dolomite_sfe package

Submodules

dolomite_sfe.read_sfe_images module

dolomite_sfe.read_sfe_images.read_bio_infomats_image(path, metadata, **kwargs)

Load a BioFormatsImage from its on-disk representation.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

• path (str) – Path to the directory containing the object.

• metadata (dict) – Metadata for the object.

• kwargs – Further arguments.

Return type:

BioFormatsImage

Returns:

A BioFormatsImage.

dolomite_sfe.read_sfe_images.read_ext_image(path, metadata, **kwargs)

Load a ExtImage from its on-disk representation.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

• path (str) – Path to the directory containing the object.

• metadata (dict) – Metadata for the object.

• kwargs – Further arguments.

Return type:

ExtImage

Returns:

A ExtImage.

dolomite_sfe.read_sfe_images.read_spat_raster_image(path, metadata, **kwargs)

Load a SpatRasterImage from its on-disk representation.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

• path (str) – Path to the directory containing the object.

• metadata (dict) – Metadata for the object.

• kwargs – Further arguments.

Return type:

SpatRasterImage

Returns:

A SpatRasterImage.

dolomite_sfe.read_spatial_feature_experiment module

dolomite_sfe.read_spatial_feature_experiment.read_geometries(path, geom_type=None)

Read geometries from disk.

Parameters:

• path (str) – Path to the directory containing geometries.

• geom_type (str) – Type of geometry (‘col’, ‘row’, or ‘annot’).

Returns:

Dictionary of geometries or None if directory doesn’t exist.

dolomite_sfe.read_spatial_feature_experiment.read_graphs(path)

Read spatial graphs from disk.

Parameters:

path (str) – Path to the directory containing spatial graphs.

Returns:

Dictionary of spatial graphs or None if directory doesn’t exist.

dolomite_sfe.read_spatial_feature_experiment.read_local_results(sfe, path)

Read local results from disk and add them to the SFE object.

Parameters:

• sfe (SpatialFeatureExperiment) – SpatialFeatureExperiment object.

• path (str) – Path to the directory containing local results.

Return type:

SpatialFeatureExperiment

Returns:

Updated SpatialFeatureExperiment object.

dolomite_sfe.read_spatial_feature_experiment.read_reduced_dim_feature_data(sfe, path)

Read reduced dimension feature data from disk and add them to the SFE object.

Parameters:

• sfe (SpatialFeatureExperiment) – SpatialFeatureExperiment object.

• path (str) – Path to the directory containing reduced dimensions.

Return type:

SpatialFeatureExperiment

Returns:

Updated SpatialFeatureExperiment object.

dolomite_sfe.read_spatial_feature_experiment.read_simple_feature(path, metadata, **kwargs)

Load a GeoDataFrame from its on-disk representation.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

• path (str) – Path to the directory containing the object.

• metadata (dict) – Metadata for the object.

• kwargs – Further arguments.

Return type:

GeoDataFrame

Returns:

A GeoDataFrame object containing the coordinates.

dolomite_sfe.read_spatial_feature_experiment.read_spatial_feature_experiment(path, metadata, **kwargs)

Load a SpatialFeatureExperiment from its on-disk representation.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

• path (str) – Path to the directory containing the object.

• metadata (dict) – Metadata for the object.

• kwargs – Further arguments.

Return type:

SpatialFeatureExperiment

Returns:

A SpatialExperiment with file-backed arrays in the assays.

dolomite_sfe.save_spatial_feature_experiment module

Module contents