allensdk.api.queries.grid_data_api module

class allensdk.api.queries.grid_data_api.GridDataApi(resolution=None, base_uri=None)

Bases: allensdk.api.queries.rma_api.RmaApi

HTTP Client for the Allen 3-D Expression Grid Data Service.

See: Downloading 3-D Expression Grid Data

DATA_MASK = 'data_mask'

DENSITY = 'density'

ENERGY = 'energy'

INJECTION_DENSITY = 'injection_density'

INJECTION_ENERGY = 'injection_energy'

INJECTION_FRACTION = 'injection_fraction'

INTENSITY = 'intensity'

PROJECTION_DENSITY = 'projection_density'

PROJECTION_ENERGY = 'projection_energy'

download_alignment3d(self, section_data_set_id, num_rows='all', count=False, **kwargs)

Download the parameters of the 3D affine tranformation mapping this section data set’s image-space stack to CCF-space (or vice-versa).

Parameters:

section_data_set_id : int

download the parameters for this data set.

Returns:

dict :

parameters of this section data set’s alignment3d

download_deformation_field(self, section_data_set_id, header_path=None, voxel_path=None, voxel_type='DeformationFieldVoxels', header_type='DeformationFieldHeader')

Download the local alignment parameters for this dataset. This a 3D vector image (3 components) describing a deformable local mapping from CCF voxels to this section data set’s affine-aligned image stack.

Parameters:

section_data_set_id : int

Download the deformation field for this data set

header_path : str, optional

If supplied, the deformation field header will be downloaded to this path.

voxel_path : str, optiona

If supplied, the deformation field voxels will be downloaded to this path.

voxel_type : str

WellKnownFileType of this dataset’s data file

header_type : str

WellKnownFileType of this dataset’s header file

download_expression_grid_data(self, section_data_set_id, include=None, path=None)

Download in zipped metaimage 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.

Returns:

file : 3-D expression grid data packaged into a compressed archive file (.zip).

download_gene_expression_grid_data(self, section_data_set_id, volume_type, path)

Download a metaimage file containing registered gene expression grid data

Parameters:

section_data_set_id : int

Download data from this experiment

volume_type : str

Download this type of data (options are GridDataApi.ENERGY, GridDataApi.DENSITY, GridDataApi.INTENSITY)

path : str

Download to this path

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 for additional documentation.