% browseLISST - display a LISST file
%
% browseLISST('file',filename) opens the file given by filename for browsing
%

% Written by Marinna Martini for the U.S. Geological Survey 
% Coastal & Marine Program Woods Hole Field Center, Woods Hole, MA
% http://woodshole.er.usgs.gov/ Please report bugs to mmartini@usgs.gov

% Last Modified by GUIDE v2.5 21-Jul-2008 13:31:13

function varargout = browseLISST(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @browseLISST_OpeningFcn, ...
                   'gui_OutputFcn',  @browseLISST_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
% End initialization code - DO NOT EDIT


% --- Executes just before browseLISST is made visible.
function browseLISST_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to browseLISST (see VARARGIN)

% Choose default command line output for browseLISST
handles.output = hObject;
%    figure1: 1.000034179687500e+002
%     sliderColorMin: 1.060206298828125e+002
%       axes1: 1.010040283203125e+002
%      output: 1.000034179687500e+002
% slider 1 controls color min
% slider 2 controls which ??
% slider 3 controls color max

% look for a filename in the varargin
handles.mydata.lisstfile = [];
for i = 1:length(varargin),
    if strcmpi(varargin{i},'file'), handles.mydata.lisstfile = varargin{i+1}; end
end
if isempty(handles.mydata.lisstfile),
    [filename, pathname] = uigetfile({'*.cdf; *.nc','netCDF files'},'Select a netCDF file containing LISST data');
    if ~filename, return; end
    handles.mydata.lisstfile = fullfile(pathname, filename);
end

% open the netCDF file and do the basic checks
cdf = netcdf(handles.mydata.lisstfile); % for passing to other methods
handles.mydata.cdf = cdf;
set(handles.figure1,'UserData',cdf); % store the netCDF file pointer here so I can close it later
set(handles.figure1,'DeleteFcn','if ~isempty(get(gcf,''UserData'')), close(get(gcf,''UserData'')); end'); % and this is the code that will close it

if isempty(cdf), disp(['Unable to open netCDF file ',handles.mydata.lisstfile]); return; end
dimnames = ncnames(dim(cdf));
flag = 0;
for i=1:length(dimnames), % make sure this is a LISST data file
    if strcmp(dimnames{i},'size') || strcmp(dimnames{i},'rings'), flag = 1; end
end
if ~flag, disp('This is not a LISST file'); close(cdf); return; end

% dimensioning and indexing setup
% the size class / ring dimension
handles.mydata.nrings = length(cdf('rings'));
if isempty(handles.mydata.nrings) || (handles.mydata.nrings < 1),
    handles.mydata.nrings = length(cdf('size'));
end
for n=1:handles.mydata.nrings, handles.mydata.lstrings{n} = sprintf('%d',n); end
handles.mydata.rings = [1 handles.mydata.nrings];
handles.mydata.iring = 1; 
% the time dimension (the burst start)
handles.mydata.nbursts = length(cdf('time'));
if isempty(handles.mydata.nbursts) || (handles.mydata.nbursts < 1),
    handles.mydata.nbursts = length(cdf('burst'));
end
if isempty(handles.mydata.nbursts) || (handles.mydata.nbursts < 1),
    handles.mydata.nbursts = length(cdf('TIM'));
end
handles.mydata.burstNum = 1:handles.mydata.nbursts; % need these for a lookup table
disp('Reading in time stamps....')
tj = cdf{'time'}(:);
if ~isempty(tj),
    tj = tj+cdf{'time2'}(:)./(24*3600*1000);
else
    tj = cdf{'TIM'}(:);
end
handles.mydata.tm = datenum(gregorian(tj));

set(handles.textFileName,'string',sprintf('Now browsing file %s',handles.mydata.lisstfile))

n=1;
varnames = ncnames(var(cdf));
for i=1:length(varnames), % remove burstnum and time
    if strcmp(varnames{i},'depth') ||...
            strcmp(varnames{i},'lat') || strcmp(varnames{i},'lon') ||...
            strcmp(varnames{i},'time') || strcmp(varnames{i},'time2') ||...
            strcmp(varnames{i},'size') || strcmp(varnames{i},'rings') ||...
            strcmp(varnames{i},'zscat') || strcmp(varnames{i},'rec'),
        % do nothing
    else
        handles.mydata.varnames{n} = varnames{i}; 
        n=n+1;
    end
end
handles.mydata.vartoplot = handles.mydata.varnames{1};
handles.mydata.newvar = 1; % when a new variable is selected 

% slider 1 - min color axis
handles.mydata.ccmin = 1e-35;
handles.mydata.ccmax = 0.0001;
set(handles.textColorMinMin,'string',sprintf('%g',handles.mydata.ccmin));
set(handles.textColorMinMax,'string',sprintf('%g',handles.mydata.ccmax));
% slider 1 limits -- maybe change the view zoom for the number of samples
set(handles.sliderColorMin,'Value',handles.mydata.ccmin,'Min',handles.mydata.ccmin,...
    'Max',handles.mydata.ccmax,'SliderStep',[0.01 0.1]);
set(handles.sliderColorMin,'Tooltipstring','Set the minimum of the color axis')
% slider 3 - max color limit range selector - labels
set(handles.textColorMaxMin,'string',sprintf('%g',handles.mydata.ccmin));
set(handles.textColorMaxMax,'string',sprintf('%g',handles.mydata.ccmax));
set(handles.sliderColorMax,'Value',handles.mydata.ccmin,'Min',handles.mydata.ccmin,...
    'Max',handles.mydata.ccmax,'SliderStep',[0.01 0.1]);
set(handles.sliderColorMax,'Tooltipstring','Select the maximum of the color axis')

% put varnames into listbox here
set(handles.listboxVar2Plot,'string',handles.mydata.varnames,'Value',1);
set(handles.listboxVar2Plot,'Tooltipstring','Select data to display')

% put colormap names into listbox here
handles.mydata.colormaps = {'default','jet','HSV','hot','cool','spring','summer','autumn',...
    'winter','gray','bone','copper','pink','lines'};
handles.mydata.ccolormap = 'default'; % current color map
set(handles.listboxColorMap,'string',handles.mydata.colormaps,'Value',1);
set(handles.listboxColorMap,'Tooltipstring','Select colormap')

% set contents of first and last bin
set(handles.editFirstBin,'String',sprintf('%d',handles.mydata.rings(1)));
set(handles.editFirstBin,'Tooltipstring','enter the first cell to plot')
set(handles.editLastBin,'String',sprintf('%d',handles.mydata.rings(2)));
set(handles.editLastBin,'Tooltipstring','enter the last cell to plot')

% Update handles structure
guidata(hObject, handles);

% This sets up the initial plot - only do when we are invisible
% so window can get raised using example.
if strcmp(get(hObject,'Visible'),'off')
    updateplot(hObject, handles)
end

% UIWAIT makes browseLISST wait for user response (see UIRESUME)
% uiwait(handles.figure1);

%% ------------------ updates the plot - this is a user function
function updateplot(hObject, handles) 
cdf = handles.mydata.cdf;
vartoplot = handles.mydata.vartoplot; % this will be the selection
axes(handles.axes1);
cla;

% two D variables
if strcmp(vartoplot,'vconc') || strcmp(vartoplot,'intensity'),
    % time, ring, lat, lon
    data = cdf{vartoplot}(:, handles.mydata.rings(1):handles.mydata.rings(2), :, :);
    ndims = 2;
    if strcmp(vartoplot,'vconc'),
        rings = cdf{'size'}(handles.mydata.rings(1):handles.mydata.rings(2));
    elseif strcmp(vartoplot,'intensity'),
        rings = cdf{'rings'}(handles.mydata.rings(1):handles.mydata.rings(2));
    end
elseif strcmp(vartoplot,'field_zscat') || strcmp(vartoplot,'factory_zscat') ||...
        strcmp(vartoplot,'ring_data'),
    data = cdf{vartoplot}(:);
    ndims = 0;
else % time, depth, lat, lon
    data = cdf{vartoplot}(:, :, :, :);
    ndims = 1;
end

    
if ndims == 2,
    if handles.mydata.newvar,
        dmin = gmin(gmin(data)');
        dmax = gmax(gmax(data)');
        dmed = gmedian(gmedian(data)');
        dmean = gmean(gmean(data)');
        dstd = gstd(gstd(data)');
        sstep = (dmax-dmin)/10000;
        lstep = (dmax-dmin)/1000;
        smin = dmin;
        if strcmp(vartoplot,'vconc'),
            smax = dmed+10*dstd;
        elseif strcmp(vartoplot,'intensity'),
            smax = dmax;
        end
        set(handles.textDataLims,'string',sprintf('Data values range from %7g to %7g', dmin,dmax));
        % reset the slider for the data for new variable limits
        set(handles.textColorMinMin,'string',sprintf('%7g',smin));
        set(handles.textColorMinMax,'string',sprintf('%7g',smax));
        set(handles.sliderColorMin,'Value',smin,'Min',smin,...
            'Max',smax,'SliderStep',[0.01 0.1]); %[0.0001 0.001]);
        set(handles.textColorMaxMin,'string',sprintf('%7g',smin));
        set(handles.textColorMaxMax,'string',sprintf('%7g',smax));
        set(handles.sliderColorMax,'Value',smax,'Min',smin,...
            'Max',smax,'SliderStep',[0.01 0.1]); %,[0.0001 0.001]);
        set(handles.editColorMinValue,'string',sprintf('%7g',smin));
        set(handles.editColorMaxValue,'string',sprintf('%7g',smax));
        handles.mydata.ccmin = smin;
        handles.mydata.ccmax = smax;
        %clims = [smin smax];
    end


    if isnan(handles.mydata.ccmin) || isnan(handles.mydata.ccmax),
        clims = [handles.mydata.cmin handles.mydata.cmax];
        disp('NaNs in color limits')
    elseif handles.mydata.ccmin > handles.mydata.ccmax,
        disp('min color limit greater than max')
    else
        clims = [handles.mydata.ccmin handles.mydata.ccmax];
    end
    
    imagesc(handles.mydata.tm,rings,data',clims)
    datetick('x',6,'keepticks','keeplimits')
    colormap(handles.mydata.ccolormap);
    cbar=colorbar;
    set(get(cbar,'Ylabel'),'String',cdf{vartoplot}.units(:))
    if strcmp(vartoplot,'vconc'),
        ylabel(sprintf('size, %s',cdf{'size'}.units(:)))
    elseif strcmp(vartoplot,'intensity'),
        ylabel(sprintf('Scatter angle, %s',cdf{'rings'}.units(:)))
    end
else
    if ndims,
        plot(handles.mydata.tm,data)
        datetick('x',6,'keepticks','keeplimits')
    else
        plot(data)
        xlabel('Ring Number')
    end
    ylabel(sprintf('%s, %s',vartoplot,cdf{vartoplot}.units(:)))
end
handles.mydata.newvar = 0;

guidata(hObject, handles);

% --- Outputs from this function are returned to the command line.
function varargout = browseLISST_OutputFcn(hObject, eventdata, handles)
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure

% --- Executes during object creation, after setting all properties.
function sliderColorMin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to sliderColorMin (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, change
%       'usewhitebg' to 0 to use default.  See ISPC and COMPUTER.
usewhitebg = 1;
if usewhitebg
    set(hObject,'BackgroundColor',[.9 .9 .9]);
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
% The actual step size is a function of the specified SliderStep and the 
% total slider range (Max - Min). The default, [0.01 0.10], provides 
% a 1 percent change for clicks on the arrow button and a 10 percent 
% change for clicks in the trough. 

% --- Executes on slider movement.
function sliderColorMin_Callback(hObject, eventdata, handles)
% hObject    handle to sliderColorMin (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

newvalue = get(hObject,'Value');
if newvalue < handles.mydata.ccmax,
    handles.mydata.ccmin = newvalue;
else
end
set(handles.editColorMinValue,'string',sprintf('%g',handles.mydata.ccmin));
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);

% --- Executes during object creation, after setting all properties.
function sliderColorMax_CreateFcn(hObject, eventdata, handles)
% hObject    handle to sliderColorMax (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, change
%       'usewhitebg' to 0 to use default.  See ISPC and COMPUTER.
usewhitebg = 1;
if usewhitebg
    set(hObject,'BackgroundColor',[.9 .9 .9]);
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end


% --- Executes on slider movement.
function sliderColorMax_Callback(hObject, eventdata, handles)
% hObject    handle to sliderColorMax (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
newvalue = get(hObject,'Value');
if newvalue > handles.mydata.ccmin,
    handles.mydata.ccmax = newvalue;
else
    disp(sprintf('%7g new max value <= %7g color minimum',...
        newmax,handles.mydata.ccmin))
end
set(handles.editColorMaxValue,'string',sprintf('%7g',handles.mydata.ccmax));
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);

% --- Executes during object creation, after setting all properties.
function listboxVar2Plot_CreateFcn(hObject, eventdata, handles)
% hObject    handle to listboxVar2Plot (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

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


% --- Executes on selection change in listboxVar2Plot.
function listboxVar2Plot_Callback(hObject, eventdata, handles)
% hObject    handle to listboxVar2Plot (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = get(hObject,'String') returns listboxVar2Plot contents as cell array
%        contents{get(hObject,'Value')} returns selected item from listboxVar2Plot
list = get(hObject,'String');
handles.mydata.vartoplot = list{get(hObject,'Value')};
handles.mydata.newvar = 1; % tell update plot that we have switched.. new data loading
guidata(hObject, handles);
updateplot(hObject, handles);

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

% Hints: contents = get(hObject,'String') returns listboxColorMap contents as cell array
%        contents{get(hObject,'Value')} returns selected item from listboxColorMap
list = get(hObject,'String');
handles.mydata.ccolormap = list{get(hObject,'Value')};
guidata(hObject, handles);
updateplot(hObject, handles);

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

% Hint: listbox 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 editFirstBin_Callback(hObject, eventdata, handles)
% hObject    handle to editFirstBin (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of editFirstBin as text
%        str2double(get(hObject,'String')) returns contents of editFirstBin as a double
newcell = round(str2double(get(hObject,'String')));
if newcell < 1, newcell = 1; end
if newcell > handles.mydata.nrings, newcell = handles.mydata.nrings; end

handles.mydata.rings(1) = newcell;
handles.mydata.newvar = 1; % tell update plot that we have switched.. new data loading
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);


% --- Executes during object creation, after setting all properties.
function editFirstBin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editFirstBin (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



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

% Hints: get(hObject,'String') returns contents of editLastBin as text
%        str2double(get(hObject,'String')) returns contents of editLastBin as a double
newcell = round(str2double(get(hObject,'String')));
if newcell < 1, newcell = 1; end
if newcell > handles.mydata.nrings, newcell = handles.mydata.nrings; end

handles.mydata.rings(2) = newcell;
handles.mydata.newvar = 1; % tell update plot that we have switched.. new data loading
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);

% --- Executes during object creation, after setting all properties.
function editLastBin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editLastBin (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

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

% Hints: get(hObject,'String') returns contents of editColorMaxValue as text
%        str2double(get(hObject,'String')) returns contents of editColorMaxValue as a double
newvalue = str2double(get(hObject,'String'));
if newvalue > handles.mydata.ccmin,
    handles.mydata.ccmax = newvalue;
else
    disp(sprintf('Value ignored: %7g <= %7g color minimum',...
        newmax,handles.mydata.ccmin))
end
set(handles.editColorMaxValue,'string',sprintf('%7g',handles.mydata.ccmax));

% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);

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

% Hints: get(hObject,'String') returns contents of editColorMinValue as text
%        str2double(get(hObject,'String')) returns contents of editColorMinValue as a double
newvalue = get(hObject,'Value');
if newvalue < handles.mydata.ccmax,
    handles.mydata.ccmin = newvalue;
else
    disp(sprintf('Value ignored: %7g >= %7g color maximum',...
        newvalue,handles.mydata.ccmax))
end
set(handles.editColorMinValue,'string',sprintf('%g',handles.mydata.ccmin));
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);