neurochat.nc_config module

This module implements Configuration Class for NeuroChaT software.

@author: Md Nurul Islam; islammn at tcd dot ie

class neurochat.nc_config.Configuration(filename=[])

Bases: object

The Configuration object is the placeholder for all NeuroChaT settings.

The object consists of specification of data and analysis along with the parameters for each analysis type.

It also facilitates saving these setting to a .ncfg file and retriving them from the .ncfg file. The .ncfg file is a YAML-formatted file.

filename

Full file name of the configuration storage (.ncfg)

Type:str

format

Recording system or format of the data file

Type:str

analysis_mode

Mode of analysis in NeuroChaT. Options are ‘Single Unit’, ‘Single Session’ and ‘Listed Units’

Type:str

mode_id

Numeric ID of modes in NeuroChaT Respectively 0, 1, and 2 for the three modes

Type:int

graphic_format

File format for output graphics. Options are ‘PDF’ or ‘Postscript’

Type:str

unit_no

Unit number to be analyzed. Used in ‘Single Unit’ mode

Type:int

spatial_file

Full file of the spatial dataset

Type:str

spike_file

Full file of the spike dataset

Type:str

lfp_file

Full file of the lfp dataset

Type:str

nwb_file

Full file of the NWB format dataset

Type:str

excel_dir

Full file of the Excel list of unit. Used only in ‘Listed Units’ mode

Type:str

analyses

Dictionary of analysis methods as key and their selection as boolean values

Type:dict

parameters

(key: value) pairs of parameter names and their values

Type:dict

special_analysis

A dict indicating a menu analysis method.

Type:dict

get_all_modes()

Return the analysis modes in NeuroChaT.

Parameters:None – Returns:dict – Modes and their IDs

get_analysis(name=None)

Return the selection of an analysis.

If name is ‘all’, selection values for all the analyses are returned.

Parameters:name (str) – Name of the analysis. Enter ‘all’ for returning values for all the analyses Returns:bool – True if selected, False if not.

get_analysis_list()

Return a list of analyses.

Parameters:None – Returns:list – List of analysis names.

get_analysis_mode()

Return the mode of analysis and mode ID.

Parameters:None – Returns:(str, int) – Analysis mode set, ID of analysis mode

get_cell_type()

Return the type of cell set to analyse.

Parameters:None – Returns:str – Cell type set for analyses

get_config_dir()

Return the directory of configuration file.

Parameters:None – Returns:str – Name of the configuration file

get_config_file()

Return the name of the configuration file.

Parameters:None – Returns:str – Name of configuration file

get_data_dir()

Return the data directory.

Parameters:None – Returns:str – Data directory

get_data_format()

Return the data format or recording system.

Parameters:None – Returns:str – Data format or recording system

get_excel_file()

Return the filename of the Excel list.

Parameters:None – Returns:str – Filename of the Excel list

get_graphic_format()

Return output graphics file format.

Parameters:None – Returns:str – Export format of output graphics

get_lfp_file()

Return the filename of the lfp data.

Parameters:None – Returns:str – Filename of the lfp data

get_nwb_file()

Return the filename of the HDF5 data.

Parameters:None – Returns:str – Filename of the HDF5 data

get_param_list()

Return the list of all parameters.

Parameters:None – Returns:list – List of parameter names

get_params(name=None)

Get the value of parameter.

If a list of parameter names are provided, then a list of values are returned.

Parameters:name (str or list of str) – Name of the parameter(s) Returns:params – Parameter value(s)

get_params_by_analysis(analysis=None)

Return the parameters and their values for a given analysis.

Parameters:analysis (str) – Name of the analysis Returns:params (dict) – Dictionary of parameters and their values

get_spatial_file()

Return the filename of the spatial data.

Parameters:None – Returns:str – Filename of the spatial data

get_special_analysis()

Get the special analysis dictionary.

Parameters:None – Returns:dict – Dictionary of special analyses.

get_spike_file()

Return the filename of the spike data.

Parameters:None – Returns:str – Filename of spike data

get_unit_no()

Return the unit number that is already set.

Parameters:None – Returns:str – Unit number

load_config(filename=None)

Import the configuration data from a .ncfg file.

Parameters:filename (str) – Name of the configuration file Returns:None

save_config(filename=None)

Export the configuration data to .ncfg file.

Parameters:filename (str) – Name of the configuration file Returns:None

set_analysis(name=None, value=None)

Set the selection of an analysis.

Parameters:

• name (str) – Name of the analysis
• value (bool) – Boolean value to indicate analysis selection

Returns:

None

set_analysis_mode(analysis_mode=None)

Set the mode of analysis.

Parameters:analysis_mode (str) – Mode of the analysis Returns:None

set_cell_type(cell_type=None)

Set the type of cell to analyse.

Parameters:cell_type (str) – Cell type of interest Returns:None

set_config_dir(directory=None)

Set the directory of configuration file.

Parameters:directory (str) – Directory of configuration file Returns:None

set_config_file(filename)

Set the name of the configuration file.

Parameters:directory (str) – Name of configuration file Returns:None

set_data_dir(directory=None)

Set the data directory.

Parameters:directory (str) – Data directory Returns:None

set_data_format(file_format=None)

Set the format of the data or recording system.

Parameters:file_format (str) – Format of the data or recording system Returns:None

set_excel_file(excel_file=None)

Set filename of the Excel list.

Parameters:excel_file (str) – Filename of the Excel list Returns:None

set_graphic_format(graphic_format=None)

Set output graphics file format.

Parameters:graphic_format (str) – Format of output graphic export. Options are ‘PDF’ or ‘Postscript’. Returns:None

set_lfp_file(lfp_file=None)

Set filename of the lfp data.

Parameters:lfp_file (str) – Filename of the lfp data Returns:None

set_nwb_file(nwb_file=None)

Set filename of the HDF5 data.

Parameters:nwb_file (str) – Filename of the HDF5 data Returns:None

set_param(name=None, value=None)

Set the value of a parameter.

Parameters:

• name (str) – Name of the parameter
• value (any) – Value of the parameter

Returns:

None

set_spatial_file(spatial_file=None)

Set filename of the spatial data.

Parameters:spatial_file (str) – Filename of the spatial data Returns:None

set_special_analysis(in_dict={})

Set special analysis to the input dictionary.

Parameters:in_dict (dict) – Dictionary to set special analysis to. Returns:None

set_spike_file(spike_file=None)

Set filename of the spike data.

Parameters:spike_file (str) – Filename of the spike data Returns:None

set_unit_no(unit_no=None)

Set the unit no to analyse in ‘Single Unit’ analysis.

Parameters:unit_no (int) – Unit number the user is intending to analyse Returns:None