bachelor_thesis/DataAnalysisToolbox/ampAtStim_curveset.m

function ampAtStim_curveset(files, varargin)
%% Amplitude during a stimulation analysed over the trials 
% This function helps to analyse time effects on the amplitude of the
% membrane potential during stimulation. The amplitude values are obtained
% from the 'ampAtStim' function and are plotted with one curve per trial.
% -------------------------------------------------------------------------
% Input     [additional arguments are positional, 
% -----      optional arguments are name-value pairs]
%
%   files:      ID of the datafile(s) in the data directory 
%                   type: integer or vector
%   Trials:     select the trials which should be used. Default: 'all'
%   (additional)    type: integer or vector
%   Filter:     select between three filter options: 
%   (optional)      'hn' applys a hum-noise-remove filter 
%                   'hnhfn' additonally applys a low pass filter to remove 
%                       high frequency noise 
%                   If not set, it will be set to "no" (default). 
%   StimCell:   set whether to plot the data for a stimulated T-cell ('T') 
%   (optional):     or a stimulated interneuron ('INT'). Default: 'T'
% 
% ------
% Output 
% ------
%   visually output of the plot(s)
% ------------------------------------------------------------------------- 
% Program by: Bjarne Schultze [last modified 09.03.2022] 
% -------------------------------------------------------------------------

%% Preperations
% parse the user input
[file_num, trials, filter_choice, ~, ~, stimCell, ~,~,~] = ...
    parse_input_peakfun(files, varargin{:});

% load a file with different colors
load("../AdditionalFiles/colorShades.mat", 'colorShades');
load("../AdditionalFiles/standard_stimulus.mat", "standard_stimulus");

% obtain the amplitudes for the requested files
amps = ampAtStim(file_num, 'Filter', filter_choice);

% obtain the amplitudes of the current pulses
[stim_peaks, ~] = findpeaks(standard_stimulus, 10000);

% find negative stimului (therefor inverting the stimulus data)
[min_stim_peaks, ~] = ...
    findpeaks(-standard_stimulus, 10000, 'MinPeakHeight', 0);
% invert the peak values back
min_stim_peaks = -min_stim_peaks;

% concatenating positive and nagative stimlus peak data
all_stim_peaks = [min_stim_peaks; stim_peaks];
% sort the values for the current in ascending order
all_stim_peaks = sort(all_stim_peaks);

%% Plot the results
for file = 1:length(file_num)
    trial_num = size(amps{file,1}.AmplitudeT,2);
    % select the trials according to the stimulated cell (stimCell)
    if isequal(stimCell, "INT")
        stimulated = setdiff(1:trial_num, amps{file,1}.stimulatedT, ...
            'stable');
        plot_title = sprintf("File: %02.f - Interneuron stimulated", ...
            file_num(file));
    else
        stimulated = amps{file,1}.stimulatedT(:);
        plot_title = sprintf("File: %02.f - T-cell stimulated", ...
            file_num(file));
    end
    % if requested, select only certain trials
    if ~isequal(trials, 'all')
        stimulated = intersect(trials, stimulated);
    end
    
    % check if there are trials selected for which the data can be plotted
    if ~isempty(stimulated)
        % plot the data for the first selected trial
        figure('Position',[120,67,1278,694]);
        plot(all_stim_peaks, amps{file,1}.AmplitudeT(:,stimulated(1)), ...
            '-o', 'Color', colorShades.blue(1,:))
        hold on;
        plot(all_stim_peaks, amps{file,1}.AmplitudeINT(:,stimulated(1)), ...
            '-o', 'Color', colorShades.red(1,:));
        title(plot_title);
        xlabel("stimulation current [nA]"); 
        ylabel("amplitude of the membrane potential [mV]");
        yline(0, 'Color', [0.6 0.6 0.6])
        legend("T-cell", "Interneuron", 'Location','best', ...
            'AutoUpdate','off');
        
        % plot the data for all the other trials, each with a brighter
        % color shade
        for col = 2:length(stimulated)
            % if not enough color shades are available, all later trials
            % get the birghtest shade
            if col > length(colorShades.blue(:,1))
                plot_colorT = colorShades.blue(end,:);
                plot_colorINT = colorShades.red(end,:);
            else
                plot_colorT = colorShades.blue(col,:);
                plot_colorINT = colorShades.red(col,:);
            end
            plot(all_stim_peaks, ...
                amps{file,1}.AmplitudeT(:,stimulated(col)), '-o', ...
                'Color', plot_colorT)
            plot(all_stim_peaks, ...
                amps{file,1}.AmplitudeINT(:,stimulated(col)), '-o', ...
                'Color', plot_colorINT);
        end
        hold off;
    else
        % display an error message when there was no trial to plot
        fprintf("\nBad trial selection for file %g. No plot created!\n", ...
            file_num(file));
    end
end

% end of function definition
end