sliceomatic.m

医学图像处理matlab工具箱

function sliceomatic(p1,p2)
% SLICEOMATIC - Slice and isosurface volume exploration GUI
%
% SLICEOMATIC(DATA) - Use 3D double matrix DATA as a volume data
%
% Example:
%
%       [x,y,z] = meshgrid(-2:.2:2, -2:.25:2, -2:.16:2);
%       v = x .* exp(-x.^2 - y.^2 - z.^2);
%       sliceomatic(v)
%
% Using SLICEOMATIC with no arguments is equivalent to the above
% example.
%
% Using the GUI:
% -------------
% The white bars on the top, left, and right allow insertion of
% new slices on the X, Y, and Z planes.  Click in an empty area to
% add a new slice or surface.  Click on a control arrow to add a
% new slice or surface.
%
% The colored bar at the bottom is used to place and position an
% isosurface.  The color in the bar indicates a position (as seen
% in the slice) where the isosurface will go.
%
% When the rotate camera button is on, the popup menu will control
% the camera.  Turn off camera rotation in order to get individual
% control over properties of the slices and isosurfaces.
%
% The defaults menu provides default features of newly created
% slices and surfaces.  The AllSlices menu controls properties of
% all the slices and surfaces in the scene.  Use popup menus on the
% objects themselves, or the control arrows to change indivudual
% properties.
%
% If the data is very large, a reduced model of the data is created.
% This reduced data set is used for interactivly positioning
% isosurfaces.
%
% The Colormap popdown controls the currenlty active colormap.
% This map is used to color the slices.  The Alphamap popdown
% controls the alphamap used on the slices.
%
% Doing Cool Stuff:
% ----------------
%
% Exploration:
% You can get a quick feel of the current data set by adding a
% slice using the ColorTexture option.  Such a slice can be dragged
% through the data very quickly.
%
% Highlight an Area:
% If certain values in your data are interesting (very large, very
% small, or very median values) you can use transparency to make
% parts of your slices disappear.  Choose AlphaTexture options from
% the defaults, and sweep some slices across your data.  Use the
% AlphaMap to pick out certain data sets.  The exaple given here
% looks best with the `vdown' alphamap.
%
% You can also add a contour onto a slice to further extract shapes
% from the data you are exploring.
%
% Hidden Shapes:
% Use the isosurface control bar to create an isosurface.  Be
% patient with this control.  It often takes a while for the
% surface to be created.  Click and hold the mouse button down
% until the first surface appears.  Drag the surface through the
% values until you get something you like, then let go.  If your
% data set is very large, you will need to wait while the new and
% more accurate isosurface is created.
%
% Volumes:
% You can simulate a volume object by creating lots of stacked
% slices.  Simply use the proper Alphamap and transparent textures
% to highlight the correct data, and a large stack of slices will
% let you simulate a volume object.
%
% BUGS:
% ----
%
% 1) Sliceomatic does not use the `slice' command.  All slices are
%    created by explicitly extracting data from the volume.  As such,
%    only slices at integer values are allowed.
% 
%
% See Also: SLICE, ISOSURFACE, ISOCAPS, CONTOURC, COLORMAP, SURFACE
  
% This is version 2.0 of sliceomatic.
%
% Sliceomatic is a tool I wrote for fun.  There are no warrenties
% expressed or implied.

% Written by Eric Ludlam <[e-mail]>
% Copyright 2000, 2001, 2002 The MathWorks Inc
% 
% Slightly modified to work with MIA_gui.m (medical image analysis) by Laszlo Balkay
% ([e-mail]). 2003
%   1. at the startup the program sets up 3 default slices at the half of the axis
%   2. scaling the axis (DataAspectRatio) regarding the pixelsize of the input volume
%      The pixelsize info should come from the "scaninfo" structure by the p2 argin.
%   3. If the size(volume,1 or 2) > 128, then the volume will be resized to 128*128*size(volume,3)  
%   4. more colormap is added to the sliceomaticfigure.m

  if nargin==0
    [x,y,z] = meshgrid(-2:.2:2, -2:.25:2, -2:.16:2);
    v = x .* exp(-x.^2 - y.^2 - z.^2);
    sliceomatic(v)
    return
  end

  if isa(p1,'double')
% $$$     if nargin==4
% $$$       d.Xv=p1;
% $$$       d.Yv=p2;
% $$$       d.Zv=p3
% $$$       p1=p4;
% $$$     else
% $$$       d.Yv=1:size(p1,1);
% $$$       d.Xv=1:size(p1,2);
% $$$       d.Zv=1:size(p1,3);
% $$$     end
    
    scaninfo = p2;
    RenderSize = 128;
    imaVOL = uint16(p1);
    if scaninfo.imfm(1) > RenderSize
        % setting up the progression bar
		info.color=[1 0 0];
		info.title='Sliceomatic in progress ...';
		info.size=1;
		info.pos='topleft';
		hpbar = progbar(info);
        imaVOLr = uint16(zeros(RenderSize,RenderSize,scaninfo.num_of_slice));
        for i = 1: scaninfo.num_of_slice
            progbar(hpbar,round(i/scaninfo.num_of_slice*100));
            imaVOLr(:,:,i) = imresize(imaVOL(:,:,i), [RenderSize RenderSize],'bilinear');
        end
        close(hpbar);
	else
        imaVOLr = imaVOL;
    end
    d.data=double(imaVOLr);
    d.UseGenericOpenGL = scaninfo.UseGenericOpenGL;
    pixsize = scaninfo.pixsize;
    d = sliceomaticfigure(d);
    d = sliceomaticsetdata(d);
    setappdata(gcf,'sliceomatic',d);
    %set the axis aspect ratio referring to the pixelsize info 
    currPBA = get(gca,'PlotBoxAspectratio');
    %DataAspectRatio = [size(d.data,1)*pixsize(1) ...
    %    size(d.data,2)*pixsize(2) size(d.data,3)*pixsize(3)];
    %set(gca,'DataAspectRatio',DataAspectRatio.*(currPBA));
    newPBA = [size(imaVOL,1)*pixsize(1) ...
        size(imaVOL,2)*pixsize(2) size(imaVOL,3)*pixsize(3)];
    set(gca,'DataAspectRatioMode','auto');
    set(gca,'PlotBoxAspectRatio',newPBA);
    
    setappdata(gcf,'sliceomatic',d);
    zoom(1.2);
    colormap(scaninfo.colormap);
    
 %set up the default X slice   
    hX = findall(gcf,'tag','Xslice');
    %axis(hX);
    X = round(size(d.data,1)/2);
    newa=arrow(hX,'down',[X 0]);
    set(gcf,'currentaxes',d.axmain);
    new=localslice(d.data, X, [], []);
    setappdata(new,'controlarrow',newa);
    setappdata(newa(2),'arrowslice',new);
    set(new,'alphadata',get(new,'cdata'),'alphadatamapping','scaled');
    set(newa,'buttondownfcn','sliceomatic Xmove');
    set([new newa],'uicontextmenu',d.uic);
    d.draggedarrow=newa(2);
    dragprep(newa(2));
    setpointer(gcf,'SOM leftright');
    set(d.motionmetaslice,'visible','off');
    dragfinis(d.draggedarrow);
    
    setappdata(gcf,'sliceomatic',d);
%set up the default Y slice
    hY = findall(gcf,'tag','Yslice');
    axis(hY);
    Y = round(size(d.data,2)/2);
    newa=arrow(hY,'right',[0 Y]);
    set(gcf,'currentaxes',d.axmain);
    new=localslice(d.data, [], Y, []);
    setappdata(new,'controlarrow',newa);
    setappdata(newa(2),'arrowslice',new);
    set(new,'alphadata',get(new,'cdata'),'alphadatamapping','scaled');
    set(newa,'buttondownfcn','sliceomatic Ymove');
    set([new newa],'uicontextmenu',d.uic);
    d.draggedarrow=newa(2);
    dragprep(newa(2));
    setpointer(gcf,'SOM topbottom');
    set(d.motionmetaslice,'visible','off');
    dragfinis(d.draggedarrow);
    
    setappdata(gcf,'sliceomatic',d);
%set up the default Z slice
    hZ = findall(gcf,'tag','Zslice');
    axis(hZ);
    Z = round(size(d.data,3)/2);
    newa=arrow(hZ,'left', [0 Z]);
    set(gcf,'currentaxes',d.axmain);
    new=localslice(d.data, [], [], Z);
    set(new,'alphadata',get(new,'cdata'),'alphadatamapping','scaled');
    setappdata(new,'controlarrow',newa);
    setappdata(newa(2),'arrowslice',new);
    set(newa,'buttondownfcn','sliceomatic Zmove');
    set([new newa],'uicontextmenu',d.uic);
    d.draggedarrow=newa(2);
    dragprep(newa(2));
    setpointer(gcf,'SOM topbottom');
    set(d.motionmetaslice,'visible','off');
    dragfinis(d.draggedarrow);
    
    setappdata(gcf,'sliceomatic',d);
  else 
    % Interpret commands
    d=getappdata(gcf,'sliceomatic');
    try
      switch p1
       case 'Xnew'
        if strcmp(get(gcf,'selectiontype'),'normal')
          pt=get(gcbo,'currentpoint');
          axis(gcbo);
          X=pt(1,1);
          newa=arrow(gcbo,'down',[X 0]);
          set(gcf,'currentaxes',d.axmain);
          new=localslice(d.data, X, [], []);
          setappdata(new,'controlarrow',newa);
          setappdata(newa(2),'arrowslice',new);
          set(new,'alphadata',get(new,'cdata'),'alphadatamapping','scaled');
          set(newa,'buttondownfcn','sliceomatic Xmove');
          set([new newa],'uicontextmenu',d.uic);
          % Make sure whatever buttonupfcn on the figure is run now to "turn
          % off" whatever was going on before we got our callback on the
          % arrow.
          buf = get(gcf,'windowbuttonupfcn');
          if ~strcmp(buf,'')
            eval(buf);
          end
          d.draggedarrow=newa(2);
          dragprep(newa(2));
          setpointer(gcf,'SOM leftright');
          set(d.motionmetaslice,'visible','off');
        end
       case 'Ynew'
        if strcmp(get(gcf,'selectiontype'),'normal')
          pt=get(gcbo,'currentpoint');
          Y=pt(1,2);
          newa=arrow(gcbo,'right',[0 Y]);
          set(gcf,'currentaxes',d.axmain);
          new=localslice(d.data, [], Y, []);
          setappdata(new,'controlarrow',newa);
          setappdata(newa(2),'arrowslice',new);
          set(new,'alphadata',get(new,'cdata'),'alphadatamapping','scaled');
          set(newa,'buttondownfcn','sliceomatic Ymove');
          set([new newa],'uicontextmenu',d.uic);
          % Make sure whatever buttonupfcn on the figure is run now to "turn
          % off" whatever was going on before we got our callback on the
          % arrow.
          buf = get(gcf,'windowbuttonupfcn');
          if ~strcmp(buf,'')
            eval(buf);
          end
          d.draggedarrow=newa(2);
          dragprep(newa(2));
          setpointer(gcf,'SOM topbottom');
          set(d.motionmetaslice,'visible','off');
        end % if strcmp(get(gcf,
       case 'Znew'
        if strcmp(get(gcf,'selectiontype'),'normal')
          pt=get(gcbo,'currentpoint');
          Y=pt(1,2);
          newa=arrow(gcbo,'left', [0 Y]);
          set(gcf,'currentaxes',d.axmain);
          new=localslice(d.data, [], [], Y);
          set(new,'alphadata',get(new,'cdata'),'alphadatamapping','scaled');
          setappdata(new,'controlarrow',newa);
          setappdata(newa(2),'arrowslice',new);
          set(newa,'buttondownfcn','sliceomatic Zmove');
          set([new newa],'uicontextmenu',d.uic);
          % Make sure whatever buttonupfcn on the figure is run now to "turn
          % off" whatever was going on before we got our callback on the
          % arrow.
          buf = get(gcf,'windowbuttonupfcn');
          if ~strcmp(buf,'')
            eval(buf);
          end
          d.draggedarrow=newa(2);
          dragprep(newa(2));
          setpointer(gcf,'SOM topbottom');
          set(d.motionmetaslice,'visible','off');
        end % if strcmp(get(gcf,
       case 'ISO'
        if strcmp(get(gcf,'selectiontype'),'normal')
          pt=get(gcbo,'currentpoint');
          V=pt(1,1);
          newa=arrow(gcbo,'up',[V 0]);
          set(gcf,'currentaxes',d.axmain);
          new=localisosurface(d.reducelims,d.reduce,d.reducesmooth,V);
          set([newa new],'uicontextmenu',d.uiciso);
          setappdata(new,'controlarrow',newa);
          setappdata(new,'reduced',1);
          setappdata(newa(2),'arrowiso',new);
          set(newa,'buttondownfcn','sliceomatic ISOmove');
          % Make sure whatever buttonupfcn on the figure is run now to "turn
          % off" whatever was going on before we got our callback on the
          % arrow.
          buf = get(gcf,'windowbuttonupfcn');
          if ~strcmp(buf,'')
            eval(buf);
          end	
          d.draggedarrow=newa(2);
          dragprep(newa(2));
          setpointer(gcf,'SOM leftright');
        end % if strcmp(get(gcf,
       case 'Xmove'
        if strcmp(get(gcf,'selectiontype'),'normal')
          [a s]=getarrowslice;
          d.draggedarrow=a;
          dragprep(a);
        end
       case 'Ymove'
        if strcmp(get(gcf,'selectiontype'),'normal')
          [a s]=getarrowslice;
          d.draggedarrow=a;
          dragprep(a);
        end
       case 'Zmove'
        if strcmp(get(gcf,'selectiontype'),'normal')
          [a s]=getarrowslice;
          d.draggedarrow=a;
          dragprep(a);
        end
       case 'ISOmove'
        if strcmp(get(gcf,'selectiontype'),'normal')
          [a s]=getarrowslice;
          d.draggedarrow=a;
          dragprep(a);
        end      
       case 'up'
        if strcmp(get(gcf,'selectiontype'),'normal')
          dragfinis(d.draggedarrow);
        end
       case 'motion'
        % Make sure our cursor is ok
        a=d.draggedarrow;			% The arrow being dragged
        s=getappdata(a,'arrowslice');	% The slice to 'move'
        if isempty(s)
          s=getappdata(a,'arrowiso');	% or the isosurface
        end
        aa=get(a,'parent');		% arrow's parent axes
        pos=getappdata(a,'arrowcenter');	% the line the arrow points at.
        apos=get(aa,'currentpoint');
        if aa==d.axx | aa==d.axiso
          % We are moving an X slice
          xdiff=apos(1,1)-pos(1,1);
          v=get(a,'vertices');
          v(:,1)=v(:,1)+xdiff;
          set([a getappdata(a,'arrowedge')],'vertices',v);
          np=[ apos(1,1) 0 ];
          % This might be a slice, or an isosurface!
          if aa==d.axiso
            new=localisosurface(d.reducelims,d.reduce,d.reducesmooth,...
                                apos(1,1),s);
            setappdata(new,'reduced',1);
            movetipforarrow(d.tip, aa, apos(1,1), [ apos(1,1) 6 ], 'bottom','center')
          else
            if round(apos(1,1))~=round(pos(1,1))
              localslice(d.data, apos(1,1), [], [],s);
            end
            movetipforarrow(d.tip, aa, apos(1,1), [ apos(1,1) .5 ],'top','center')
          end
        else
          % We are moving a Y or Z slice
          ydiff=apos(1,2)-pos(1,2);
          v=get(a,'vertices');
          v(:,2)=v(:,2)+ydiff;
          set([a getappdata(a,'arrowedge')],'vertices',v);
          np=[ 0 apos(1,2) ];
          if aa==d.axy
            if round(apos(1,2))~=round(pos(1,2))
              localslice(d.data, [], apos(1,2), [], s);
            end
            movetipforarrow(d.tip, aa, apos(1,2), [ 5.5 apos(1,2) ], 'middle','left');
          else
            if round(apos(1,2))~=round(pos(1,2))
              localslice(d.data, [], [], apos(1,2), s);
            end
            movetipforarrow(d.tip, aa, apos(1,2), [ .5 apos(1,2) ], 'middle','right');
          end
        end
        setappdata(a,'arrowcenter',np);
        drawnow;
        %
        % IsoSurface context menu items
        %
       case 'isotogglevisible'
        [a s]=getarrowslice;
        if propcheck(s,'visible','on')
          set(s,'visible','off');
        else
          set(s,'visible','on');
        end
       case 'isodelete'
        [a s]=getarrowslice;
        if numel(a)==1
          delete(getappdata(a,'arrowedge'));
        end
        cap=getappdata(s,'sliceomaticisocap');
        if ~isempty(cap)
          delete(cap);
        end
        delete(s);
        delete(a);
       case 'isoflatlight'
        [a s]=getarrowslice;
        set(s,'facelighting','flat');
       case 'isosmoothlight'
        [a s]=getarrowslice;
        set(s,'facelighting','phong');
       case 'isocolor'
        [a s]=getarrowslice;
        c=uisetcolor(get(s,'facecolor'));
        set(s,'facecolor',c);