siibra 1.0a1__1-py3-none-any.whl

siibra/VERSION

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+1.0.0-alpha.1

siibra/__init__.py

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+# Copyright 2018-2024
+# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from .commons import (
+    logger,
+    QUIET,
+    VERBOSE,
+    MapType,
+    MapIndex,
+    set_log_level,
+    __version__
+)
+
+from .core import (
+    atlas as _atlas,
+    parcellation as _parcellation,
+    space as _space
+)
+from .volumes import parcellationmap as _parcellationmap
+from .retrieval.requests import (
+    EbrainsRequest as _EbrainsRequest,
+    CACHE as cache
+)
+from .retrieval.cache import Warmup, WarmupLevel
+
+from . import configuration
+from . import experimental
+from .configuration import factory
+from . import features, livequeries
+from siibra.locations import Point, PointCloud
+
+import os as _os
+logger.info(f"Version: {__version__}")
+logger.warning("This is a development release. Use at your own risk.")
+logger.info(
+    "Please file bugs and issues at https://github.com/FZJ-INM1-BDA/siibra-python."
+)
+
+# forward access to some functions
+set_ebrains_token = _EbrainsRequest.set_token
+fetch_ebrains_token = _EbrainsRequest.fetch_token
+find_regions = _parcellation.find_regions
+from_json = factory.Factory.from_json
+
+
+def __getattr__(attr: str):
+    # lazy loading of some classes for package-level functions.
+    if attr == 'atlases':
+        return _atlas.Atlas.registry()
+    elif attr == 'spaces':
+        return _space.Space.registry()
+    elif attr == 'parcellations':
+        return _parcellation.Parcellation.registry()
+    elif attr == 'maps':
+        return _parcellationmap.Map.registry()
+    elif attr == 'use_configuration':
+        return configuration.Configuration.use_configuration
+    elif attr == 'extend_configuration':
+        return configuration.Configuration.extend_configuration
+    else:
+        raise AttributeError(f"No such attribute: {__name__}.{attr}")
+
+
+# convenient access to reference space templates
+def get_template(space_spec: str, **kwargs):
+    return (
+        _space.Space
+        .get_instance(space_spec)
+        .get_template(**kwargs)
+    )
+
+
+# convenient access to parcellation maps
+def get_map(parcellation: str, space: str, maptype: MapType = MapType.LABELLED, **kwargs):
+    return (
+        _parcellation.Parcellation
+        .get_instance(parcellation)
+        .get_map(space=space, maptype=maptype, **kwargs)
+    )
+
+
+# convenient access to regions of a parcellation
+def get_region(parcellation: str, region: str):
+    return (
+        _parcellation.Parcellation
+        .get_instance(parcellation)
+        .get_region(region)
+    )
+
+
+def set_feasible_download_size(maxsize_gbyte):
+    from .volumes import volume
+    volume.gbyte_feasible = maxsize_gbyte
+    logger.info(f"Set feasible download size to {maxsize_gbyte} GiB.")
+
+
+def set_cache_size(maxsize_gbyte: int):
+    """
+    siibra runs maintainance on its local cache to keep it under a predetermined
+    size of 2 gigabytes. This method changes the cache size.
+
+    Parameters
+    ----------
+    maxsize_gbyte : int
+    """
+    assert maxsize_gbyte >= 0
+    cache.SIZE_GIB = maxsize_gbyte
+    logger.info(f"Set cache size to {maxsize_gbyte} GiB.")
+
+
+if "SIIBRA_CACHE_SIZE_GIB" in _os.environ:
+    set_cache_size(float(_os.environ.get("SIIBRA_CACHE_SIZE_GIB")))
+
+
+def warm_cache(level=WarmupLevel.INSTANCE):
+    """
+    Preload preconfigured siibra concepts.
+
+    Siibra relies on preconfigurations that simplify integrating various
+    concepts such as parcellations, refernce spaces, and multimodal data
+    features. By preloading the instances, siibra commits all preconfigurations
+    to the memory at once instead of commiting them when required.
+    """
+    Warmup.warmup(level)
+
+
+def __dir__():
+    return [
+        "atlases",
+        "spaces",
+        "parcellations",
+        "features",
+        "use_configuration",
+        "extend_configuration",
+        "get_region",
+        "find_regions",
+        "get_map",
+        "get_template",
+        "MapType",
+        "Point",
+        "PointCloud",
+        "QUIET",
+        "VERBOSE",
+        "fetch_ebrains_token",
+        "set_ebrains_token",
+        "vocabularies",
+        "__version__",
+        "cache",
+        "warm_cache",
+        "set_cache_size",
+        "from_json",
+    ]