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def __init__(self, base_dir=None, **kwargs):
BrainGlobeAtlasBase.__init__(self, base_dir=base_dir, **kwargs)
# get mouse connectivity cache and structure tree
self.mcc = MouseConnectivityCache(
manifest_file=os.path.join(
self.mouse_connectivity_cache, "manifest.json"
)
)
self.structure_tree = self.mcc.get_structure_tree()
# 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,
def launch(self, resolution, weighting, inj_f_thresh, vol_thresh):
resolution = int(resolution)
weighting = int(weighting)
inj_f_thresh = float(inj_f_thresh)/100.
vol_thresh = float(vol_thresh)
project = dao.get_project_by_id(self.current_project_id)
manifest_file = self.file_handler.get_allen_mouse_cache_folder(project.name)
manifest_file = os.path.join(manifest_file, 'mouse_connectivity_manifest.json')
cache = MouseConnectivityCache(resolution=resolution, manifest_file=manifest_file)
# the method creates a dictionary with information about which experiments need to be downloaded
ist2e = dictionary_builder(cache, False)
# the method downloads experiments necessary to build the connectivity
projmaps = download_an_construct_matrix(cache, weighting, ist2e, False)
# the method cleans the file projmaps in 4 steps
projmaps = pms_cleaner(projmaps)
# download from the AllenSDK the annotation volume, the template volume
vol, annot_info = cache.get_annotation_volume()
template, template_info = cache.get_template_volume()
# rotate template in the TVB 3D reference:
template = rotate_reference(template)
# Authors: Joseph Knox
# License: Allen Institute Software License
import numpy as np
import pandas as pd
from allensdk.core import json_utilities
from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
from .base import VoxelData
from .masks import Mask
from .voxel_model_api import VoxelModelApi
from ..models.voxel import VoxelConnectivityArray
class VoxelModelCache(MouseConnectivityCache):
"""Cache class extending MouseConnectivityCache to cache voxel model data.
Parameters
----------
resolution: int
Resolution of grid data to be downloaded when accessing projection volume,
the annotation volume, and the annotation volume. Must be one of (10, 25,
50, 100). Default is 25.
ccf_version: string
Desired version of the Common Coordinate Framework. This affects the annotation
volume (get_annotation_volume) and structure masks (get_structure_mask).
Must be one of (MouseConnectivityApi.CCF_2015, MouseConnectivityApi.CCF_2016).
Default: MouseConnectivityApi.CCF_2016
cache: boolean
def __init__(self):
# get mouse connectivity cache and structure tree
self.mcc = MouseConnectivityCache(
manifest_file=os.path.join(
self.mouse_connectivity_cache, "manifest.json"
)
)
self.structure_tree = self.mcc.get_structure_tree()
# 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]),