from laptop

Author: murphyk2

demos/bookDemos/Bayesian_statistics/bayesChangeOfVar.m

@@ -19,5 +19,5 @@
 xticklabelRot(data.varNames)
 set(gca,'yticklabel', data.varNames);
 title('pairwise mutual information in autompg data')
-printPmtkFigure('miMixedDemoColor')
+printPmtkFigure('miMixedDemoColor2', 'png')
 

demos/bookDemos/Information_theory/miMixedDemo.m

@@ -1,4 +1,10 @@
-% bishop-5-4
+% Visualize difference between KL(p,q) and KL(q,p) where p is a mix of two
+% 2d Gaussians, and q is a single 2d Gaussian
+% This is Figure bishop-5-4
+
+%PMTKauthor Cody Severinski
+
+clear all
 
 mu = [-1,-1; 1,1];
 
@@ -29,23 +35,31 @@
 
 f = f1 + f2;
 % (a)
-contour(x1,x2,f,'b',4,'linewidth',3);
+figure
+contour(x1,x2,f); %,'b',4,'linewidth',3);
 hold on;
-contour(x1,x2,klf,'r',4,'linewidth',3);
+contour(x1,x2,klf); %'r',4,'linewidth',3);
 hold off;
-print('bishop-5-4a.pdf'); close all;
+axis square
+printPmtkFigure('KLfwd')
+%print('bishop-5-4a.pdf'); close all;
 
 % (b)
-contour(x1,x2,f,'b',4,'linewidth',3);
+figure
+contour(x1,x2,f); %,'b',4,'linewidth',3);
 hold on;
-contour(x1,x2,kll,'r',4,'linewidth',3);
+contour(x1,x2,kll); %'r',4,'linewidth',3);
 hold off;
-print('bishop-5-4b.pdf'); close all;
+printPmtkFigure('KLreverse1')
+%print('bishop-5-4b.pdf'); close all;
 
 %(c)
-contour(x1,x2,f,'b',4,'linewidth',3);
+figure
+contour(x1,x2,f); %,'b',4,'linewidth',3);
 hold on;
-contour(x1,x2,klr,'r',4,'linewidth',3);
+contour(x1,x2,klr); %,'r',4,'linewidth',3);
 hold off;
-print('bishop-5-4c.pdf'); close all;
+axis equal
+printPmtkFigure('KLreverse1')
+%print('bishop-5-4c.pdf'); close all;
 

demos/bookDemos/Variational_inference/KLfwdReverseMixGauss.m

@@ -21,11 +21,10 @@
     prior.dof = 15;
 end
 
-
 model = hmmFitEm(data, 2, 'gauss', 'verbose', true, 'piPrior', [3 2], ...
-    'emissionPrior', prior, 'nRandomRestarts', 3)
-
+    'emissionPrior', prior, 'nRandomRestarts', 2, 'maxIter', 10)
+break
 
 X = hmmSample(model, 200, 10);
-m2 = hmmFitEm(X, 5, 'gauss', 'verbose', true);
+%m2 = hmmFitEm(X, 5, 'gauss', 'verbose', true);
 

demos/otherDemos/hmmGaussTest.m

@@ -1,22 +1,25 @@
-function printPmtkFigure(filename)
-% print current figure to specified file in .pdf format
+function printPmtkFigure(filename, format)
+% print current figure to specified file in .pdf (or other) format
 
 % This file is from pmtk3.googlecode.com
 
+if nargin <2, format = 'pdf'; end
 
 if false % set to false to turn off printing
    %printFolder = 'C:\kmurphy\dropbox\PML\Figures\pdfFigures';
    printFolder = '/Users/kpmurphy/MLbook/Figures/pdfFigures';
-  pdfcrop;
-    fname = sprintf('%s/%s.pdf', printFolder, filename);
+   if strcmpi(format, 'pdf')
+       pdfcrop;
+   end
+    fname = sprintf('%s/%s.%s', printFolder, filename, format);
     fprintf('printing to %s\n', fname);
     if exist(fname,'file'), delete(fname); end % prevent export_fig from appending
-    if 1
+    if 0
         %opts = struct('Color', 'rgb', 'Resolution', 1200, 'fontsize', 12);
         opts = struct('Color', 'rgb', 'Resolution', 1200);
         exportfig(gcf, fname, opts, 'Format', 'pdf' );
     else
-        set(gca,'Color','none')
+        set(gca,'Color','none') % turn off gray background
         set(gcf,'Color','none')
         export_fig(fname)
     end

matlabTools/graphics/printPmtkFigure.m

@@ -1,3 +1,35 @@
 This is an experimental directory containing translations of a few 
 pmtk3 demos from Matlab to python. Over time, we hope to port
 more and more functionality.
+
+--------
+
+Below I include some notes based on Kevin Murphy's experience
+getting python 2.6 to work on a Mac OS X
+(written from the perspective of a matlab user and someone interested
+in data analysis/ scientific computing)
+
+- diveintopython.org is a free 300 page book (pdf format) which is not too basic
+  but not too advanced. Sometimes reading a pdf is easier than reading
+  many small html pages.
+
+- The site below contains ipython, numpy, scipy and matplotlib all bundled
+together for Mac OS X 10.6
+  http://stronginference.com/scipy-superpack
+
+- The site below sells ($200 per year per user) a bundle of 75 of the
+  latest packages, focussing on scientific comptuation
+http://www.enthought.com/
+
+- to install packages do this:
+1. Download setuptools from http://pypi.python.org/pypi/setuptools#downloads
+2. sudo sh setuptools-0.6c11-py2.6.egg
+3. Stores it in/ Library/Python/2.6/site-packages
+4. Run something like this:  sudo easy_install-2.6 networkx
+
+- the networkx package (http://networkx.lanl.gov) supports graph
+  operations.
+
+- to automatically execute a startup file,
+put this in your .bashrc
+  export PYTHONSTARTUP=/Users/kpmurphy/pystart.py