% browsehydraburst - browse ADV burst file data by burst (works for PCADP too)
%
% browsehydraburst('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

% 16 Nov 2005
% -- call gregorian instead of gregoria
% 14 Sep 2005
% -- fix the problem of missing bursts (in the case of multiple samplign
% scenarios) now handled gracefully
% Version 2.5
% 15 Mar 2005 There is a java bug in version R14 (no SP) and lower that
% limits how far numerically a slider will go.  To turn off java so this
% works, use feature('javafigures',0) or upgrade to R14 SP2

% Last Modified by GUIDE v2.5 26-Apr-2005 13:34:29

function varargout = browsehydraburst(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @browsehydraburst_OpeningFcn, ...
                   'gui_OutputFcn',  @browsehydraburst_OutputFcn, ...
                   'gui_LayoutFcn',  [], ...
                   'gui_Callback',   []);
if nargin & isstr(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 browsehydraburst is made visible.
function browsehydraburst_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 browsehydraburst (see VARARGIN)

% Choose default command line output for browsehydraburst
handles.output = hObject;
%    figure1: 1.000034179687500e+002
%     slider1: 1.060206298828125e+002
%       axes1: 1.010040283203125e+002
%      output: 1.000034179687500e+002
% slider 1 controls time shift
% slider 2 controls which burst
% slider 3 controls which profiles

% look for a filename in the varargin
handles.mydata.burstfile = [];
for i = 1:length(varargin),
    if strcmp(varargin{i},'file'), handles.mydata.burstfile = varargin{i+1}; end
end
if isempty(handles.mydata.burstfile),
    [filename, pathname, filterindex] = uigetfile('*.*','Open a netCDF file containing burst Hydra data');
    if ~filename, return; end
    handles.mydata.burstfile = fullfile(pathname, filename);
end

% open the netCDF file and do the basic checks
cdf = netcdf(handles.mydata.burstfile); % 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.burstfile]); return; end
dimnames = ncnames(dim(cdf));
flag = 0;
for i=1:length(dimnames), % make sure this is a burst data file
    if strcmp(dimnames{i},'sample') || strcmp(dimnames{i},'profile'), flag = 1; end
end
if ~flag, close(cdf); return; end
handles.mydata.ispcadp = 0;
if findstr(cdf.INST_TYPE(:),'PCADP'), % find out if this is a PCADP
    % PCADP raw data file shape is
    handles.mydata.ispcadp = 1;
    handles.mydata.ncells = length(cdf{'depth'});
    for n=1:handles.mydata.ncells, handles.mydata.lstrings{n} = sprintf('%d',n); end
else
    handles.mydata.ncells  = 1;
    handles.mydata.ispcadp = 0;
end

set(handles.text7,'string',sprintf('Now browsing file %s',handles.mydata.burstfile))

n=1;
varnames = ncnames(var(cdf));
for i=1:length(varnames), % remove burstnum and time
    if strcmp(varnames{i},'burst') || strcmp(varnames{i},'profile') || ...
            strcmp(varnames{i},'depth') || strcmp(varnames{i},'lat') || strcmp(varnames{i},'lon') ||...
            strcmp(varnames{i},'time') || strcmp(varnames{i},'time2') || strcmp(varnames{i},'burstNum'),
        % do nothing
    else
        handles.mydata.varnames{n} = varnames{i}; 
        n=n+1;
    end
end
handles.mydata.vartoplot = handles.mydata.varnames{1};

handles.mydata.iburst = 1;
handles.mydata.icell = 1;
s = size(cdf{'time'});
handles.mydata.nbursts = s(1); handles.mydata.nsamples = s(2);
handles.mydata.nsamplesinview = handles.mydata.nsamples;
handles.mydata.samples = [1 handles.mydata.nsamplesinview];
if handles.mydata.nsamples < 500,
    handles.mydata.minsamplesinview = 1;
else handles.mydata.minsamplesinview = 500;
end
disp('Loading the burst numbers, one moment...')
handles.mydata.burstNum = cdf{'burst'}(:); % need these for a lookup table
if isempty(handles.mydata.burstNum), handles.mydata.burstNum = cdf{'burstNum'}(:); end

% slider 1 - zoom within a burst
set(handles.text1,'string',sprintf('%3.0f',handles.mydata.minsamplesinview));
set(handles.text4,'string',sprintf('%3.0f in view',handles.mydata.nsamples));
% slider 1 limits -- maybe change the view zoom for the number of samples
set(handles.slider1,'Value',handles.mydata.nsamples,'Min',handles.mydata.minsamplesinview,...
    'Max',handles.mydata.nsamples,'SliderStep',[1/handles.mydata.nsamples 5/handles.mydata.nsamples]);
set(handles.slider1,'Tooltipstring','Restrict the number of samples in view (zoom)')

% slider 2 - burst selector - labels
%set(handles.text2,'string',sprintf('%d',cdf{'burst'}(1)));
set(handles.text2,'string',sprintf('%d',handles.mydata.burstNum(1)));
%set(handles.text6,'string',sprintf('%d bursts',cdf{'burst'}(end)));
set(handles.text6,'string',sprintf('%d bursts',handles.mydata.burstNum(end)));
% slider 2 limits (burstnumber in view)
set(handles.slider2,'Value',handles.mydata.burstNum(1),'Min',handles.mydata.burstNum(1),...
    'Max',handles.mydata.burstNum(handles.mydata.nbursts),...
    'SliderStep',[1/handles.mydata.nbursts 100/handles.mydata.nbursts])
set(handles.slider2,'Tooltipstring','Select burst number to display')

% slider 3 - sample selector - labels
set(handles.text3,'string',sprintf('%d',1));
if ~handles.mydata.ispcadp, 
    set(handles.text5,'string',sprintf('%d samples in burst',length(cdf('sample'))));
else set(handles.text5,'string',sprintf('%d samples in burst',length(cdf('profile'))));
end
%set slider 3 limits
set(handles.slider3,'Value',1,'Min',handles.mydata.samples(1),'Max',handles.mydata.samples(2))
set(handles.slider3,'Tooltipstring','Select which part of burst to display (if zoomed)')

% put varnames into listbox here
set(handles.listbox1,'string',handles.mydata.varnames,'Value',1);
set(handles.listbox1,'Tooltipstring','Select data to display')

% set the goto box to the first burst
set(handles.edit1,'String',sprintf('%d',handles.mydata.burstNum(handles.mydata.iburst)));
set(handles.edit1,'Tooltipstring','enter a burst number to jump to')

% 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 browsehydraburst 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
samples = handles.mydata.samples;
%disp(sprintf('updateplot: iburst = %d',handles.mydata.iburst))
tm1 = datenum(gregorian(cdf{'time'}(handles.mydata.iburst,samples(1))));
tm1 = tm1+cdf{'time2'}(handles.mydata.iburst,samples(1))./(24*3600*1000);
cburst = cdf{'burst'}(handles.mydata.iburst);
axes(handles.axes1);
cla;
data = cdf{vartoplot}(handles.mydata.iburst,samples(1):samples(2),:);
plot(samples(1):samples(2),data);
ylabel(cdf{vartoplot}.units(:));
text(0.05,0.05,sprintf('%s at %s, burst #%d, samples #%d to %d',cdf{vartoplot}.long_name(:),...
    datestr(tm1), cburst, samples(1), samples(2)),'units','normalized');
if handles.mydata.ispcadp, 
    if ~isvector(data), legend(handles.mydata.lstrings,'Location','EastOutside'); end
end
% Update handles structure
guidata(hObject, handles);

% --- Outputs from this function are returned to the command line.
function varargout = browsehydraburst_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 slider1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider1 (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 slider1_Callback(hObject, eventdata, handles)
% hObject    handle to slider1 (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

handles.mydata.nsamplesinview = round(get(hObject,'Value'));
% now reset the view limits accordingly, use the first point as the anchor
handles.mydata.samples(2) = handles.mydata.samples(1)+handles.mydata.nsamplesinview-1;
if handles.mydata.samples(2) > handles.mydata.nsamples, 
    handles.mydata.samples(2) = handles.mydata.nsamples;
    handles.mydata.samples(1) = handles.mydata.nsamples-handles.mydata.nsamplesinview;
end
if handles.mydata.samples(1) <= 0, handles.mydata.samples(1) = 1; end
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);


% --- Executes during object creation, after setting all properties.
function slider2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider2 (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 slider2_Callback(hObject, eventdata, handles)
% hObject    handle to slider2 (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
cburst = round(get(hObject,'Value'));
handles.mydata.iburst = find(handles.mydata.burstNum == cburst);
if isempty(handles.mydata.iburst),
    disp('selected burst number not found, using the next in sequence')
    handles.mydata.iburst = find(handles.mydata.burstNum > cburst,1,'first');
end    
%disp(sprintf('slider2: cburst = %d; iburst = %d',cburst,handles.mydata.iburst))
set(handles.edit1,'String',sprintf('%d',cburst));
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);

% --- Executes during object creation, after setting all properties.
function slider3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider3 (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 slider3_Callback(hObject, eventdata, handles)
% hObject    handle to slider3 (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
%disp(handles.mydata.pcprof)
handles.mydata.samples(1) = round(get(hObject,'Value'));
% now reset the view limits accordingly, use middle as the anchor
handles.mydata.samples(2) = handles.mydata.samples(1)+handles.mydata.nsamplesinview-1;
if handles.mydata.samples(2) > handles.mydata.nsamples, 
    handles.mydata.samples(2) = handles.mydata.nsamples;
    handles.mydata.samples(1) = handles.mydata.nsamples-handles.mydata.nsamplesinview;
end
if handles.mydata.samples(1) <= 0, handles.mydata.samples(1) = 1; end
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);

% --- Executes during object creation, after setting all properties.
function listbox1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to listbox1 (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 listbox1.
function listbox1_Callback(hObject, eventdata, handles)
% hObject    handle to listbox1 (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 listbox1 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from listbox1
list = get(hObject,'String');
handles.mydata.vartoplot = list{get(hObject,'Value')};
guidata(hObject, handles);
updateplot(hObject, handles);

function edit1_Callback(hObject, eventdata, handles)
% hObject    handle to edit1 (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 edit1 as text
%        str2double(get(hObject,'String')) returns contents of edit1 as a double
cburst = str2num(get(hObject,'String'));
cburst = round(cburst); % just in case the user doesn't enter an integer
handles.mydata.iburst = find(handles.mydata.burstNum == cburst);
% should be one value...
if isempty(handles.mydata.iburst), % figure out if we are too high or too low
    if handles.mydata.iburst < handles.mydata.burstNum(1),
        handles.mydata.iburst = 1;
        disp('selected burst number is less than the smallest burst number in the file,')
        disp('using the smallest...')
    elseif handles.mydata.iburst > handles.mydata.nbursts;
        handles.mydata.iburst = handles.mydata.burstNum(end);
        disp('selected burst number is greater than the greatest burst number in the file,')
        disp('using the largest...')
    else,
        disp('selected burst number not found, using the next in sequence')
        handles.mydata.iburst = find(handles.mydata.burstNum > cburst,1,'first');
    end    
elseif length(handles.mydata.iburst) > 1,
    disp('There are repetetive burst numbers in this cdf file!')
    disp('using the smallest...')
    handles.mydata.iburst = min(handles.mydata.iburst);
end
set(handles.slider2,'Value',cburst);
% Update handles structure
guidata(hObject, handles);
updateplot(hObject, handles);


% --- Executes during object creation, after setting all properties.
function edit1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit1 (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
    set(hObject,'BackgroundColor','white');
else
    set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end


% --- Executes on button press in export_button.
function export_button_Callback(hObject, eventdata, handles)
% hObject    handle to export_button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%
% create a netCDF file with just the burst
cburst = handles.mydata.burstNum(handles.mydata.iburst);
[pname, fname] = fileparts(name(handles.mydata.cdf));
newname = fullfile(pname,[fname '_' num2str(cburst) '.cdf']);
if exist(newname,'file'),
    button = questdlg(sprintf('Do you want to overwrite %s?', newname),...
        'Wanring!','No');
    if strcmp(button,'No') | strcmp(button, 'Cancel'),
        return
    end
end
% create the file
cdfe = netcdf(newname,'clobber');
% let the user add a comment
answer = inputdlg('Enter a comment about this burst','Add metadata',1,{''});
cdfe.forensic_comment = answer{1};
% copy the global objects
ncobj = att(handles.mydata.cdf);
for n = 1:length(ncobj), copy(ncobj{n},cdfe); end
% set up the dimensions
ncobj = dim(handles.mydata.cdf);
rdim = recdim(handles.mydata.cdf);
for n = 1:length(ncobj), 
    if strcmp(name(rdim),name(ncobj{n})),
        cdfe(name(rdim)) = 0; % make the record dimension
    else
        copy(ncobj{n},cdfe);
    end
end
% make empty variables
ncobj = var(handles.mydata.cdf);
for n = 1:length(ncobj), 
    copy(ncobj{n},cdfe,0,1); % copy atts only 
end
% populate variables with data
ncobje = var(cdfe);
for n = 1:length(ncobj), 
    ncobje{n}(1,:,:) = ncobj{n}(handles.mydata.iburst,:,:);
end
% (handles.mydata.iburst,:,:)
disp(sprintf('Burst %d copied to %s',cburst,newname))
close(cdfe)