prelim_UDS_analysis.m

%% prelim_UDS_analysis

% this script uses multiunit activity and filtered LFP traces to ID indices
% of probable upstates. An optional plotting function can be used as an
% additional sanity check
%(c) Constance Holman & Roberto De Filippo

%INPUT
%1. LFP file downsampled to 200 Hz. Rows are channels, and columns are time
%samples, Format = 'DSC-xxxxxx_xH_downsampled.mat'
%2. Files generated by Kilosort2 algorithm (Pachitariu et al., 2016) for spikes orting/multiunit
%analysis, e.g. ('spike_time.npy')

% Required: 'Spikes' package from Harris lab. See https://github.com/cortex-lab/spikes
% Required: 'npy-matlab' package (or equivalent) if Kilosort files in
% python, see https://github.com/kwikteam/npy-matlab

%OUTPUT
% row matrix of start and stop indices of detected upstates

load('your filename here') %downsampled LFP file, rows = channels, columns = time points
fs=200;
mychan=   1;%SELECT which channel to use to extract the 1-4 Hz trace
rec_length=round(length(dsdata)/fs/60);%recording length in minutes

%get spike time information
spikeStruct = loadKSdir(pwd);

rate = 0.1; %spike count bin size
[spikecountovertime]=spikeovertime(spikeStruct.st,rate,rec_length);
spikecountovertime=interp(spikecountovertime,20); %smoothing
spikecountovertime(spikecountovertime<0)=0;

onechan=dsdata(mychan,:);

[s] = spectrogram(onechan,fs/100,1,200,fs,'yaxis');
plim = abs(s);
delta_filtered=mean(plim(1:4,:));%mean 1-4 hz

%gamma_filtered=mean(plim(41:101,:)); %not used in current script

filteredTrace = sgolayfilt(delta_filtered,3,15);

[start_us,stop_us]=search_wrapper(onechan,filteredTrace,fs,mychan,spikecountovertime,rec_length,[]);
%% save US indices for future us (i.e. in batch processing scripts

%final script output
indices = horzcat(start_us,stop_us);
name2save ='US_indices.mat';
save(name2save,'indices')

%% Associated Mini-Functions
%%
function [spikecountovertime]=spikeovertime(st,rate,rec_length)%rate = rate of sampling,e.g. 0.1 sample every 100ms

[spikecountovertime,edges]=histcounts(st,0:rate:60*rec_length);
spikecountovertime=spikecountovertime/rate;

end
%%
function [start_us,stop_us]=search_wrapper(onechan,filteredTrace,fs,mychan,spikecountovertime,rec_length,XY)

%search for stop and start indices of us based on (1) LFP
%and (2) MUA
%TODO make this sequential rather than running script twice...

[start_LFP,stop_LFP]  = find_upstates(onechan,filteredTrace,fs,mychan,2); %find upstates according to power frequency
[start_spikes,stop_spikes]  = find_upstates(onechan,spikecountovertime,fs,mychan,1);%find upstates according to spike count

% go through detected deflections of LFP
for i=1:numel(start_LFP)
    us_lfpmua(start_LFP(i):stop_LFP(i))=1;
end
us_lfpmua(end+1:stop_spikes(end))=0; %append any extra period of elevated mua


%generate final indices to save
start_us=[];
stop_us=[];

%iterate through periods of elevated spiking
for i=1:numel(start_spikes)
    if sum(us_lfpmua(start_spikes(i):stop_spikes(i)))~=0 %find deflections in trace that are already contained within periods of elevated spiking
        start_us = vertcat(start_us,start_spikes(i)); %save this deflection as an upstate
        stop_us = vertcat(stop_us,stop_spikes(i));
    end
end


% %  %% Optional plotting functions for additional sanity check
% %  % TODO: fix bug with axes and way indices are save

% % figure
% % plot(onechan(mychan,:),'k')
% %
% % hold on
% % for i=1: numel(start_us)
% % rectangle('Position',[start_us(i) -1000 stop_us(i)-start_us(i) 2000],'LineStyle', 'none','FaceColor',[246/255 71/255 64/255 0.5])
% % end
% %     if ~isempty(XY)
% %         for i=1:2: numel(XY(:,1))
% %             rectangle('Position',[XY(i,1) -1000 XY(i+1,1)-XY(i,1) 2000],'LineStyle', 'none','FaceColor',[21/255 193/255 47/255 0.5])
% %         end
% %     end
% % xticks(0:fs*60:fs*rec_length*60)
% % xticklabels(0:60)
% % xlabel('time(m)')
% % title('raw trace')
% % xlim([1 numel(onechan(mychan,:))])
% % ylim([-1000 1000])
% %
% % figure
% % ax1=subplot(3,1,2)
% %
% % % if (filteredTrace) < fs*60*10 %added 12.02.19 by CH for bug in short 190207 RH baseline
% % %     p = plot:numel(filteredTrace),filteredTrace,1:numel(filteredTrace),(movmedian(filteredTrace,2000)+std(filteredTrace(1:length(filteredTrace))/2))%added 12.02.19 by CH for bug in short 190207 RH baseline
% % % else
% %  p=plot(1:numel(filteredTrace),filteredTrace,1:numel(filteredTrace),(movmedian(filteredTrace,2000)+std(filteredTrace(1:fs*60*10))*2));
% % % end
% % p(1).LineWidth = 2;p(2).LineWidth = 4; p(1).Color='k'
% % title('1-4 Hz power')
% % set(gca,'xticklabel',{[]})
% % hold on
% % for i=1: numel(start_spikes(1,:))
% % rectangle('Position',[start_spikes(i) 0 stop_spikes(i)-start_spikes(i) 50],'LineStyle', 'none','FaceColor',[255/255 49/255 46/255 0.5])
% % end
% % for i=1: numel(start_LFP(1,:))
% % rectangle('Position',[start_LFP(i) 0 stop_LFP(i)-start_LFP(i) 50],'LineStyle', 'none','FaceColor',[71/255 121/255 152/255 0.5])
% % end
% %
% % ax3=subplot(3,1,3)
% % p=plot(1:numel(spikecountovertime),spikecountovertime,1:numel(spikecountovertime),(movmedian(spikecountovertime,2000)+std(spikecountovertime(1:fs*60*10))/2))
% % title('Spike rate/s')
% % p(1).LineWidth = 2;;p(2).LineWidth = 4;; p(1).Color='k'
% % hold on
% % for i=1: numel(start_LFP(1,:))
% % rectangle('Position',[start_LFP(i) 0 stop_LFP(i)-start_LFP(i) 200],'LineStyle', 'none','FaceColor',[71/255 121/255 152/255 0.5])
% % end
% %
% %
% % xticks(0:fs*60:fs*rec_length*60)
% % xticklabels(0:60)
% % xlabel('time(m)')
% % set(gcf,'color','w');
% %
% % ax2=subplot(3,1,1)
% % plot(onechan(mychan,:),'k')
% % set(gca,'xticklabel',{[]})
% % hold on
% % for i=1: numel(start_us)
% % rectangle('Position',[start_us(i) -1000 stop_us(i)-start_us(i) 2000],'LineStyle', 'none','FaceColor',[246/255 71/255 64/255 0.5])
% % end
% % % if isempty(XY)~=1
% % % for i=1:2: numel(XY(:,1))
% % % rectangle('Position',[XY(i,1) -1000 XY(i+1,1)-XY(i,1) 2000],'LineStyle', 'none','FaceColor',[21/255 193/255 47/255 0.5])
% % % end
% % % end
% % title('raw trace')
% % %linkaxes([ax1,ax2,ax3],'x')
% % xlim([1 numel(onechan(mychan,:))/24])
% % fprintf('When RIGHT-click, the point is selected \n When LEFT-click, ZOOM-IN is performed right into the selected point \n When DOUBLE-click, ZOOM-OUT is done \n A) If ENTER is pressed, the selection is terminated. If no point was already selected, the outputs are empty \n B) If BACKSPACE key is pressed, the last selected point isdeleted and the selection continues.')
% %
% % if exist(ginput2(false,'r*')); %X = select rubbish upstates
% %     XX=ginput2(false,'r*');
% %         for i=2:2:numel(XX(:,1))
% %         start_us(start_us>XX(i-1,1)&start_us<XX(i,1))=[];
% %         stop_us(stop_us>XX(i-1,1)&stop_us<XX(i,1))=[];
% %     end
% % end

end
%%
function [start_temp,stop_temp]  = find_upstates(onechan,trace2analyze,fs,klik,mua_or_lfp)
%spike_or_freqpower==1   for lfp
%spike_or_freqpower==2   for mua

upstatelimit=4; %maximum us length in seconds

if (trace2analyze) < fs*60*10 %added 12.02.19 by CH as catch for  very short recs (<10 min) baselines
    overthreshold =trace2analyze>movmedian(trace2analyze,2000)+2*std(trace2analyze(1:length(trace2analyze)));%added 12.02.19 by CH for bug in 190207RH baseline
else
    overthreshold=trace2analyze>movmedian(trace2analyze,2000)+2*std(trace2analyze(1:fs*60*10));
end

start_temp=strfind( [0 overthreshold 0], [ 0 1 ] ); %start  upstate
stop_temp=strfind( [0 overthreshold 0], [ 1 0 ] ); %stop upstate

for i=2:numel(start_temp)
    if start_temp(i)-stop_temp(i-1)<fs/100*35 %if gap between two overthreshold<350 ms FILL IT!
        overthreshold(stop_temp(i-1):start_temp(i))=1;
    end
end
start_temp=strfind( [0 overthreshold 0], [ 0 1 ] );
stop_temp=strfind( [0 overthreshold 0], [ 1 0 ] );
%%
if mua_or_lfp==2 %analyze mua, check max and min length of frequency deflections
    
    for i=1:numel(start_temp)
        if stop_temp(i)-start_temp(i)<fs/100*10 %no shorter than 20ms
            overthreshold(start_temp(i):stop_temp(i))=0; %if so, get rid of it
        end
    end
    
    for i=1:numel(start_temp)
        if stop_temp(i)-start_temp(i)>fs*upstatelimit %no longer than upstate limit
            overthreshold(start_temp(i):stop_temp(i))=0;
        end
    end
   
    %find remaining epochs
    start_temp= strfind( [0 overthreshold 0], [ 0 1   ] );
    stop_temp= strfind( [0 overthreshold 0], [  1   0  ] );
    
  % check for epochs at beginning and end of recording
  % extend candidate periods to add initial deflection/return to baseline
  % 10uV is used here, may have to modify depending on noise
  
    for i=1:numel(start_temp)
        if onechan(start_temp(i))>10
            while onechan(start_temp(i))>10
                if start_temp(i)==1
                    break
                end
                start_temp(i)= start_temp(i)-1;
            end
        end
        
        if onechan(start_temp(i))<-10
            while onechan(start_temp(i))<-10
                if start_temp(i)==1
                    break
                end
                start_temp(i)= start_temp(i)-1;
            end
        end
    end
    for i=1:numel(stop_temp)
        if onechan(stop_temp(i))>10
            while onechan(stop_temp(i))>10
                if stop_temp(i)==length(onechan)
                    break
                end
                stop_temp(i)= stop_temp(i)+1;
                
            end
        end
        if onechan(stop_temp(i))<-10
            while onechan(stop_temp(i))<-10
                stop_temp(i)= stop_temp(i)+1;
            end
        end
    end
    
    % plot(onechan(:,klik))
    % hold on
    % for i=1: numel(start_spikes(1,:))
    % rectangle('Position',[start_spikes(i) 0 stop_spikes(i)-start_spikes(i) 500],'LineStyle', 'none','FaceColor',[1 0 0 0.5])
    % end
end
end
%%
% ginput2
% Carlos Adrian Vargas Aguilera (2020). ginput2.m v3.1 (Nov 2009) (https://www.mathworks.com/matlabcentral/fileexchange/20645-ginput2-m-v3-1-nov-2009), MATLAB Central File Exchange. Retrieved October 25, 2020.

function  [X,Y,BUTTON,SCALEMAT] = ginput2(varargin)
%GINPUT2   Graphical input from mouse with zoom, pan, plot and scaling.
%
%   SYNTAX:
%                        XY = ginput2;
%                        XY = ginput2(DoScale);          true or false
%                        XY = ginput2(...,PlotOpt);      '.r' for example
%                        XY = ginput2(...,'KeepZoom');   vs. 'UnZoom'
%                        XY = ginput2(N,...);
%                        XY = ginput2(...);
%                     [X,Y] = ginput2(...);
%              [X,Y,BUTTON] = ginput2(...);
%     [X,Y,BUTTON,SCALEMAT] = ginput2(...);
%
%   INPUT:
%     DoScale    - Single logical specifying whether the IMAGE should be
%                  interactively scaled (georeferenced), or it can be the
%                  2x4 SCALEMAT matrix for automatically scaling.
%                  DEFAULT: false (do not scales/georeferences)
%     PlotOpt    - String and/or parameter/value pairs specifying the drawn
%                  points optional inputs (see PLOT for details).
%                  DEFAULT: 'none' (do not plot any point)
%     'KeepZoom' - When finishing selection by default the zoom is
%                  restored. By using this option this feature is ignored.
%                  DEFAULT: 'UnZoom' (restores original axis limits)
%     N          - Number of points to be selected. One of 0,1,2,...,Inf
%                  DEFAULT: Inf (selects until ENTER or ESCAPE is pressed)
%
%   OUTPUT:
%     XY        - [X(:) Y(:)] axis coordinate(s).
%     X         - X-coordinate(s).
%     Y         - Y-coordinate(s).
%     BUTTON    - Last pressed button.
%     SCALEMAT  - 2x4 matrix specifying the coordinates of two different
%                 points (1) and (2) in the Image coordinates (pixels) and
%                 the User coordinates (data):
%                                                Point 1     Point 2
%                   Image coord (pixels):     [ (I1x,I1y)   (I2x,I2y)
%                   User  coord (data)  :       (U1x,U1y)   (U2x,U2y) ]
%                 to be use for scaling/georeferencing.
%
%   DESCRIPTION:
%     This program uses MATLAB's GINPUT function to get the coordinates
%     of a mouse-selected point in the current figure (see GINPUT for
%     details), but with five major improvements:
%                  1. ZOOMING  (left click)
%                  2. PANNING  (dragging mouse)
%                  3. DELETING (last selected point)
%                  4. PLOTING  (temporarily the selected points)
%                  5. SCALING or GEOREFERENCE IMAGES.
%     The differences are:
%      a) Obviously, the SCALEOPT and PlotOpt optional arguments.
%      b) When click is made outside the axes, it is ignored.
%      c) When LEFT-click, ZOOM-IN is performed right into the selected
%         point (PANNING).
%      d) When RIGHT-click, the point is selected (normal).
%      e) When DOUBLE-click, ZOOM-OUT is done.
%      f) When MIDDLE-click, ZOOM-RESET is done (see ZOOM for details).
%      g) When dragging while pressed left-click PAN is done (until the
%         button is released).
%      h) When pressed any KEY follows the next rules:
%          A) If ENTER is pressed, the selection is terminated. If no point
%             was already selected, the outputs are empty's.
%          B) If BACKSPACE key is pressed, the last selected point is
%             deleted and the selection continues.
%          C) If SPACEBAR the mouse current position or NANs coordinates
%             are saved, depending whether the mouse was inside or outside
%             any of the current figure axes, respectively. In this latter
%             case, the selection is NOT counted as one of the N points.
%             Besides, when drawing the color is changed. Then, the outputs
%             may not be of length N.
%
%   NOTE:
%     * Optional inputs use its DEFAULT value when not given or [].
%     * Optional outputs may or not be called.
%     * String inputs may be shortened, as long as they are unambiguous.
%       Case is ignored.
%     * The function can be used for interactively digitalize/vectorize
%       RASTER images with:
%       >> ginput(true)
%     * The function can be used only as a georeference function with
%       >> ginput2(0,true)
%     * The scale/georeference only works when the current axes has an
%       IMAGE type children (see Image for details).
%     * The x and y data from axes and image are changed when scale/
%       georeference is used.
%     * The drawn points are deleted from the graphics once the selection
%       is finished.
%     * The priority of the inputs are: N, then SCALEOPT and finally
%       PlotOpt. If the first (integer) is missing, the next is taken into
%       account (logical or 2x4 matrix) and so on.
%
%   EXAMPLE:
%     % Selects until ENTER is pressed:
%         xy = ginput2;
%     % Selects 5 points:
%         [x,y] = ginput2(5);
%     % Gets pressed button:
%         [x,y,button] = ginput2(1);
%     % Scales image and select 4 points temporarily coloring them in
%       black. Besides to not ZOOM OUT at the end:
%         imagesc(peaks(40))
%         [x,y,button,scalemat] = ginput2(4,true,'k*','KeepZoom');
%         hold on, plot(x,y,'or'), hold off
%
%   SEE ALSO:
%     GINPUT, PLOT.
%
%
%   ---
%   MFILE:   ginput2.m
%   VERSION: 3.1 (Nov 12, 2009) (<a href="matlab:web('http://www.mathworks.com/matlabcentral/fileexchange/authors/11258')">download</a>)
%   MATLAB:  7.7.0.471 (R2008b)
%   AUTHOR:  Carlos Adrian Vargas Aguilera (MEXICO)
%   CONTACT: nubeobscura@hotmail.com

%   REVISIONS:
%   1.0      Released. (Jul 09, 2008)
%   2.0      Changed default YESERROR value and fixed a bug there. Changed
%            behavior when N==1. Fixed bug with zoom out. Changed default
%            selection keys. Changed default selection click mouse: from
%            left one to the right one. (Jun 08, 2009)
%   2.1      Fixed bugs related with points deletion. Added new 'KeepZoom'
%            feature. (Aug 20, 2009)
%   3.0      Now it PANs when dragging. Updated help. (Nov 05, 2009)
%   3.1      Now returns when N==1 and pressed not predefined KEYS or one
%            of DELECTION or RETURN buttons. (Nov 12, 2009)

%   DISCLAIMER:
%   ginput2.m is provided "as is" without warranty of any kind, under the
%   revised BSD license.

%   Copyright (c) 2008-2009 Carlos Adrian Vargas Aguilera


% INPUTS CHECK-IN
% -------------------------------------------------------------------------

% PARAMETERS
% Defaults:
X        = [];
Y        = [];
BUTTON   = [];
SCALEMAT = [];
N        = Inf;
DoScale  = false;
PlotOpt  = {'none'};
UnZoom   = 'UnZoom';
% Constants KEYs (on my personal keyboard):
DOUBLECLICK    =   0;
LEFTCLICK      =   1;
MIDDLECLICK    =   2;
RIGHTCLICK     =   3;
BACKSPACE      =   8;
ESCAPE         =  27;
LEFTARROW      =  28;
RIGHTARROW     =  29;
UPARROW        =  30;
DOWNARROW      =  31;
SPACEBAR       =  32;
DELETE         = 127;
ASCII          = [ ...
    33:64  ...  UP-KEYS
    65:90  ...  UP-LETTERS
    91:96  ... LOW-KEYS
    97:122 ... LOW-LETTERS
    123:126 ... LOW-KEY
    161:255 ...     FOREING
    ];
% Functionality:
% NOTE: I left all this KEYs because the user may use this special case for
% other special purposes outside this function.
% % First version default:
% % SELECTS   = [LEFTCLICK ASCII ESCAPE LEFTARROW RIGHTARROW ...
% %              UPARROW DOWNARROW SPACEBAR DELETE];
% % ZOOMIN    = RIGHTCLICK;
SELECTS   = [RIGHTCLICK SPACEBAR]; % Selection  buttons
DELETES   = BACKSPACE;             % Deletion   buttons
FINISHES  = [];                    % Finishes   buttons
ZOOMIN    = LEFTCLICK;             % ZOOM(2)    buttons
ZOOMRESET = MIDDLECLICK;           % ZOOM RESET buttons
ZOOMOUT   = DOUBLECLICK;           % ZOOM OUT   buttons
% Other parameters
secpause  = 0.3;    % Seconds to wait for double-click response.
YESERROR  = false;  % If there is an error with GINPUT, it tells to display
% an ERROR or a WARNING message.

% Checks number of inputs:
if nargout>4
    error('CVARGAS:ginput2:tooManyOutputs',...
        'At most 4 outputs are allowed.')
end

% Checks N:
if ~isempty(varargin) && ~isempty(varargin{1}) && ...
        isfloat(varargin{1})
    N           = round(abs(varargin{1}(1))); % Forced unique, positive
    varargin(1) = [];                         % integer.
end

% Checks DoScale:
if ~isempty(varargin) && ~isempty(varargin{1}) && ...
        ((islogical(varargin{1})) || (ndims(varargin{1})==2 && ...
        all(size(varargin{1})==[2 4])))
    DoScale     = varargin{1};
    varargin(1) = [];
end

% Checks UnZoom:
if ~isempty(varargin)
    if ~isempty(varargin{1}) && ischar(varargin{1})
        if     strncmpi(varargin(1),'UnZoom'  ,max(length(varargin{1}),2))
            UnZoom = 'UnZoom';
            varargin(1) = [];
        elseif strncmpi(varargin(1),'KeepZoom',max(length(varargin{1}),2))
            UnZoom = 'KeepZoom';
            varargin(1) = [];
        end
    elseif (length(varargin)>1) && ~isempty(varargin{end}) && ...
            ischar(varargin{end})
        if     strncmpi(varargin(end),'UnZoom'  ,max(length(varargin{1}),2))
            UnZoom = 'UnZoom';
            varargin(end) = [];
        elseif strncmpi(varargin(end),'KeepZoom',max(length(varargin{1}),2))
            UnZoom = 'KeepZoom';
            varargin(end) = [];
        end
    end
end

% Checks PlotOpt:
if ~isempty(varargin) && ~isempty(varargin{1})
    PlotOpt = varargin;
end
clear varargin

% Checks DoScale:
if ~islogical(DoScale)
    SCALEMAT = DoScale;
    DoScale = true;
end

% SCALES/GEOREFERENCE?:
if DoScale
    method = 'linear';
    extrap = 'extrap';
    ha     = gca;
    hi     = findobj(get(ha,'Children'),'Type','image');
    axes(ha)
    if ~isempty(hi)
        hi    = hi(1);
        xlim  = get(ha,'XLim');
        ylim  = get(ha,'YLim');
        zlim  = get(ha,'ZLim');
        z     = repmat(max(zlim),1,5);
        xdata = get(hi,'XData');
        ydata = get(hi,'YData');
        if isempty(SCALEMAT) % interactively
            I1x = round(min(xdata)); I2x = round(max(xdata));
            I1y = round(min(ydata)); I2y = round(max(ydata));
            % Default (equal):
            U1x = I1x; U2x = I2x;
            U1y = I1y; U2y = I2y;
            hgeo     = [];
            dlgTitle = 'Georeference image';
            lineNo   = 1;
            
            while true
                % Selects first corner:
                theans = ...
                    questdlg('Select the first corner (1 of 2):',dlgTitle,'OK','OK');
                if ~strcmp(theans,'OK'), return, end
                pause(secpause)
                
                [I1x,I1y] = ginput2(1,false,'none','UnZoom');
                I1x       = round(I1x);
                I1y       = round(I1y);
                if ~ishandle(ha), return, end
                if (ha==gca) && ~isempty(I1x) && ~isnan(I1x)
                    axis(ha,[xlim ylim])
                    hgeo(1) = line([xlim NaN I1x I1x],[I1y I1y NaN ylim],z,'color','m');
                    prompt  = {'X-coordinate at 1st corner:',...
                        'Y-coordinate at 1st corner:'};
                    def     = {int2str(I1x),int2str(I1y)};
                    answer  = inputdlg(prompt,dlgTitle,lineNo,def);
                    answer  = str2num(char(answer{:}));
                    break
                end
            end
            axes(ha)
            
            % Checks inputs:
            if ~isempty(answer) && isfloat(answer) && (length(answer)==2) && ...
                    all(isfinite(answer))
                U1x = answer(1); U1y = answer(2);
                secondcorner = true;
            else
                secondcorner = false;
                warning('CVARGAS:ginput2:incorrectGeoreference',...
                    'Ignored incorrect georeference corners.')
            end
            
            while secondcorner
                % Selects second corner:
                theans = ...
                    questdlg('Select the second corner (2 of 2):',dlgTitle,'OK','OK');
                if ~strcmp(theans,'OK'), return, end
                pause(secpause)
                
                [I2x,I2y] = ginput2(1,false,'none','UnZoom');
                I2x       = round(I2x);
                I2y       = round(I2y);
                if ~ishandle(ha), return, end
                if (ha==gca) && ~isempty(I2x) && ~isnan(I2x) && ...
                        (I2x~=I1x) && (I2y~=I1y)
                    axis(ha,[xlim ylim])
                    hgeo(2) = line([xlim NaN I2x I2x],[I2y I2y NaN ylim],z,'color','c');
                    prompt  = {'X-coordinate at 2nd corner:',...
                        'Y-coordinate at 2nd corner:'};
                    def     = {int2str(I2x),int2str(I2y)};
                    answer  = inputdlg(prompt,dlgTitle,lineNo,def);
                    answer  = str2num(char(answer{:}));
                    break
                end
            end
            axes(ha)
            
            % Checks inputs:
            if secondcorner && ~isempty(answer) && isfloat(answer) && ...
                    (length(answer)==2) && all(isfinite(answer))
                U2x = answer(1); U2y = answer(2);
            else
                warning('CVARGAS:ginput2:incorrectGeoreference',...
                    'Ignored incorrect georeference corners.')
            end
            
            % Deletes corner's lines:
            if any(ishandle(hgeo))
                delete(hgeo(ishandle(hgeo)))
            end
            
            % Scale matrix:
            SCALEMAT = [I1x I1y I2x I2y; U1x U1y U2x U2y];
        else
            % Continue
        end
    else
        warning('CVARGAS:ginput2:noImageFound',...
            'No image found in the current axes to georeference.')
    end
    
    % OK, set the scaling then:
    if ~isempty(SCALEMAT)
        xdata = interp1(SCALEMAT(1,[1 3]),SCALEMAT(2,[1 3]),xdata,method,extrap);
        ydata = interp1(SCALEMAT(1,[2 4]),SCALEMAT(2,[2 4]),ydata,method,extrap);
        xlim2 = interp1(SCALEMAT(1,[1 3]),SCALEMAT(2,[1 3]),xlim ,method,extrap);
        ylim2 = interp1(SCALEMAT(1,[2 4]),SCALEMAT(2,[2 4]),ylim ,method,extrap);
        set(hi,'XData',xdata);
        set(hi,'YData',ydata);
        set(ha,'XLim' ,sort(xlim2,'ascend'));
        set(ha,'YLim' ,sort(ylim2,'ascend'));
        % Reverses axis directions:
        if diff(xlim)*diff(xlim2)<1
            if strcmp(get(ha,'XDir'),'normal')
                set(ha,'XDir','reverse')
            else
                set(ha,'XDir','normal')
            end
        end
        if diff(ylim)*diff(ylim2)<1
            if strcmp(get(ha,'YDir'),'normal')
                set(ha,'YDir','reverse')
            else
                set(ha,'YDir','normal')
            end
        end
    end
    axis(ha,'normal')
    
end

% DRAWS?:
if strcmpi(PlotOpt{1},'none')
    yesdraw = false;
else
    yesdraw = true;
end
% Optional parameters:
if yesdraw
    hpoints  = [];
    % Check for linestyle color:
    yescolor     = true;
    Nplotopt     = length(PlotOpt);
    yeslinestyle = rem(Nplotopt,2);
    if yeslinestyle % Given LineStyle
        for k = 1:length(PlotOpt{1})
            switch lower(PlotOpt{1}(k))
                case 'y', yescolor = false; break
                case 'm', yescolor = false; break
                case 'c', yescolor = false; break
                case 'r', yescolor = false; break
                case 'g', yescolor = false; break
                case 'b', yescolor = false; break
                case 'w', yescolor = false; break
                case 'k', yescolor = false; break
                otherwise, % no color specified
            end
        end
    end
    if ~yescolor && (Nplotopt*yeslinestyle~=1)
        for k = yeslinestyle+1:2:Nplotopt    % Given 'Color'
            if strncmpi(PlotOpt{k},'co',2), yescolor = false; break, end
        end
    end
    if yescolor
        contnan  = 1;
        colors   = get(gca,'ColorOrder');
        ncolors  = size(colors,1);
        color    = colors(1,:);
    end
end


% -------------------------------------------------------------------------
% MAIN
% -------------------------------------------------------------------------

cont       = 0;
alim.ha    = [];
alim.la    = {};
undoPtrFig = [];

while cont<N     % Principal loop
    
    % GINPUT:
    try
        [x,y,button] = ginput(1);
    catch % Changed for compatibility.
        % GINPUT error:
        if YESERROR
            error('CVARGAS:ginput2:executionError',lasterr)
        else
            warning('CVARGAS:ginput2:executionError',lasterr)
            if nargout<2  % Fixed BUG 29 SEP, 2008
                X = [X Y];
            end
            return
        end
    end
    
    % Axes clicked:
    ha = gca;
    
    % Gets limits:
    if ~any(alim.ha==ha)
        alim.ha(end+1) = ha;
        alim.la{end+1} = axis;
    end
    
    % Sets zoom:
    zlim = getappdata(ha,'zoom_zoomOrigAxesLimits');
    if isempty(zlim) % Fixed BUG, SEP 2008
        zoom reset
        zlim = getappdata(ha,'zoom_zoomOrigAxesLimits');
    end
    
    % Checks if DOUBLE clicks:
    pause(secpause) % Gives time for response
    if strcmp(get(gcf,'selectiontype'),'open')
        button = DOUBLECLICK;
    end
    
    % Checks if ENTER or FINISHES button:
    if isempty(button) || ismember(button,FINISHES)
        % Finishes selection:
        if (N==1) && isempty(X) % New feature v3.1
            BUTTON = button;
        end
        break
    end
    
    % Checks if DELETION button:
    if ismember(button,DELETES)
        if ~isempty(X)
            inan = isnan(X(end));
            if yesdraw
                if ~inan
                    % Deletes last drawn point:
                    if ~isempty(hpoints) && ishandle(hpoints(end)) % Fixed bug Aug 2009
                        delete(hpoints(end)), hpoints(end) = [];
                    end
                elseif yescolor
                    % Change color as necessary:
                    contnan = contnan-1;
                    color   = colors(mod(contnan-1,ncolors)+1,:);
                end
            end
            % Deletes the last selected point:
            X(end)      = [];
            Y(end)      = [];
            BUTTON(end) = [];
            % Checks if the last point was NaN:
            if ~inan
                cont = cont-1;
            end
        elseif N==1
            % Finishes selection: New feature v3.1
            BUTTON = button;
            break
        end
        continue
    end
    
    % Checks if ZOOM OUT button:
    if ismember(button,ZOOMOUT)
        undoPtrFig = gcf;
        setptr(undoPtrFig,'glassminus')
        zoom out
        continue
    end
    
    % Checks if ZOOM RESET button:
    if ismember(button,ZOOMRESET)
        zoom reset
        continue
    end
    
    % Checks if the mouse was inside an axes of the current figure;
    lim     = axis;
    outside = x<lim(1) || x>lim(2) || y<lim(3) || y>lim(4);
    
    % Checks if ZOOM IN with PAN:
    if ismember(button,ZOOMIN) && ~outside
        % Dragging rectangle:
        undoPtrFig = gcf;
        setptr(undoPtrFig,'closedhand')
        rbbox
        ydrag = get(gca,'CurrentPoint');
        xdrag = ydrag(1,1)-x;
        ydrag = ydrag(1,2)-y;
        % Do the PANNING:
        if  any(abs([xdrag ydrag])>eps*1000000)
            % Only PAN (dragging):
            lim(1:4) = lim(1:4) - [xdrag xdrag ydrag ydrag];
            axis(lim)
        else
            % PAN (centers the last point) and ZOOM in:
            setptr(undoPtrFig,'glassplus')
            lim = [x+diff(lim(1:2))/2*[-1 1] y+diff(lim(3:4))/2*[-1 1]];
            axis(lim)
            zoom(2)
        end
        continue
    end
    
    % Checks if SELECTS button:
    if ismember(button,SELECTS)
        
        % Sets NaNs if outside the axes:
        if outside
            if ~isnumeric(N)
                % Change color:
                if yesdraw && yescolor
                    contnan = contnan+1;
                    color   = colors(mod(contnan-1,ncolors)+1,:);
                end
                % Adds NaNs but the point counters do not take it into account:
                X      = [X;      NaN];
                Y      = [Y;      NaN];
                BUTTON = [BUTTON; button];
            else
                % Ignores the point
            end
        else
            % Draws the result:
            if yesdraw
                % Search for last point:
                x0 = []; y0 = []; z0 = [];
                inan = isnan([NaN; X; NaN]);
                if ~inan(end-1)
                    inan        = find(inan);
                    nlastpoints = inan(end)-inan(end-1)-1;
                    npoints     = length(hpoints);
                    range       = npoints-nlastpoints+1:npoints;
                    hlastaxes   = get(hpoints(range),'Parent');
                    if iscell(hlastaxes), hlastaxes = [hlastaxes{:}]; end
                    [loc,loc] = ismember(ha,hlastaxes);
                    if loc
                        x0 = get(hpoints(range(loc)),'XData');
                        y0 = get(hpoints(range(loc)),'YData');
                        z0 = get(hpoints(range(loc)),'ZData');
                    end
                end
                holdon = ishold;
                if ~holdon, hold on, end
                h = plot([x0 x],[y0 y],PlotOpt{:});
                % Elevates the value:
                z = get(ha,'ZLim'); z = z(2);
                set(h,'Zdata',[z0 z])
                % Sets the color:
                if yescolor
                    set(h,'Color',color)
                end
                hpoints = [hpoints; h];
                if ~holdon, hold off, end
                % Restores limits:
                axis(lim)
            end
            
            % Centers the selected point if ZOOM-IN: 29 SEP,2008
            if all((lim~=zlim(1:4)))
                lim = [x+diff(lim(1:2))/2*[-1 1] y+diff(lim(3:4))/2*[-1 1]];
                axis(lim)
            end
            
            % Saves the result:
            X      = [X;      x];
            Y      = [Y;      y];
            BUTTON = [BUTTON; button];
            cont   = cont+1;
        end
        continue
    end
    
    % Checks if any other button pressed inside the axes:
    if ~outside
        X      = [X;      x];
        Y      = [Y;      y];
        BUTTON = [BUTTON; button];
        cont   = cont+1;
    else
        if N==1 % New feature v3.1
            BUTTON = button;
            break
        end
        % ignores the selection
    end
    
end

% Returns pointer.
if ~isempty(undoPtrFig) && ishandle(undoPtrFig)
    setptr(undoPtrFig,'arrow')
end

% Deletes drawn points if still exist:
if yesdraw && any(ishandle(hpoints))
    delete(hpoints(ishandle(hpoints)))
end

% Returns original limits.
if ~strcmp(UnZoom,'KeepZoom') && ~isempty(alim.ha)
    alim.ha(~ishandle(alim.ha)) = [];
    for k = 1:length(alim.ha)
        temp = axis(alim.ha(k));
        if ~all(temp(1:4)==alim.la{k}(1:4))
            axis(alim.ha(k),alim.la{k})
        end
    end
end


% OUTPUTS CHECK-OUT
% -------------------------------------------------------------------------

if nargout<2
    X = [X Y];
end
end