% 
% Written by:
% -- 
% John L. Weatherwax                2005-08-14
% 
% email: wax@alum.mit.edu
% 
% Please send comments and especially bug reports to the
% above email address.
% 
%-----

addpath( '../../Code/eda_data' );
addpath( '../../Code/eda_toolbox' );  

close all; drawnow; 
clc; 
clear; 

randn('seed',0); rand('seed',0); 

% Modifications on Example 3.5
% This shows how to use the LLE and ISOMAP routines on the scurve dataset
%
load scurve; 

% these are loaded in from the "scurve" file, but I want to remember what they are ...
N=2000;
d = 2; 
K = 12; 

% Now run the ISOMAP - we need the distances for input.
dists = squareform(pdist(X'));
options.dims = 1:10;               % These are for ISOMAP.
options.display = 0;
[Yiso, Riso, Eiso] = isomap(dists, 'k', 7, options);
% To get the coordinates, look in the structure Yiso. Note that the
% coordinates are also in the form dim x observ. If we want a 2-D
% scatter plot, then we use the 2nd record. Typing in Yiso at the
% command line shows what is in the structure.
tt = linspace( -pi, +pi, N ); 
scatter(Yiso.coords{2}(1,:), Yiso.coords{2}(2,:), 12, tt, '+');
axis tight; 
title( 'isomap projection of the scurve data' ); 
saveas( gcf, '../../WriteUp/Graphics/Chapter3/prob_3_11_isomap', 'epsc' );