allensdk.api.queries.grid_data_api module¶
- class allensdk.api.queries.grid_data_api.GridDataApi(resolution=None, base_uri=None)[source]¶
Bases:
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(section_data_set_id, num_rows='all', count=False, **kwargs)[source]¶
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_idint
download the parameters for this data set.
- Returns:
- dict
parameters of this section data set’s alignment3d
- download_deformation_field(section_data_set_id, header_path=None, voxel_path=None, voxel_type='DeformationFieldVoxels', header_type='DeformationFieldHeader')[source]¶
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_idint
Download the deformation field for this data set
- header_pathstr, optional
If supplied, the deformation field header will be downloaded to this path.
- voxel_pathstr, optiona
If supplied, the deformation field voxels will be downloaded to this path.
- voxel_typestr
WellKnownFileType of this dataset’s data file
- header_typestr
WellKnownFileType of this dataset’s header file
- download_expression_grid_data(section_data_set_id, include=None, path=None)[source]¶
Download in zipped metaimage format.
- Parameters:
- section_data_set_idinteger
What to download.
- includelist of strings, optional
Image volumes. ‘energy’ (default), ‘density’, ‘intensity’.
- pathstring, optional
File name to save as.
- Returns:
- file3-D expression grid data packaged into a compressed archive file (.zip).
- download_gene_expression_grid_data(section_data_set_id, volume_type, path)[source]¶
Download a metaimage file containing registered gene expression grid data
- Parameters:
- section_data_set_idint
Download data from this experiment
- volume_typestr
Download this type of data (options are GridDataApi.ENERGY, GridDataApi.DENSITY, GridDataApi.INTENSITY)
- pathstr
Download to this path
- download_projection_grid_data(section_data_set_id, image=None, resolution=None, save_file_path=None)[source]¶
Download in NRRD format.
- Parameters:
- section_data_set_idinteger
What to download.
- imagelist of strings, optional
Image volume. ‘projection_density’, ‘projection_energy’, ‘injection_fraction’, ‘injection_density’, ‘injection_energy’, ‘data_mask’.
- resolutioninteger, optional
in microns. 10, 25, 50, or 100 (default).
- save_file_pathstring, optional
File name to save as.
Notes
See Downloading 3-D Projection Grid Data for additional documentation.