drcme.bin.run_existing_spca_on_new_data¶

Script to apply an existing set of sPCA loadings to a new data set.

class drcme.bin.run_existing_spca_on_new_data.DatasetParameters(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)[source]¶

Parameter schema for input datasets

DatasetParameters¶
key	description	default	field_type	json_type
fv_h5_file	HDF5 file with feature vectors	NA	`InputFile`	str
metadata_file	Metadata file in CSV format	None	`InputFile`	str
dendrite_type	Filter for dendrite type using information in metadata (all, spiny, aspiny)	all	`String`	str
allow_missing_structure	Whether or not structure value for cell in metadata can be missing	False	`Boolean`	bool
allow_missing_dendrite	Whether or not dendrite type value for cell in metadata can be missing	False	`Boolean`	bool
need_ramp_spike	Whether or not to exclude cells that did not fire an action potential from the ramp stimulus	True	`Boolean`	bool
limit_to_cortical_layers	List of cortical layers to limit the data set (using the metadata file)	[]	`List`	str
id_file	Text file with specimen IDs to use. Cells with IDs not in the file will be excluded.	None	`InputFile`	str

class drcme.bin.run_existing_spca_on_new_data.SpcaTransformParameters(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)[source]¶

Parameter schema for sPCA using existing transform

This schema is designed to be a schema_type for an ArgSchemaParser object

SpcaTransformParameters¶
key	description	default	field_type	json_type
input_json	file path of input json file	NA	`InputFile`	str
output_json	file path to output json file	NA	`OutputFile`	str
log_level	set the logging level of the module	ERROR	`LogLevel`	str
orig_transform_file	sPCA loadings file	NA	`InputFile`	str
orig_datasets	schema for loading one or more specific datasets for the analysis	(REQUIRED)	`DatasetParameters`	list
new_datasets	schema for loading one or more specific datasets for the analysis	(REQUIRED)	`DatasetParameters`	list
params_file	JSON file with sPCA parameters	NA	`InputFile`	str
output_file	CSV with transformed values	NA	`OutputFile`	str

Functions

main(orig_transform_file, orig_datasets, …)

Main runner function for script.

Classes

`DatasetParameters`([extra, only, exclude, …])	Parameter schema for input datasets
`SpcaTransformParameters`([extra, only, …])	Parameter schema for sPCA using existing transform