[linearalg] updated code for octave

linearalgebra/code/coordinaterafo2.m

@@ -1,52 +0,0 @@
-% some vectors:
-x = [ -1:0.02:1 ];
-y = x*0.5 + 0.1*randn( size(x) );
-plot( x, y, '.b' );
-hold on
-plot( x(10), y(10), '.r' );
-
-% new coordinate system:
-%e1 = [ 3/5 4/5 ];
-%e2 =  [ -4/5 3/5 ];
-e1 = [ 3 4 ];
-e2 =  [ -4 3 ];
-me1 = sqrt( e1*e1' );
-e1 = e1/me1;
-me2 = sqrt( e2*e2' );
-e2 = e2/me2;
-quiver( 0.0, 0.0 , e1(1), e1(2), 1.0, 'r' )
-quiver( 0.0, 0.0 , e2(1), e2(2), 1.0, 'g' )
-axis( 'equal' )
-
-% project [x y] onto e1 and e2:
-
-% % the long way:
-% nx = zeros( size( x ) );  % new x coordinate
-% ny = zeros( size( y ) );  % new y coordinates
-% for k=1:length(x)
-%     xvec = [ x(k) y(k) ];
-%     nx(k) = xvec * e1';
-%     ny(k) = xvec * e2';
-% end
-% plot( nx, ny, '.g' );
-
-% the short way:
-%nx = [ x' y' ] * e1';
-%nx = [x; y]' * e1';
-% nx = e1 * [ x; y ];
-% ny = e2 * [ x; y ];
-% plot( nx, ny, '.g' );
-
-% even shorter:
-n = [e1; e2 ] * [ x; y ];
-plot( n(1,:), n(2,:), '.g' );
-
-
-
-
-
-
-
-
-
-hold off

linearalgebra/code/coordinatetrafo.m

@@ -35,3 +35,4 @@ xlabel( 'x' );
 ylabel( 'y' );
 
 hold off;
+pause;

linearalgebra/code/covareigen.m

@@ -38,11 +38,11 @@ function covareigen( x, y, pm, w, h )
         colormap( 'gray' );
     else
         % scatter plot:
-        scatter( x, y, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+	    scatter( x, y ); %, 'b', 'filled', 'MarkerEdgeColor', 'white' );
     end
 
     % plot eigenvectors:
-    quiver( ones( 1, 2 ).*mean( x ), ones( 1, 2 )*mean(y), v(1,:).*sqrt(diag(d))', v(2,:).*sqrt(diag(d))', 'r', 'LineWidth', 3, 'AutoScale', 'off', 'AutoScaleFactor', 1.0, 'MaxHeadSize', 0.7 )
+    quiver( ones( 1, 2 ).*mean( x ), ones( 1, 2 )*mean(y), v(1,:).*sqrt(diag(d))', v(2,:).*sqrt(diag(d))', 'r', 'LineWidth', 3 ); %, 'AutoScale', 'off', 'AutoScaleFactor', 1.0, 'MaxHeadSize', 0.7 )
 
     xlabel( 'x' );
     ylabel( 'y' );
@@ -76,7 +76,7 @@ function covareigen( x, y, pm, w, h )
             contourf( xp, yp, gauss )
         end
     else
-        scatter( nc(:,1), nc(:,2), 'b', 'filled', 'MarkerEdgeColor', 'white' );
+      scatter( nc(:,1), nc(:,2) ); %, 'b', 'filled', 'MarkerEdgeColor', 'white' );
     end
     xlabel( 'x' );
     ylabel( 'y' );

linearalgebra/code/covareigen3.m

@@ -15,29 +15,29 @@ function covareigen3( x, y, z )
 
     % scatter plot:
     view( 3 );
-    scatter3( x, y, z, 0.1, 'b', 'filled', 'MarkerEdgeColor', 'blue' );
+scatter3( x, y, z, 0.1, 'b', 'filled' ); %, 'MarkerEdgeColor', 'blue' );
     xlabel( 'x' );
     ylabel( 'y' );
     zlabel( 'z' );
     grid on;
     
     % plot eigenvectors:
-    quiver3( ones( 1, 3 ).*mean( x ), ones( 1, 3 )*mean(y), ones( 1, 3 )*mean(z), v(1,:).*sqrt(diag(d))', v(2,:).*sqrt(diag(d))', v(3,:).*sqrt(diag(d))', 'r', 'LineWidth', 3, 'AutoScale', 'off', 'AutoScaleFactor', 1.0, 'MaxHeadSize', 0.7 )
+    quiver3( ones( 1, 3 ).*mean( x ), ones( 1, 3 )*mean(y), ones( 1, 3 )*mean(z), v(1,:).*sqrt(diag(d))', v(2,:).*sqrt(diag(d))', v(3,:).*sqrt(diag(d))', 'r' ); %, 'LineWidth', 3, 'AutoScale', 'off', 'AutoScaleFactor', 1.0, 'MaxHeadSize', 0.7 )
     
     %axis( 'equal' );
     hold off;
 
     % 2D scatter plots:
     subplot( 2, 6, 4 );
-    scatter( x, y, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( x, y, 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'x' )
     ylabel( 'y' )
     subplot( 2, 6, 5 );
-    scatter( x, z, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( x, z, 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'x' )
     ylabel( 'z' )
     subplot( 2, 6, 6 );
-    scatter( y, z, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( y, z, 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'y' )
     ylabel( 'z' )
 
@@ -51,7 +51,7 @@ function covareigen3( x, y, z )
     y = y - mean( y );
     % project onto eigenvectors:
     nx = [ x y z ] * v(:,inx);
-    scatter( nx(:,1), nx(:,2), 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( nx(:,1), nx(:,2), 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'ex' )
     ylabel( 'ey' )
     axis( 'equal' );

linearalgebra/code/covareigen3examples.m

@@ -1,6 +1,3 @@
-scrsz = get( 0, 'ScreenSize' );
-set( 0, 'DefaultFigurePosition', [ scrsz(3)/2 scrsz(4)/2 scrsz(3)/2 scrsz(4)/2 ] );
-
 n = 10000;
 
 % three distributions:
@@ -17,3 +14,4 @@ for k = 1:4
 end
 f = figure( 1 );
 covareigen3( x, y, z );
+pause;

linearalgebra/code/covareigenexamples.m

@@ -1,6 +1,3 @@
-scrsz = get( 0, 'ScreenSize' );
-set( 0, 'DefaultFigurePosition', [ scrsz(3)/2 scrsz(4)/2 scrsz(3)/2 scrsz(4)/2 ] );
-
 % correlation coefficients:
 n = 10000;
 x = randn( n, 1 );
@@ -10,9 +7,9 @@ for r = 0.01:0.19:1
     clf( f );
     y = r*x + sqrt(1-r^2)*randn( n, 1 );
     covareigen( x, y, 0, 5.0, 3.0 );
-    key = waitforbuttonpress;
+    %key = waitforbuttonpress;
+    pause( 1.0 );
 end
-return
 
 % two distributions:
 n = 10000;
@@ -21,14 +18,12 @@ y1 = randn( n/2, 1 );
 x2 = randn( n/2, 1 );
 y2 = randn( n/2, 1 );
 f = figure( 1 );
-pause( 'on' );
 for d = 0:1:5
     fprintf( 'Distance = %g\n', d );
     clf( f  );
     d2 = d / sqrt( 2.0 );
     x = [ x1; x2 ];
     y = [ y1+d2; y2-d2 ];
-    scrsz = get(0,'ScreenSize');
     covareigen( x, y, 0, 10.0, 7.0 );
     %key = waitforbuttonpress;
     pause( 1.0 );

linearalgebra/code/matrixbox.m

@@ -41,5 +41,5 @@ function matrixbox( m, s )
     text( 0.8, 0.1, sprintf( '%.3g', m(2,1) ), 'Units', 'normalized' )
     text( 0.9, 0.1, sprintf( '%.3g', m(2,2) ), 'Units', 'normalized' )
     title( s );
-    waitforbuttonpress;
+    pause(1.0);
 end

linearalgebra/code/pca2d.m

@@ -39,7 +39,7 @@ function pca2d( x, y, pm, w, h )
         colormap( 'gray' );
     else
         % scatter plot:
-        scatter( x, y, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+	    scatter( x, y, 'b', 'filled' );%, 'MarkerEdgeColor', 'white' );
     end
 
     % plot eigenvectors:
@@ -80,7 +80,7 @@ function pca2d( x, y, pm, w, h )
         end
     else
         % scatter plot:
-        scatter( nc(:,1), nc(:,2), 'b', 'filled', 'MarkerEdgeColor', 'white' );
+	    scatter( nc(:,1), nc(:,2), 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     end
     xlabel( 'n_x' );
     ylabel( 'n_y' );

linearalgebra/code/pca2dexamples.m

@@ -1,6 +1,3 @@
-scrsz = get( 0, 'ScreenSize' );
-set( 0, 'DefaultFigurePosition', [ scrsz(3)/2 scrsz(4)/2 scrsz(3)/2 scrsz(4)/2 ] );
-
 % correlation coefficients:
 n = 10000;
 x = randn( n, 1 );
@@ -27,7 +24,6 @@ for d = 0:1:5
     d2 = d / sqrt( 2.0 );
     x = [ x1; x2 ];
     y = [ y1+d2; y2-d2 ];
-    scrsz = get(0,'ScreenSize');
     pca2d( x, y, 0, 10.0, 7.0 );
     waitforbuttonpress;
 end

linearalgebra/code/pca3d.m

@@ -15,29 +15,29 @@ function pca3d( x, y, z )
 
     % scatter plot:
     view( 3 );
-    scatter3( x, y, z, 0.1, 'b', 'filled', 'MarkerEdgeColor', 'blue' );
+    scatter3( x, y, z ); % , 0.1, 'b', 'filled', 'MarkerEdgeColor', 'blue' );
     xlabel( 'x' );
     ylabel( 'y' );
     zlabel( 'z' );
     grid on;
     
     % plot eigenvectors:
-    quiver3( ones( 1, 3 ).*mean( x ), ones( 1, 3 )*mean(y), ones( 1, 3 )*mean(z), v(1,:).*sqrt(diag(d))', v(2,:).*sqrt(diag(d))', v(3,:).*sqrt(diag(d))', 'r', 'LineWidth', 3, 'AutoScale', 'off', 'AutoScaleFactor', 1.0, 'MaxHeadSize', 0.7 )
+    quiver3( ones( 1, 3 ).*mean( x ), ones( 1, 3 )*mean(y), ones( 1, 3 )*mean(z), v(1,:).*sqrt(diag(d))', v(2,:).*sqrt(diag(d))', v(3,:).*sqrt(diag(d))', 'r' ); %, 'LineWidth', 3, 'AutoScale', 'off', 'AutoScaleFactor', 1.0, 'MaxHeadSize', 0.7 )
     
     %axis( 'equal' );
     hold off;
 
     % 2D scatter plots:
     subplot( 2, 6, 4 );
-    scatter( x, y, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( x, y, 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'x' )
     ylabel( 'y' )
     subplot( 2, 6, 5 );
-    scatter( x, z, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( x, z, 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'x' )
     ylabel( 'z' )
     subplot( 2, 6, 6 );
-    scatter( y, z, 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( y, z, 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'y' )
     ylabel( 'z' )
 
@@ -51,10 +51,11 @@ function pca3d( x, y, z )
     y = y - mean( y );
     % project onto eigenvectors:
     nx = [ x y z ] * v(:,inx);
-    scatter( nx(:,1), nx(:,2), 'b', 'filled', 'MarkerEdgeColor', 'white' );
+    scatter( nx(:,1), nx(:,2), 'b', 'filled' ); %, 'MarkerEdgeColor', 'white' );
     xlabel( 'ex' )
     ylabel( 'ey' )
     axis( 'equal' );
     hold off;
 
 end
+

linearalgebra/code/pca3dexamples.m

@@ -17,3 +17,4 @@ for k = 1:4
 end
 f = figure( 1 );
 pca3d( x, y, z );
+pause

linearalgebra/code/simplematrixbox.m

@@ -17,5 +17,5 @@ function simplematrixbox( a, s )
     xlim( [-2 2 ] )
     ylim( [-2 2] )
     title( s );
-    waitforbuttonpress;
+    pause(1.0);
 end

linearalgebra/code/spikesortingwave.m

@@ -5,21 +5,22 @@ load( 'extdata' );
 dt = time( 2) - time(1);
 tinx = round(spiketimes/dt)+1;
 
-% plot voltage trace with dettected spikes:
+% plot voltage trace with detected spikes:
 figure( 1 );
 clf;
 plot( time, voltage, '-b' )
 hold on
 scatter( time(tinx), voltage(tinx), 'r', 'filled' );
-xlabel( 'time [ms]' );
+xlabel( 'time [s]' );
 ylabel( 'voltage' );
+xlim([0.1, 0.4])
 hold off
 
 % spike waveform snippets:
 w = ceil( 0.005/dt );
-vs = [];
+vs = zeros(length(tinx), 2*w);
 for k=1:length(tinx)
-    vs = [ vs; voltage(tinx(k)-w:tinx(k)+w-1) ];
+    vs(k,:) = voltage(tinx(k)-w:tinx(k)+w-1);
 end
 ts = time(1:size(vs,2));
 ts = ts - ts(floor(length(ts)/2));
@@ -78,9 +79,9 @@ kx = ones( size( nx ) );
 kx(nx<kthresh) = 2;
 
 subplot( 4, 1, 2 );
-scatter( nx(kx==1), ny(kx==1), 'r', 'filled', 'MarkerEdgeColor', 'white' );
+scatter( nx(kx==1), ny(kx==1), 10.0, 'r', 'filled' ); %, 'MarkerEdgeColor', 'white' );
 hold on;
-scatter( nx(kx==2), ny(kx==2), 'g', 'filled', 'MarkerEdgeColor', 'white' );
+scatter( nx(kx==2), ny(kx==2), 10.0, 'g', 'filled' ); %, 'MarkerEdgeColor', 'white' );
 hold off;
 xlabel( 'projection onto eigenvector 1' );
 ylabel( 'projection onto eigenvector 2' );
@@ -113,6 +114,7 @@ hold off
 % spike trains:
 figure( 1 );
 hold on;
-scatter( time(tinx(kinx1)), voltage(tinx(kinx1)), 100.0, 'r', 'filled' );
+scatter( time(tinx(kinx1)), voltage(tinx(kinx1)), 10.0, 'r', 'filled' );
-scatter( time(tinx(kinx2)), voltage(tinx(kinx2)), 100.0, 'g', 'filled' );
+scatter( time(tinx(kinx2)), voltage(tinx(kinx2)), 10.0, 'g', 'filled' );
 hold off;
+pause