Source code for allensdk.api.queries.grid_data_api

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from .rma_api import RmaApi


[docs]class GridDataApi(RmaApi): '''HTTP Client for the Allen 3-D Expression Grid Data Service. See: `Downloading 3-D Expression Grid Data <http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data>`_ ''' INJECTION_DENSITY = 'injection_density' PROJECTION_DENSITY = 'projection_density' INJECTION_FRACTION = 'injection_fraction' INJECTION_ENERGY = 'injection_energy' PROJECTION_ENERGY = 'projection_energy' DATA_MASK = 'data_mask' ENERGY = 'energy' DENSITY = 'density' INTENSITY = 'intensity' def __init__(self, resolution=None, base_uri=None): super(GridDataApi, self).__init__(base_uri) if resolution is None: resolution = 25 self.resolution = resolution
[docs] def download_expression_grid_data(self, section_data_set_id, include=None, path=None): '''Download in NRRD format. Parameters ---------- section_data_set_id : integer What to download. include : list of strings, optional Image volumes. 'energy' (default), 'density', 'intensity'. path : string, optional File name to save as. i Returns ------- file : 3-D expression grid data packaged into a compressed archive file (.zip). Notes ----- ''' if include is not None: include_clause = ''.join(['?include=', ','.join(include)]) else: include_clause = '' url = ''.join([self.grid_data_endpoint, '/download/', str(section_data_set_id), include_clause]) if path is None: path = str(section_data_set_id) + '.zip' self.retrieve_file_over_http(url, path)
[docs] def download_projection_grid_data(self, section_data_set_id, image=None, resolution=None, save_file_path=None): '''Download in NRRD format. Parameters ---------- section_data_set_id : integer What to download. image : list of strings, optional Image volume. 'projection_density', 'projection_energy', 'injection_fraction', 'injection_density', 'injection_energy', 'data_mask'. resolution : integer, optional in microns. 10, 25, 50, or 100 (default). save_file_path : string, optional File name to save as. Notes ----- See `Downloading 3-D Projection Grid Data <http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data#name="Downloading3-DExpressionGridData-DOWNLOADING3DPROJECTIONGRIDDATA">`_ for additional documentation. ''' params_list = [] if image is not None: params_list.append('image=' + ','.join(image)) if resolution is not None: params_list.append('resolution=%d' % (resolution)) if len(params_list) > 0: params_clause = '?' + '&'.join(params_list) else: params_clause = '' url = ''.join([self.grid_data_endpoint, '/download_file/', str(section_data_set_id), params_clause]) if save_file_path is None: save_file_path = str(section_data_set_id) + '.nrrd' self.retrieve_file_over_http(url, save_file_path)