py

@@ -0,0 +1,216 @@
+from api.common import data_decorator, get_filename, NotFound
+from api.models.volumes.volume import MapType
+from api.siibra_api_config import ROLE
+from typing import Union, Dict, Tuple
+
+@data_decorator(ROLE)
+def get_map(parcellation_id: str, space_id: str, maptype: Union[MapType, str]) -> Dict:
+    """Get a map instance, based on specification
+    
+    Args:
+        parcellation_id: lookup id of the parcellation of the map
+        space_id: lookup id of the space of the map
+        maptype: maptype, either LABELLED or STATISTICAL
+    
+    Returns:
+        Requested map instance, serialized into dict
+    
+    Raises:
+        AssertionError: if the supplied maptype is invalid type
+        NotFound: Map with the specification not found
+    """
+    import siibra
+    from api.serialization.util import instance_to_model
+
+    maptype_string = None
+    # check maptype name and value both matches
+    if isinstance(maptype, MapType):
+        assert maptype.name == maptype.value, f"str enum, expecting .name and .value to equal"
+        maptype_string = maptype.name
+    if isinstance(maptype, str):
+        maptype_string = maptype
+
+    assert maptype_string is not None, f"maptype is neither MapType nor str"
+
+    siibra_maptype = siibra.MapType[maptype_string]
+    assert siibra_maptype.name == maptype_string, f"Expecting maptype.name to match"
+
+    returned_map = siibra.get_map(parcellation_id, space_id, siibra_maptype)
+
+    if returned_map is None:
+        raise NotFound
+
+    return instance_to_model(
+        returned_map
+    ).dict()
+
+
+def cache_region_statistic_map(parcellation_id: str, region_id: str, space_id: str) -> Tuple[str, bool]:
+    """Retrieve and save regional statistical map (if necessary), and then return the path of the map.
+
+    Args:
+        parcellation_id: lookup id of the parcellation of the map
+        region_id: lookup id of the region of the map
+        space_id: lookup id of the space of the map
+    
+    Returns:
+        path to statistical map, if a cached file is returned
+    """
+    import os
+    full_filename = get_filename("statistical_map", parcellation_id, region_id, space_id, ext=".nii.gz")
+    if os.path.isfile(full_filename):
+        return full_filename, True
+
+    import siibra
+    import nibabel as nib
+    error_text = f"Map with parc id '{parcellation_id}', space id '{space_id}'"
+
+    stat_map = siibra.get_map(parcellation_id, space_id, siibra.MapType.STATISTICAL)
+    assert stat_map is not None, f"{error_text} returns None"
+
+    volume_data = stat_map.fetch(region=region_id)
+
+    error_text = f"{error_text}, with region_id '{region_id}'"
+    assert isinstance(volume_data, nib.Nifti1Image), f"{error_text}, volume provided is not of type Nifti1Image"
+
+    nib.save(volume_data, full_filename)
+    import json
+    import time
+    with open(f"{full_filename}.{str(int(time.time()))}.json", "w") as fp:
+        json.dump({
+            "prefix": "statistical_map",
+            "parcellation_id": parcellation_id,
+            "region_id": region_id,
+            "space_id": space_id,
+        }, fp=fp, indent="\t")
+    return full_filename, False
+
+@data_decorator(ROLE)
+def get_region_statistic_map(parcellation_id: str, region_id: str, space_id: str):
+    """Retrieve and save regional statistical map (if necessary), and then return the path of the map.
+
+    Args:
+        parcellation_id: lookup id of the parcellation of the map
+        region_id: lookup id of the region of the map
+        space_id: lookup id of the space of the map
+    
+    Returns:
+        path to statistical map, if a cached file is returned
+    """
+    return cache_region_statistic_map(parcellation_id, region_id, space_id)
+
+@data_decorator(ROLE)
+def get_region_statistic_map_info(parcellation_id: str, region_id: str, space_id: str):
+    """Retrieve and save regional statistical map (if necessary), and then return the path of the map.
+
+    Args:
+        parcellation_id: lookup id of the parcellation of the map
+        region_id: lookup id of the region of the map
+        space_id: lookup id of the space of the map
+    
+    Returns:
+        dict of min an max of the statistical map
+    """
+    full_filename, _cache_flag = cache_region_statistic_map(parcellation_id, region_id, space_id)
+
+    import nibabel as nib
+    import numpy as np
+
+    nii = nib.load(full_filename)
+    data = nii.get_fdata()
+    return {
+        "min": np.min(data),
+        "max": np.max(data),
+    }
+
+@data_decorator(ROLE)
+def get_parcellation_labelled_map(parcellation_id: str, space_id: str, region_id:str=None):
+    """Retrieve and save labelled map / regional mask (if necessary), and then return the path of the map.
+
+    Args:
+        parcellation_id: lookup id of the parcellation of the map
+        region_id: lookup id of the region of the map
+        space_id: lookup id of the space of the map
+    
+    Returns:
+        path to labelled map/regional mask, if a cached file is returned
+    """
+    import os
+    full_filename = get_filename("labelled_map", parcellation_id, space_id, region_id if region_id else "", ext=".nii.gz")
+    if os.path.isfile(full_filename):
+        return full_filename, True
+
+    import siibra
+    import nibabel as nib
+    error_text = f"Map with parc id '{parcellation_id}', space id '{space_id}'"
+
+    volume_data = None
+    if region_id is not None:
+        region = siibra.get_region(parcellation_id, region_id)
+        volume_data = region.fetch_regional_map(space_id, siibra.MapType.LABELLED)
+    else:
+        labelled_map = siibra.get_map(parcellation_id, space_id, siibra.MapType.LABELLED)
+        assert labelled_map is not None, f"{error_text} returns None"
+        volume_data = labelled_map.fetch()
+
+    assert isinstance(volume_data, nib.Nifti1Image), f"{error_text}, volume provided is not of type Nifti1Image"
+
+    nib.save(volume_data, full_filename)
+    import json
+    import time
+    with open(f"{full_filename}.{str(int(time.time()))}.json", "w") as fp:
+        json.dump({
+            "prefix": "labelled_map",
+            "parcellation_id": parcellation_id,
+            "space_id": space_id,
+            "region_id": region_id,
+        }, fp=fp, indent="\t")
+    return full_filename, False
+
+# @data_decorator(ROLE)
+# def assign_point(parcellation_id: str, space_id: str, point: str, assignment_type: str, sigma_mm: float):
+#     import siibra
+#     from api.serialization.util import instance_to_model
+#     m = siibra.get_map(parcellation_id, space_id, assignment_type)
+#     p = siibra.Point(point, space=space_id, sigma_mm=sigma_mm)
+#     df = m.assign(p)
+
+#     try:
+#         return instance_to_model(df, detail=True).dict()
+#     except Exception as e:
+#         raise e
+
+@data_decorator(ROLE)
+def get_resampled_map(parcellation_id: str, space_id: str):
+    """Retrieve and save a labelled map, resampled in space (if necessary), and then return the path of the map.
+
+    Args:
+        parcellation_id: lookup id of the parcellation of the map
+        space_id: lookup id of the target space of the sampled map
+    
+    Returns:
+        path to statistical map, if a cached file is returned
+    """
+    import os
+    full_filename = get_filename("resampled_map", parcellation_id, space_id, ext=".nii.gz")
+    if os.path.isfile(full_filename):
+        return full_filename, True
+
+    import siibra
+    import nibabel as nib
+    parcellation: siibra.core.parcellation.Parcellation = siibra.parcellations[parcellation_id]
+    parcellation_map = parcellation.get_map(siibra.spaces[space_id], siibra.MapType.LABELLED)
+    nii = parcellation_map.get_resampled_template()
+
+    assert isinstance(nii, nib.Nifti1Image), f"resample failed... returned not of type nii"
+
+    import time
+    import json
+    nib.save(nii, full_filename)
+    with open(f"{full_filename}.{str(int(time.time()))}.json", "w") as fp:
+        json.dump({
+            "prefix": "resampled_map",
+            "parcellation_id": parcellation_id,
+            "space_id": space_id,
+        }, indent="\t", fp=fp)
+    return full_filename, False

api/common/data_handlers/features/__init__.py

@@ -1 +1 @@
-from . import types
+from . import types, misc

api/common/data_handlers/features/misc.py

@@ -0,0 +1,24 @@
+from api.common import data_decorator
+from api.siibra_api_config import ROLE
+from api.models.vocabularies.genes import GeneModel
+
+@data_decorator(ROLE)
+def get_genes(find:str=None):
+    """Get all genes
+
+    Args:
+        string to find in vocabularies
+    
+    Returns:
+        List of the genes."""
+
+    from siibra.vocabularies import GENE_NAMES
+    if find == None:
+        return_list = [v for v in GENE_NAMES]
+    else:
+        return_list = GENE_NAMES.find(find)
+
+    return [GeneModel(
+        symbol=v.get("symbol"),
+        description=v.get("description")
+        ).dict() for v in return_list]

api/server/volcabularies/__init__.py

@@ -7,7 +7,8 @@
 from api.siibra_api_config import ROLE
 from api.common import router_decorator
 from api.models.vocabularies.genes import GeneModel
-from api.common.data_handlers.vocabularies.gene import get_genes
+# from api.common.data_handlers.vocabularies.gene import get_genes
+from api.common.data_handlers.features.misc import get_genes
 
 TAGS= ["vocabularies"]
 """HTTP vocabularies tags"""

api/server/volumes/parcellationmap.py

@@ -10,6 +10,13 @@
 from api.models.volumes.volume import MapType
 from api.models._commons import DataFrameModel
 from api.common import router_decorator, get_filename, logger, NotFound
+from api.common.data_handlers.core.misc import (
+    get_map as old_get_map,
+    get_resampled_map as old_get_resampled_map,
+    get_parcellation_labelled_map as old_get_parcellation_labelled_map,
+    get_region_statistic_map as old_get_region_statistic_map,
+    get_region_statistic_map_info as old_get_region_statistic_map_info
+)
 from new_api.v3.data_handlers.map import assign, get_map, statistical_map_info_json, statistical_map_nii_gz, labelled_map_nii_gz, resampled_template
 from api.server.util import SapiCustomRoute
 import os
@@ -20,20 +27,23 @@
 router = APIRouter(route_class=SapiCustomRoute, tags=TAGS)
 """HTTP map router"""
 
+# still use the old worker. New worker not stable (?)
 @router.get("", response_model=MapModel)
 @version(*FASTAPI_VERSION)
-@router_decorator(ROLE, func=get_map)
+@router_decorator(ROLE, func=old_get_map)
 def get_siibra_map(parcellation_id: str, space_id: str, map_type: MapType,  name: str= "", *, func):
     """Get map according to specification"""
     if func is None:
         raise HTTPException(500, f"func: None passsed")
     return func(parcellation_id, space_id, map_type, name)
 
+
+# still use the old worker. New worker not stable (?)
 @router.get("/resampled_template", response_class=FileResponse, tags=TAGS, description="""
 Return a resampled template volume, based on labelled parcellation map.
 """)
 @version(*FASTAPI_VERSION)
-@router_decorator(ROLE, func=resampled_template)
+@router_decorator(ROLE, func=old_get_resampled_map)
 def get_resampled_map(parcellation_id: str, space_id: str, *, func):
     """Get resampled map according to specification"""
     if func is None:
@@ -50,6 +60,7 @@ def get_resampled_map(parcellation_id: str, space_id: str, *, func):
     return FileResponse(full_filename, headers=headers)
 
 
+# still use the old worker. New worker not stable (?)
 @router.get("/labelled_map.nii.gz", response_class=FileResponse, tags=TAGS, description="""
 Returns a labelled map if region_id is not provided.
 
@@ -58,7 +69,7 @@ def get_resampled_map(parcellation_id: str, space_id: str, *, func):
 region_id MAY refer to ANY region on the region hierarchy, and a combined mask will be returned.
 """)
 @version(*FASTAPI_VERSION)
-@router_decorator(ROLE, func=labelled_map_nii_gz)
+@router_decorator(ROLE, func=old_get_parcellation_labelled_map)
 def get_parcellation_labelled_map(parcellation_id: str, space_id: str, region_id: str=None, *, func):
     """Get labelled map according to specification"""
     if func is None:
@@ -76,13 +87,14 @@ def get_parcellation_labelled_map(parcellation_id: str, space_id: str, region_id
     return FileResponse(full_filename, headers=headers)
 
 
+# still use the old worker. New worker not stable (?)
 @router.get("/statistical_map.nii.gz", response_class=FileResponse, tags=TAGS, description="""
 Returns a statistic map.
 
 region_id MUST refer to leaf region on the region hierarchy.
 """)
 @version(*FASTAPI_VERSION)
-@router_decorator(ROLE, func=statistical_map_nii_gz)
+@router_decorator(ROLE, func=old_get_region_statistic_map)
 def get_region_statistical_map(parcellation_id: str, region_id: str, space_id: str, name: str="", *, func):
     """Get statistical map according to specification"""
     if func is None:
@@ -92,7 +104,7 @@ def get_region_statistical_map(parcellation_id: str, region_id: str, space_id: s
         "content-type": "application/octet-stream",
         "content-disposition": f'attachment; filename="statistical_map.nii.gz"'
     }
-    full_filename, cache_flag = func(parcellation_id=parcellation_id, region_id=region_id, space_id=space_id, name=name)
+    full_filename, cache_flag = func(parcellation_id=parcellation_id, region_id=region_id, space_id=space_id)
     if cache_flag:
         headers[cache_header] = "hit"
     assert os.path.isfile(full_filename), f"file saved incorrectly"
@@ -102,15 +114,17 @@ class StatisticModelInfo(BaseModel):
     min: float
     max: float
 
+
+# still use the old worker. New worker not stable (?)
 @router.get("/statistical_map.info.json", response_model=StatisticModelInfo, tags=TAGS)
 @version(*FASTAPI_VERSION)
-@router_decorator(ROLE, func=statistical_map_info_json)
+@router_decorator(ROLE, func=old_get_region_statistic_map_info)
 def get_region_statistical_map_metadata(parcellation_id: str, region_id: str, space_id: str, name: str="", *, func):
     """Get metadata of statistical map according to specification"""
     if func is None:
         raise HTTPException(500, f"func: None passsed")
 
-    data = func(parcellation_id=parcellation_id, region_id=region_id, space_id=space_id, name=name)
+    data = func(parcellation_id=parcellation_id, region_id=region_id, space_id=space_id)
     return StatisticModelInfo(**data)
 
 @router.get("/assign", response_model=DataFrameModel, tags=TAGS)

api/siibra_api_config.py

@@ -70,7 +70,7 @@ def get_config_dir_short_hash(path_to_config: str):
     "features",
     "volumes",
     "compounds",
-    "vocabularies",
+    # "vocabularies",
 ]
 
 class CELERY_CONFIG: