Source code for allensdk.api.queries.mouse_atlas_api

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from allensdk.core import sitk_utilities
from allensdk.api.cache import Cache, cacheable

from .reference_space_api import ReferenceSpaceApi
from .grid_data_api import GridDataApi
from .rma_pager import pageable



[docs]class MouseAtlasApi(ReferenceSpaceApi, GridDataApi): ''' Downloads Mouse Brain Atlas grid data, reference volumes, and metadata. ''' MOUSE_ATLAS_PRODUCTS = (1,) DEVMOUSE_ATLAS_PRODUCTS = (3,) MOUSE_ORGANISM = (2,) HUMAN_ORGANISM = (1,)
[docs] @cacheable() @pageable(num_rows=2000, total_rows='all') def get_section_data_sets(self, gene_ids=None, product_ids=None, **kwargs): ''' Download a list of section data sets (experiments) from the Mouse Brain Atlas project. Parameters ---------- gene_ids : list of int, optional Filter results based on the genes whose expression was characterized in each experiment. Default is all. product_ids : list of int, optional Filter results to a subset of products. Default is the Mouse Brain Atlas. Returns ------- list of dict : Each element is a section data set record, with one or more gene records nested in a list. ''' if product_ids is None: product_ids = list(self.MOUSE_ATLAS_PRODUCTS) criteria = 'products[id$in{}]'.format(','.join(map(str, product_ids))) if gene_ids is not None: criteria += ',genes[id$in{}]'.format(','.join(map(str, gene_ids))) return self.model_query(model='SectionDataSet', criteria=criteria, include='genes', **kwargs)
[docs] @cacheable() @pageable(num_rows=2000, total_rows='all') def get_genes(self, organism_ids=None, chromosome_ids=None, **kwargs): ''' Download a list of genes Parameters ---------- organism_ids : list of int, optional Filter genes to those appearing in these organisms. Defaults to mouse (2). chromosome_ids : list of int, optional Filter genes to those appearing on these chromosomes. Defaults to all. Returns ------- list of dict: Each element is a gene record, with a nested chromosome record (also a dict). ''' if organism_ids is None: organism_ids = list(self.MOUSE_ORGANISM) criteria = '[organism_id$in{}]'.format(','.join(map(str, organism_ids))) if chromosome_ids is not None: criteria += ',[chromosome_id$in{}]'.format(','.join(map(str, chromosome_ids))) return self.model_query(model='Gene', criteria=criteria, include='chromosome', **kwargs)
[docs] @cacheable(strategy='create', reader = sitk_utilities.read_ndarray_with_sitk, pathfinder=Cache.pathfinder(file_name_position=1, path_keyword='path')) def download_expression_density(self, path, experiment_id): self.download_gene_expression_grid_data( experiment_id, GridDataApi.DENSITY, path)
[docs] @cacheable(strategy='create', reader = sitk_utilities.read_ndarray_with_sitk, pathfinder=Cache.pathfinder(file_name_position=1, path_keyword='path')) def download_expression_energy(self, path, experiment_id): self.download_gene_expression_grid_data( experiment_id, GridDataApi.ENERGY, path)
[docs] @cacheable(strategy='create', reader = sitk_utilities.read_ndarray_with_sitk, pathfinder=Cache.pathfinder(file_name_position=1, path_keyword='path')) def download_expression_intensity(self, path, experiment_id): self.download_gene_expression_grid_data( experiment_id, GridDataApi.INTENSITY, path)