set_parameters.m

function par = set_parameters()

% LOAD PARAMS
par.segments_length = 5;             % length (in minutes) of segments in which the data is cutted (default 5min).
par.sr = 30000;                      % sampling rate (in Hz). This parameter will be only used if the data file don't have a sr.


% PLOTTING PARAMETERS
par.cont_segment = true;
par.max_spikes_plot = 1000;          % max. number of spikes to be plotted
par.print2file = true;               % If is not true, print the figure (only for batch scripts).
par.cont_plot_samples = 100000;      % number of samples used in the one-minute (maximum) sample of continuous data to plot.
par.to_plot_std = 1;                 % # of std from mean to plot
par.all_classes_ax = 'mean';         % 'mean'/'all'. If it's 'mean' only the mean waveforms will be ploted in the axes with all the classes
par.plot_feature_stats = false;


% SPC PARAMETERS
par.mintemp = 0.00;                  % minimum temperature for SPC
par.maxtemp = 0.251;                 % maximum temperature for SPC
par.tempstep = 0.01;                 % temperature steps
par.SWCycles = 100;                  % SPC iterations for each temperature (default 100)
par.KNearNeighb = 11;                % number of nearest neighbors for SPC
par.min_clus = 20;                   % minimum size of a cluster (default 60)
par.randomseed = 0;                  % if 0, random seed is taken as the clock value (default 0)
%par.randomseed = 147;               % If not 0, random seed
%par.temp_plot = 'lin';              % temperature plot in linear scale
par.temp_plot = 'log';               % temperature plot in log scale

par.c_ov = 0.7;                      % Overlapping coefficient to use for the inclusion criterion.
par.elbow_min  = 0.4;                %Thr_border parameter for regime border detection.

% DETECTION PARAMETERS
par.tmax = 'all';                    % maximum time to load
%par.tmax= 180;                      % maximum time to load (in sec)
par.tmin= 0;                         % starting time for loading (in sec)
par.w_pre = 20;                      % number of pre-event data points stored (default 20)
par.w_post = 44;                     % number of post-event data points stored (default 44))
par.alignment_window = 10;           % number of points around the sample expected to be the maximum
par.stdmin = 5;                      % minimum threshold for detection
par.stdmax = 50;                     % maximum threshold for detection
par.detect_fmin = 300;               % high pass filter for detection
par.detect_fmax = 3000;              % low pass filter for detection (default 1000)
par.detect_order = 4;                % filter order for detection. 0 to disable the filter.
par.sort_fmin = 300;                 % high pass filter for sorting
par.sort_fmax = 3000;                % low pass filter for sorting (default 3000)
par.sort_order = 2;                  % filter order for sorting. 0 to disable the filter.
par.ref_ms = 1.5;                    % detector dead time, minimum refractory period (in ms)
par.detection = 'pos';               % type of threshold ('pos','neg','both')
% par.detection = 'neg';
% par.detection = 'both';

% INTERPOLATION PARAMETERS
par.int_factor = 5;                  % interpolation factor
par.interpolation = 'y';             % interpolation with cubic splines (default)
% par.interpolation = 'n';


% FEATURES PARAMETERS
par.min_inputs = 10;         % number of inputs to the clustering
par.max_inputs = 0.75;       % number of inputs to the clustering. if < 1 it will the that proportion of the maximum.
par.scales = 4;                        % number of scales for the wavelet decomposition
par.features = 'wav';                % type of feature ('wav' or 'pca')
%par.features = 'pca'


% FORCE MEMBERSHIP PARAMETERS
par.template_sdnum = 3;             % max radius of cluster in std devs.
par.template_k = 10;                % # of nearest neighbors
par.template_k_min = 10;            % min # of nn for vote
%par.template_type = 'mahal';       % nn, center, ml, mahal
par.template_type = 'center';       % nn, center, ml, mahal
par.force_feature = 'spk';          % feature use for forcing (whole spike shape)
%par.force_feature = 'wav';         % feature use for forcing (wavelet coefficients).
par.force_auto = true;              %automatically force membership (only for batch scripts).

% TEMPLATE MATCHING
par.match = 'y';                    % for template matching
%par.match = 'n';                   % for no template matching
par.max_spk = 40000;                % max. # of spikes before starting templ. match.
par.permut = 'y';                   % for selection of random 'par.max_spk' spikes before starting templ. match.
% par.permut = 'n';                 % for selection of the first 'par.max_spk' spikes before starting templ. match.

% HISTOGRAM PARAMETERS
par.nbins = 100;                    % # of bins for the ISI histograms
par.bin_step = 1;                   % percentage number of bins to plot