mcmodels.core.VoxelModelApi¶

class mcmodels.core.VoxelModelApi(base_uri=None)[source]¶

HTTP Client extending MouseConnectivityApi to download model data.

Methods

build_query_url(self, stage_clauses[, fmt]) Combine one or more RMA query stages into a single RMA query.

build_reference_aligned_image_channel_volumes_url(…) Construct url to download the red, green, and blue channels aligned to the 25um adult mouse brain reference space volume.

build_schema_query(self[, clazz, fmt]) Build the URL that will fetch the data schema.

build_volumetric_data_download_url(self, …) Construct url to download 3D reference model in NRRD format.

calculate_injection_centroid(self, …[, …]) Compute the centroid of an injection site.

cleanup_truncated_file(self, file_path) Helper for removing files.

construct_well_known_file_download_url(self, …) Join data api endpoint and id.

debug_clause(self[, debug_value]) Construct a debug clause for use in an rma::options clause.

do_query(self, url_builder_fn, …) Bundle an query url construction function with a corresponding response json traversal function.

do_rma_query(self, rma_builder_fn, …) Bundle an RMA query url construction function with a corresponding response json traversal function.

download_alignment3d(self, section_data_set_id) Download the parameters of the 3D affine tranformation mapping this section data set’s image-space stack to CCF-space (or vice-versa).

download_annotation_volume(self, …) Download the annotation volume at a particular resolution.

download_deformation_field(self, …[, …]) Download the local alignment parameters for this dataset.

download_expression_grid_data(self, …[, …]) Download in zipped metaimage format.

download_gene_expression_grid_data(self, …) Download a metaimage file containing registered gene expression grid data

download_model_files(self, file_name[, …]) Download data.

download_mouse_atlas_volume(self, age, …) Download a reference volume (annotation, grid annotation, atlas volume)

download_projection_grid_data(self, …[, …]) Download in NRRD format.

download_reference_aligned_image_channel_volumes(…)

Returns:

download_structure_mask(self, structure_id, …) Download an indicator mask for a specific structure.

download_structure_mesh(self, structure_id, …) Download a Wavefront obj file containing a triangulated 3d mesh built from an annotated structure.

download_template_volume(self, resolution, …) Download the registration template volume at a particular resolution.

download_volumetric_data(self, data_path, …) Download 3D reference model in NRRD format.

experiment_correlation_search(self, \*\*kwargs) Select a seed experiment and a domain over which the similarity comparison is to be made.

experiment_injection_coordinate_search(self, …) User specifies a seed location within the 3D reference space.

experiment_source_search(self, \*\*kwargs) Search over the whole projection signal statistics dataset to find experiments with specific projection profiles.

experiment_spatial_search(self, \*\*kwargs) Displays all SectionDataSets with projection signal density >= 0.1 at the seed point.

filter(self, key, value) serialize a single RMA query filter clause.

filters(self, filters) serialize RMA query filter clauses.

get_experiment_detail(self, experiment_id) Retrieve the experiments data.

get_experiments(self, structure_ids, \*\*kwargs) Fetch experiment metadata from the Mouse Brain Connectivity Atlas.

get_experiments_api(self) Fetch experiment metadata from the Mouse Brain Connectivity Atlas via the ApiConnectivity table.

get_manual_injection_summary(self, experiment_id) Retrieve manual injection summary.

get_projection_image_info(self, …) Fetch meta-information of one projection image.

get_reference_aligned_image_channel_volumes_url(…) Retrieve the download link for a specific data set.

get_schema(self[, clazz]) Retrieve schema information.

json_msg_query(self, url[, dataframe]) Common case where the url is fully constructed and the response data is stored in the ‘msg’ field.

load_api_schema(self) Download the RMA schema from the current RMA endpoint

model_query(self, \*args, \*\*kwargs) Construct and execute a model stage of an RMA query string.

model_stage(self, model, \*\*kwargs) Construct a model stage of an RMA query string.

only_except_tabular_clause(self, …) Construct a clause to filter which attributes are returned for use in an rma::options clause.

options_clause(self, \*\*kwargs) build rma:: options clause.

order_clause(self[, order_list]) Construct a debug clause for use in an rma::options clause.

pipe_stage(self, pipe_name, parameters) Connect model and service stages via their JSON responses.

quote_string(self, the_string) Wrap a clause in single quotes.

read_data(self, parsed_json) Return the message data from the parsed query.

retrieve_file_over_http(self, url, file_path) Get a file from the data api and save it.

retrieve_parsed_json_over_http(self, url[, post]) Get the document and put it in a Python data structure

retrieve_xml_over_http(self, url) Get the document and put it in a Python data structure

service_query(self, \*args, \*\*kwargs) Construct and Execute a single-stage RMA query to send a request to a connected service.

service_stage(self, service_name[, parameters]) Construct an RMA query fragment to send a request to a connected service.

set_api_urls(self, api_base_url_string) Set the internal RMA and well known file download endpoint urls based on a api server endpoint.

set_default_working_directory(self, …) Set the working directory where files will be saved.

tuple_filters(self, filters) Construct an RMA filter clause.

download_connection_density
download_connection_strength
download_data_mask
download_injection_density
download_injection_fraction
download_nodes
download_normalized_connection_density
download_normalized_connection_strength
download_projection_density
download_source_mask_params
download_target_mask_params
download_weights
get_structure_unionizes

__init__(self, base_uri=None)¶

Methods

__init__(self[, base_uri])