writeSpykingCircusParameters.m

function writeSpykingCircusParameters(cfg)

% WRITESPYKINGCIRCUSPARAMETERS writes .params and .prb file for Spyking Circus
%
% use as
%   writeSpykingCircusParameters(cfg)
%
% The .params file is based on the one in the template folder of EpiCode.
% Change this file to have new default values.
%
% Mandatory inputs
%
% cfg.directorylist     % list of folders with the neuralynx raw files
% cfg.circus.channel    % list of channels to process with Spyking-Circus
% cfg.datasavedir       % where to save the data
%
% Optional cfg fields
%
% cfg.circus.params.SECTION.SETTING % any setting for params file, e.g.:
%
% cfg.circus.params.detection.spike_thresh  = '6';
% cfg.circus.params.filtering.cut_off       = '300, auto';
% cfg.circus.params.filtering.remove_median = 'False';
% cfg.circus.params.clustering.max_elts     = '20000';
%
% cfg.circus.part_list  % Array of integers with the parts numbers to
%                         analyze. Can be 'all'. Default = 'all'

% This file is part of EpiCode, see
% http://www.github.com/stephenwhitmarsh/EpiCode for documentation and details.
%
%   EpiCode is free software: you can redistribute it and/or modify
%   it under the terms of the GNU General Public License as published by
%   the Free Software Foundation, either version 3 of the License, or
%   (at your option) any later version.
%
%   EpiCode is distributed in the hope that it will be useful,
%   but WITHOUT ANY WARRANTY; without even the implied warranty of
%   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%   GNU General Public License for more details.
%
%   You should have received a copy of the GNU General Public License
%   along with EpiCode. If not, see <http://www.gnu.org/licenses/>.

% get the default options
cfg.circus.part_list        = ft_getopt(cfg.circus, 'part_list', 'all');
cfg.circus.paramfile        = ft_getopt(cfg.circus, 'paramfile', []);
cfg.circus.channelname      = ft_getopt(cfg.circus, 'channelname', []);

% add external/iniconfig path if not already
mfile_name = mfilename('fullpath');
pathstr    = fileparts(fileparts(mfile_name));
pathCell   = regexp(path, pathsep, 'split');

if ispc  % Windows is not case-sensitive
    onPath = any(strcmpi(fullfile(pathstr, ['external', filesep, 'iniconfig']), pathCell));
else
    onPath = any(strcmp(fullfile(pathstr, ['external', filesep, 'iniconfig']), pathCell));
end
if ~onPath
    addpath(fullfile(pathstr, ['external', filesep, 'iniconfig']));
end

if strcmp(cfg.circus.part_list, 'all')
    cfg.circus.part_list = 1:size(cfg.directorylist,2);
end

if isempty(cfg.circus.paramfile)
    [p, ~, ~]               = fileparts(mfilename('fullpath'));
    [p, ~, ~]               = fileparts(p);
    fname_params_default    = fullfile(p, 'templates', 'SpykingCircus.params');
else
    fname_params_default    = cfg.circus.paramfile;
end

if ~exist(fname_params_default, 'file')
    error('Template file does not exist: %s\n', fname_params_default);
else
    fprintf('Using template for defaults: %s\n', fname_params_default);
end

for ipart = cfg.circus.part_list

    subjdir = cfg.prefix(1:end-1);
    partdir = ['p', num2str(ipart)];

    % read Spyking-Circus params file
    ini = IniConfig();
    ini.ReadFile(fname_params_default);

    % remove inline comments
    [sections, count_sections] = ini.GetSections();
    for sectioni = 1 : count_sections
        [keys, count_keys] = ini.GetKeys(sections{sectioni});
        for keysi = 1 : count_keys
            old     = ini.GetValues(sections{sectioni}, keys{keysi});
            temp    = split(old,{'#'});
            ini.SetValues(sections{sectioni}, keys{keysi}, temp{1});
        end
    end

    % there should be a better way to do this that removes double code...
    if isempty(cfg.circus.channelname)
        nb_channels     = size(cfg.circus.channel,2);
        
        % adjust parameters common to all
        fname_prb       = ['Adtech_', num2str(nb_channels), 'chan.prb'];
        h1 = ini.SetValues('data', {'file_format','stream_mode','mapping','suffix','overwrite','output_dir'}, {'neuralynx','None', fname_prb, '','False','SpykingCircus'});
        h2 = ini.SetValues('noedits', {'filter_done','artefacts_done','ground_done','median_done'}, {'False','False','False','False'});

        % add artefact file to params only if needed
        temp = dir(fullfile(cfg.datasavedir, subjdir, partdir, '*.dead'));
        if isempty(temp)
            continue
        end
        if temp(1).bytes == 0
            h3 = ini.SetValues('triggers', {'dead_file','dead_unit','ignore_times'}, {'','timestep','False'});
        else
            h3 = ini.SetValues('triggers', {'dead_file','dead_unit','ignore_times'}, {'SpykingCircus_artefacts_samples.dead','timestep','True'});
        end
        
        % replace settings with those defined in cfg.circus.params
        if isfield(cfg.circus, 'params')
            if ~isempty(cfg.circus.params)
                for field = string(fields(cfg.circus.params))'
                    for setting = string(fields(cfg.circus.params.(field)))'
                        h4 = ini.SetValues(char(field), char(setting), cfg.circus.params.(field).(setting));
                        fprintf('Set: [%s] %s to %s\n', field, setting, cfg.circus.params.(field).(setting));                        
                        if h4 ~= 1, error('Something went wrong with adjusting parameters; does the field not exist in the template?'); end
                    end
                end
            end
        end
        
        if nb_channels == 1
            h0 = ini.SetValues('filtering', {'remove_median'}, {'False'});
            if h0 ~= 1, error('Something went wrong with adjusting parameters'); end
        end
        
        filename    = 'SpykingCircus.params';
        fname_params    = fullfile(cfg.datasavedir, subjdir, partdir, filename);
        status          = ini.WriteFile(fname_params);
        if status == false
            error('Couldn''t write file %s', fname_params);
        else
            fprintf('Succesfully wrote SpykingCircus settings to %s\n', fname_params);
        end
        writeProbeFile(nb_channels, fullfile(cfg.datasavedir, subjdir, partdir, fname_prb));

    else

        for chandir = unique(cfg.circus.channelname)

            % add artefact file to params only if needed
            temp        = strcmp(cfg.circus.channelname, chandir);
            nb_channels = sum(temp);

            % adjust parameters common to all
            fname_prb       = ['Adtech_', num2str(nb_channels), 'chan.prb'];
            h1 = ini.SetValues('data', {'file_format','stream_mode','mapping','suffix','overwrite','output_dir'}, {'neuralynx','None', fname_prb, '','False','SpykingCircus'});
            h2 = ini.SetValues('noedits', {'filter_done','artefacts_done','ground_done','median_done'}, {'False','False','False','False'});

            temp        = dir(fullfile(cfg.datasavedir, subjdir, partdir, string(chandir), '*.dead'));
            if isempty(temp)
                continue
            end
            if temp(1).bytes == 0
                h3 = ini.SetValues('triggers', {'dead_file','dead_unit','ignore_times'}, {'','timestep','False'});
            else
                h3 = ini.SetValues('triggers', {'dead_file','dead_unit','ignore_times'}, {'SpykingCircus_artefacts_samples.dead','timestep','True'});
            end
            if any([h1; h2; h3] ~= 1), error('Something went wrong with adjusting parameters'); end

            % replace settings with those defined in cfg.circus.params
            if isfield(cfg.circus, 'params')
                if ~isempty(cfg.circus.params)
                    for field = string(fields(cfg.circus.params))'
                        for setting = string(fields(cfg.circus.params.(field)))'
                            h4 = ini.SetValues(char(field), char(setting), cfg.circus.params.(field).(setting));
                            if h4 ~= 1, error('Something went wrong with adjusting parameters'); end
                            fprintf('Set: [%s] %s to %s\n', field, setting, cfg.circus.params.(field).(setting));
                        end
                    end
                end
            end
              
            if nb_channels == 1
                h0 = ini.SetValues('filtering', {'remove_median'}, {'False'});
                if h0 ~= 1, error('Something went wrong with adjusting parameters'); end
            end

            filename        = 'SpykingCircus.params';            
            fname_params    = char(fullfile(cfg.datasavedir, subjdir, partdir, string(chandir), filename));
            fname_prb       = ['Adtech_', num2str(nb_channels), 'chan.prb'];
            status          = ini.WriteFile(fname_params);
            if status == false
                error('Couldn''t write file %s', fname_params);
            else
                fprintf('Succesfully wrote SpykingCircus settings to %s\n', fname_params);
            end
            writeProbeFile(nb_channels, fullfile(cfg.datasavedir, subjdir, partdir, string(chandir), fname_prb));
            
        end
    end
end