% flagbadadv - interactively flag bad ADV data 
%
% flagbadadv('QualityFile', cdfqFile,'settings', settings) 
%
% cdfqFile = neCDF quality file generated by adr2cdf
% Results and settings are returned to the qFile
% settings.currentBeam: 1    the beam operated on
% settings.new_bad: {[]; []; []; [1 2 3]; []} 
%       5 cell matrix of arrays of burst numbers of known
%       bad data to add to mask override
% settings.new_good: {[]; [101]; []; [1 2 3]; [35]} 
%       5 cell matrix of arrays of burst numbers of
%       known good data to pass to mask override
% settings.new_scutoff: 5 element array with a new velocity standard
%       deviation threshold
% settings.new_ccutoff: 5 element array with a new correlation threshold
%
% Note: this gui is constrained to 5 subbursts because that's all there is
%       room to plot.  The file flagbadadv.fig is required by flagbadadv.m
% Note: using the mouse pointer or the edit field to add bursts to the
%       override lists is very sticky, it will not be undone by changing the
%       cutoff thresholds

%
% 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
%
% 11/17/05
% allow user to work on partial burst ranges.  Leave as a hidden feature
% for now.  If a range is specified and the user changes a threshold, the 
% threshold will be recorded in the qfile, and loaded the next time
% flagbadadv is run... which might wipe out previous mask settings
% useage is:
% BurstNumRange = [m:n]; % have flagbadadv work on a subset of bursts
% 11/16/05
% -- fix a few little issues, including making the color scheme simpler.
% Version 2.0 10/19/05 
% use the netCDF qaulity file and improve logic
% Version 1.2 3/9/05 go back to the version needing flagbadadv.fig.  Handle
%   systems without pressure sensors
% Version 1.1 1/11/05   make flagbadadv.fig unnecessary in distribution
% Version 1.0 11/19/04  change toggles to overrides for good and bad points
%   allow user to preload these overrides
%   change bottom plot to psdev
%   change all flags points to red
% Version 0.5 9/15/04 added correlation cutoff
% Version 0.0 10/11/04


function varargout = flagbadadv(varargin)
% FLAGBADADV M-file for flagbadadv.fig
%      FLAGBADADV, by itself, creates a new FLAGBADADV or raises the existing
%      singleton*.
%
%      H = FLAGBADADV returns the handle to a new FLAGBADADV or the handle to
%      the existing singleton*.
%
%      FLAGBADADV('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in FLAGBADADV.M with the given input
%      arguments.
%
%      FLAGBADADV('Property','Value',...) creates a new FLAGBADADV or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before flagbadadv_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to flagbadadv_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

% Copyright 2002-2003 The MathWorks, Inc.

% TODO freeze zoom until user unzooms by tracking the axis limits and
% resetting them

% Last Modified by GUIDE v2.5 22-Nov-2005 10:31:35

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

handles.mydata = [];
for i = 1:2:length(varargin),
    if strcmp(varargin{i},'QualityFile'), handles.mydata.cdfqFile = varargin{i+1}; end
    if strcmp(varargin{i},'settings'), handles.mydata.settings = varargin{i+1}; end
    if strcmp(varargin{i},'BurstNumRange'), handles.mydata.BurstNumRange = varargin{i+1}; end
end
if ~isfield(handles.mydata,'cdfqFile'),
    [filename, pathname] = uigetfile('*.*','Open a netCDF file containing burst Hydra data');
    if ~filename, return; end
    handles.mydata.cdfqFile = fullfile(pathname, filename);
end
if ~isfield(handles.mydata,'settings'), handles.mydata.settings = []; end
if ~isfield(handles.mydata.settings,'new_bad'), handles.mydata.settings.new_bad = {[],[],[],[],[]}; end
if ~isfield(handles.mydata.settings,'new_good'), handles.mydata.settings.new_good = {[],[],[],[],[]}; end
if ~isfield(handles.mydata.settings,'currentBeam'), handles.mydata.settings.currentBeam = 1; end
if ~isfield(handles.mydata,'BurstNumRange'), handles.mydata.BurstNumRange = []; end
    
% get data from qfile
if exist(handles.mydata.cdfqFile,'file'),
    handles.mydata.cdfq = netcdf(handles.mydata.cdfqFile,'write');
    if isempty(handles.mydata.cdfq),
        disp(sprintf('Failure to open netCDF burst file %s',handles.mydata.cdfqFile))
        return
    end
else
    disp(sprintf('Failure to find netCDF burst file %s',handles.mydata.cdfqFile))
    return
end

handles.mydata.currentBeam = handles.mydata.settings.currentBeam;
if isfield(handles.mydata, 'currentBeam'),
    if handles.mydata.currentBeam > length(handles.mydata.cdfq('axis')),
        handles.mydata.currentBeam = length(handles.mydata.cdfq('axis'));
    elseif handles.mydata.currentBeam < 1,
        handles.mydata.currentBeam = 1;
    end
else
    handles.mydata.currentBeam = 1;
end


idx = [];
% get the quality data
handles.mydata.burstNum = handles.mydata.cdfq{'burst'}(:);
% check the burst range requested
if isempty(handles.mydata.BurstNumRange), % user wants all the bursts
    handles.mydata.iBurstNumRange(1) = 1;
    handles.mydata.iBurstNumRange(2) = length(handles.mydata.burstNum);
else % user has specified a range, so make sure it's valid and look up the indeces
    idx = find(handles.mydata.burstNum == handles.mydata.BurstNumRange(1),1,'first');
    if isempty(idx),
        disp('Can''t find requested starting burst number, ')
        disp(sprintf('using first burst in qulity file = %d',handles.mydata.burstNum(1)));
        handles.mydata.iBurstNumRange(1) = 1;
    else handles.mydata.iBurstNumRange(1) = idx;
    end
    idx = find(handles.mydata.burstNum == handles.mydata.BurstNumRange(2),1,'first');
    if isempty(idx),
        disp('Can''t find requested ending burst number, ')
        disp(sprintf('using last burst in qulity file = %d',handles.mydata.burstNum(end)));
        handles.mydata.iBurstNumRange(2) = length(handles.mydata.burstNum);
    else handles.mydata.iBurstNumRange(2) = idx;
    end
end
% iBurstNumRange is now an accurate index range to the file
% the indeces now used by flagbadadv will refer to the subset of data
% loaded as follows:
disp(sprintf('Reading burst %d to %d from the quality file....',...
    handles.mydata.cdfq{'burst'}(handles.mydata.iBurstNumRange(1)),...
    handles.mydata.cdfq{'burst'}(handles.mydata.iBurstNumRange(2))))
b1 = handles.mydata.iBurstNumRange(1); b2 = handles.mydata.iBurstNumRange(2);
handles.mydata.burstNum = handles.mydata.cdfq{'burst'}(b1:b2);  % reread the burt numbers for the subset we're working on
handles.mydata.tm = datenum(gregorian(handles.mydata.cdfq{'time'}(b1:b2)+handles.mydata.cdfq{'time2'}(b1:b2)./(1000*3600*24)));
handles.mydata.stdv(:,:) = handles.mydata.cdfq{'flagbadadv_stdv'}(b1:b2,handles.mydata.currentBeam,:); % should be [nbursts x 5 subbursts]
handles.mydata.mcor(:,:) = handles.mydata.cdfq{'flagbadadv_mcor'}(b1:b2,handles.mydata.currentBeam,:); % should be [nbursts x 5 subbursts]
handles.mydata.stdp = handles.mydata.cdfq{'flagbadadv_stdp'}(b1:b2);
handles.mydata.cdfqFile = handles.mydata.cdfqFile;
handles.mydata.nSubbursts = length(handles.mydata.cdfq('subburst'));
handles.mydata.ivthsubbads(:,:) = handles.mydata.cdfq{'flagbadadv_ivthsubbads'}(b1:b2,handles.mydata.currentBeam,:); 
handles.mydata.icthsubbads(:,:) = handles.mydata.cdfq{'flagbadadv_icthsubbads'}(b1:b2,handles.mydata.currentBeam,:); 
handles.mydata.nBursts = length(handles.mydata.tm);
handles.mydata.scutoff = handles.mydata.cdfq{'flagbadadv_scutoff'}(handles.mydata.settings.currentBeam,:);
handles.mydata.ccutoff = handles.mydata.cdfq{'flagbadadv_ccutoff'}(handles.mydata.settings.currentBeam,:);
handles.mydata.mask(:,:) = handles.mydata.cdfq{'flagbadadv_mask'}(b1:b2,handles.mydata.settings.currentBeam,:);
handles.mydata.override_as_bad(:,:) = handles.mydata.cdfq{'flagbadadv_override_as_bad'}(b1:b2,handles.mydata.settings.currentBeam,:);
handles.mydata.override_as_good(:,:) = handles.mydata.cdfq{'flagbadadv_override_as_good'}(b1:b2,handles.mydata.settings.currentBeam,:);

idx = [];
% then, add any new overrides the user has provided
for iSubburst = 1:handles.mydata.nSubbursts,
    % translate burst numbers to file indexes
    for n = 1:length(handles.mydata.settings.new_bad{iSubburst}),
        idx(n) = find(handles.mydata.settings.new_bad{iSubburst}(n) == handles.mydata.burstNum,1,'first');
    end
    % then into a mask
    if ~isempty(idx), handles.mydata.override_as_bad(idx,iSubburst) = ones(size(idx)); end
end
idx = [];
% repeat for the good overrides
for iSubburst = 1:handles.mydata.nSubbursts,
    % translate burst numbers to file indexes
    for n = 1:length(handles.mydata.settings.new_good{iSubburst}),
        idx(n) = find(handles.mydata.settings.new_good{iSubburst}(n) == handles.mydata.burstNum,1,'first');
    end
    % then into a mask
    if ~isempty(idx), handles.mydata.override_as_good(idx,iSubburst) = ones(size(idx)); end 
end
if isfield(handles.mydata.settings,'new_scutoff'), 
    for iSubburst = 1:handles.mydata.nSubbursts,
        handles.mydata.scutoff(iSubburst) = handles.mydata.settings.new_scutoff(iSubburst);
    end
end
if isfield(handles.mydata.settings,'new_ccutoff'), 
    for iSubburst = 1:handles.mydata.nSubbursts,
        handles.mydata.ccutoff(iSubburst) = handles.mydata.settings.new_ccutoff(iSubburst);
    end
end
% apply these
handles.mydata = flagbads(hObject, handles);

% calculated the stats for pressure for plotting later
if isempty(handles.mydata.stdp), % we're only making one plot of pressure std, so plot the mean of the subburst values
    handles.mydata.stdpm = ones(size(handles.mydata.burstNum)).*NaN;
else handles.mydata.stdpm = mean(handles.mydata.stdp,2);
end

% set the cutoff boxes to the cutoff used based on the seed
for iSubburst = 1:handles.mydata.nSubbursts,
    buffer = sprintf('%6.2f',handles.mydata.scutoff(iSubburst));
    eval(sprintf('set(handles.editscutoff%d,''String'',buffer);',iSubburst))
    buffer = sprintf('%6.2f',handles.mydata.ccutoff(iSubburst));
    eval(sprintf('set(handles.editccutoff%d,''String'',buffer);',iSubburst))
end
set(handles.editTogBurst,'String','?,?')

% update the objects
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')
    updateplots(hObject, handles, 'init')
    % save the initial axes limits for fiddling with zoom later.
    kids = get(handles.figure1,'children');
    for i = 1:length(kids),
        iAx = [];
        buf = get(kids(i),'tag');
        if findstr(buf, 'cor'),
            iAx = 1; iPlot = str2num(buf(end));
        elseif findstr(buf, 'std'),
            iAx = 2; iPlot = str2num(buf(end));
        end
        if ~isempty(iAx),
            handles.oxLims{iPlot,iAx} = get(kids(i),'xlim');
            handles.oyLims{iPlot,iAx} = get(kids(i),'ylim');
            handles.cxLims{iPlot,iAx} = handles.oxLims{iPlot,iAx};
            handles.cyLims{iPlot,iAx} = handles.oyLims{iPlot,iAx};
        end
    end
end

handles.mydata.initialize = 1;

% make sure the delete function is called when the figure is closed
set(handles.figure1,'DeleteFcn',...
    ['disp(''Saving marks to quality file''); ',...
    'handles = guidata(gcbo); ',...
    'b1 = handles.mydata.iBurstNumRange(1); b2 = handles.mydata.iBurstNumRange(2); ',...
    'handles.mydata.cdfq{''flagbadadv_scutoff''}(handles.mydata.settings.currentBeam,:) = handles.mydata.scutoff; ',...
    'handles.mydata.cdfq{''flagbadadv_ccutoff''}(handles.mydata.settings.currentBeam,:) = handles.mydata.ccutoff; ',...
    'handles.mydata.cdfq{''flagbadadv_mask''}(b1:b2,handles.mydata.settings.currentBeam,:) = handles.mydata.mask; ',...
    'handles.mydata.cdfq{''flagbadadv_override_as_bad''}(b1:b2,handles.mydata.settings.currentBeam,:) = handles.mydata.override_as_bad; ',...
    'handles.mydata.cdfq{''flagbadadv_override_as_good''}(b1:b2,handles.mydata.settings.currentBeam,:) = handles.mydata.override_as_good; ',...
    'close (handles.mydata.cdfq);']); 

% update the objects
guidata(hObject, handles);

return

% UIWAIT makes flagbadadv wait for user response (see UIRESUME)
% this is not good, as one can't concurrently do anything else (like run
% ncbrowse or browsehydraburst concurrently.
% However, not using uwait means that I can't return results via varargout
% hence dumping the results to the workspace during the delete_fcn call
% uiwait(handles.figure1);

% ------------------ updates the plot - this is a user function
function updateplots(hObject, handles, zoomcontrol) 
if strcmp(get(gcf,'visible'),'off'), init = 1; 
else init = 0; end % must check here
theBlockStdAxes = {handles.axes1, handles.axes2, handles.axes3, handles.axes4, handles.axes5};
theStdStdAxes = handles.axes6;
axes(theStdStdAxes);
cla;
if isfield(handles.mydata,'tm'),
    plot(handles.mydata.tm,handles.mydata.stdpm)
    set(gca,'xlim',[handles.mydata.tm(1) handles.mydata.tm(end)])
    datetick('x','keeplimits','keepticks')
else
    plot(handles.mydata.burstNum,handles.mydata.stdpm)
    set(gca,'xlim',[handles.mydata.burstNum(1) handles.mydata.burstNum(end)])
    xlabel('Burst Number')
end
%set(gca,'ylim',[0 20])
ylabel('mean PSDEV for all')
for iPlot = 1:length(theBlockStdAxes),
    allbads = find(handles.mydata.mask(:,iPlot));
    overbads = find(handles.mydata.override_as_bad(:,iPlot));
    overgoods = find(handles.mydata.override_as_good(:,iPlot));
    axes(theBlockStdAxes{iPlot});
    xl = get(gca,'xlim');
    cla;
    % the way plotyy works, the std vel plots ends u on top and active
    [theAx, theLine1, theLine2] = plotyy(handles.mydata.burstNum,handles.mydata.mcor(:,iPlot),...
        handles.mydata.burstNum,handles.mydata.stdv(:,iPlot));    % activate only
    set(theLine2,'ButtonDownFcn','flagbadadv(''stdvline_ButtonDownFcn'',gcbo,[],guidata(gcbo))',...
        'UserData',iPlot); % label the subbursts so we know which one we get later when the user clicks
    set(get(theAx(1),'ylabel'),'string',sprintf('Cor %d',iPlot));
    set(theAx(1),'tag',sprintf('cor%d',iPlot));
    set(theAx(2),'tag',sprintf('std%d',iPlot));
    % use 'line' here instead to add lines, plot is destroying the axis object
    theLine6 = line(handles.mydata.burstNum,ones(handles.mydata.nBursts,1).*handles.mydata.ccutoff(iPlot),...
        'linestyle','--','color',get(theLine1,'color'));
    axes(theAx(2))
    theLine3 = line(handles.mydata.burstNum,ones(handles.mydata.nBursts,1).*handles.mydata.scutoff(iPlot),...
        'linestyle','--','color',get(theLine2,'color'));
    theMaskMarkers = line(handles.mydata.burstNum(allbads),handles.mydata.stdv(allbads,iPlot),'linestyle','none','marker','.','color','r');
    theOverBadMarkers = line(handles.mydata.burstNum(overbads),handles.mydata.stdv(overbads,iPlot),'linestyle','none','marker','*','color','r');
    theOverGoodMarkers = line(handles.mydata.burstNum(overgoods),handles.mydata.stdv(overgoods,iPlot),'linestyle','none','marker','o','color','r');
    set(theMaskMarkers,'ButtonDownFcn','flagbadadv(''stdvline_ButtonDownFcn'',gcbo,[],guidata(gcbo))',...
        'UserData',iPlot); % label the subbursts so we know which one we get later when the user clicks    
    set(get(theAx(2),'ylabel'),'string',sprintf('STD Vel %d',iPlot))
    %if strcmp(zoomcontrol,'init'),
        set(theAx,'xlim',[handles.mydata.burstNum(1) handles.mydata.burstNum(end)]) % really only need this the first time
    %elseif strcmp(zoomcontrol,'hold'),
        % restore the axes to what the user had zoomed to when something was pushed
    %    set(theAx(1),'ylim',handles.cyLims{iPlot,1}); %cor
    %    set(theAx(2),'ylim',handles.cyLims{iPlot,2});
    %    set(theAx(1),'xlim',handles.cxLims{iPlot,1}); % std
    %    set(theAx(2),'xlim',handles.cxLims{iPlot,2});
    %end
    linkaxes(theAx,'x') % now both plotyy axes will zoom together
    if iPlot == 1,
        title(['Beam ',int2str(handles.mydata.settings.currentBeam),...
            ' quality data by subburst from ',handles.mydata.cdfqFile],'interpreter','none')
    elseif iPlot == 5,
        set(get(theAx(2),'xlabel'),'string','Burst Number')        
    end
end

% ------------------ finds the baddata based on Vel STD cutoffs set by user
function mydata = flagbads(hObject, handles)
% first, clear the mask
handles.mydata.mask = zeros(size(handles.mydata.mask));
for iSubburst = 1:handles.mydata.nSubbursts,
    % assume user changed the cutoff value, find the new indeces that are bad
    ivthsubbads = find(handles.mydata.stdv(:,iSubburst) >= handles.mydata.scutoff(iSubburst));
    if ~isempty(ivthsubbads),
        handles.mydata.ivthsubbads(ivthsubbads,iSubburst) = ones(size(ivthsubbads));
    end
    icthsubbads = find(handles.mydata.mcor(:,iSubburst) < handles.mydata.ccutoff(iSubburst));
    if ~isempty(icthsubbads),
        handles.mydata.icthsubbads(icthsubbads,iSubburst) = ones(size(icthsubbads));
    end
    % first shot at a mask is the union of subbursts failing the thresholds
    idx = union(ivthsubbads, icthsubbads);
    % these are the new bad points based on the current threshold settings
    handles.mydata.mask(idx,iSubburst) = ones(size(idx));
    % now apply the user overides, forcing good and bad
    idx = find(handles.mydata.override_as_bad(:,iSubburst)); % indeces to bad data
    if ~isempty(idx), handles.mydata.mask(idx,iSubburst) = ones(size(idx)); end % force these as marked bad  
    idx = find(handles.mydata.override_as_good(:,iSubburst)); % indeces to good data
    if ~isempty(idx), handles.mydata.mask(idx,iSubburst) = zeros(size(idx)); end % force these as marked good  
end

% Update handles structure
guidata(hObject, handles);
% return the flags to the calling function
mydata = handles.mydata;
return

% --- Outputs from this function are returned to the command line.
function varargout = flagbadadv_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)

% this function gets called during initialization!

return

function editscutoff5_Callback(hObject, eventdata, handles)
% hObject    handle to editscutoff5 (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 editscutoff5 as text
%        str2double(get(hObject,'String')) returns contents of editscutoff5 as a double
handles.mydata.scutoff(5) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes5,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 5;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);

updateplots(hObject, handles, 'hold');

% --- Executes during object creation, after setting all properties.
function editscutoff5_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editscutoff5 (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

function editscutoff4_Callback(hObject, eventdata, handles)
% hObject    handle to editscutoff4 (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 editscutoff4 as text
%        str2double(get(hObject,'String')) returns contents of editscutoff4 as a double
handles.mydata.scutoff(4) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes4,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 4;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);

updateplots(hObject, handles, 'hold');

% --- Executes during object creation, after setting all properties.
function editscutoff4_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editscutoff4 (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

function editscutoff3_Callback(hObject, eventdata, handles)
% hObject    handle to editscutoff3 (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 editscutoff3 as text
%        str2double(get(hObject,'String')) returns contents of editscutoff3 as a double
handles.mydata.scutoff(3) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes3,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 3;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');
return

% --- Executes during object creation, after setting all properties.
function editscutoff3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editscutoff3 (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

function editscutoff2_Callback(hObject, eventdata, handles)
% hObject    handle to editscutoff2 (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 editscutoff2 as text
%        str2double(get(hObject,'String')) returns contents of editscutoff2 as a double
handles.mydata.scutoff(2) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes2,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 2;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);

updateplots(hObject, handles, 'hold');


% --- Executes during object creation, after setting all properties.
function editscutoff2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editscutoff2 (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



function editscutoff1_Callback(hObject, eventdata, handles)
% hObject    handle to editscutoff1 (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 editscutoff1 as text
%        str2double(get(hObject,'String')) returns contents of editscutoff1 as a double
handles.mydata.scutoff(1) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes1,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 1;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);

updateplots(hObject, handles, 'hold');


% --- Executes during object creation, after setting all properties.
function editscutoff1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editscutoff1 (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

%flagbadadv('axes1_ButtonDownFcn',gcbo,[],guidata(gcbo))
% --- Executes on mouse press over axes background.
function axes1_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('click')

% --- Executes on mouse press over axes background.
function stdvline_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)
% I set this in the line object to the subburst # and beam earlier
data = get(hObject,'UserData'); 
iPlot = data(1);
cb = get(gca,'CurrentPoint');
cb = round(cb(1,1));
% note that cp is the burst number, not an index into the array of burst numbers
% now must find which index has that burst number
icb = near(handles.mydata.burstNum, cb); % index that was toggled
% the user wants to invert the current state by mouse click
handles.mydata.mask(icb,iPlot) = ~handles.mydata.mask(icb,iPlot);
% now we must save this as an override
if handles.mydata.mask(icb,iPlot), % true means this is known bad
    handles.mydata.override_as_bad(icb, iPlot) = 1;
    handles.mydata.override_as_good(icb, iPlot) = 0;
    disp(sprintf('Selected Burst #%d in Subburst %d in beam %d added to Bad Override list',cb,iPlot,handles.mydata.currentBeam))
else
    handles.mydata.override_as_good(icb, iPlot) = 1;
    handles.mydata.override_as_bad(icb, iPlot) = 0;
    disp(sprintf('Selected Burst #%d in Subburst %d in beam %d added to Good Override list',cb,iPlot,handles.mydata.currentBeam))
end
% update the mask
handles.mydata = flagbads(hObject, handles);
buf = get(gca,'tag');
if findstr(buf, 'cor'), iAx = 1; iPlot = str2num(buf(end));
elseif findstr(buf, 'std'), iAx = 2; iPlot = str2num(buf(end));
end
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');

% Update handles structure
guidata(hObject, handles);

updateplots(hObject, handles, 'hold');




function editccutoff1_Callback(hObject, eventdata, handles)
% hObject    handle to editccutoff1 (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 editccutoff1 as text
%        str2double(get(hObject,'String')) returns contents of editccutoff1 as a double
handles.mydata.ccutoff(1) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes1,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 1;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');


% --- Executes during object creation, after setting all properties.
function editccutoff1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editccutoff1 (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

function editccutoff2_Callback(hObject, eventdata, handles)
% hObject    handle to editccutoff2 (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 editccutoff2 as text
%        str2double(get(hObject,'String')) returns contents of editccutoff2 as a double
handles.mydata.ccutoff(2) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes2,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 2;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');


% --- Executes during object creation, after setting all properties.
function editccutoff2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editccutoff2 (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



function editccutoff3_Callback(hObject, eventdata, handles)
% hObject    handle to editccutoff3 (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 editccutoff3 as text
%        str2double(get(hObject,'String')) returns contents of editccutoff3 as a double
handles.mydata.ccutoff(3) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes3,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 3;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');


% --- Executes during object creation, after setting all properties.
function editccutoff3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editccutoff3 (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



function editccutoff4_Callback(hObject, eventdata, handles)
% hObject    handle to editccutoff4 (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 editccutoff4 as text
%        str2double(get(hObject,'String')) returns contents of editccutoff4 as a double
handles.mydata.ccutoff(4) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes4,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 4;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');


% --- Executes during object creation, after setting all properties.
function editccutoff4_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editccutoff4 (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



function editccutoff5_Callback(hObject, eventdata, handles)
% hObject    handle to editccutoff5 (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 editccutoff5 as text
%        str2double(get(hObject,'String')) returns contents of editccutoff5 as a double
handles.mydata.ccutoff(5) = str2num(get(hObject,'String'));
handles.mydata = flagbads(hObject, handles);
% the user may have zoomed, so save the limits
buf = get(handles.axes5,'tag');
if findstr(buf, 'cor'), iAx = 1; 
elseif findstr(buf, 'std'), iAx = 2; 
end
iPlot = 5;
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');
% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');


% --- Executes during object creation, after setting all properties.
function editccutoff5_CreateFcn(hObject, eventdata, handles)
% hObject    handle to editccutoff5 (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





function editTogBurst_Callback(hObject, eventdata, handles)
% hObject    handle to editTogBurst (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 editTogBurst as text
%        str2double(get(hObject,'String')) returns contents of editTogBurst as a double

% the burst is asked for as #, #
[cb, buffer] = strtok(get(hObject,'String'),',');
[iPlot, buffer] = strtok(buffer,',');
cb = round(str2num(char(cb))); % chosen burst
iPlot = round(str2num(char(iPlot))); % chosen subburst plot
if isempty(cb) | isempty(iPlot), 
    set(hObject,'String','?,?')
    guidata(hObject, handles);
    disp('User entered burst or subburst missing')
    return
end
if iPlot < 1 | iPlot > 5,
    set(hObject,'String','?,?')
    guidata(hObject, handles);
    disp('User entered subburst out of bounds')
    return
end
% note that cp is the burst number, not an index into the array of burst numbers
% now must find which index has that burst number
icb = near(handles.mydata.burstNum, cb);
% the user wants to invert the current state by entering the burst number
handles.mydata.mask(icb,iPlot) = ~handles.mydata.mask(icb,iPlot);
% now we must save this as an override
if handles.mydata.mask(icb,iPlot), % true means this is known bad
    handles.mydata.override_as_bad(icb, iPlot) = 1;
    handles.mydata.override_as_good(icb, iPlot) = 0;
    disp(sprintf('Selected Burst #%d in Subburst %d in beam %d added to Bad Override list',cb,iPlot,handles.mydata.currentBeam))
else
    handles.mydata.override_as_good(icb, iPlot) = 1;
    handles.mydata.override_as_bad(icb, iPlot) = 0;
    disp(sprintf('Selected Burst #%d in Subburst %d in beam %d added to Good Override list',cb,iPlot,handles.mydata.currentBeam))
end

% update the mask
handles.mydata = flagbads(hObject, handles);

buf = get(gca,'tag');
if findstr(buf, 'cor'), iAx = 1; iPlot = str2num(buf(end));
elseif findstr(buf, 'std'), iAx = 2; iPlot = str2num(buf(end));
end
handles.cxLims{iPlot,iAx} = get(gca,'xlim');
handles.cyLims{iPlot,iAx} = get(gca,'ylim');

% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');

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




% ********************** this button currently removed from the figure
% --- Executes on button press in reset_zoom.
function reset_zoom_Callback(hObject, eventdata, handles)
% hObject    handle to reset_zoom (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
for iPlot = 1:handles.mydata.nSubbursts,
    for iAx = 1:2
        eval(sprintf('theAx = handles.axes%d;',iPlot))
        handles.cxLims{iPlot,iAx} = handles.oxLims{iPlot,iAx};
        handles.cyLims{iPlot,iAx} = handles.oyLims{iPlot,iAx};
    end
end
% Update handles structure
guidata(hObject, handles);
updateplots(hObject, handles, 'init');



% --- Executes on button press in cleargood.
function cleargood_Callback(hObject, eventdata, handles)
% hObject    handle to cleargood (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
handles.mydata.override_as_good = zeros(size(handles.mydata.override_as_good));
% update the mask
handles.mydata = flagbads(hObject, handles);
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');


% --- Executes on button press in clearbad.
function clearbad_Callback(hObject, eventdata, handles)
% hObject    handle to clearbad (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
handles.mydata.override_as_bad = zeros(size(handles.mydata.override_as_bad));
% update the mask
handles.mydata = flagbads(hObject, handles);
guidata(hObject, handles);
updateplots(hObject, handles, 'hold');