DeepSqueak.m

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DeepSqueak 2.7.0                                                        %
% Copyright (c) 2021 Kevin Coffey , Ruby Marx, & Robert Ciszek         %
%                                                                         %
% Licensed under the BSD 3-Clause Licence:                                %
% https://opensource.org/licenses/BSD-3-Clause                            %
%                                                                         %
% Unless required by applicable law or agreed to in writing, software     %
% distributed under the License is distributed on an "AS IS" BASIS,       %
% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function varargout = DeepSqueak(varargin)

set(groot,'defaultFigureVisible','on');
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
    'gui_Singleton',  gui_Singleton, ...
    'gui_OpeningFcn', @DeepSqueak_OpeningFcn, ...
    'gui_OutputFcn',  @DeepSqueak_OutputFcn, ...
    'gui_LayoutFcn',  [] , ...
    'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end

% --- Executes just before DeepSqueak is made visible.
function DeepSqueak_OpeningFcn(hObject, eventdata, handles, varargin)
% Very Important Logo (Mouse from hjw)
disp '                                                                                                                                 .---.'
disp '                                                                                                                                /  .  \  '
disp '                                                                                                       ) _     _               |\_/|   |'
disp '                                                                                                      ( (^)-~-(^)              |   |   |'
disp '    ._______________________________________________________________________________________________,-.\_( 0 0 )__,-.__________|___|__,|'
disp '   /  .-.                                                                                           ''M''   \   /   ''M''                  |'
disp '  |  /   \                                                                                                 >o<                         |'
disp '  | |\_.  |                                                                                                                            |  '
disp '  |\|  | /|        ,---,                                    .--.--.                                                         ,-.        |  '
disp '  | `---'' |      .''  .'' `\                      ,-.----.   /  /    ''.   ,----.                                          ,--/ /|        |'
disp '  |       |    ,---.''     \                     \    /  \ |  :  /`. /  /   /  \-.         ,--,                        ,--. :/ |        |'
disp '  |       |    |   |  .`\  |                    |   :    |;  |  |--`  |   :    :|       ,''_ /|                        :  : '' /         |'
disp '  |       |    :   : |  ''  |   ,---.     ,---.  |   | .\ :|  :  ;_    |   | .\  .  .--. |  | :    ,---.     ,--.--.   |  ''  /          |'
disp '  |       |    |   '' ''  ;  :  /     \   /     \ .   : |: | \  \    `. .   ; |:  |,''_ /| :  . |   /     \   /       \  ''  |  :          |'
disp '  |       |    ''   | ;  .  | /    /  | /    /  ||   |  \ :  `----.   \''   .  \  ||  '' | |  . .  /    /  | .--.  .-. | |  |   \         | '
disp '  |       |    |   | :  |  ''.    '' / |.    '' / ||   : .  |  __ \  \  | \   `.   ||  | '' |  | | .    '' / |  \__\/: . . ''  : |. \        |'
disp '  |       |    ''   : | /  ; ''   ;   /|''   ;   /|:     |`-'' /  /`--''  /  `--''""| |:  | : ;  ; | ''   ;   /|  ," .--.; | |  | '' \ \       |'
disp '  |       |    |   | ''` ,/  ''   |  / |''   |  / |:   : :   ''--''.     /     |   | |''  :  `--''   \''   |  / | /  /  ,.  | ''  : |--''        |'
disp '  |       |    ;   :  .''    |   :    ||   :    ||   | :     `--''---''      |   | ::  ,      .-./|   :    |;  :   .''   \;  |,''           |'
disp '  |       |    |   ,.''       \   \  /  \   \  / `---''.|                   `---''.| `--`----''     \   \  / |  ,     .-./''--''             |'
disp '  |       |    ''---''          `----''    `----''    `---`                     `---`                `----''   `--`---''                     |'
disp '  |       |                                                                                                                            |'
disp '  \       |____________________________________________________________________________________________________________________________/'
disp '   \     /'
disp '    `---'''
disp '  '
disp '  '
disp '  '

% Set Handles
hFig = hObject;
handles.hFig=hFig;

% % Fullscreen
% warning ('off','all');
% pause(0.00001);
% frame_h = get(handle(gcf),'JavaFrame');
% set(frame_h,'Maximized',1);

% Create a class to hold the data
squeakfolder = fileparts(mfilename('fullpath'));

% Add to MATLAB path and check for toolboxes
if ~isdeployed
    % Add DeepSqueak to the path
    addpath(squeakfolder);
    addpath(genpath(fullfile(squeakfolder, 'Functions')));
    savepath
    
    %% Display error message if running on matlab before 2017b or toolboxes not found
    if verLessThan('matlab','9.9')
        errordlg(['Warning, DeepSqueak V3 requires MATLAB 20201 or later. It looks like you are use MATLAB ' version('-release')],'upgrade your matlab')
    end
    
    try
        verLessThan('nnet','1');
    catch
        warning('Deep Learning Toolbox not found')
    end
    
    try
        verLessThan('curvefit','1');
    catch
        warning('Curve Fitting Toolbox not found')
    end
    
    try
        verLessThan('vision','1');
    catch
        warning('Computer Vision System Toolbox not found')
    end
    
    try
        verLessThan('images','1');
    catch
        warning('Image Processing Toolbox not found')
    end
    
    try
        verLessThan('parallel','1');
    catch
        warning('Parallel Computing Toolbox not found')
    end
end

handles.data = squeakData(squeakfolder);

set ( hFig, 'Color', [.1 .1 .1] );
handles.output = hObject;
cd(handles.data.squeakfolder);

%% Display version
try % Read the current changelog and find the version (## number)
    fid = fopen(fullfile(handles.data.squeakfolder,'CHANGELOG.md'));
    changelog = fscanf(fid,'%c');
    fclose(fid);
    tokens = regexp(changelog, '## ([.\d])+', 'tokens');
    handles.DSVersion =  tokens{1}{:};
catch
    handles.DSVersion = '? -- can''t read CHANGELOG.md. Make sure you have the latest version!';
end
fprintf(1,'%s %s\n\n', 'DeepSqueak version', handles.DSVersion);
try % Check if a new version is avaliable by comparing changelog to whats online
    WebChangelog = webread('https://raw.githubusercontent.com/DrCoffey/DeepSqueak/master/CHANGELOG.md');
    [changes, tokens] = regexp(WebChangelog, '## ([.\d])+', 'start', 'tokens');
    WebVersion = tokens{1}{:};
    if ~strcmp(WebVersion, handles.DSVersion)
        fprintf(1,'%s\n%s\n\n%s\n',...
            'A new version of DeepSqueak is avaliable.',...
            '<a href="https://github.com/DrCoffey/DeepSqueak">Download it here!</a>',...
            WebChangelog(1:changes(2)-1))
    end
catch
    fprintf(1,'Can''t check for a updates online right now\n');
end

% set(handles.spectogramWindow,'Visible', 'off');
% set(handles.epochSpect,'Visible', 'off');
% set(handles.topRightButton, 'Visible', 'off');
% set(handles.topLeftButton, 'Visible', 'off');

if ~(exist(fullfile(handles.data.squeakfolder,'Background.png'), 'file')==2)
    disp('Background image not found')
    background = zeros(280);
    fonts = listTrueTypeFonts;
    background = insertText(background,[10 8],'DeepSqueak','Font',char(datasample(fonts,1)),'FontSize',30);
    background = insertText(background,[10 80],'DeepSqueak','Font',char(datasample(fonts,1)),'FontSize',30);
    background = insertText(background,[10 150],'DeepSqueak','Font',char(datasample(fonts,1)),'FontSize',30);
    background = insertText(background,[10 220],'DeepSqueak','Font',char(datasample(fonts,1)),'FontSize',30);
    handles.background = background;
else
    handles.background=imread('Background.png');
end
if ~(exist(fullfile(handles.data.squeakfolder,'DeepSqueak.fig'), 'file')==2)
    errordlg('"DeepSqueak.fig" not found');
end


% Cool Background Image
imshow(handles.background, 'Parent', handles.focusWindow);
set(handles.focusWindow,'Color',[0.1 0.1 0.1],'YColor',[1 1 1],'XColor',[1 1 1]);
set(handles.focusWindow,'XTick',[]);
set(handles.focusWindow,'YTick',[]);
update_folders(hObject, eventdata, handles);
handles = guidata(hObject);  % Get newest version of handles

% Set the sliders to the saved values
% set(handles.TonalitySlider, 'Value', handles.data.settings.EntropyThreshold);

% Set the page and focus window dropdown boxes to the values defined in
% squeakData, and set the current value to the one closest to the save value.
handles.epochWindowSizePopup.String = compose('%gs', handles.data.pageSizes);
[~, handles.epochWindowSizePopup.Value] =  min(abs(handles.data.pageSizes - handles.data.settings.pageSize));
handles.focusWindowSizePopup.String = compose('%gs', handles.data.focusSizes);
[~, handles.focusWindowSizePopup.Value] =  min(abs(handles.data.focusSizes - handles.data.settings.focus_window_size));
    
guidata(hObject, handles);

set(handles.contourWindow,'Color',[0.1 0.1 0.1],'YColor',[1 1 1],'XColor',[1 1 1],'Box','off','Clim',[0,1]);
set(handles.contourWindow,'XTickLabel',[]);
set(handles.contourWindow,'XTick',[]);
set(handles.contourWindow,'YTick',[]);

set(handles.waveformWindow,'Color',[0.1 0.1 0.1],'YColor',[1 1 1],'XColor',[1 1 1],'Box','off','Clim',[0,1]);
set(handles.waveformWindow,'XTickLabel',[]);
set(handles.waveformWindow,'XTick',[]);
set(handles.waveformWindow,'YTick',[]);

C = spatialPattern([1000,10000],-2);
imagesc(C(1:900,1:10000),'Parent', handles.spectogramWindow);
colormap(handles.spectogramWindow,inferno);
set(handles.spectogramWindow,'Color',[0.1 0.1 0.1],'YColor',[1 1 1],'XColor',[1 1 1]);
set(handles.spectogramWindow,'XTickLabel',[]);
set(handles.spectogramWindow,'XTick',[]);
set(handles.spectogramWindow,'YTick',[]);

% imagesc(C(900:1000,1:10000),'Parent', handles.detectionAxes);
% colormap(handles.detectionAxes,inferno);
set(handles.detectionAxes,'Color',[64/255 10/255 103/255],'YColor',[1 1 1],'XColor',[1 1 1]);
set(handles.detectionAxes,'XTickLabel',[]);
set(handles.detectionAxes,'XTick',[]);
set(handles.detectionAxes,'YTick',[]);
set(handles.spectogramWindow,'Parent',handles.hFig);


% Set the list of colormaps
handles.popupmenuColorMap.String = {
    'inferno'
    'magma'
    'plasma'
    'viridis'
    'cubehelix'
    'gray'
    'jet'
    'turbo'
    'hot'
    'parula'
    'hsv'
    'cool'
    'spring'
    'summer'
    'autumn'
    'winter'
    'bone'
    'copper'
    'pink'};


function varargout = DeepSqueak_OutputFcn(hObject, eventdata, handles)
shg;
varargout{1} = handles.output;

% --- Executes on button press in PlayCall.
function PlayCall_Callback(hObject, eventdata, handles)
% Play the sound within the boxs
audio = handles.data.AudioSamples(...
    handles.data.calls.Box(handles.data.currentcall, 1),...
    handles.data.calls.Box(handles.data.currentcall, 1) + handles.data.calls.Box(handles.data.currentcall, 3));
playbackRate = handles.data.audiodata.SampleRate * handles.data.settings.playback_rate; % set playback rate
audio = resample(audio, 192000, playbackRate);
audio = audio - mean(audio);
% Use a window funtion to smooth the beginning and end to remove clicks
w = hamming(2000);
audio(1:1000) = audio(1:1000) .* w(1:1000);
audio(end-999:end) = audio(end-999:end) .* w(1001:2000);
% Bandpass Filter
% audio = bandpass(audio,[handles.data.calls.Box(handles.data.currentcall, 2), handles.data.calls.Box(handles.data.currentcall, 2) + handles.data.calls.Box(handles.data.currentcall, 4)] * 1000,handles.data.audiodata.SampleRate);
soundsc(audio,192000);


% --- Executes on button press in NextCall.
function NextCall_Callback(hObject, eventdata, handles)
if handles.data.currentcall < height(handles.data.calls) % If not the last call
    handles.data.currentcall=handles.data.currentcall+1;
    handles.data.focusCenter = handles.data.calls.Box(handles.data.currentcall,1) + handles.data.calls.Box(handles.data.currentcall,3)/2;
end
handles.data.current_call_valid = true;
update_fig(hObject, eventdata, handles);


% --- Executes on button press in PreviousCall.
function PreviousCall_Callback(hObject, eventdata, handles)
if handles.data.currentcall > 1 % If not the first call
    handles.data.currentcall=handles.data.currentcall-1;
    handles.data.focusCenter = handles.data.calls.Box(handles.data.currentcall,1) + handles.data.calls.Box(handles.data.currentcall,3)/2;
end
handles.data.current_call_valid = true;
update_fig(hObject, eventdata, handles);


% --- Executes on selection change in Networks Folder Pop up.
function neuralnetworkspopup_Callback(hObject, eventdata, handles)
guidata(hObject, handles);

% --- Executes during Networks Folder Pop up.
function neuralnetworkspopup_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on selection change in Audio Folder Pop up.
function AudioFilespopup_Callback(hObject, eventdata, handles)
guidata(hObject, handles);

% --- Executes during Audio Folder Pop up.
function AudioFilespopup_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on selection change in Detection Folder Pop up.
function popupmenuDetectionFiles_Callback(hObject, eventdata, handles)
guidata(hObject, handles);

% --- Executes during Detection Folder Pop up.
function popupmenuDetectionFiles_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on button press in AcceptCall.
function AcceptCall_Callback(hObject, eventdata, handles)
handles.data.calls.Accept(handles.data.currentcall) = true;
handles.update_position_axes = 1;
NextCall_Callback(hObject, eventdata, handles)

% --- Executes on button press in RejectCall.
function RejectCall_Callback(hObject, eventdata, handles)
handles.data.calls.Accept(handles.data.currentcall) = false;
handles.update_position_axes = 1;
NextCall_Callback(hObject, eventdata, handles)

% --- Executes during MAIN AXES CREATION
function focusWindow_CreateFcn(hObject, eventdata, handles)

function slide_focus(focus_offset, hObject, eventdata, handles)
% Move the focus window one unit over
new_position = handles.data.focusCenter + focus_offset;
new_position = min(new_position, handles.data.audiodata.Duration - handles.data.settings.focus_window_size ./ 2);
new_position = max(new_position, handles.data.settings.focus_window_size ./ 2);
handles.data.focusCenter = new_position;

if new_position > handles.data.windowposition + handles.data.settings.pageSize
    forwardButton_Callback(hObject, eventdata, handles);
elseif new_position < handles.data.windowposition
    backwardButton_Callback(hObject, eventdata, handles);
else
    calls_within_window = find(...
        handles.data.calls.Box(:,1) > new_position - handles.data.settings.focus_window_size/2 & ...
        handles.data.calls.Box(:,1) < new_position + handles.data.settings.focus_window_size/2 | ...
        sum(handles.data.calls.Box(:,[1,3]),2) > new_position - handles.data.settings.focus_window_size/2 &...
        sum(handles.data.calls.Box(:,[1,3]),2) < new_position + handles.data.settings.focus_window_size/2);
    if ~isempty(calls_within_window)
        handles.data.currentcall = calls_within_window(1);
        
        handles.data.current_call_valid = true;
    end
    
    guidata(hObject,handles);
    update_fig(hObject, eventdata, handles);
end

function score_Callback(hObject, eventdata, handles)

% --- Executes during object creation, after setting all properties.
function score_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function status_Callback(hObject, eventdata, handles)

% --- Executes during object creation, after setting all properties.
function status_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on key press with focus on figure1 or any of its controls.
function figure1_WindowKeyPressFcn(hObject, eventdata, handles)
%disp(eventdata);
switch eventdata.Character
    case 'p'
        PlayCall_Callback(hObject, eventdata, handles)
    case {'e', 29} % char(29) is right arrow key
        NextCall_Callback(hObject, eventdata, handles)
    case {'q', 28} % char(28) is left arrow key
        PreviousCall_Callback(hObject, eventdata, handles)
    case 'a'
        AcceptCall_Callback(hObject, eventdata, handles)
    case 'r'
        RejectCall_Callback(hObject, eventdata, handles)
    case 'd'
        rectangle_Callback(hObject, eventdata, handles)
    case 127 % Delete key
        handles.data.calls(handles.data.currentcall,:) = [];
        SortCalls(hObject, [], handles, 'time', 0, handles.data.currentcall - 1);
    case 30 % char(30) is up arrow key
        slide_focus(+ handles.data.settings.focus_window_size, hObject, eventdata, handles)
    case 31 % char(31) is down arrow key
        slide_focus(- handles.data.settings.focus_window_size, hObject, eventdata, handles)
    case 32 % 'space'
        forwardButton_Callback(hObject, eventdata, handles);
    case handles.data.labelShortcuts
        %% Update the call labels
        % Index of the shortcut
        idx = contains(handles.data.labelShortcuts, eventdata.Character);
        handles.data.calls.Type(handles.data.currentcall) = categorical(handles.data.settings.labels(idx));
        update_fig(hObject, eventdata, handles);
end
% drawnow

function figure1_KeyPressFcn(hObject, eventdata, handles)

% --- Executes during object creation, after setting all properties.
function popupmenuColorMap_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes during object creation, after setting all properties.
function freq_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on button press in rectangle.
function rectangle_Callback(hObject, eventdata, handles)
current_box = drawrectangle( 'Parent',handles.focusWindow,...
                            'FaceAlpha',0,...
                            'LineWidth',1 );
% Don't do anything if the new box is empty  
if current_box.Position(3) == 0 || current_box.Position(4) == 4
    delete(current_box)
    return
end
new_box = table();
new_box.Box = current_box.Position;
new_box.Score = 1;
new_box.Type = categorical({'USV'});
new_box.Accept = true;
handles.data.calls = [handles.data.calls; new_box];

%Now delete the roi and render the figure. The roi will be rendered along
%with the existing boxes.
handles.data.current_call_valid = true;
SortCalls(hObject, eventdata, handles, 'time', 0, -1);
delete(current_box)

% --------------------------------------------------------------------
function select_audio_Callback(hObject, eventdata, handles)
% Find audio in folder
path=uigetdir(handles.data.settings.audiofolder,'Select Audio File Folder');
if isnumeric(path);return;end
handles.data.settings.audiofolder = path;
handles.data.saveSettings();
update_folders(hObject, eventdata, handles);

% --------------------------------------------------------------------
function load_networks_Callback(hObject, eventdata, handles)
% Find networks
path=uigetdir(handles.data.settings.networkfolder,'Select Network Folder');
if isnumeric(path);return;end
handles.data.settings.networkfolder = path;
handles.data.saveSettings();
update_folders(hObject, eventdata, handles);

function load_detectionFolder_Callback(hObject, eventdata, handles)
% Find audio in folder
path=uigetdir(handles.data.settings.detectionfolder,'Select Detection File Folder');
if isnumeric(path);return;end
handles.data.settings.detectionfolder = path;
handles.data.saveSettings();
update_folders(hObject, eventdata, handles);

% --------------------------------------------------------------------
function folders_Callback(hObject, eventdata, handles)

% --------------------------------------------------------------------
function export_raven_Callback(hObject, eventdata, handles)
% Export current file as a txt file for viewing in Raven
% http://www.birds.cornell.edu/brp/raven/RavenOverview.html
raventable = [{'Selection'} {'View'} {'Channel'} {'Begin Time (s)'} {'End Time (s)'} {'Low Freq (Hz)'} {'High Freq (Hz)'} {'Delta Time (s)'} {'Delta Freq (Hz)'} {'Avg Power Density (dB FS)'} {'Annotation'} {'Begin Path'} {'File Offset'}];
View = 'Spectrogram 1';
Channel = 1;
for i = 1:height(handles.data.calls)
    if handles.data.calls.Accept(i)
        Selection = i;
        BeginTime = handles.data.calls.Box(i, 1);
        EndTime = sum(handles.data.calls.Box(i ,[1, 3]));
        LowFreq = handles.data.calls.Box(i, 2) * 1000;
        HighFreq = sum(handles.data.calls.Box(i, [2, 4])) * 1000;
        DeltaTime = EndTime - BeginTime;
        DeltaFreq = HighFreq - LowFreq;
        AvgPwr = 1;
        Annotation = handles.data.calls.Accept(i);
        BeginPath = handles.data.audiodata.Filename;
        FileOffset = handles.data.calls.Box(i, 1);
        raventable = [raventable; {Selection} {View} {Channel} {BeginTime} {EndTime} {LowFreq} {HighFreq} {DeltaTime} {DeltaFreq} {AvgPwr} {Annotation} {BeginPath} {FileOffset}];
    end
end
a  = cell2table(raventable);
handles.current_file_id = get(handles.popupmenuDetectionFiles,'Value');
current_detection_file = handles.detectionfiles(handles.current_file_id).name;
ravenname=[strtok(current_detection_file,'.') '_Raven.txt'];
[FileName,PathName] = uiputfile(ravenname,'Save Raven Truth Table (.txt)');
writetable(a,[PathName FileName],'delimiter','\t','WriteVariableNames',false);
guidata(hObject, handles);

% --------------------------------------------------------------------
function export_Callback(hObject, eventdata, handles)

function training_Callback(hObject, eventdata, handles)

% --------------------------------------------------------------------
function customlabels_Callback(hObject, eventdata, handles)
% Define call categories
prompt = {
    'Label 1  --- Key 1'
    'Label 2  --- Key 2'
    'Label 3  --- Key 3'
    'Label 4  --- Key 4'
    'Label 5  --- Key 5'
    'Label 6  --- Key 6'
    'Label 7  --- Key 7'
    'Label 8  --- Key 8'
    'Label 9  --- Key 9'
    'Label 10  --- Key 0'
    'Label 11  --- Key -'
    'Label 12  --- Key ='
    'Label 13  --- Key !'
    'Label 14  --- Key @'
    'Label 15  --- Key #'   
    'Label 16  --- Key $'   
    'Label 17  --- Key %'
    'Label 18  --- Key ^'    
    'Label 19  --- Key &'
    'Label 20  --- Key *'
    'Label 21  --- Key ('
    'Label 22  --- Key )'
    'Label 23  --- Key _'
    'Label 24  --- Key +'    
    };

dlg_title = 'Set Custom Label Names';
num_lines=[1,60]; options.Resize='off'; options.WindowStyle='modal'; options.Interpreter='none';
old_labels = handles.data.settings.labels;
new_labels = inputdlgcol(prompt,dlg_title,num_lines,old_labels,options,3);
if ~isempty(new_labels)
    handles.data.settings.labels = new_labels;
    handles.data.saveSettings();
    update_folders(hObject, eventdata, handles);
end
guidata(hObject, handles);

% --------------------------------------------------------------------
function Change_Playback_Rate_Callback(hObject, eventdata, handles)
prompt = {'Playback Rate: (default = 0.0.5)'};
dlg_title = 'Change Playback Rate';
num_lines=1; options.Resize='off'; options.WindowStyle='modal'; options.Interpreter='tex';
defaultans = {num2str(handles.data.settings.playback_rate)};
rate = inputdlg(prompt,dlg_title,num_lines,defaultans);
if isempty(rate); return; end

[newrate,~,errmsg] = sscanf(rate{1},'%f',1);
disp(errmsg);
if ~isempty(newrate)
    handles.data.settings.playback_rate = newrate;
    handles.data.saveSettings();
    update_folders(hObject, eventdata, handles);
end
guidata(hObject, handles);


% --------------------------------------------------------------------
function Help_Callback(hObject, eventdata, handles)

% --------------------------------------------------------------------
function Untitled_3_Callback(hObject, eventdata, handles)

% --------------------------------------------------------------------
function CallClassification_Callback(hObject, eventdata, handles)

% --------------------------------------------------------------------
function ChangeContourThreshold_Callback(hObject, eventdata, handles)
% Change the contour threshold
prompt = {'Entropy Threshold: (range = 0-1, default = 0.215)', 'Amplitude Percentile Threshold: (range = 0-1, default = 0.825)'};
dlg_title = 'New Contour Threshold:';
num_lines=[1 50]; options.Resize='off'; options.WindowStyle='modal'; options.Interpreter='tex';
defaultans = {num2str(handles.data.settings.EntropyThreshold),num2str(handles.data.settings.AmplitudeThreshold)};
threshold = inputdlg(prompt,dlg_title,num_lines,defaultans);
if isempty(threshold); return; end

[EntropyThreshold,~,errmsg] = sscanf(threshold{1},'%f',1);
disp(errmsg);
[AmplitudeThreshold,~,errmsg] = sscanf(threshold{2},'%f',1);
disp(errmsg);

if ~isempty(EntropyThreshold) && ~isempty(AmplitudeThreshold)

    if AmplitudeThreshold < .001 || AmplitudeThreshold > .999
        disp('Warning! Amplitude Percentile Threshold Must be (0 > 1), Reverting to Default (.825)');
        AmplitudeThreshold = handles.data.defaultSettings.AmplitudeThreshold;
    end
    if EntropyThreshold < .001 || EntropyThreshold > .999
        disp('Warning! Entropy Threshold Must be (0 > 1), Reverting to Default (.215)');
        EntropyThreshold = handles.data.defaultSettings.EntropyThreshold;
    end

    handles.data.settings.EntropyThreshold = EntropyThreshold;
    handles.data.settings.AmplitudeThreshold = AmplitudeThreshold;
    handles.data.saveSettings();
    update_folders(hObject, eventdata, handles);
    try
        update_fig(hObject, eventdata, handles);
    catch
        disp('Could not update figure. Is a call loaded?')
    end
end
guidata(hObject, handles);

% --------------------------------------------------------------------
function ViewManual_Callback(hObject, eventdata, handles)
web('https://github.com/DrCoffey/DeepSqueak/wiki','-browser');

% --------------------------------------------------------------------
function AboutDeepSqueak_Callback(hObject, eventdata, handles)
title = 'About DeepSqueak';

d = dialog('Position',[300 350 500  600],'Name',title,'WindowStyle','Normal','Visible', 'off','Color', [0,0,0]);
movegui(d,'center');
ha = axes(d,'Units','Normalized','Position',[0,0,1,1]);

A = zeros(128);
A = insertText(A,[64,20],'Coffey & Marx, 2019','TextColor','white','BoxColor','Black','AnchorPoint','Center','FontSize',11);
A = insertText(A,[64,64],'DeepSqueak','TextColor','white','BoxColor','Black','AnchorPoint','Center');
A = insertText(A,[64,80],['Version ' handles.DSVersion],'TextColor','white','BoxColor','Black','AnchorPoint','Center','FontSize',11);

A = A(:,:,1);

P = [64, 64];
D = 3;
T = [1,0,-1,0;0,1,0,-1];	% 4 directions
k = 0;

handle_image = imshow(A,[0,1],'parent',ha);

btn = uicontrol('Parent',d,...
    'Units','Normalized',...
    'Position',[.42 .01 .16 .06],...
    'String','Okay',...
    'Callback','delete(gcf)');
set(d,'Visible','on')

while isvalid(handle_image)
    k = k+1;
    a = A(P(1),P(2));
    A(P(1),P(2)) = ~a;
    if ( a )
        D = mod(D+1,4);
    else
        D = mod(D-1,4);
    end
    P = P+T(:,D+1);
    handle_image.CData = A;
    pause(.01)
end

% --- Executes on slider movement.
function TonalitySlider_Callback(hObject, eventdata, handles)
handles.data.settings.EntropyThreshold=(get(hObject,'Value'));
handles.data.saveSettings();
update_fig(hObject, eventdata, handles);

% --- Executes during object creation, after setting all properties.
function TonalitySlider_CreateFcn(hObject, eventdata, handles)
% hObject    handle to TonalitySlider (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

% --------------------------------------------------------------------
function submit_a_bug_Callback(hObject, eventdata, handles)
% hObject    handle to submit_a_bug (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
web('https://github.com/UEFepilepsyAIVI/DeepSqueak/issues','-browser');

% --- Executes on slider movement.
function optimization_slider_Callback(hObject, eventdata, handles)
hObject.Value = round(hObject.Value);

% --- Executes on button press in backwardButton.
function backwardButton_Callback(hObject, eventdata, handles)
% handles.data.windowposition = max(0, handles.data.windowposition - handles.data.settings.pageSize);
handles.data.focusCenter = max(0, handles.data.windowposition - handles.data.settings.focus_window_size ./ 2);
% get_closest_call_to_focus(hObject, eventdata, handles);

jumps = floor(handles.data.focusCenter / handles.data.settings.pageSize);
handles.data.windowposition = jumps*handles.data.settings.pageSize;

calls_within_window = find(handles.data.calls.Box(:,1) < handles.data.windowposition + handles.data.settings.pageSize, 1, 'last');
if ~isempty(calls_within_window)
    handles.data.currentcall = calls_within_window;
    handles.data.current_call_valid = true;
end

update_fig(hObject, eventdata, handles);


% --- Executes on button press in forwardButton.
function forwardButton_Callback(hObject, eventdata, handles)
% handles.data.windowposition = min(handles.data.audiodata.Duration - handles.data.settings.pageSize, handles.data.windowposition + handles.data.settings.pageSize);
handles.data.focusCenter = handles.data.windowposition + handles.data.settings.pageSize + handles.data.settings.focus_window_size ./ 2;
handles.data.focusCenter = min(handles.data.focusCenter, handles.data.audiodata.Duration - handles.data.settings.focus_window_size ./ 2);

jumps = floor(handles.data.focusCenter / handles.data.settings.pageSize);
handles.data.windowposition = jumps*handles.data.settings.pageSize;

% handles.data.focusCenter = max(0, handles.data.windowposition - handles.data.settings.focus_window_size ./ 2);
% get_closest_call_to_focus(hObject, eventdata, handles);

calls_within_window = find(handles.data.calls.Box(:,1) > handles.data.windowposition, 1);
if ~isempty(calls_within_window)
    handles.data.currentcall = calls_within_window;
    handles.data.current_call_valid = true;
end

update_fig(hObject, eventdata, handles);
% guidata(hObject, handles);

function get_closest_call_to_focus(hObject, eventdata, handles)
calls_within_window = find(...
    handles.data.calls.Box(:,1) > handles.data.windowposition &...
    sum(handles.data.calls.Box(:,[1,3]),2) < handles.data.windowposition + handles.data.settings.pageSize);
if ~isempty(calls_within_window)
    callMidpoints = handles.data.calls.Box(calls_within_window,1) + handles.data.calls.Box(calls_within_window,3)/2;
    [~, closestCall] = min(abs(callMidpoints - handles.data.focusCenter));
    handles.data.currentcall = calls_within_window(closestCall);
    handles.data.current_call_valid = true;
end
update_fig(hObject, eventdata, handles);

% --- Executes during object creation, after setting all properties.
function epochWindowSizePopup_CreateFcn(hObject, eventdata, handles)
% hObject    handle to epochWindowSizePopup (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
padding = cellstr(get(hObject,'String')); 
seconds = regexp(padding{get(hObject,'Value')},'([\d*.])*','match');
seconds = str2num(seconds{1});
handles.data.settings.pageSize = seconds;
guidata(hObject, handles);

% --- Executes on selection change in spectogramScalePopup.
function spectogramScalePopup_Callback(hObject, eventdata, handles)
% hObject    handle to spectogramScalePopup (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns spectogramScalePopup contents as cell array
%        contents{get(hObject,'Value')} returns selected item from spectogramScalePopup
update_fig(hObject, [], handles);

% --- Executes during object creation, after setting all properties.
function spectogramScalePopup_CreateFcn(hObject, eventdata, handles)
% hObject    handle to spectogramScalePopup (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

function SpectogramMax_Callback(hObject, eventdata, handles)
% hObject    handle to SpectogramMax (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
    set(hObject, 'String', num2str(get_spectogram_max(hObject, handles))); 
    guidata(hObject,handles);
    update_fig(hObject, [], handles);

% --- Executes during object creation, after setting all properties.
function SpectogramMax_CreateFcn(hObject, eventdata, handles)
% hObject    handle to SpectogramMax (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes during object creation, after setting all properties.
function focusWindowSizePopup_CreateFcn(hObject, eventdata, handles)
% hObject    handle to focusWindowSizePopup (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

padding = cellstr(get(hObject,'String')); 
seconds = regexp(padding{get(hObject,'Value')},'([\d*.])*','match');
seconds = str2double(seconds{1});
handles.data.settings.focus_window_size = seconds;
guidata(hObject, handles);

% --- Executes on button press in topLeftButton.
function topLeftButton_Callback(hObject, eventdata, handles)
% hObject    handle to topLeftButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
    slide_focus(handles.data.settings.focus_window_size*(-1), hObject, eventdata, handles)

% --- Executes on button press in topRightButton.
function topRightButton_Callback(hObject, eventdata, handles)
% hObject    handle to topRightButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
    slide_focus(handles.data.settings.focus_window_size*(1), hObject, eventdata, handles)

% --- Executes on button press in loadAudioFile.
function loadAudioFile_Callback(hObject, eventdata, handles)
h = waitbar(0,'Loading Audio Please wait...');
update_folders(hObject, eventdata, handles);
handles = guidata(hObject);

if nargin == 3 % if "Load Calls" button pressed
    if isempty(handles.audiofiles)
        close(h);
        errordlg(['No valid audio files in current audio folder. Select a folder containing audio with '...
            '"File -> Select Audio Folder", then choose the desired file in the "Audio Files" dropdown box.'])
        return
    end
    handles.current_file_id = get(handles.AudioFilespopup,'Value');
    handles.current_audio_file = handles.audiofiles(handles.current_file_id).name;
end

handles.data.audiodata = audioinfo(fullfile(handles.data.settings.audiofolder,handles.current_audio_file));

Calls = table(zeros(0,4),[],[],[], 'VariableNames', {'Box', 'Score', 'Type', 'Accept'});
% Calls.Box = [0 0 1 1];
% Calls.Score = 0;
% Calls.Type = categorical({'NA'});
% Calls.Power = 1;
% Calls.Accept = false;
handles.data.calls = Calls;
% Position of the focus window
handles.data.focusCenter = handles.data.settings.focus_window_size ./ 2;
initialize_display(hObject, eventdata, handles);
close(h);

% --- Executes during object creation, after setting all properties.
function detectionAxes_CreateFcn(hObject, eventdata, handles)
% hObject    handle to detectionAxes (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% --------------------------------------------------------------------
function contributorToolsMenu_Callback(hObject, eventdata, handles)
web('https://gitter.im/DeepSqueak_Community/General')

% --------------------------------------------------------------------
function Untitled_2_Callback(hObject, eventdata, handles)
% hObject    handle to Untitled_2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% --- Executes on button press in invert_cmap.
function invert_cmap_Callback(hObject, eventdata, handles)
colormap(handles.spectogramWindow, flipud(colormap(handles.spectogramWindow)))
colormap(handles.focusWindow, flipud(colormap(handles.focusWindow)))

% --- Executes during object creation, after setting all properties.
function waveformWindow_CreateFcn(hObject, eventdata, handles)
% hObject    handle to waveformWindow (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: place code in OpeningFcn to populate waveformWindow


% --------------------------------------------------------------------
function Keyboard_Shortcuts_Callback(hObject, eventdata, handles)
% Display a list of keyboard shortcuts
Keyboard_Shortcuts = [
    "Save file", "ctrl + s"
    "Next call", "e, right arrow"
    "Previous call", "q, left arrow"
    "Accept call", "a"
    "Reject call", "r"
    "Delete call", "delete, right click"
    "Redraw box", "d"
    "Play call audio", "p"
    "Set call label", "See ""Add Custom Labels"", double click"
    "Slide foucs forward", "up arrow"
    "Slide foucs back", "down arrow"
    "Next page", "space"
    ];
CreateStruct.Interpreter = 'tex';
CreateStruct.WindowStyle = 'modal';
msgbox(['\fontname{Courier}\fontsize{12}' sprintf('%-20s |   %s\n', Keyboard_Shortcuts')], 'Keyboard Shortcuts', CreateStruct)