MATLAB

To access the lab version of MATLAB log on to ringo.ams.sunysb.edu and type the following:

matlab -nojvm

While running matlab, one can still use the unix commands by adding "!" in the beginning. For example, to open a file using vim, type the following:

!vim file.txt

This opens MATLAB without using the java interface (the virtual machine).

Making large plots

First create a new figure, maximize it. Add these commands after the plot() and before making labels and printing. This will create a 1000 x 1000 px plot

 set(gcf,'Position',[1 1 1000 1000]); 
 set(gcf,'PaperPositionMode','auto');
 set(gca,'FontSize',12);

The parm 'PaperPositionMode' set as 'auto' will have matlab print the figure as it appers on screen. see following link.

http://www.mathworks.com/help/techdoc/creating_plots/f3-124745.html

Note that if you have a multi-paneled graph each panel have its own handle.

subpanel in a panel

figure(1)
h = uipanel
subplot(1,1,1,'Parent',h),plot([1:.1:10],sin([1:.1:10]/10*pi))
h2 = uipanel('Parent',h,'position',[0.4108    0.4096    0.2090    0.2157])
subplot(1,1,1,'Parent',h2),plot([1:.1:10],sin([1:.1:10]/10*pi))

make the background white.

set(h,'BackgroundColor',[1 1 1])
set(h,'ShadowColor',[1 1 1])
set(h2,'ShadowColor',[1 1 1])
set(h2,'BackgroundColor',[1 1 1])

Heatmap and colormap

Here are some possible color maps.

  map =[1 0 0;     %red
        1 0.3 0.3; %light red
        1 0.7 0.7;
        1 1 1;     %white
        0.7 0.7 1;
        0.3 0.3 1; %light blue
        0 0 1];    %blue
  v1 = ones(1,101);
  x  = [0:100]/100;
  map  = [(1-x)' (1-x)' v1'; 0 0 0; 0 0 0; v1' x' x']; %white - blue - black - red - white
  map  = [ v1' x' x'; 1 1 1; 1 1 1;(1-x)' (1-x)' v1']; %red - white - blue

Make a heatmap using the one of the color maps above.

H1 is a NXM matrixs

  val1 = max(max(abs(H1)));
  val2 = max(max(abs(std1)));
  figure(num),
  imagesc(H1), % makes heatmap
  colorbar,
  caxis([-val1,val1]) % this specifics the range of the color axis 
                      % zero is in the center
  colormap(map)

Useful Matlab Functions written by Rizzo group

fourier_fit

This Matlab function fits Fourier series to data, written by Trent E. Balius