%SEGMENTGUI   GUI to do simple segmentation
%   OUT = SEGMENTGUI(IN) presents a GUI with a view of IN and
%   its histogram, and allows the user to select a threshold
%   for segmentation. OUT will contain the thresholded image
%   when the user is finished.
%
%   The threshold value can be changed by clicking on the
%   histogram. This will update the display. The image on
%   the left shows the grey-value image, the one on the
%   right the thresholded one.
%
%   In case of a 3D image, it is possible to change the view
%   by selecting one of the radiobuttons near the top. Also,
%   you can change the slice by clicking with the left and
%   right mouse buttons on one of the images.

%(c) by Cris Luengo, August 2001

% If you don't want either <enter> or <esc> to do what they do
% now, comment out the section in the function 'KeyPress' that
% handles these keys. This section is commented.
function out = segmentgui(in)

% Handle Callback functions
if ischar(in)
   switch(in)
   case 'DIP_GetParamList'
      out = struct('menu','Point',...
                   'display','Segment GUI',...
                   'inparams',struct('name',       {'in'},...
                                     'description',{'Input image'},...
                                     'type',       {'image'},...
                                     'dim_check',  {0},...
                                     'range_check',{[]},...
                                     'required',   {1},...
                                     'default',    {'a'}...
                                    ),...
                   'outparams',struct('name',       {'out'},...
                                      'description',{'Output image'},...
                                      'type',       {'image'}...
                                     )...
                  );
   case 'imageclick'
      ImageClick;
   case 'histclick'
      HistogramClick;
   case 'chngorient'
      ChangeOrientation;
   case 'sliceselect'
      SliceSelect;
   case 'keypress'
      KeyPress;
   otherwise
      error('Input must be an image!')
   end
   return
end

% Parse input image
if ~isa(in,'dip_image')
   in = dip_image(in);
end
in = squeeze(in);
if ndims(in)<2 | ndims(in)>3
   error('Only 2D and 3D images supported.')
end
if isa(dip_array(in),'double')
   in = dip_image(in,'sfloat');
end

% Create figure window
figh = figure;
dtu = get(0,'units');
set(0,'units','pixels');
dts = get(0,'ScreenSize');
dts = dts(3:4);
set(0,'units',dtu);
sz = [880,400];
set(figh,'units','pixels','position',[dts-sz-[10,100],sz],...
    'colormap',[0,0,0;1,0,0;gray(128)],...
    'color',get(0,'defaultuicontrolbackground'),...
    'KeyPressFcn','segmentgui(''keypress'')');
% Create image display
axhb = axes('parent',figh,'units','pixels',...
            'position',[sz(1)-256-20,60,256,256],...
            'visible','off','ydir','reverse','DataAspectRatio',[1,1,1]);
axhg = axes('parent',figh,'units','pixels',...
            'position',[sz(1)-512-40,60,256,256],...
            'visible','off','ydir','reverse','DataAspectRatio',[1,1,1]);
udata.img = in;
imsz = size(in);
if ndims(in)==3
   udata.orientation = 3; % axis along which we look: 3 = x-y slices.
                          % 1 = y-z slices.
   udata.slice = 0;
   imsz(udata.orientation) = [];
else
   udata.orientation = 0; % meaning 2D.
end
udata.imghb = image('parent',axhb);
udata.imghg = image('parent',axhg);
set(axhb,'xlim',[0,imsz(1)]+0.5,'ylim',[0,imsz(2)]+0.5);
set(axhg,'xlim',[0,imsz(1)]+0.5,'ylim',[0,imsz(2)]+0.5);
if ndims(in)==3
   set(udata.imghb,'ButtonDownFcn','segmentgui(''imageclick'')');
   set(udata.imghg,'ButtonDownFcn','segmentgui(''imageclick'')');
   % For 3D display: create buttons
   uicontrol('parent',figh,'style','text',...
             'position',[sz(1)-256-60-100,60+256+5,100,20],...
             'horizontalalignment','right',...
             'string','slice number:  ');
   udata.slicetxt = uicontrol('parent',figh,'style','edit',...
             'position',[sz(1)-256-60,60+256+5,60,20],...
             'string',num2str(udata.slice),...
             'horizontalalignment','left',...
             'callback','segmentgui(''sliceselect'')');
   udata.mxslc = uicontrol('parent',figh,'style','text',...
             'position',[sz(1)-256,60+256+5,100,20],...
             'string',['  (out of ',num2str(size(udata.img,udata.orientation)),')']);
   uicontrol('parent',figh,'style','radiobutton','string','X-Y',...
             'position',[sz(1)-512+130,60+256+30,50,20],'tag','3',...
             'callback','segmentgui(''chngorient'')','value',1);
   uicontrol('parent',figh,'style','radiobutton','string','X-Z',...
             'position',[sz(1)-512+130+70,60+256+30,50,20],'tag','2',...
             'callback','segmentgui(''chngorient'')','value',0);
   uicontrol('parent',figh,'style','radiobutton','string','Y-Z',...
             'position',[sz(1)-512+130+140,60+256+30,50,20],'tag','1',...
             'callback','segmentgui(''chngorient'')','value',0);
end
% Create histogram display
udata.histh = axes('parent',figh,'units','pixels',...
                   'position',[600-512-40,60,256,256],...
                   'box','on');
[hist,bins] = diphist(in,[]);
line('parent',udata.histh,'xdata',bins,'ydata',hist,...
     'ButtonDownFcn','segmentgui(''histclick'')');
yrange = [0,max(hist(2:end-1))];
set(udata.histh,'xlim',bins([1,end]),'ylim',yrange,'ytick',yrange);
                        % I do this because max and min values are too frequent.
udata.threshv = IsoDataThreshold(hist,bins);
udata.threshh = line('parent',udata.histh,...
                     'xdata',[udata.threshv,udata.threshv],...
                     'ydata',yrange,'color',[1,0,0],'EraseMode','xor',...
                     'ButtonDownFcn','segmentgui(''histclick'')');
set(figh,'ButtonDownFcn','segmentgui(''histclick'')');
set(udata.histh,'ButtonDownFcn','segmentgui(''histclick'')');
% Display image
DisplayImage(udata);
% Create control buttons
uicontrol('parent',figh,'String','Ok',...
          'position',[sz(1)-100,20,80,30],...
          'Callback','set(gcbf,''tag'',''OK'')');
uicontrol('parent',figh,'String','Cancel',...
          'position',[sz(1)-200,20,80,30],...
          'Callback','set(gcbf,''tag'',''CANCEL'')');
% Save data into figure window
set(figh,'userdata',[]);
set(figh,'userdata',udata); % This avoids a very slow update MATLAB sometimes does.
% Wait for user to finish
waitfor(figh,'tag');
ok = 0;
if ishandle(figh)
   if strcmp(get(figh,'tag'),'OK')
      ok = 1;
      udata = get(figh,'userdata');
   end
   delete(figh);
end
% Perform segmentation
if ok
   out = in>=udata.threshv;
else
   error('Operation cancelled');
end
% Done!


% Send a new image to the image display (update both)
function DisplayImage(udata)
switch udata.orientation
case 0
   data = udata.img;
case 1
   data = squeeze(udata.img(udata.slice,:,:));
case 2
   data = squeeze(udata.img(:,udata.slice,:));
case 3
   data = squeeze(udata.img(:,:,udata.slice));
end
g = uint8(stretch(data,0,100,129,2));
b = uint8(data >= udata.threshv);
set(udata.imghg,'cdata',g);
set(udata.imghb,'cdata',b);

% Send a new image to the binary image display
function DisplayBinaryImage(udata)
switch udata.orientation
case 0
   data = udata.img;
case 1
   data = squeeze(udata.img(udata.slice,:,:));
case 2
   data = squeeze(udata.img(:,udata.slice,:));
case 3
   data = squeeze(udata.img(:,:,udata.slice));
end
b = uint8(data >= udata.threshv);
set(udata.imghb,'cdata',b);

% Callback for clicking on the image
function ImageClick
figh = gcbf;
if ~isempty(figh)
   udata = get(figh,'userdata');
   imsz = size(udata.img);
   switch get(figh,'selectiontype')
   case 'normal' % left mouse click
      if udata.slice>=imsz(udata.orientation)-1
         return
      end
      udata.slice = udata.slice+1;
   case 'alt'    % right mouse click
      if udata.slice<=0
         return
      end
      udata.slice = udata.slice-1;
   end
   DisplayImage(udata);
   set(udata.slicetxt,'string',num2str(udata.slice));
   set(figh,'userdata',[]);
   set(figh,'userdata',udata); % This avoids a very slow update MATLAB sometimes does.
end

% Callback for pressing a key
function KeyPress
figh = gcbf;
if ~isempty(figh)
   udata = get(figh,'userdata');
   imsz = size(udata.img);
   switch get(figh,'currentcharacter')
   case {'n','N'} % next
      if udata.orientation==0 | udata.slice>=imsz(udata.orientation)-1
         return
      end
      udata.slice = udata.slice+1;
   case {'p','P'} % previous
      if udata.orientation==0 | udata.slice<=0
         return
      end
      udata.slice = udata.slice-1;
   %--- Handles escape and enter keys that terminate the dialog box.
   case 27        % <esc>
      set(gcbf,'tag','CANCEL');
      return
   case 13        % <enter>
      set(gcbf,'tag','OK');
      return
   %---
   end
   DisplayImage(udata);
   set(udata.slicetxt,'string',num2str(udata.slice));
   set(figh,'userdata',[]);
   set(figh,'userdata',udata); % This avoids a very slow update MATLAB sometimes does.
end

% Callback for the edit box (selecting a slice number)
function SliceSelect
figh = gcbf;
if ~isempty(figh)
   udata = get(figh,'userdata');
   imsz = size(udata.img);
   udata.slice = str2num(get(udata.slicetxt,'string'));
   if udata.slice >= imsz(udata.orientation)
      udata.slice = imsz(udata.orientation)-1;
   elseif udata.slice <= 0
      udata.slice = 0;
   end
   DisplayImage(udata);
   set(udata.slicetxt,'string',num2str(udata.slice));
   set(figh,'userdata',[]);
   set(figh,'userdata',udata); % This avoids a very slow update MATLAB sometimes does.
end

% Callback for the orientation checkboxes
function ChangeOrientation
[box,figh] = gcbo;
if ~isempty(figh)
   set(findobj(figh,'type','uicontrol','style','radiobutton'),'value',0);
   set(box,'value',1);
   udata = get(figh,'userdata');
   udata.orientation = str2num(get(box,'tag'));
   imsz = size(udata.img);
   if udata.slice >= imsz(udata.orientation)
      udata.slice = imsz(udata.orientation)-1;
   end
   imsz(udata.orientation) = [];
   set(get(udata.imghb,'parent'),'xlim',[0,imsz(1)]+0.5,'ylim',[0,imsz(2)]+0.5);
   set(get(udata.imghg,'parent'),'xlim',[0,imsz(1)]+0.5,'ylim',[0,imsz(2)]+0.5);
   DisplayImage(udata);
   set(udata.slicetxt,'string',num2str(udata.slice));
   set(udata.mxslc,'string',['  (out of ',num2str(size(udata.img,udata.orientation)),')']);
   set(figh,'userdata',[]);
   set(figh,'userdata',udata); % This avoids a very slow update MATLAB sometimes does.
end

% Callback for clicking on the histogram
function HistogramClick
figh = gcbf;
if ~isempty(figh)
   udata = get(figh,'userdata');
   pt = get(udata.histh,'CurrentPoint');
   xlim = get(udata.histh,'xlim');
   if pt(1,1)>=xlim(1) & pt(1,1)<=xlim(2)
      udata.threshv = pt(1,1);
      set(udata.threshh,'xdata',[pt(1,1),pt(1,1)]);
      DisplayBinaryImage(udata);
      set(figh,'userdata',[]);
      set(figh,'userdata',udata); % This avoids a very slow update MATLAB sometimes does.
   end
end

% Isodata threshold algorithm
function threshold_new = IsoDataThreshold(histogram,bins)
min_val = bins(1);
max_val = bins(end);
range = max_val-min_val;
interval = bins(2)-bins(1);
threshold_old = min_val;
threshold_new = min_val + range/2;
while (threshold_new - threshold_old < interval/10)
   mask = (bins < threshold_new);
   mean1 = sum(bins(mask).*histogram(mask)) ./ sum(histogram(mask));
   mask = (bins >= threshold_new);
   mean2 = sum(bins(mask).*histogram(mask)) ./ sum(histogram(mask));
   threshold_old = threshold_new;
   threshold_new = (mean1 + mean2) ./ 2;
end