drcme.load_data.load_h5_data

drcme.load_data.load_h5_data(h5_fv_file, params_file, metadata_file=None, dendrite_type='all', need_structure=False, need_ramp_spike=True, include_dend_type_null=True, limit_to_cortical_layers=None, id_file=None)[source]

Load dictionary for sPCA processing from HDF5 file

The data can also be filtered by several metadata values.

Parameters

  • h5_fv_file (str) – Path to feature vector HDF5 file

  • params_file (str) – Path to sPCA parameters JSON file

  • metadata_file (str, optional) – Path to metadata CSV file

  • dendrite_type ({'all', 'spiny', 'aspiny'}, optional) – Dendrite type for filtering (only used if metadata file is supplied)

  • need_structure (bool, optional) – Requires that structure is present (only used if metadata file is supplied)

  • need_ramp_spike (bool, optional) – Requires that the ramp spike is non-zero (aka not missing)

  • include_dend_type_null (bool, optional) – Also include cells without a dendrite type available regardless of what dendrite_type is specified (only used if metadata file is supplied)

  • limit_to_cortical_layers (list, optional) – List of cortical layers that metadata must match for inclusion (only used if metadata file is supplied)

  • id_file (str, optional) – Path to text file with IDs to use

Returns

  • data_for_spca (dict) – Dictionary of data sets for sPCA analysis

  • specimen_ids (array) – The specimen IDs for the cells in the data sets