How to use the allensdk.api.queries.mouse_connectivity_api.MouseConnectivityApi function in allensdk

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github BrancoLab / BrainRender / brainrender / atlases / aba.py View on Github external
# get ontologies API and brain structures sets
        self.oapi = OntologiesApi()

        # get reference space
        self.space = ReferenceSpaceApi()
        self.spacecache = ReferenceSpaceCache(
            manifest=os.path.join(
                self.annotated_volume_fld, "manifest.json"
            ),  # downloaded files are stored relative to here
            resolution=int(self.resolution[0]),
            reference_space_key="annotation/ccf_2017",  # use the latest version of the CCF
        )
        self.annotated_volume, _ = self.spacecache.get_annotation_volume()

        # mouse connectivity API [used for tractography]
        self.mca = MouseConnectivityApi()

        # Get tree search api
        self.tree_search = TreeSearchApi()
github BrancoLab / BrainRender / brainrender / atlases / mouse.py View on Github external
# get ontologies API and brain structures sets
        self.oapi = OntologiesApi()

        # get reference space
        self.space = ReferenceSpaceApi()
        self.spacecache = ReferenceSpaceCache(
            manifest=os.path.join(
                self.annotated_volume_fld, "manifest.json"
            ),  # downloaded files are stored relative to here
            resolution=self.resolution,
            reference_space_key="annotation/ccf_2017",  # use the latest version of the CCF
        )
        self.annotated_volume, _ = self.spacecache.get_annotation_volume()

        # mouse connectivity API [used for tractography]
        self.mca = MouseConnectivityApi()

        # Get tree search api
        self.tree_search = TreeSearchApi()
github AllenInstitute / mouse_connectivity_models / mcmodels / core / voxel_model_api.py View on Github external
"""
Module containing VoxelModelApi.
"""
# Authors: Joseph Knox 
# License: Allen Institute Software License

from allensdk.api.cache import cacheable, Cache
from allensdk.api.queries.mouse_connectivity_api import MouseConnectivityApi


class VoxelModelApi(MouseConnectivityApi):
    '''HTTP Client extending MouseConnectivityApi to download model data.
    '''
    HTTP_MODEL_DIRECTORY = "http://download.alleninstitute.org/publications/"\
            "A_high_resolution_data-driven_model_of_the_mouse_connectome/"

    NODES_FILE = "nodes.csv.gz"
    WEIGHTS_FILE = "weights.csv.gz"
    SOURCE_MASK_FILE = "source_mask_params.json"
    TARGET_MASK_FILE = "target_mask_params.json"

    CONNECTION_DENSITY_FILE = 'connection_density.csv.gz'
    CONNECTION_STRENGTH_FILE = 'connection_strength.csv.gz'
    NORMALIZED_CONNECTION_DENSITY_FILE = 'normalized_connection_density.csv.gz'
    NORMALIZED_CONNECTION_STRENGTH_FILE = 'normalized_connection_strength.csv.gz'

    def download_model_files(self, file_name, save_file_path=None):