GUI_run

Set the GUI Layout
Select the Folder with Data Files
Select the Files to Process
Select Channels to Process
Process the First Image
Process All Images
Control the Vertical Display Props
Save Fitting Settings
Load Fitting Settings

Set the GUI Layout

function [] = GUI_run_me()

%

close all;
clear all;

S.GUI_flag = 1;   % variable to tell Nano6_Flatten_surf_poly that it was called from the GUI.

SCR = get(0,'Screensize');  % Get screensize.
S.fh = figure('numbertitle','off',...
              'menubar','none',...
              'units','pixels',...
              'position',[SCR(3)/2-400 ,SCR(4)/2-300 , 1200, 750],...
              'name','GUI',...
              'resize','on');

S.plots = uipanel('BackgroundColor','white', 'units', 'pixel', 'Position', [15 150 1170 530], 'visible', 'on');
% For the image:
S.ax1 = axes('units','pixels', 'position',[20 100 500 400], 'Parent', S.plots, 'visible', 'off');
% For the histogram:
S.ax2 = axes('units','pixels', 'position',[630 100 460 400], 'Parent', S.plots, 'visible', 'off');

S.initialText = uicontrol('style', 'text', 'units','pixels', 'position',[480 300 250 200], ...
                    'string',{'- Select the starting directory', '- Select files to process', '- Select the channels to process', ...
                    '- Choose the parameters', '- and Click "Process single image"'},...
                    'BackgroundColor', 'white', 'fontsize',11, 'fontangle', 'italic', 'HorizontalAlignment', 'left', 'visible', 'on');

% Sets the Color bar to display
S.ColorBarText          = uicontrol('Style', 'text', 'String', 'Colorbar: ',...
                                    'Position', [350 20  70 20], 'Fontsize', 11, 'BackgroundColor','white', 'Parent', S.plots);
S.ColorBarSelect        = uicontrol('Style', 'popup',...                  % Channel selection for the plotting
                                    'String', { 'Sky',...
                                                'Autumn',...
                                                'Bone',...
                                                'Cool',...
                                                'Copper',...
                                                'Flag',...
                                                'Gray',...
                                                'Hot',...
                                                'HSV',...
                                                'Jet',...
                                                'Pink',...
                                                'Spring',...
                                                'Summer',...
                                                'Winter'},...
                                    'Position', [425 22 150 20], 'fontsize', 11, 'Parent', S.plots);



% For channel display selection:
S.channelDisplayText    = uicontrol('Style', 'text', 'String', 'Display: ',...
                                    'Position', [600 20 70 20], 'Fontsize', 11, 'BackgroundColor','white', 'Parent', S.plots);
S.channelDisplaySelect  = uicontrol('Style', 'popup',...                  % Channel selection for the plotting
                                    'String', {'Height', 'Deflection'}',...
                                    'Position', [675 22 150 20], 'fontsize', 11, 'Parent', S.plots);

% Channel State to plot
S.j                     = uicontrol('Style', 'text', 'position', [700 700 140 40], 'string', '1', 'visible', 'off'); % text that is never visible; to know which channel we are dealing with
S.image_to_plot         = uicontrol('Style', 'text',...
                                    'position', [700 700 140 40], 'string', '1', 'visible', 'off'); % text that is never visible; to know which image (final, raw, etc) to plot

S.raw_vs_processed      = uicontrol('Style', 'popup',...
                                    'String', 'Final image and histogram|Raw image and histogram|After 1st median correction|After 1st poly flattening|After 2nd median correction|After 2nd poly flattening',...
                                    'Position', [850 22 300 20], 'fontsize', 11, 'Parent', S.plots, 'enable', 'off');

S.pb(1) = uicontrol(    'style','pushbutton',...
                        'units','pixels',...
                        'position',[970 20 200 40],...
                        'string','Process all images',...
                        'fontsize',12, 'enable', 'off');

S.pb(2) = uicontrol(    'style','pushbutton',...
                        'units','pixels',...
                        'position',[720 20 200 40],...
                        'string','Process single image',...
                        'fontsize',12, 'enable', 'off');

S.selectFile            = uicontrol('style','pushbutton', 'units','pixels',...
                                    'position',[720 70 200 25], 'string','Select images to process:', 'fontsize',10);
S.selectFileText        = uicontrol('style', 'edit', 'units', 'pixels',...
                                    'position',[920 70 250 25], 'string','', 'fontsize',10);

S.selectFolder          = uicontrol('style','pushbutton', 'units','pixels',...
                                    'position',[720 105 200 25], 'string','Change starting folder:', 'fontsize',10);
S.selectFolderText      = uicontrol('style', 'edit', 'units', 'pixels',...
                                    'position',[920 105 250 25], 'string','C:\', 'fontsize', 10);

S.channelsSelection     = uipanel(  'BackgroundColor','white', 'title', 'Channels to process', 'units', 'pixel',...
                                    'position', [15 20 680 120], 'fontsize', 12, 'visible', 'on');
for k = 1:8
    strposition = [-53+k*80 40 70 40];
    S.channelProcessText(k) = uicontrol('Style','text', 'string', {'Channel ', num2str(k)}, 'position', strposition, 'visible', 'on', 'HorizontalAlignment', 'center','BackgroundColor','white', 'fontsize',10, 'Parent', S.channelsSelection);
end
for k = 1:8
    strposition = [-25+k*80 25 30 20];
    if k == 1
        S.channelProcessSelect(k) = uicontrol('Style','Check', 'position', strposition, 'Value', 1, 'visible', 'on', 'BackgroundColor','white', 'Parent', S.channelsSelection);
    else
        S.channelProcessSelect(k) = uicontrol('Style','Check', 'position', strposition, 'Value', 0, 'visible', 'on', 'BackgroundColor','white', 'Parent', S.channelsSelection);
    end
end

% S.plot_parameters = uipanel('BackgroundColor','white', 'units', 'pixel', 'Position', [640 75 420 50], 'visible', 'on');
% S.plot_intermediate_steps = uicontrol('Style','text', 'string', 'Plot intermediate steps', 'position', [640 100 140 20], 'fontsize', 10, 'Parent', S.plot_parameters, 'visible', 'on');
% S.plot_intermediate_steps = uicontrol('Style','Check', 'position', [700 60 30 20], 'Value', 0, 'Parent', S.plot_parameters, 'visible', 'on');

% Channels explanation panel
S.channels_explanation_panel = uipanel('Title','Units','FontSize',12.5, 'units', 'pixel', 'Position', [20 50 190 250], 'visible', 'off');
channels_titles = ['Height: [nm]          '; ...
                   'Height Sensor: [nm]   '; ...
                   'Deflection: [V]       '; ...
                   'Phase: [°]            '; ...
                   'Amplitude: [mV]       '; ...
                   'Amplitude Error: [mV] '; ...
                   'Potential: [V]        '; ...
                   'Peak Force Error: [nN]'; ...
                   'DMTModulus: [MPa]     '; ...
                   'logDMTMod: [log(MPa)] '; ...
                   'Adhesion: [nN]        '; ...
                   'Deformation: [nm]     '; ...
                   'Dissipation: [eV]     '; ...
                   'Input1: [nm]          '; ...
                   'Input2: [mV]          '];
S.channel_info_Units = ['[nm]   ';'[nm]   '; '[V]    '; '[°]    '; '[mV]   '; '[mV]   '; '[V]    '; '[nN]   '; '[MPa]  '; 'lg(MPa)'; '[nN]   '; '[nm]   '; '[eV]   '; '[nm]   ';  '[mV]   '];

for k = 1:size(S.channel_info_Units,1)
    strposition = [15 220-k*15 140 20];
    S.channels_explanation(k) = uicontrol('Style','text', 'string', channels_titles(k,:), 'fontsize', 12, 'position', strposition, 'Parent', S.channels_explanation_panel, 'horizontalAlignment', 'left', 'visible', 'on');
end

channels_titles = ['Height        '; ...
                   'Height Sensor '; ...
                   'Deflection    '; ...
                   'Phase         '; ...
                   'Amplitude     '; ...
                   'Amplitude err '; ...
                   'Potential     '; ...
                   'Peak Force err'; ...
                   'DMTModulus    '; ...
                   'logDMTMod     '; ...
                   'Adhesion      '; ...
                   'Deformation   '; ...
                   'Dissipation   '; ...
                   'Input1        '; ...
                   'Input2        '];

% Parameters per channel panel
S.parameters_panel = uipanel('Title','Parameters per channel','FontSize',12, 'BackgroundColor','white', 'units', 'pixel', 'Position', [230 35 950 645], 'visible', 'off');
S.axText = axes('units','pixels', 'position',[30 530 900 50], 'Parent', S.parameters_panel, 'XColor', 'w', 'YColor', 'w',  'visible', 'on');


Med_corr_1_init_values                              = ['Y','Y','N','N','Y','Y','Y','Y','N','N','N','N','N','N','N','N'];
Med_corr_2_init_values                              = ['Y','Y','N','N','Y','Y','Y','Y','N','N','N','N','N','N','N','N'];
vert_med_corr_init_values                           = ['N','N','N','N','N','N','N','N','N','N','N','N','N','N','N','N'];
poly_order_horiz_init_values                        = [ 3,  2,  0,  0,  0,  0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0 ]+ones(1,length(vert_med_corr_init_values));     % +1 because index 0 doesn't exist in matlab;
poly_order_vert_init_values                         = [ 3,  2,  0,  0,  0,  0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0 ]+ones(1,length(vert_med_corr_init_values));     % +1 because index 0 doesn't exist in matlab;
peak_fit_values                                     = [ 2,  2,  1,  1,  2,  1,  2,  1,  1,  1,  1,  1,  1,  1,  1,  1 ]+ones(1,length(vert_med_corr_init_values));
peak_shift_values                                   = [ 2,  2,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1 ]+ones(1,length(vert_med_corr_init_values));
peak_flatten_values                                 = [ 2,  2,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1 ]+ones(1,length(vert_med_corr_init_values));
min_peak_dist_initial_values                        = [ 5.0e-0,  5.0e-0,  0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,  0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0];
min_std_initial_values                              = [ 5.0e-2,  5.0e-2,  2.0e+0,   2.0e-1,   5.0e-2,   1.0e+1,   5.0e-3,   1.0e-3,  1.0e-2,   1.0e-2,   1.0e-2,   1.0e-2,   1.0e-2,   1.0e-2,   1.0e-2 ,  1.0e-2];
max_std_initial_values                              = [ 5.0e-1,  5.0e-1,  2.0e+1,   2.0e+0,   1.0e-0,   4.0e+1,   2.0e-2,   5.0e-2,  1.0e-1,   1.0e-1,   1.0e-1,   1.0e-1,   1.0e-1,   1.0e-1,   1.0e-1,   1.0e-1];
z_ref_values                                        = [ 0.0e-0,  0.0e-0,  0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,  0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0,   0.0e-0];
min_z_values                                        = [ 0.0e+0,  0.0e+0, -3.0e+1,  -5.0e+0,  -1.0e+1,  -1.0e+2,  -1.0e-2,  -1.0e-1, -1.0e-0,  -1.0e-0,  -1.0e-0,  -1.0e-0,  -1.0e-0,  -1.0e-0,  -1.0e-0 , -1.0e-0];
max_z_values                                        = [10.0e+0, 10.0e+0,  3.0e+1,   5.0e+0,   1.0e+1,   1.0e+2,   3.0e-2,   1.0e-1,  1.0e-0,   1.0e-0,   1.0e-0,   1.0e-0,   1.0e-0,   1.0e-0,   1.0e-0,   1.0e-0];


col_spacing = (900-195)/size(S.channel_info_Units,1);

for k = 1:size(S.channel_info_Units,1)
   %for l = 1:16
        % - Titles - %
        text((175+k*col_spacing)/900, 0.1, channels_titles(k,:),'Fontsize', 12,'HorizontalAlignment', 'Left','Rotation',90);

%         S.Titles                                    = uicontrol(    'Style', 'text', 'String', channels_titles(k,:),...
%                                                                     'Position',  strposition,...
%                                                                     'Fontsize', 12,...
%                                                                     'Parent', S.parameters_panel, 'BackgroundColor','white',...
%                                                                     'HorizontalAlignment', 'left',...
%                                                                     'Visible', 'on');

        % - Median correction - %
        S.Med_corr_text                             = uicontrol(    'Style', 'text', 'String', 'Median correction:',...
                                                                    'Position', [15 495 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'HorizontalAlignment', 'left',...
                                                                    'Visible', 'on');
            strposition                             = [195+k*col_spacing 497 30 20];
            if (Med_corr_1_init_values(k) == 'Y')
                S.Med_corr(k)                       = uicontrol(    'Style','Check',...
                                                                    'Position', strposition, 'Value', 1,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'Visible', 'on');
            else
                S.Med_corr(k)                       = uicontrol(    'Style','Check',...
                                                                    'Position', strposition, 'Value', 0,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'Visible', 'on');
            end

        % - Median correction 2 - %
        S.Med_corr_2_text                           = uicontrol(    'Style', 'text', 'String', 'Median correction 2:',...
                                                                    'Position', [15 465 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'HorizontalAlignment', 'left',...
                                                                    'Visible', 'on');

            strposition                             = [195+k*col_spacing 467 30 20];
            if (Med_corr_2_init_values(k) == 'Y')
                S.Med_corr_2(k)                     = uicontrol(    'Style','Check',...
                                                                    'Position', strposition, 'value', 1,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'Visible', 'on');
            else
                S.Med_corr_2(k)                     = uicontrol(    'Style','Check',...
                                                                    'Position', strposition, 'value', 0,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'Visible', 'on');
            end


        % - Vertical median correction - %
        S.vert_med_corr_text                        = uicontrol(    'Style', 'text', 'String', 'Vertical median correction:',...
                                                                    'Position', [15 435 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [195+k*col_spacing 437 30 20];
            if (vert_med_corr_init_values(k) == 'Y')
                S.vert_med_corr(k)                  = uicontrol(    'Style','Check','position', strposition,...
                                                                    'value', 1, 'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');
            else
                S.vert_med_corr(k)                  = uicontrol(    'Style','Check','position', strposition,...
                                                                    'value', 0, 'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');
            end


        % - Polynomial flattening order, horizontal - %
        S.poly_order_horiz_text                     = uicontrol(    'Style', 'text', 'String', 'Poly order horiz:',...
                                                                    'Position', [15 405 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 407 30 20];
            S.poly_order_horiz(k)                   = uicontrol(     'Style','popup','String','0|1|2|3',...
                                                                     'position', strposition, 'Value', poly_order_horiz_init_values(k),...
                                                                     'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                     'visible', 'on');


        % - Polynomial flattening order, vertical - %
        S.poly_order_vert_text                      = uicontrol(    'Style', 'text', 'String', 'Poly order vert:',...
                                                                    'Position', [15 375 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 377 30 20];
            S.poly_order_vert(k)                    = uicontrol(    'Style','popup','String','0|1|2|3',...
                                                                    'position', strposition, 'value', poly_order_vert_init_values(k),...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % % - Min Peak Distance - %
        S.min_peak_distance_reference_text          = uicontrol(    'Style', 'text', 'String', 'z height reference:',...
                                                                    'Position', [15 345 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 347 30 20];
            S.min_peak_distance(k)                  = uicontrol(    'Style','edit','position', strposition,...
                                                                    'Parent', S.parameters_panel, 'string', min_peak_dist_initial_values(k), 'BackgroundColor','white',...
                                                                    'visible', 'on');


        % - min_spacing_stdev_user - %
        S.min_spacing_stdev_user_text               = uicontrol(    'Style', 'text', 'String', 'Min spacing standard deviation:',...
                                                                    'Position', [15 315 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 317 30 20];
            S.min_spacing_stdev_user(k)             = uicontrol(    'Style','edit','position', strposition,...
                                                                    'Parent', S.parameters_panel, 'string', min_std_initial_values(k), 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % - max_spacing_stdev_user - %
        S.max_spacing_stdev_user_text               = uicontrol(    'Style', 'text', 'String', 'Max spacing standard deviation:',...
                                                                    'Position', [15 285 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 287 30 20];
            S.max_spacing_stdev_user(k)             = uicontrol(    'Style','edit','position', strposition,....
                                                                    'Parent', S.parameters_panel, 'string', max_std_initial_values(k), 'BackgroundColor','white',...
                                                                    'visible', 'on');


        % - calc_flatten_lim - %
        S.Calc_flatten_lim_text                     = uicontrol (   'Style', 'text', 'String', 'Calc. flatten limits:',...
                                                                    'Position', [15 255 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [195+k*col_spacing 257 30 20];
            S.Calc_flatten_lim(k)                   = uicontrol(    'Style','Check','position', strposition, 'value', 1,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % - overwrite_Z lim -%
        S.overwrite_xlim_text                       = uicontrol (   'Style', 'text', 'String', 'Overwrite Z Limits:',...
                                                                    'Position', [15 225 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
             strposition                            = [195+k*col_spacing 227 30 20];
             S.overwrite_xlim(k)                    = uicontrol(    'Style','Check','position', strposition, 'value', 1,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % % - Z Reference Value - %
        S.z_height_reference_text                   = uicontrol(    'Style', 'text', 'String', 'z height reference:',...
                                                                    'Position', [15 345 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 347 30 20];
            S.z_height_reference(k)                 = uicontrol(    'Style','edit','position', strposition,...
                                                                    'Parent', S.parameters_panel, 'string', z_ref_values(k), 'BackgroundColor','white',...
                                                                    'visible', 'on');


        % - min_z - %
        S.min_z_text                                = uicontrol(    'Style', 'text', 'String', 'Minimum z:',...
                                                                    'Position', [15 195 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 197 30 20];
            S.min_z(k)                              = uicontrol(    'Style','edit','position', strposition,...
                                                                    'Parent', S.parameters_panel, 'string', min_z_values(k), 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % - max_z - %
        S.max_z_text                                = uicontrol(    'Style', 'text', 'String', 'Maximum z:',...
                                                                    'Position', [15 165 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'HorizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 167 30 20];
            S.max_z(k)                              = uicontrol(    'Style','edit','position', strposition,...
                                                                    'Parent', S.parameters_panel, 'string', max_z_values(k), 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % - peaks_fit - %
        S.peaks_fit_text                            = uicontrol(    'Style', 'text', 'String', 'Number of peaks to fit:',...
                                                                    'Position', [15 135 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'HorizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 137 30 20];
            S.peaks_fit(k)                          = uicontrol(    'Style','popup','String','0|1|2|3',...
                                                                    'Position', strposition, 'value', peak_fit_values(k),...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % - peak_reference_height - %
        S.peak_reference_height_text                = uicontrol(    'Style', 'text', 'String', 'Peak to shift:',...
                                                                    'Position', [15 105 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 107 30 20];
            S.peak_reference_height(k)              = uicontrol(    'Style','popup','String','0|1|2|3',...
                                                                    'Position', strposition, 'value', peak_shift_values(k),...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % - sort_peaks - %
        S.sort_peaks_text                           = uicontrol (   'Style', 'text', 'String', 'Sort peaks in position order:',...
                                                                    'Position', [15 75 200 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','White',...
                                                                    'HorizontalAlignment', 'Left', 'Visible', 'on');
            strposition                             = [195+k*col_spacing 77 30 20];
            S.sort_peaks(k)                         = uicontrol(    'Style','Check','position', strposition, 'value', 1,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');

        % - peak_to_flatten - %
        S.peak_to_flatten_text                      = uicontrol(    'Style', 'text', 'String', 'Peak to flatten (position order):',...
                                                                    'Position', [15 45 180 20], 'Fontsize', 12,...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'horizontalAlignment', 'left', 'visible', 'on');
            strposition                             = [190+k*col_spacing 47 30 20];
            S.peak_to_flatten(k)                    = uicontrol(    'Style','popup','String','0|1|2|3',...
                                                                    'Position', strposition, 'value', peak_flatten_values(k),...
                                                                    'Parent', S.parameters_panel, 'BackgroundColor','white',...
                                                                    'visible', 'on');



   %end
end










S.other_parameters_panel    = uipanel('Title','Other parameters','FontSize',12, 'BackgroundColor','white', 'units', 'pixel', 'Position', [20 400 190 280], 'visible', 'off');
S.disp_scale_bar_text       = uicontrol('Style','text','string', 'Scale Bar: ',                         'Position',[10  5   100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.disp_scale_bar            = uicontrol('Style','Check',                                                'Position',[120 5   40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on', 'Value', 1);
S.disp_grain_analysis_text  = uicontrol('Style','text','string', 'Grain Analysis: ',                    'Position',[10  30  100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.disp_grain_analysis       = uicontrol('Style','Check',                                                'Position',[120 30  40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on', 'Value', 1);
S.scale_bar_length_text     = uicontrol('Style','text','string', 'Scale Bar (nm): ',                    'position',[10  55  100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.scale_bar_length          = uicontrol('Style','edit',                                                 'position',[120 55  40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on','string', 1000);
S.crop_fraction_text        = uicontrol('Style','text','string', 'Crop Fraction: ',                     'position',[10  80  100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.crop_fraction             = uicontrol('Style','edit',                                                 'position',[120 80  40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on','string', 0);
S.thresh_range_text         = uicontrol('Style','text','string', 'Threshold Range: ',                   'position',[10  105 100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.thresh_range              = uicontrol('Style','edit',                                                 'position',[120 105 40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on','string', 2);
S.peak_threshold_text       = uicontrol('Style','text','string', 'Peak Threshold: ',                    'position',[10  130 100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.peak_threshold            = uicontrol('Style','edit',                                                 'position',[120 130 40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on','string', 0);
S.min_peak_distance_text    = uicontrol('Style','text','string', 'Min Peak Dist: ',                     'position',[10  155 100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.min_peak_distance         = uicontrol('Style','edit',                                                 'position',[120 155 40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on','string', 8);
S.min_peak_height_text      = uicontrol('Style','text','string', 'Min Peak Height: ',                   'position',[10  180 100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.min_peak_height           = uicontrol('Style','edit',                                                 'position',[120 180 40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on', 'string', 100);
S.smoothing_level_text      = uicontrol('Style','text','string', {'Histogram', 'Smoothing Level: '},    'position',[10  205 100 40], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.smoothing_level           = uicontrol('Style','edit',                                                 'position',[120 205 40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on', 'string', 5);
S.histogram_bins_text       = uicontrol('Style','text','string', 'Histogram Bins: ',                    'position',[10  230 100 20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white', 'Fontsize', 12, 'horizontalAlignment', 'left', 'visible', 'on');
S.histogram_bins            = uicontrol('Style','edit',                                                 'position',[120 230 40  20], 'Parent', S.other_parameters_panel, 'BackgroundColor', 'white',                                                'visible', 'on','string', 256 );



S.save = uicontrol('style','pushbutton','units','pixels', 'position',[55 355 120 30], 'string','Save parameters','Fontsize', 12, 'visible', 'off');
S.load = uicontrol('style','pushbutton','units','pixels', 'position',[55 315 120 30], 'string','Load parameters','Fontsize', 12, 'visible', 'off');


% Toggles will act as the tabs.
S.tg(1) = uicontrol('style','toggle',...
                    'units','pixels',...
                    'position',[5 700 140 40],...
                    'string','MAIN','fontweight', 'bold',...
                    'fontsize', 11, ...
                    'val',1);
S.tg(2) = uicontrol('style','toggle',...
                    'units','pixels',...
                    'position',[145 700 140 40],...
                    'string','PARAMETERS','fontweight', 'bold',...
                    'fontsize', 11, ...
                    'value',0,...
                    'enable','on');
S.tg(3) = uicontrol('style','toggle',...
                    'units','pixels',...
                    'position',[285 700 120 40],...
                    'string','HELP', 'fontweight', 'bold',...
                    'fontsize', 11, ...
                    'value',0,...
                    'enable','on');
S.tg(4) = uicontrol('style','toggle',...
                    'units','pixels',...
                    'position',[405 700 120 40],...
                    'string','ABOUT', 'fontweight', 'bold',...
                    'fontsize', 11, ...
                    'value',0,...
                    'enable','on');

S.text_waiting = uicontrol('style', 'text', 'units', 'pixels', 'position', [17 155 1160 515], 'string', 'Processing...', 'horizontalAlignment', 'center', 'BackgroundColor', 'white', 'fontsize', 14, 'visible', 'off');

% Text in "About" tab
S.tx = uicontrol('style','text',...
                 'units','pixels',...
                 'position',[40 20 1020 660],...
                 'visible','off',...
                 'string',{' ','This is a', 'first attempt to',...
                 'create a GUI','with Matlab.',' ','Copyright:',...
                 'LBNI, EPFL','2011'},...
                 'Fontsize',12,'fontweight','bold');


% Test in "Help" tab
S.explanations = uicontrol('style','text',...
                 'units','pixels',...
                 'position',[40 20 1020 660],...
                 'visible','off',...
                 'string',{' ','This is a', 'tab to write',...
                 'some explanations'},...
                 'Fontsize',12,'horizontalAlignment','left');

S.slider_z_reference = uicontrol('style','slide',...
                 'unit','pix',...
                 'position',[130 15 150 20],...
                 'min', str2double(get(S.min_z(1), 'string')),'max',str2double(get(S.max_z(1), 'string')),...
                 'value', str2double(get(S.z_height_reference(1), 'string')), ...
                 'parent', S.plots, 'enable', 'off', 'visible', 'off');
S.slider_val = uicontrol('style', 'text', 'position', [130 42 150 20], 'string', get(S.z_height_reference(1), 'string'), 'Fontsize', 12, 'backgroundcolor', 'white', 'parent', S.plots, 'visible', 'off');
S.slider_min = uicontrol('style', 'edit', 'position', [75 15 50 20],   'string', get(S.min_z(1), 'string'),              'Fontsize', 12, 'backgroundcolor', 'white', 'parent', S.plots, 'visible', 'off');
S.slider_max = uicontrol('style', 'edit', 'position', [285 15 50 20],  'string', get(S.max_z(1), 'string'),              'Fontsize', 12, 'backgroundcolor', 'white', 'parent', S.plots, 'visible', 'off');

%W = {'style','edit','units','pixels','position'};  % Save some typing.

S.Offset_data = 0;

% -- Set the callback functions. --%
set(S.pb(1),'callback',{@processAllImages_call,S})
set(S.pb(2),'callback',{@processOneImage_call,S})
set(S.tg(:),{'callback'},{{@tg_call,S}})
set(S.raw_vs_processed,'callback',{@plots_call,S});
set(S.ColorBarSelect,'callback',{@colorbar_call,S});
set(S.channelDisplaySelect, 'callback', {@display_channels_call,S});
set(S.save, 'callback', {@save_call,S});
set(S.load, 'callback', {@load_call,S});
set(S.selectFolder, 'callback', {@selectFolder_call,S});
set(S.selectFile, 'callback', {@selectFile_call,S});
set(S.slider_z_reference, 'callback', {@slider_z_call,S});
set([S.slider_min; S.slider_max], 'callback', {@slider_min_max_call,S});
set([S.min_z(:); S.max_z(:); S.z_height_reference(:)] , 'callback', {@change_slider_z_call,S});
set(S.channelProcessSelect(:), 'callback', {@selectChannels_call,S});

Select the Folder with Data Files

function [] = selectFolder_call(varargin)

[~,S] = varargin{[1,3]};  % Get the structure.
S.folder = uigetdir;
set(S.selectFolderText, 'string', S.folder);

Select the Files to Process

function [] = selectFile_call(varargin)

[~,S] = varargin{[1,3]};  % Get the structure.
[S.Filename, S.ImageDir] = uigetfile({'*.*','Nanoscope Files (*.*)'}, 'Pick files', get(S.selectFolderText, 'string'),...
                                     'MultiSelect','on') ;
assignin('base', 'Filename', S.Filename);
set(S.selectFileText, 'string', [S.Filename{1}, ', ...']);
channelsInfo = getChannelInfo(S.Filename, S.ImageDir);
for k = 1:min(size(channelsInfo, 1),8)
    set(S.channelProcessText(k), 'string', {channelsInfo(k, 1).Name});
end
set(S.pb(2), 'enable', 'on');   % Enables the "Process single image" button now that the file to process has been selected
selectChannels_call(varargin);   % Disable all the parameters of channels that are not processed

Select Channels to Process

function [] = selectChannels_call(varargin)

if size(varargin,2) == 1 % callback was called from processOneImage_call
    varargin = varargin{1};
    [~,S] = varargin{[1,3]};  % Get the structure.
else
    [~,S] = varargin{[1,3]};  % Get the structure.
end
[display_nb ~] = find(cell2mat(get(S.channelProcessSelect, 'value'))==1);
channels = get(S.channelProcessText(display_nb), 'string');
if (length(channels)>1)
    channels = [channels{1:length(channels)}];
else
    channels{1,1} = 'Channel ';
    channels{2,1} = num2str(display_nb);
end


enabled_channels = zeros(1, 15);
for i = 1:length(channels)
    switch channels{i}
        case 'Height'
           enabled_channels(1) = 1;
        case 'Deflection'
           enabled_channels(2) = 1;
        case 'Phase'
           enabled_channels(3) = 1;
        case 'Amplitude'
            enabled_channels(4) = 1;
        case 'Amplitude Error'
            enabled_channels(5) = 1;
        case 'Potential'
            enabled_channels(6) = 1;
        case 'Peak Force Error'
            enabled_channels(7) = 1;
        case 'DMTModulus'
            enabled_channels(8) = 1;
        case 'LogDMTModulus'
            enabled_channels(9) = 1;
        case 'Adhesion'
            enabled_channels(10) = 1;
        case 'Deformation'
            enabled_channels(11) = 1;
        case 'Dissipation'
            enabled_channels(12) = 1;
        case 'Input1'
            enabled_channels(13) = 1;
        case 'Input2'
            enabled_channels(14) = 1;
        case 'Height Sensor'
            enabled_channels(15) = 1;
    end
end

for k = 1:size(S.channel_info_Units,1)
    if enabled_channels(k) == 0    % channels that do not exist and the ones that are not selected = disabled channels
        set(S.Med_corr(k), 'enable', 'off');
        set(S.Med_corr_2(k),'enable', 'off');
        set(S.vert_med_corr(k), 'enable', 'off');
        set(S.poly_order_horiz(k), 'enable', 'off');
        set(S.poly_order_vert(k), 'enable', 'off');
        set(S.z_height_reference(k), 'enable', 'off');
        set(S.min_spacing_stdev_user(k), 'enable', 'off');
        set(S.max_spacing_stdev_user(k), 'enable', 'off');
        set(S.min_z(k), 'enable', 'off');
        set(S.max_z(k), 'enable', 'off');
        set(S.peaks_fit(k), 'enable', 'off');
        set(S.peak_reference_height(k), 'enable', 'off');
        set(S.peak_to_flatten(k), 'enable', 'off');
        set(S.Calc_flatten_lim(k), 'enable', 'off');
        set(S.overwrite_xlim(k), 'enable', 'off');
        set(S.sort_peaks(k), 'enable', 'off');
    else  % enabled channels
        set(S.Med_corr(k), 'enable', 'on');
        set(S.Med_corr_2(k),'enable', 'on');
        set(S.vert_med_corr(k), 'enable', 'on');
        set(S.poly_order_horiz(k), 'enable', 'on');
        set(S.poly_order_vert(k), 'enable', 'on');
        set(S.z_height_reference(k), 'enable', 'on');
        set(S.min_spacing_stdev_user(k), 'enable', 'on');
        set(S.max_spacing_stdev_user(k), 'enable', 'on');
        set(S.min_z(k), 'enable', 'on');
        set(S.max_z(k), 'enable', 'on');
        set(S.peaks_fit(k), 'enable', 'on');
        set(S.peak_reference_height(k), 'enable', 'on');
        set(S.peak_to_flatten(k), 'enable', 'on');
        set(S.Calc_flatten_lim(k), 'enable', 'on');
        set(S.overwrite_xlim(k), 'enable', 'on');
        set(S.sort_peaks(k), 'enable', 'on');
    end
end

Process the First Image

function [] = processOneImage_call(varargin)

% Callback for pushbutton "Process one image"
delete('Nano6_variables.mat');
[~,S] = varargin{[1,3]};
set(S.text_waiting, 'visible', 'on');
set(S.initialText, 'visible', 'off');
set(varargin{3}.tg(2:4),'enable','off');  % Turn off the other tabs.
set(varargin{3}.pb(1:2),'enable', 'off'); % Turn off the "Process one image" and "Process all images" buttons
S.processAll = 0; % To tell Nano6_Flatten_surf_poly that it has to process only one image
pause(0.1)
Nano6_Flatten_surf_poly_GUI;
set(varargin{3}.tg(2:4),'enable','on');  % Turn on the other tabs.
set(varargin{3}.pb(1:2),'enable', 'on'); % Turn on the "Process one image" and "Process all images" buttons
set(S.raw_vs_processed, 'enable', 'on');
load('Nano6_variables') % Loads the variables used in Nano6_Flatten_surf_poly
display_channels_call(varargin)
j = str2double(get(S.j, 'string'));
set(S.slider_z_reference, 'min', str2double(get(S.min_z(j), 'string')));
set(S.slider_z_reference, 'max', str2double(get(S.max_z(j), 'string')));
set(S.slider_z_reference, 'value', str2double(get(S.z_height_reference(j), 'string')));
set(S.slider_val, 'string', [get(S.z_height_reference(j), 'string'), ' ', S.channel_info_Units(j,:)]);
set(S.slider_min, 'string', get(S.min_z(j), 'string'));
set(S.slider_max, 'string', get(S.max_z(j), 'string'));
set(S.channelDisplaySelect, 'enable', 'on');
images(:,:,j) = final_images(:,:,j);
S.Offset_data = 0;
plot_nice_image_in_GUI;
set(S.text_waiting, 'visible', 'off');
[display_nb ~] = find(cell2mat(get(S.channelProcessSelect, 'value'))==1);
disp_str = get(S.channelProcessText(display_nb), 'string');
set(S.channelDisplaySelect, 'string', [disp_str{1:length(disp_str)}]);
set(S.channelDisplaySelect, 'value', 1);
set(S.slider_z_reference, 'enable', 'on');
set([S.slider_z_reference; S.slider_val; S.slider_min; S.slider_max], 'visible', 'on');

Process All Images

function [] = processAllImages_call(varargin)

% Callback for pushbutton "Process all images"
[~,S]                                       = varargin{[1,3]};
set(varargin{3}.tg(2:4),'enable','off');  % Turn off the other tabs.
set(varargin{3}.pb(1:2),'enable', 'off'); % Turn off the "Process one image" and "Process all images" buttons
set(S.raw_vs_processed, 'enable', 'off')
set(S.channelDisplaySelect, 'enable', 'off');
S.processAll                                = 1; % Variable to tell Nano6_Flatten_surf_poly that it has to process only all images (if processAll = 1), or only one image (if processAll = 0)
S.Offset_data                               = 0;
Nano6_Flatten_surf_poly_GUI;
set(varargin{3}.tg(2:4),'enable','on');  % Turn on the other tabs.
set(varargin{3}.pb(1:2),'enable', 'on'); % Turn on the "Process one image" and "Process all images" buttons

Control the Vertical Display Props

function [] = slider_z_call(varargin)
% Callback to change z_reference_height with slider; can only be called
% when image to display is the final image, because slider is disabled else
[~,S] = varargin{[1,3]};  % Get the structure.
j = str2double(get(S.j, 'string')); % j = channel
set(S.z_height_reference(j), 'string', num2str(get(S.slider_z_reference, 'value')));
load('Nano6_variables') % Loads the variables used in Nano6_Flatten_surf_poly to be able to plot the image
set(S.slider_val, 'string', [get(S.z_height_reference(j), 'string'), ' ', S.channel_info_Units(j,:)]);
S.Offset_data = 0;
images(:,:,j) = final_images(:,:,j);
plot_nice_image_in_GUI; % to refresh the image with the new offset
S.Offset_data = 0;
function [] = slider_min_max_call(varargin)
% Callback for when min_z or max_z was changed (limits of the slider)
[~,S] = varargin{[1,3]};  % Get the structure.
j = str2double(get(S.j, 'string')); % j = channel
set(S.slider_z_reference, 'value', (str2double(get(S.slider_min, 'string'))+str2double(get(S.slider_max, 'string')))/2)
set(S.slider_z_reference, 'min', str2double(get(S.slider_min, 'string')));
set(S.min_z(j), 'string', get(S.slider_min, 'string'));
set(S.slider_z_reference, 'max', str2double(get(S.slider_max, 'string')));
set(S.max_z(j), 'string', get(S.slider_max, 'string'));
if get(S.image_to_plot, 'string') == '1' % Final image
    load('Nano6_variables') % Loads the variables used in Nano6_Flatten_surf_poly to be able to plot the image
    images(:,:,j) = final_images(:,:,j);
    plot_nice_image_in_GUI; % to refresh the image with the new offset
else % if not final image, then edit min and max is disabled so do nothing
end
function [] = change_slider_z_call(varargin)
% Callback for changing the min, max and current values of the slider
[~,S] = varargin{[1,3]};  % Get the structure.
load('Nano6_variables') % Loads the variables used in Nano6_Flatten_surf_poly to get channel_info.Unit
j = str2double(get(S.j, 'string')); % j = channel
set(S.slider_z_reference, 'min', str2double(get(S.min_z(j), 'string')));
set(S.slider_z_reference, 'max', str2double(get(S.max_z(j), 'string')));
set(S.slider_z_reference, 'value', str2double(get(S.z_height_reference(j), 'string')));
set(S.slider_val, 'string', [get(S.z_height_reference(j), 'string'), ' ', S.channel_info_Units(j,:)]);
set(S.slider_min, 'string', get(S.min_z(j), 'string'));
set(S.slider_max, 'string', get(S.max_z(j), 'string'));
if get(S.image_to_plot, 'string') == '1' % Final image
    images(:,:,j) = final_images(:,:,j);
    plot_nice_image_in_GUI;
else
end
function [] = display_channels_call(varargin)
% Callback for the popup allowing the choice of which channel to display
if size(varargin,2) == 1 % callback was called from processOneImage_call
    varargin = varargin{1};
    [~,S] = varargin{[1,3]};  % Get the structure.
    for k = 1:7
        if get(S.channelProcessSelect(k), 'value') == 1
           channel_name = get(S.channelProcessText(k), 'string');
           channel_name = channel_name{1};
           break;
        end
    end
else
    [~,S] = varargin{[1,3]};  % Get the structure.
    channel_string = get(S.channelDisplaySelect, 'string');
    channel_name = channel_string(get(S.channelDisplaySelect, 'Value'));
    channel_name = channel_name{1};
end
        switch channel_name
                case 'Height'
                     set(S.j, 'string', '1');
                case 'Deflection'
                     set(S.j, 'string', '2');
                case 'Phase'
                     set(S.j, 'string', '3');
                case 'Amplitude'
                     set(S.j, 'string', '4');
                case 'Amplitude Error'
                     set(S.j, 'string', '5');
                case 'Potential'
                     set(S.j, 'string', '6');
                case 'Peak Force Error'
                     set(S.j, 'string', '7');
                case 'DMTModulus'
                     set(S.j, 'string', '8');
                case 'LogDMTModulus'
                     set(S.j, 'string', '9');
                case 'Adhesion'
                     set(S.j, 'string', '10');
                case 'Deformation'
                     set(S.j, 'string', '11');
                case 'Dissipation'
                     set(S.j, 'string', '12');
                case 'Input1'
                     set(S.j, 'string', '13');
                case 'Input2'
                     set(S.j, 'string', '14');
                case 'Height Sensor'
                     set(S.j, 'string', '15');
        end
j = str2double(get(S.j, 'string'));
set(S.image_to_plot, 'string', '1') % if we change the channel to display, always displays first the final image
load('Nano6_variables') % Loads the variables used in Nano6_Flatten_surf_poly to be able to plot the image
set(S.slider_z_reference, 'min', str2double(get(S.min_z(j), 'string'))); % Refresh the slider's parameters
set(S.slider_z_reference, 'max', str2double(get(S.max_z(j), 'string')));
set(S.slider_z_reference, 'value', str2double(get(S.z_height_reference(j), 'string')));
set(S.slider_val, 'string', [get(S.z_height_reference(j), 'string'), ' ', S.channel_info_Units(j,:)]);
set(S.slider_min, 'string', get(S.min_z(j), 'string'));
set(S.slider_max, 'string', get(S.max_z(j), 'string'));
popup_items = [1, 1, get(S.Med_corr(j), 'value'), 1,1, get(S.Med_corr_2(j), 'value'), 1];
images_str = {'Final image and histogram'; 'Raw image and histogram'; 'After 1st median correction';'After General Tilt Correction'; 'After 1st poly flattening'; 'After 2nd median correction'; 'After 2nd poly flattening'};
set(S.raw_vs_processed, 'string', images_str(popup_items == 1));
set(S.raw_vs_processed,'value', 1);
images(:,:,j) = final_images(:,:,j);
set(S.slider_z_reference, 'enable', 'on');
plot_nice_image_in_GUI;
function [] = plots_call(varargin)
% Callback for the popup "Display raw image and histogram|Display processed image and histogram".
[~,S] = varargin{[1,3]};  % Get the structure.
set(S.image_to_plot, 'string', num2str(get(S.raw_vs_processed,'value')));  % Get the user's choice.
j = str2double(get(S.j, 'string')); % j = channel
load('Nano6_variables') % Loads the variables used in Nano6_Flatten_surf_poly to be able to plot the image
%string = images_str(str2double(get(S.image_to_plot, 'string')));
all_strings = get(S.raw_vs_processed, 'string');
value       = get(S.raw_vs_processed, 'value');
switch all_strings{value}   %string{1}
    case 'Final image and histogram'
        images(:,:,j) = final_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'on');
        set(S.image_to_plot, 'string', '1');
    case 'Raw image and histogram'
        images(:,:,j) = raw_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '2');
    case 'After 1st median correction'
        images(:,:,j) = med_corr_1_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '3');
    case 'After General Tilt Correction'
        images(:,:,j) = ini_tilt_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '4');
    case 'After 1st poly flattening'
        images(:,:,j) = poly_flat_1_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '5');
    case 'After 2nd median correction'
        images(:,:,j) = med_corr_2_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '6');
    case 'After 2nd poly flattening'
        images(:,:,j) = poly_flat_2_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '7');
end
plot_nice_image_in_GUI;
function [] = colorbar_call(varargin)
% Callback for the popup "Display raw image and histogram|Display processed image and histogram".
[~,S] = varargin{[1,3]};  % Get the structure.
set(S.image_to_plot, 'string', num2str(get(S.raw_vs_processed,'value')));  % Get the user's choice.
j = str2double(get(S.j, 'string')); % j = channel
load('Nano6_variables') % Loads the variables used in Nano6_Flatten_surf_poly to be able to plot the image
%string = images_str(str2double(get(S.image_to_plot, 'string')));
all_strings = get(S.raw_vs_processed, 'string');
value       = get(S.raw_vs_processed, 'value');
switch all_strings{value}   %string{1}
    case 'Final image and histogram'
        images(:,:,j) = final_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'on');
        set(S.image_to_plot, 'string', '1');
    case 'Raw image and histogram'
        images(:,:,j) = raw_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '2');
    case 'After 1st median correction'
        images(:,:,j) = med_corr_1_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '3');
    case 'After General Tilt Correction'
        images(:,:,j) = ini_tilt_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '4');
    case 'After 1st poly flattening'
        images(:,:,j) = poly_flat_1_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '5');
    case 'After 2nd median correction'
        images(:,:,j) = med_corr_2_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '6');
    case 'After 2nd poly flattening'
        images(:,:,j) = poly_flat_2_images(:,:,j);
        set(S.slider_z_reference, 'enable', 'off');
        set(S.image_to_plot, 'string', '7');
end
plot_nice_image_in_GUI;
function [] = tg_call(varargin)

% Callback for tabs
[h,S] = varargin{[1,3]};  % Get calling handle and structure.

if get(h,'val')==0  % Here the Toggle is already pressed.
    set(h,'val',1) % To keep the Tab-like functioning.
end
% Each case of the switch has one toggle associated with it.  When a toggle
% is selected the uicontrols which belong to it are made visible, and the
% others are made invisible.  This way each toggle has, in effect, its own
% GUI.  All uicontrols are part of the main GUI, some are simply hidden
% when each toggle is selected.  This mimics the action of tabs.
switch h
    case S.tg(1)
        set(S.tg([2,3,4]),'val',0)
        set([S.plots;S.pb(:); S.channelsSelection; S.selectFolder; S.selectFile;...
            S.selectFolderText; S.selectFileText],{'visible'},{'on'})
        set([S.tx; S.parameters_panel; S.channels_explanation_panel; S.other_parameters_panel;...
            S.explanations; S.save; S.load; S.initialText],{'visible'},{'off'})
    case S.tg(2)
        set(S.tg([1,3,4]),{'val'},{0})
        set([S.parameters_panel; S.channels_explanation_panel; S.other_parameters_panel; S.save; S.load],'visible','on')
        set([S.plots;S.pb(:);S.tx; S.channelsSelection; S.explanations; S.selectFolder; S.selectFile;...
            S.selectFolderText; S.selectFileText; S.initialText],{'visible'},{'off'})
    case S.tg(3)
        set(S.tg([1,2,4]),{'val'},{0})
        set([S.parameters_panel; S.channels_explanation_panel; S.other_parameters_panel; S.plots;S.pb(:);S.tx; ...
            S.channelsSelection; S.save; S.load; S.selectFolder; S.selectFile; S.selectFolderText; S.selectFileText; S.initialText],'visible','off')
        set([S.explanations],{'visible'},{'on'})
    otherwise
        set(S.tg([1,2,3]),{'val'},{0})
        set(S.tx,'visible','on')
        set([S.plots;S.pb(:); S.channelsSelection; S.parameters_panel; S.channels_explanation_panel; S.other_parameters_panel; ...
            S.explanations; S.save; S.load; S.selectFolder; S.selectFile; S.selectFolderText; S.selectFileText; S.initialText],{'visible'},{'off'})
end

Save Fitting Settings

    function [] = save_call(varargin)

    % Callback for the button "Save". Saves the current parameters
    %[FileName,PathName] = uiputfile('settings.m','Save as');
    S = varargin{3};
    histogram_bins                  = get(S.histogram_bins, 'string');
    smoothing_level                 = get(S.smoothing_level, 'string');
    min_peak_height                 = get(S.min_peak_height, 'string');
    min_peak_distance               = get(S.min_peak_distance, 'string');
    thresh_range                    = get(S.thresh_range, 'string');
    for k = 1:size(S.channel_info_Units,1)
        Med_corr(k)                 = get(S.Med_corr(k), 'value');
        Med_corr_2(k)               = get(S.Med_corr_2(k),'value');
        vert_med_corr(k)            = get(S.vert_med_corr(k), 'value');
        poly_order_horiz(k)         = get(S.poly_order_horiz(k), 'value');
        poly_order_vert(k)          = get(S.poly_order_vert(k), 'value');
        z_height_reference(k)       = str2double(get(S.z_height_reference(k), 'string'));
        min_spacing_stdev_user(k)   = str2double(get(S.min_spacing_stdev_user(k), 'string'));
        max_spacing_stdev_user(k)   = str2double(get(S.max_spacing_stdev_user(k), 'string'));
        min_z(k)                    = str2double( get(S.min_z(k), 'string'));
        max_z(k)                    = str2double(get(S.max_z(k), 'string'));
        peaks_fit(k)                = get(S.peaks_fit(k), 'value');
        peak_reference_height(k)    = get(S.peak_reference_height(k), 'value');
        peak_to_flatten(k)          = get(S.peak_to_flatten(k), 'value');
        Calc_flatten_lim(k)         = get(S.Calc_flatten_lim(k), 'value');
        overwrite_xlim(k)           = get(S.overwrite_xlim(k), 'value');
        sort_peaks(k)               = get(S.sort_peaks(k), 'value');
    end

    uisave({'histogram_bins', 'smoothing_level', 'min_peak_height', 'min_peak_distance', ...
        'thresh_range', 'Med_corr', 'Med_corr_2', 'vert_med_corr',...
        'poly_order_horiz', 'poly_order_vert', ...
        'z_height_reference', 'min_spacing_stdev_user', 'max_spacing_stdev_user', 'min_z', ...
        'max_z', 'peaks_fit', 'peak_reference_height', 'peak_to_flatten', ...
        'Calc_flatten_lim', 'overwrite_xlim', 'sort_peaks'},'Settings.mat');

Load Fitting Settings

    function [] = load_call(varargin)
    % Callback for the button "Load".  Loads the parameters previously saved
    % with the button "Save".
    [~,S] = varargin{[1,3]};  % Get the structure.
    uiopen('Settings.mat');
    set(S.histogram_bins, 'string', histogram_bins);
    set(S.smoothing_level, 'string', smoothing_level);
    set(S.min_peak_height, 'string', min_peak_height);
    set(S.min_peak_distance, 'string', min_peak_distance);
    set(S.thresh_range, 'string', thresh_range);
    for k = 1:size(S.channel_info_Units,1)
       set(S.Med_corr(k), 'value', Med_corr(k));
       set(S.Med_corr_2(k), 'value', Med_corr_2(k));
       set(S.vert_med_corr(k), 'value', vert_med_corr(k));
       set(S.poly_order_horiz(k), 'value', poly_order_horiz(k));
       set(S.poly_order_vert(k), 'value', poly_order_vert(k));
       set(S.z_height_reference(k), 'string', z_height_reference(k));
       set(S.min_spacing_stdev_user(k), 'string', min_spacing_stdev_user(k));
       set(S.max_spacing_stdev_user(k), 'string', max_spacing_stdev_user(k));
       set(S.min_z(k), 'string', min_z(k));
       set(S.max_z(k), 'string', max_z(k));
       set(S.peaks_fit(k), 'value', peaks_fit(k));
       set(S.peak_reference_height(k), 'value', peak_reference_height(k));
       set(S.peak_to_flatten(k), 'value', peak_to_flatten(k));
       set(S.Calc_flatten_lim(k), 'value', Calc_flatten_lim(k));
       set(S.overwrite_xlim(k), 'value', overwrite_xlim(k));
       set(S.sort_peaks(k), 'value', sort_peaks(k));
    end

Contents

Set the GUI Layout

Select the Folder with Data Files

Select the Files to Process

Select Channels to Process

Process the First Image

Process All Images

Control the Vertical Display Props

Save Fitting Settings

Load Fitting Settings