spectraViewer_old.m

function spectraViewer_old

% Viewer for excitation and emission spectra of fluorescent dyes
%
% Data organization inside spectra files:
% All files are expected to be comma separated lists with a header line.
% The header line is ignored, data are expected to be (in this order):
% Wavelength (abs), Absorption coef, Wavelength (em), Emission coef.
%
% The file names should contain the best excitation wavelength as the only
% number (anywhere within the string).
%
% Convert Excel files to csv files:
% - Make sure the excel sheet uses '.' as a decimal separator. If not, go
% to File -> Options -> Advanced -> Editing options -> Use system separator
% and change accordingly. Then, go to File -> Export -> Change File Type ->
% CSV -> Save as and save file. The region settings of your OS might result
% in semicolon-separated lists (instead of comma-separated lists). If so,
% go to Windows Start menu - Region and language - Additional settings - 
% List separator and set it to comma.
%
% This is a good resource for spectra: https://www.chroma.com/spectra-viewer
%
% Stephan Junek, 2015

%Find files
fn = [dir('*.txt')' dir('*.csv')'];

% Sort files according to the wavelength number contained in the file name
for f=1:numel(fn)
    wl(f) = str2double(cell2mat(regexp(fn(f).name,'\d','match')));
    spectra(f).wavelength = wl(f);
end
[sortFn sortIdx] = sort(wl);
fn = fn(sortIdx);
spectra = spectra(sortIdx);

% Import data from files
for f = 1:numel(fn)
    spectra(f).name = fn(f).name;
    spectra(f).data = readData(fn(f).name);
end

% Make Gui
guiSz = [100 100 1200 600];
gui = figure('Position',guiSz);
colorCode = jet(numel(fn));
% Checkboxes for spectra
for f = 1:numel(fn)
    cb_fn(f) = uicontrol('Style','Checkbox','String',spectra(f).name(1:end-4),...
        'Value',0, 'Position',[10 guiSz(4)-20-f*20 150 18],...
        'Backgroundcolor',get(gui,'Color'),'Callback',@updateSpectra,...
        'ForegroundColor',colorCode(f,:));
end

% "None" button
uicontrol('Style','pushbutton','Position',[10 guiSz(4)-50-f*20 150 18], 'String','None', ...
    'Callback', @deselect);

% Checkboxes for laser lines
colorLaserLine = jet(30);
colorLUT = linspace(400,700,30);
laserlines = [355, 405, 458, 488, 514, 561, 594, 633];
for f = 1:numel(laserlines)
    cb_ll(f) = uicontrol('Style','Checkbox','String',[num2str(laserlines(f)) ' nm'],...
        'Value',0, 'Position',[10 guiSz(4)-20-(numel(fn)+3+f)*20 150 18],...
        'Backgroundcolor',get(gui,'Color'),'Callback',@updateSpectra,...
        'ForegroundColor',colorLaserLine(find(colorLUT>laserlines(f),1),:));
end

% Axes for conventional display of spectra, spectra of deselected dyes will
% be made invisible
ax(1) = axes('Position',[0.15 0.1 0.55 0.8]);
hold on
for f = 1:numel(fn)
    plEx(f) = plot(spectra(f).data(:,1),spectra(f).data(:,2)/max(spectra(f).data(:,2)),'LineStyle','--','Color',colorCode(f,:),'LineWidth',4);
    plEm(f) = plot(spectra(f).data(:,3),spectra(f).data(:,4)/max(spectra(f).data(:,4)),'Color',colorCode(f,:),'LineWidth',3);
end

for f = 1:numel(laserlines)
    plLl(f) = plot(laserlines(f)*[1 1],get(gca,'YLim'),'Color',colorLaserLine(find(colorLUT>laserlines(f),1),:),'LineWidth',2);
end
set(gca,'YLim',[0 1]);
set([plEx plEm plLl], 'Visible','off')
xlabel('wavelength [nm]');

% Axes for combined (2D) display of excitation and emission spectra
ax(2) = axes('Position',[0.75 0.1 0.2 0.8]);
hold all
% Calculate matrices (product of exc and em spectra) and display as contour plots
% Data will be interpolated to reduce calculation and plotting time
wEx = linspace(400,700,100);
wEm = linspace(500,800,100);
for f = 1:numel(fn)
    % Make sure no wavelength value appears twice and remove NaN values
    [c, idx] = unique(spectra(f).data(:,1));
    notNaN = ~isnan(spectra(f).data(idx,1)) & ~isnan(spectra(f).data(idx,2));
    interEx = interp1(spectra(f).data(idx(notNaN),1),spectra(f).data(idx(notNaN),2),wEx);
    
    [c, idx] = unique(spectra(f).data(:,3));
    notNaN = ~isnan(spectra(f).data(idx,3)) & ~isnan(spectra(f).data(idx,4));
    interEm = interp1(spectra(f).data(idx(notNaN),3),spectra(f).data(idx(notNaN),4),wEm);
    
    % Calculate and plot combined spectrum
    m = repmat(interEx/max(interEx),[100 1]).*repmat(interEm'/max(interEm),[1 100]);
    [c, pl2d(f)] = contour(wEx,wEm,m,[0.99 0.75 0.5 0.25],'Color',colorCode(f,:),'LineWidth',3);    
end
for f = 1:numel(laserlines)
    plLl2d(f) = plot(laserlines(f)*[1 1],get(gca,'YLim'),'Color',colorLaserLine(find(colorLUT>laserlines(f),1),:),'LineWidth',2); 
end
set([pl2d plLl2d], 'Visible','off');
xlabel('\lambda_{exc} [nm]');
ylabel('\lambda_{em} [nm]');
set(gca,'YLim',[500 700]);

% Callback and helper functions
    function updateSpectra(varargin)
        % updates display of spectra
        checked = find(cell2mat(get(cb_fn,'Value')));
        set([plEx plEm pl2d], 'Visible','off');
        set([plEx(checked) plEm(checked) pl2d(checked)], 'Visible','on');
        legend(pl2d(checked),fn(checked).name);
        checked = find(cell2mat(get(cb_ll,'Value')));
        set([plLl plLl2d], 'Visible','off');
        set([plLl(checked) plLl2d(checked)],'Visible','on');
    end

    function deselect(varargin)
        % Deselect all dyes
       set(cb_fn,'Value',0);
       updateSpectra
    end

    function out = readData(in)
        % Import data (adopted from code created by "Import data" button)
        
        % Initialize variables.
        delimiter = ',';
        startRow = 2;
        % Read columns of data as strings:
        % For more information, see the TEXTSCAN documentation.
        formatSpec = '%s%s%s%s%[^\n\r]';
        
        % Open the text file.
        fileID = fopen(in,'r');
        % Read columns of data according to format string.
        % This call is based on the structure of the file used to generate this
        % code. If an error occurs for a different file, try regenerating the code
        % from the Import Tool.
        dataArray = textscan(fileID, formatSpec, 'Delimiter', delimiter, 'HeaderLines' ,startRow-1, 'ReturnOnError', false);
        
        % Close the text file.
        fclose(fileID);
        
        % Convert the contents of columns containing numeric strings to numbers.
        % Replace non-numeric strings with NaN.
        raw = repmat({''},length(dataArray{1}),length(dataArray)-1);
        for col=1:length(dataArray)-1
            raw(1:length(dataArray{col}),col) = dataArray{col};
        end
        numericData = NaN(size(dataArray{1},1),size(dataArray,2));
        
        for col=[1,2,3,4]
            % Converts strings in the input cell array to numbers. Replaced non-numeric
            % strings with NaN.
            rawData = dataArray{col};
            for row=1:size(rawData, 1);
                % Create a regular expression to detect and remove non-numeric prefixes and
                % suffixes.
                regexstr = '(?<prefix>.*?)(?<numbers>([-]*(\d+[\,]*)+[\.]{0,1}\d*[eEdD]{0,1}[-+]*\d*[i]{0,1})|([-]*(\d+[\,]*)*[\.]{1,1}\d+[eEdD]{0,1}[-+]*\d*[i]{0,1}))(?<suffix>.*)';
                try
                    result = regexp(rawData{row}, regexstr, 'names');
                    numbers = result.numbers;
                    
                    % Detected commas in non-thousand locations.
                    invalidThousandsSeparator = false;
                    if any(numbers==',');
                        thousandsRegExp = '^\d+?(\,\d{3})*\.{0,1}\d*$';
                        if isempty(regexp(thousandsRegExp, ',', 'once'));
                            numbers = NaN;
                            invalidThousandsSeparator = true;
                        end
                    end
                    % Convert numeric strings to numbers.
                    if ~invalidThousandsSeparator;
                        numbers = textscan(strrep(numbers, ',', ''), '%f');
                        numericData(row, col) = numbers{1};
                        raw{row, col} = numbers{1};
                    end
                catch me
                end
            end
        end
        
        
        % Replace non-numeric cells with NaN
        R = cellfun(@(x) ~isnumeric(x) && ~islogical(x),raw); % Find non-numeric cells
        raw(R) = {NaN}; % Replace non-numeric cells
        
        % Create output variable
        out = cell2mat(raw);
        % Clear temporary variables
        clearvars filename delimiter startRow formatSpec fileID dataArray ans raw col numericData rawData row regexstr result numbers invalidThousandsSeparator thousandsRegExp me R;
    end
end