%% MATLAB 3D viewer demo 3
%
% In this demo file, we will use the surface plot mode of the 3D viewer. It
% is a mode of rendering where a 3D surface mesh is created from a 2D
% image. Here, the pixel intensity of the 2D image is interpreted as the
% elevation (Z coordinates), which is enough to generate the 3D surface.
% 
% It is a mode which is particularly useful for images that have indeed a
% pixel intensity that can be interpreted as elevation, such as maps. Here,
% we try to use the surface plot mode of the 3D viewer with a surface well
% known to MATLAB users.


%% Make sure Java3D is installed
% If not, try to install it

if ~IsJava3DInstalled(true)
    return
end

%% Generate elevation data in MATLAB
% This is the well known *membrane* dataset, that serves as a generator for
% the MATLAB logo.

%%
% This will generate a 51*51 image, for which intensity should be
% interpreted as height. It is not a 3D data per se, but its rendering will
% be. 
Z = membrane(1,25);

%%
% The trouble is that Z is made of doubles, the most common MATLAB type,
% whether the 3D viewer only accepts 8-bit images. So we have do some
% conversion before rendering it. The following commands will stretch the
% range of Z to [0; 255] and cast to |uint8|.
Imin = min(Z(:));
Imax = max(Z(:));
I = uint8( 200 * (Z-Imin) / (Imax-Imin) );

%% Send data to the 3D viewer, through miji
%  Launch Miji
Miji(false);

%%
% We create an ImagePlus from the 2D image.
imp = MIJ.createImage('MATLAB peaks', I, false);

%%
% Create and display a new 3D universe.
universe = ij3d.Image3DUniverse();
universe.show();

%%
% Feed it the previous ImagePlus, but render it as a surface plot, where
% the intensity is encoded as height in a 3D space.
color = javax.vecmath.Color3f(240 / 255, 120 / 255, 20 / 255);
c = universe.addSurfacePlot(imp, ...
        javax.vecmath.Color3f(), ...
        'Matlab Peak in 3D', ...
        1, ...
        [true true true], ...
        1);

%%
% Rotate it a little, so that it shows the same orientation that of the
% actual MATLAB logo.
universe.resetView();
c.setColor(color);
c.setTransform([1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1]);
universe.fireContentChanged(c);
universe.centerSelected(c);
universe.rotateUniverse(javax.vecmath.Vector3d(-1, -0.5, +0.2), +120 * pi / 180);

%%
% Et voilą! A beautiful monochrome MATLAB logo, rendered in an accelerated
% 3D viewer. You can try the _Fullscreen_ option in the _View_ menu, to
% maximize your experience.
%
%%
% Note that it is monochrome: the MATLAB logo (type |logo| in the command
% window) has two colors: the close side is yellow-orange-ish and the back
% face is blueish. If you look at the |logo.m| code, you will see that
% MATLAB guys generated these colors using 2 different light source of 2
% different colors, which you cannot do in the 3D viewer.
%%
% 
% <<MatlabLogoInFiji.png>>
%
%%
%
% _Jean-Yves Tinevez \<jeanyves.tinevez at gmail.com\>_
%
% _Johannes Schindelin \<johannes.schindelin@gmx.de\>_
%
% _- August 2011_