function varargout = maskADCP(varargin)
% MASKADCP allows the user to view a raw ADCP file and interactively mark
% areas of data to be marked as bad in the mask (.msk) file and
% subsequently be replaced with fill values 
%
% if maskADCP invoked without arguements, it will ask for a file.
% maskADCP('file','datafilename.cdf','mask','maskfilename.msk')
%
% the mask file is open if the button in the upper right hand corner is red
% and shows the mask file name.  Click on it in this state to close the
% mask file.  When the mask file is closed (or not known) no masking is
% displayed on the plots.  When the mask file is open, any clicking of the
% mouse in an axis window will mark data!  For one-D data, you ahve to
% click on the actual line.
%

% written by Marinna Martini 
% U.S. Geological Survey Woods Hole Science Center
% Version 0.0 beta beta 28-feb-2008

%%% START USGS BOILERPLATE -------------%
% Use of this program is described in:
%
% Acoustic Doppler Current Profiler Data Processing System Manual 
% Jessica M. Côté, Frances A. Hotchkiss, Marinna Martini, Charles R. Denham
% Revisions by: Andrée L. Ramsey, Stephen Ruane
% U.S. Geological Survey Open File Report 00-458 
% Check for later versions of this Open-File, it is a living document.
%
% Program written in Matlab v7.1.0 SP3
% Program updated in Matlab 7.2.0.232 (R2006a)
% Program ran on PC with Windows XP Professional OS.
%
% "Although this program has been used by the USGS, no warranty, 
% expressed or implied, is made by the USGS or the United States 
% Government as to the accuracy and functioning of the program 
% and related program material nor shall the fact of distribution 
% constitute any such warranty, and no responsibility is assumed 
% by the USGS in connection therewith."
%
%%% END USGS BOILERPLATE --------------

% MASKADCP M-file for maskADCP.fig
%      MASKADCP, by itself, creates a new MASKADCP or raises the existing
%      singleton*.
%
%      H = MASKADCP returns the handle to a new MASKADCP or the handle to
%      the existing singleton*.
%
%      MASKADCP('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in MASKADCP.M with the given input arguments.
%
%      MASKADCP('Property','Value',...) creates a new MASKADCP or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before maskADCP_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to maskADCP_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help maskADCP

% Last Modified by GUIDE v2.5 12-Mar-2008 14:49:09

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @maskADCP_OpeningFcn, ...
                   'gui_OutputFcn',  @maskADCP_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 maskADCP is made visible.
function maskADCP_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 maskADCP (see VARARGIN)

% Choose default command line output for maskADCP
handles.output = hObject;

%    figure1: 1.000034179687500e+002
%     sliderTimeShift: 1.060206298828125e+002
%       axes1: 1.010040283203125e+002
%       axes2: 1.010040283203125e+002
%       axes3: 1.010040283203125e+002
%       axes4: 1.010040283203125e+002
%      output: 1.000034179687500e+002
% slider 1 controls time shift

% look for a filename in the varargin
handles.mydata = [];
handles.mydata.masktoggle = [];
handles.mydata.fill = 1E35;

for i = 1:length(varargin),
    if strcmp(varargin{i},'file'), handles.mydata.datafile = varargin{i+1}; end
    if strcmp(varargin{i},'mask'), handles.mydata.maskfile = varargin{i+1}; end
end
if ~isfield(handles.mydata,'datafile') || isempty(handles.mydata.datafile),
    [filename, pathname] = uigetfile('*.cdf','Open a netCDF time series file');
    if ~filename, return; end
    handles.mydata.datafile = fullfile(pathname, filename);
end
% open the netCDF file and do the basic checks
cdf = netcdf(handles.mydata.datafile); 
if isempty(cdf), disp('problem opening %s',handles.mydata.datafile); return; end
filehandles{1} = cdf;
handles.mydata.cdf = cdf; % for passing to other methods
if isfield(handles.mydata,'maskfile') && ~isempty(handles.mydata.maskfile),
    handles = getmaskfile(handles);
    filehandles{2} = handles.mydata.msk; 
else
    set(handles.maskfilebutton,'String','Push for mask file');
    set(handles.masktogglebutton,'String','Not Masking');
end

set(handles.figure1,'UserData',filehandles); % store the netCDF file pointer here so I can close it later
set(handles.figure1,'DeleteFcn','cdf = get(gcf,''UserData''); for n=1:length(cdf), disp(sprintf(''closing %s\nApply mask using postmask.m'', char(ncnames(cdf{n})))); close(cdf{n}); end; clear cdf n'); % and this is the code that will close it
clear filehandles

if isempty(cdf), disp(['Unable to open netCDF file ',handles.mydata.datafile]); return; end
dimnames = ncnames(dim(cdf));
handles.mydata.israwADCP = 0; % flag for the TIM variable
handles.mydata.isEPIC = 0;
for i=1:length(dimnames), % is this a burst data file
    if strcmp(dimnames{i},'ensemble'), handles.mydata.israwADCP = 1; end
    if strcmp(dimnames{i},'time'), handles.mydata.isEPIC = 1; end
end

set(handles.textTitle,'string',handles.mydata.datafile)

% these set up the data views
handles.mydata.Curplotset = 1;
if handles.mydata.israwADCP,
    handles.mydata.plotset = {'vel','cor','AGC','PGd','orientation',...
        'STDorientation','Press-Temp','xmit','VD','EWD'};
    handles.mydata.shapes = {'2d','2d','2d','2d','1d','1d','1d','1d','1d','1d'};
    handles.mydata.clims = {[-500 500],[0 256],[0 256],[0 100],[],[],[],[],[],[]};
    handles.mydata.varset = {{'vel1','vel2','vel3','vel4'},...
         {'cor1','cor2','cor3','cor4'},...
         {'AGC1','AGC2','AGC3','AGC4'},...
         {'PGd1','PGd2','PGd3','PGd4'},...
         {'Hdg','Ptch','Roll',''},...
         {'HdgSTD','PtchSTD','RollSTD',''},...
         {'Pressure','PressVar','Tx','sv'}, ...
         {'xmitc','xmitv','dac',''},...
         {'VDD3','VDD1','VDC',''},...
         {'EWD1','EWD2','EWD3','EWD4'} ...
         };
else    handles.mydata.plotset = {'vel','Werr, cor, AGC, PGd',...
        'orientation', 'Press, Temp, range'};
end

% variables never to be masked
handles.mydata.mask.nomaskvars = {'ensemble','Rec','D','bin','TIM'};

handles.mydata.icell = 1; 

disp('Loading time, one moment...')
if handles.mydata.israwADCP,
    handles.mydata.tm = datenum(gregorian(cdf{'TIM'}(:)));
    handles.mydata.ens = cdf{'Rec'}(:);
    handles.mydata.cells = cdf{'D'}(:);
elseif handles.mydata.isEPIC,
    handles.mydata.tm = datenum(gregorian(cdf{'time'}(:)+cdf{'time2'}(:)./(1000*24*3600)));
    handles.mydata.cells = cdf{'depth'}(:);
else
    disp('Unable to load record dimension'); return;
end
disp(sprintf('Data found from %s to %s',datestr(handles.mydata.tm(1)),datestr(handles.mydata.tm(end))))
disp(sprintf('Data found from ensemble %d to %d',handles.mydata.ens(1),handles.mydata.ens(end)))
set(handles.textStartTime,'string',sprintf('%s, #%d',...
    datestr(handles.mydata.tm(1),0),handles.mydata.ens(1)))
set(handles.textEndTime,'string',sprintf('%s, #%d',...
    datestr(handles.mydata.tm(end),0),handles.mydata.ens(end)))

handles.mydata.days2view = 3; % a random starter
% look for N days of data
dayN = find(handles.mydata.tm > handles.mydata.tm(1)+handles.mydata.days2view, 1,'first');
handles.mydata.idx2view = [1 dayN];
recspan = handles.mydata.idx2view(2) - handles.mydata.idx2view(1);
handles.mydata.timespan = handles.mydata.tm(end) - handles.mydata.tm(1);
handles.mydata.dT = gmean(diff(handles.mydata.tm)); % estimate time between ensembles

handles.mydata.nens = length(handles.mydata.tm);
% slider 1 - move along in time
% slider 1 limits -- maybe change the view zoom for the number of samples
% [min_step max_step]Slider step size. This property controls the amount
% the slider Value changes when you click the mouse on the
% arrow button (min_step) or on the slider trough (max_step).
% Specify SliderStep as a two-element vector; each value
% must be in the range [0, 1]. 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.
% start with 7 days
set(handles.sliderTimeShift,'Value',handles.mydata.tm(1),'Min',handles.mydata.tm(1),...
    'Max',handles.mydata.tm(end),'SliderStep',[handles.mydata.days2view/handles.mydata.timespan, 0.1]);
set(handles.sliderTimeShift,'Tooltipstring','Move along in time')

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

% minimum zoom in time to maximum zoom, limit by the number of ensembles
% figure out a best smallest window based on the minimum number of
% ensembles that will render well
handles.mydata.minensdisplayed = 100;
ens2view = floor(handles.mydata.days2view./handles.mydata.dT);
% max we can display is handles.mydata.nens
set(handles.sliderTimeView,'Value',ens2view,'Min',handles.mydata.minensdisplayed,...
    'Max',handles.mydata.nens,'SliderStep',[0.1 0.6]);
set(handles.sliderTimeView,'Tooltipstring','Zoom in and out in time')
set(handles.textTimeView,'string',sprintf('%5.2f days = %5.2f hours, #%d ensembles',...
    handles.mydata.days2view, handles.mydata.days2view*24, recspan))

handles.mydata.Curmask = [];
handles.mydata.TaggedAxis = [];

% because we don't know what to do with this yet
handles.output = [];

% so I can find this window later
set(gcf,'Name','maskADCP')

% because some things fail when gone through first
handles.mydata.initialize = 1;
set(gcf,'Tag','maskADCPwindow')
%disp(sprintf('slider from %s to %s', datestr(handles.mydata.tm(1), datestr(handles.mydata.tm(1)))))
% Update handles structure
guidata(gcf, handles); %guidata(hObject, handles);
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(gcf, handles); %updateplot(hObject, handles)
end

% UIWAIT makes maskADCP 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;
idx = handles.mydata.idx2view;
varset = handles.mydata.varset{handles.mydata.Curplotset}; % cell array of varnames
clims = handles.mydata.clims{handles.mydata.Curplotset};
setshape = handles.mydata.shapes{handles.mydata.Curplotset};
% is there a mask file open?
showmask = 0;
if isfield(handles.mydata,'msk') && ~isempty(handles.mydata.msk), 
    showmask = 1;
    msk = handles.mydata.msk;
end
phand = [0 0 0 0];
set(handles.textPlotStart,'string',sprintf('%s, #%d',...
    datestr(handles.mydata.tm(idx(1)),0),handles.mydata.ens(idx(1))))
set(handles.textPlotEnd,'string',sprintf('%s, #%d',...
    datestr(handles.mydata.tm(idx(2)),0),handles.mydata.ens(idx(2))))
switch setshape,
    case '2d',
        for iax = 1:4,
            eval(sprintf('axes(handles.axes%d);',iax))
            cla;
            set(gca,'DrawMode','fast')
            data = cdf{varset{iax}}(idx(1):idx(2),:)';
            phand(iax) = pcolor(handles.mydata.tm(idx(1):idx(2)),handles.mydata.cells,data);
            % image does not render well with changing color limits
            %phand(iax) = image(handles.mydata.tm(idx(1):idx(2)),handles.mydata.cells,data);
            shading flat;
            set(phand(iax),'ButtonDownFcn','maskADCP(''axes_ButtonDownFcn'',gcbo,[],guidata(gcbo))');
            if ~isempty(clims), caxis(clims); 
            else caxis('auto');
            end
            % TODO - colorbar has trouble with NaNs
            if ~isnan(cdf{varset{iax}}(idx(1):idx(2),:)'); 
                handles.mydata.caxes{iax} = colorbar('location','EastOutside'); 
            end
            ylabel(sprintf('%s, %s',varset{iax},cdf{'D'}.units(:)));
            if iax == 4, datetick('x','keepticks','keeplimits');
            else set(gca,'XTickLabel',[]);                
            end
            set(gca,'Tag',sprintf('axis%d',iax))
            if showmask,
                hold on
                mask = msk{varset{iax}}(idx(1):idx(2),:)';
                goods = find(mask == 0);
                bads = find(mask == 1);
                mask(bads) = handles.mydata.fill;
                mask(goods) = NaN;
                %mhand(iax) = image(handles.mydata.tm(idx(1):idx(2)),handles.mydata.cells,mask);
                mhand(iax) = pcolor(handles.mydata.tm(idx(1):idx(2)),handles.mydata.cells,mask);
                set(mhand(iax),'ButtonDownFcn','maskADCP(''axes_ButtonDownFcn'',gcbo,[],guidata(gcbo))');
                shading flat
                hold off
            end
            set(gca,'DrawMode','normal')
        end
    case '1d',
        for iax = 1:4,
            eval(sprintf('axes(handles.axes%d);',iax))
            cla;
            if ~isempty(cdf{varset{iax}}), % some are odd sets
                data = cdf{varset{iax}}(idx(1):idx(2),:)';
                phand(iax) = plot(handles.mydata.tm(idx(1):idx(2)),data);
                ylabel(sprintf('%s, %s',varset{iax},cdf{varset{iax}}.units(:)));
                if iax == 4, datetick('x','keepticks','keeplimits');
                else set(gca,'XTickLabel',[]);
                end
                ylims = get(gca,'Ylim');
                set(phand(iax),'ButtonDownFcn','maskADCP(''axes_ButtonDownFcn'',gcbo,[],guidata(gcbo))');
                if showmask,
                    hold on
                    mask = msk{varset{iax}}(idx(1):idx(2),:)';
                    goods = find(mask == 0);
                    bads = find(mask == 1);
                    mask(bads) = data(bads);
                    mask(goods) = NaN;
                    mhand(iax) = plot(handles.mydata.tm(idx(1):idx(2)),mask,'r');
                    set(mhand(iax),'ButtonDownFcn','maskADCP(''axes_ButtonDownFcn'',gcbo,[],guidata(gcbo))');
                    set(gca,'Ylim',ylims)
                    hold off
                end
            else % make a dummy plot
                phand(iax) = plot(handles.mydata.tm(idx(1):idx(2)),...
                    zeros(length(handles.mydata.tm(idx(1):idx(2))),1),'w');
                ylabel('none');
                if iax == 4, datetick('x','keepticks','keeplimits');
                else set(gca,'XTickLabel',[]);
                end
                ylims = get(gca,'Ylim');
                text(0.5,0.5,'Empty plot','units','normalized')
            end 
            set(gca,'Tag',sprintf('axis%d',iax))
        end
end

if handles.mydata.initialize, handles.mydata.initialize = 0; end

% Update handles structure
% gcbo = handle of objcte whos call back is executing
% note that hObject will be [] if something other than a direct callback
% calls this function
hObject = gcf;
guidata(gcf, handles); %guidata(hObject, handles);


% --- Outputs from this function are returned to the command line.
function varargout = maskADCP_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
%varargout{1} = handles.output;


% --- Executes on slider movement.
function sliderTimeShift_Callback(hObject, eventdata, handles)
% hObject    handle to sliderTimeShift (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
newtmstart = round(get(hObject,'Value')); % this is the *middle* value
%disp(datestr(newtmstart))
if newtmstart > (handles.mydata.tm(end)-handles.mydata.days2view),
    newtmstart = handles.mydata.tm(end)-handles.mydata.days2view;
elseif newtmstart < handles.mydata.tm(1),
    newtmstart = handles.mydata.tm(1);
end
handles.mydata.idx2view(1) = find(handles.mydata.tm >= newtmstart, 1,'first');
newtmend = newtmstart+handles.mydata.days2view;
if newtmend > handles.mydata.tm(end),
    newtmend = handles.mydata.tm(end);
elseif newtmend < handles.mydata.tm(1),
    newtmend = handles.mydata.tm(1)+handles.mydata.days2view;
end
handles.mydata.idx2view(2) = ...
    find(handles.mydata.tm >= newtmend, 1,'first');
disp(sprintf('viewing from %s to %s', datestr(handles.mydata.tm(handles.mydata.idx2view(1))),...
    datestr(handles.mydata.tm(handles.mydata.idx2view(2)))));

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

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


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


% --- Executes on selection change in listboxWhichPlot.
function listboxWhichPlot_Callback(hObject, eventdata, handles)
% hObject    handle to listboxWhichPlot (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 listboxWhichPlot contents as cell array
%        contents{get(hObject,'Value')} returns selected item from listboxWhichPlot
handles.mydata.Curplotset = get(hObject,'Value');
% Update handles structure
guidata(gcf, handles); %guidata(hObject, handles);
updateplot(gcf, handles); %updateplot(hObject, handles);


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


% --- Executes on mouse press over figure background, over a disabled or
% --- inactive control, or over an axes background.
function figure1_WindowButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% disp(sprintf('figure1_WindowButtonDownFcn: working in %s', get(gco,'Tag')))
% this always gets executed.  

% --- Executes on mouse press over axes background.
% had to be made the call back function of the plot object
function axes_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to axes1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%disp(sprintf('axes_ButtonDownFcn: working in %s', get(gca,'Tag')))
%don't do anything if there's no mask file open
if ~isfield(handles.mydata,'msk') || isempty(handles.mydata.msk),
    disp('No mask file open')
    return
end
% location and size of the rubberband box as [x y width height], where x and y define
% the lower left corner, and width and height define the size. initialRect is in 
% the units specified by the current figure's Units property, and measured from the
% lower left corner of the figure window.
point1 = get(gca,'CurrentPoint');    % button down detected
finalRect = rbbox;                   % return figure units
point2 = get(gca,'CurrentPoint');    % button up detected
point1 = point1(1,1:2);              % extract x and y
point2 = point2(1,1:2);
p1 = min(point1,point2);             % calculate locations
offset = abs(point1-point2);         % and dimensions
x = [p1(1) p1(1)+offset(1) p1(1)+offset(1) p1(1) p1(1)];
y = [p1(2) p1(2) p1(2)+offset(2) p1(2)+offset(2) p1(2)];
% hold on
% axis manual
% plot(x,y)
if strcmp(handles.mydata.shapes(handles.mydata.Curplotset),'2d'),
    for iax = 1:4,
        eval(sprintf('axes(handles.axes%d);',iax))
        hold on
        plot(x,y)
    end
else
    hold on
    plot(x,y)
    handles.mydata.TaggedAxis = sscanf(get(gca,'Tag'),'axis%d');
end
% now organize the results into iformation that can be added to the mask file
handles.mydata.mask.bbox = [min(x) max(x) min(y) max(y)];
% ask user if they want to apply mask all variables
handles.mydata.mask.doall = 0;
button = questdlg('Apply mask to all variables?','Masking','No');
if ~isempty(button) && strcmpi(button,'Yes'),
    handles.mydata.mask.doall = 1;
    update_maskfile(handles)
elseif strcmpi(button,'No'), 
    handles.mydata.mask.doall = 0;
    update_maskfile(handles)
else
    disp('user cancelled, no update applied to the mask file')
end
guidata(gcf, handles); %guidata(hObject, handles);
updateplot(gcf, handles); %updateplot(hObject, handles);

function update_maskfile(handles) % set the mask in the file
% first, locate the bounding box in terms of file indeces
% the bounding box is in whatever the x and y units were in the plot,
% mainly depth and time
bbox = handles.mydata.mask.bbox;
% translate x/tm into index
junk = find(handles.mydata.tm >= bbox(1),1,'first');
if ~isempty(junk), tmidx(1) = junk;
elseif bbox(1) < 1, tmidx(1) = 1;
    elseif bbox(1) > length(handles.mydata.tm),
        tmidx(1) = length(handles.mydata.tm); 
end
junk = find(handles.mydata.tm >= bbox(2),1,'first');
if ~isempty(junk), tmidx(2) = junk;
elseif bbox(2) < 1, tmidx(2) = 1;
elseif bbox(2) > length(handles.mydata.tm),
    tmidx(2) = length(handles.mydata.tm);
end
if strcmp(handles.mydata.shapes(handles.mydata.Curplotset),'2d'),
    junk = find(handles.mydata.cells >= bbox(3),1,'first');
    if ~isempty(junk), binidx(1) = junk;
    elseif bbox(3) < 1, binidx(1) = 1;
    elseif bbox(3) > handles.mydata.cells,
        binidx(1) = handles.mydata.cells;
    end
    junk = find(handles.mydata.cells >= bbox(4),1,'first');
    if ~isempty(junk), binidx(2) = junk;
    elseif bbox(4) < 1, binidx(2) = 1;
    elseif bbox(4) > handles.mydata.cells,
        binidx(2) = length(handles.mydata.cells); 
    end
else
    binidx(1) = 1;
    binidx(2) = 1;
end
% check one more time!
if (tmidx(1)<1) || (tmidx(1)>length(handles.mydata.tm)) || ...
        (tmidx(2)<1) || (tmidx(2)>length(handles.mydata.tm)) || ...
        (binidx(1)<1) || (binidx(1)>length(handles.mydata.cells)) || ...
        (binidx(2)<1) || (binidx(2)>length(handles.mydata.cells)) ,
    disp('mask was out of bounds of the range of the data in the file')
    return
end
% give it a go in the mask file
msk = handles.mydata.msk;
% what variables get the mask?
if ~handles.mydata.mask.doall, % just do the variables in the window
    varset = handles.mydata.varset{handles.mydata.Curplotset}; % cell array of varnames
    if strcmp(handles.mydata.shapes(handles.mydata.Curplotset),'1d'),
        varset = varset(handles.mydata.TaggedAxis);
    end
else
    allvars = ncnames(var(msk));
    n = 1;
    nomask = 0;
    for vidx = 1:length(allvars),
        % is this one of the never to be masked variables?
        for nmidx = 1:length(handles.mydata.mask.nomaskvars),
            if strcmp(allvars{vidx},handles.mydata.mask.nomaskvars{nmidx}),
                nomask = 1;
            end
        end
        if nomask, nomask = 0;
        else varset{n} = allvars{vidx};
            n = n+1;
        end
    end
end
disp(sprintf('RDI Ensemble number range to be masked are %d to %d',...
    msk{'Rec'}(tmidx(1)), msk{'Rec'}(tmidx(2))));
disp(sprintf('That''s from %s to %s',...
    datestr(handles.mydata.tm(tmidx(1))), datestr(handles.mydata.tm(tmidx(2)))));
% now update the mask file
if isempty(handles.mydata.masktoggle), 
    disp('mask toggle variable was empty, applying mask')
end
for ivar = 1:length(varset),
    if length(dim(msk{varset{ivar}})) == 1, % one dimensional
        theMask = ones(tmidx(2)-tmidx(1)+1,1).*handles.mydata.masktoggle;
        msk{varset{ivar}}(tmidx(1):tmidx(2)) = theMask;
        disp(sprintf('Masked %s from file index %d to %d',varset{ivar},tmidx(1),tmidx(2)))
    elseif length(dim(msk{varset{ivar}})) == 2, % two dimensional
        theMask = ones(tmidx(2)-tmidx(1)+1,binidx(2)-binidx(1)+1).*handles.mydata.masktoggle;
        msk{varset{ivar}}(tmidx(1):tmidx(2),binidx(1):binidx(2)) = theMask;
        disp(sprintf('Masked %s from file index %d to %d and bins %d to %d',...
            varset{ivar},tmidx(1),tmidx(2),binidx(1),binidx(2)))
    else % this shouldn't be in an ADCP file
        disp('This variable has more dimensions than expected in an ADCP file')
    end
end
return

% --- Executes on button press in maskfilebutton.
function maskfilebutton_Callback(hObject, eventdata, handles)
% hObject    handle to maskfilebutton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% first see if a mask file is open:
if isfield(handles.mydata,'msk') && ~isempty(handles.mydata.msk),
    close(handles.mydata.msk);
    set(handles.maskfilebutton,'BackgroundColor',[0.92549 0.913725 0.847059])
    set(handles.maskfilebutton,'String','Push for mask file')
    set(handles.masktogglebutton,'BackgroundColor',[0.92549 0.913725 0.847059])
    set(handles.masktogglebutton,'String','Not Masking')
    %msgbox(sprintf('%s is closed',handles.mydata.maskfile))
    handles.mydata.msk = [];
    handles.mydata.maskfile = [];
    handles.mydata.masktoggle = [];
    set(handles.figure1,'UserData',{handles.mydata.cdf});
else
    handles = getmaskfile(handles);
end
guidata(gcf, handles); %guidata(hObject, handles);
 updateplot(gcf, handles); %updateplot(hObject, handles);

function handles = getmaskfile(handles)
if ~isfield(handles.mydata,'maskfile'), handles.mydata.maskfile = []; end
if isempty(handles.mydata.maskfile),
    Curdir = pwd;
    pathname = fileparts(handles.mydata.datafile);
    if isempty(pathname), pathname = '.'; end
    cd(pathname);
    [filename, pathname] = uigetfile('*.msk','Open a netCDF mask file');
    cd(Curdir);
    if ~filename,
        disp('User cancelled, no mask file opened')
        return;
    end
    handles.mydata.maskfile = fullfile(pathname, filename);
end
% open the netCDF file and do the basic checks
handles.mydata.msk = netcdf(handles.mydata.maskfile,'write');
if isempty(handles.mydata.msk),
    disp('problem opening mask file %s',handles.mydata.maskfile);
    return;
end
if isempty(handles.mydata.msk.CreatedBy(:)) || ...
        ~strcmp(handles.mydata.msk.CreatedBy(:),'mkadcpmask'),
    disp('file %s is not an ADCP mask file',handles.mydata.maskfile);
    return;
end
set(handles.figure1,'UserData',{handles.mydata.cdf, handles.mydata.msk});
[pathname, filename, fileext] = fileparts(handles.mydata.maskfile);
set(handles.maskfilebutton,'String',[filename, fileext]);
set(handles.maskfilebutton,'BackgroundColor',[1 0 0]);
set(handles.masktogglebutton,'String','Masking');
set(handles.masktogglebutton,'BackgroundColor',[1 0 0]);
set(handles.masktogglebutton,'Tooltipstring','Push to switch to unmask mode')
handles.mydata.masktoggle = 1;
guidata(gcf, handles); %guidata(hObject, handles);

% --- Executes during object deletion, before destroying properties.
function figure1_DeleteFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
disp('in figure1_DeleteFcn')


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


% --------------------------------------------------------------------
function SetClims_Callback(hObject, eventdata, handles)
% hObject    handle to SetClims (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
disp('in SetClims')
clims = handles.mydata.clims{handles.mydata.Curplotset};
dlg_title = sprintf('Limits for %s',...
    handles.mydata.plotset{handles.mydata.Curplotset});
def = {num2str(clims(1)),num2str(clims(2))};
result = inputdlg({'min:','max:'},dlg_title,1,def);
if ~isempty(result),
    handles.mydata.clims{handles.mydata.Curplotset} = ...
        [str2double(result{1}), str2double(result{2})];
    guidata(gcf, handles); %guidata(hObject, handles);
    updateplot(gcf, handles); %updateplot(hObject, handles);
end


% --- Executes on slider movement.
function sliderTimeView_Callback(hObject, eventdata, handles)
% hObject    handle to sliderTimeView (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 de*middle* value
newensspan = round(get(hObject,'Value')); 
if newensspan > handles.mydata.nens,
    newensspan = handles.mydata.nens;
elseif newensspan < handles.mydata.minensdisplayed,
    newensspan = handles.mydata.minensdisplayed;
end
handles.mydata.days2view = newensspan.*handles.mydata.dT;
% handles.mydata.idx2view is the start and end netCDF file indeces we're viewing
% now move the end index in view
tmstart = handles.mydata.tm(handles.mydata.idx2view(1));
newtmend = tmstart + handles.mydata.days2view;
if newtmend > handles.mydata.tm(end),
    newtmend = handles.mydata.tm(end);
elseif newtmend < handles.mydata.tm(1),
    newtmend = handles.mydata.tm(1)+handles.mydata.days2view;
end
handles.mydata.idx2view(2) = ...
    find(handles.mydata.tm >= newtmend, 1,'first');
disp(sprintf('viewing from %s to %s', datestr(handles.mydata.tm(handles.mydata.idx2view(1))),...
    datestr(handles.mydata.tm(handles.mydata.idx2view(2)))));
set(handles.textTimeView,'string',sprintf('%5.2f days = %5.2f hours, #%d ensembles',...
    handles.mydata.days2view, handles.mydata.days2view*24, ...
    handles.mydata.idx2view(2) - handles.mydata.idx2view(1)))

% update the time slider accordingly
newstep = [handles.mydata.days2view/handles.mydata.timespan, 0.1];
if newstep(1) > 1, newstep(1) = 1; end
if newstep(1) < 0, newstep(1) = 0; end
set(handles.sliderTimeShift,'SliderStep',newstep);

% Update handles structure
guidata(gcf, handles); %guidata(hObject, handles);
updateplot(gcf, handles); %updateplot(hObject, handles);termine range of slider


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


% --- Executes on button press in masktogglebutton.
function masktogglebutton_Callback(hObject, eventdata, handles)
% hObject    handle to masktogglebutton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if isempty(handles.mydata.masktoggle),
    warndlg('Mask file is not open');
elseif handles.mydata.masktoggle, % now applying mask, switch
    set(handles.masktogglebutton,'String','Removing Mask');
    set(handles.masktogglebutton,'BackgroundColor',[0 1 0]);
    set(handles.masktogglebutton,'Tooltipstring','Push to switch to mask mode')
    handles.mydata.masktoggle = 0;
else % change to apply mask
    set(handles.masktogglebutton,'String','Masking');
    set(handles.masktogglebutton,'BackgroundColor',[1 0 0]);
    set(handles.masktogglebutton,'Tooltipstring','Push to switch to unmask mode')
    handles.mydata.masktoggle = 1;
end
guidata(gcf, handles); %guidata(hObject, handles);