database and arranges them for use in the analysis code. A data folder (mouse_struc_data_dir
or human_struc_data_dir) should appear within this directory. Note that that cleaned up
versions of these directories are provided in this repository and are available in the root
directory.'''
import os
import sys
relative_path=os.path.dirname(os.getcwd())
from allensdk.api.queries.glif_api import GlifApi
from allensdk.core.cell_types_cache import CellTypesCache
ctc = CellTypesCache(manifest_file=os.path.join(relative_path,'cell_types_manifest.json'))
import pandas as pd
from shutil import copyfile
import numpy as np
from allensdk.config import enable_console_log
enable_console_log()
#---------------------------------------------------------------------------
#----------------------SPECIFY SPECIES--------------------------------------
#---------------------------------------------------------------------------
species="mouse"
#species="human"
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
model_template_ids=[395310469, 395310479, 395310475, 471355161, 395310498] #model template ids associated with data in database
model_names=['GLIF1', 'GLIF2', 'GLIF3', 'GLIF4', 'GLIF5']
def get_files_from_LIMS_public(output_path, glif_sp_ids=None, type='mouse'):
'''This will grab cre positive data config files from LIMS and sort them and put them in
def console_log():
enable_console_log()
def test_list_cells_unmocked(cell_types_api):
from allensdk.config import enable_console_log
enable_console_log()
# this test will always require the latest warehouse
cells = cell_types_api.list_cells()
def console_log():
enable_console_log()
