nichecompass.models.utils.load_saved_files

nichecompass.models.utils.load_saved_files(dir_path, load_adata, adata_file_name='adata.h5ad', load_adata_atac=False, adata_atac_file_name='adata_atac.h5ad', map_location=None)

Helper to load saved model files.

Parts of the implementation are adapted from https://github.com/scverse/scvi-tools/blob/master/scvi/model/base/_utils.py#L55 (01.10.2022)

Parameters:

  • dir_path (str) – Path where the saved model files are stored.

  • load_adata (bool) – If True, also load the stored AnnData object.

  • adata_file_name (str (default: 'adata.h5ad')) – File name under which the AnnData object is saved.

  • load_adata_atac (bool (default: False)) – If True, also load the stored ATAC AnnData object.

  • adata_atac_file_name (str (default: 'adata_atac.h5ad')) – File name under which the ATAC AnnData object is saved.

  • map_location (Optional[Literal['cpu', 'cuda']] (default: None)) – Memory location where to map the model files to.

Return type:

Tuple[OrderedDict, dict, ndarray, AnnData]

Returns:

model_state_dict:

The stored model state dict.

var_names:

The stored variable names.

attr_dict:

The stored attributes.

adata:

The stored AnnData object.

adata_atac:

The stored ATAC AnnData object.