modifed 'makeRunDemos' so it calls each demo inside a try..catch bloc…

…k, so if a demo says 'requireXXXtoolbox', it will automatically be skipped by runDemos; the old system which said 'if ~XXXinstalled then print 'skipping'" has been removed. Alos, makeRunDEmos now skips exclued files rather than commenting them out git-svn-id: https://pmtk3.googlecode.com/svn/trunk@2764 b6abd7f4-f95b-11de-aa3c-59de0406b4f5
cinkie · Apr 6, 2011 · 690f446 · 690f446
1 parent b236367
commit 690f446
Show file tree

Hide file tree

Showing 27 changed files with 3,776 additions and 581 deletions.
diff --git a/demos/biclusterDemo.m b/demos/biclusterDemo.m
@@ -1,5 +1,5 @@
 %% Bicluster Demo
-% PMTKreallySlow
+%PMTKreallySlow
 %%
 
 % This file is from pmtk3.googlecode.com

diff --git a/demos/clusterYeast.m b/demos/clusterYeast.m
@@ -5,10 +5,7 @@
 
 % This file is from pmtk3.googlecode.com
 
-if ~bioinfoToolboxInstalled
-    disp('skipping demo, needs bioinfoToolbox');
-    return;
-end
+
 requireStatsToolbox
 requireBioinfoToolbox
 loadData('yeastData310') % 'X', 'genes', 'times');

diff --git a/demos/demoPeaksTraj.m b/demos/demoPeaksTraj.m
@@ -5,11 +5,8 @@
 
 % This file is from pmtk3.googlecode.com
 
-if ~optimToolboxInstalled
-    fprintf('%s requires optimization toolbox; skipping\n', mfilename())
-    return
-end
-%requireOptimToolbox;
+
+requireOptimToolbox;
 [X,Y] = meshgrid(linspace(-2.5,2.5,40),linspace(-3,3,50));
 Z = peaks(X,Y);
 

diff --git a/demos/demoRosen2d.m b/demos/demoRosen2d.m
@@ -4,11 +4,7 @@
 
 % This file is from pmtk3.googlecode.com
 
-if ~optimToolboxInstalled
-    fprintf('%s requires optimization toolbox; skipping\n', mfilename())
-    return
-end
-%requireOptimToolbox;
+requireOptimToolbox;
 xstart = [-1 2];
 
 % basic usage with anonymous function and numerical derivatives

diff --git a/demos/demoRosenConstrained.m b/demos/demoRosenConstrained.m
@@ -9,10 +9,7 @@ function demoRosenConstrained()
 % minimize 2d rosenbrock st x1^2 + x^2 <= 1
 % Example from p1-8 of Mathworks Optimization Toolbox manual
 
-if ~optimToolboxInstalled
-    fprintf('%s requires optimization toolbox; skipping\n', mfilename())
-    return
-end
+requiresOptimToolbox
 
 xstart = [-1 2];
  % Hessian is ignored by quasi-Newton so we use interior point

diff --git a/demos/discreteDensityModelsShootout.m b/demos/discreteDensityModelsShootout.m
@@ -13,10 +13,10 @@
 pcTrain = 0.5; pcTest = 0.5;
 pcMissing =  0.3;
 
-%dataName = 'SUN09';
+dataName = 'SUN09';
 %dataName = 'newsgroups';
 %dataName = 'newsgroups1';
-dataName = 'ases4';
+%dataName = 'ases4';
 
 switch dataName
   case 'newsgroups'
@@ -182,13 +182,12 @@
 %}
 
 
-%{
+
 m = m + 1;
 methods(m).modelname = 'dgm-init-tree';
 methods(m).fitFn = @(labels) dgmFitStruct(labels, 'nodeNames', nodeNames, 'maxFamEvals', 1000, ...
   'figFolder', figFolder, 'nrestarts', 0, 'initMethod', 'tree', 'edgeRestrict', 'MI');
 methods(m).logprobFn = @(model, labels) dgmLogprob(model, 'obs', labels);
-%}
 
 %{
 m = m + 1;
@@ -228,20 +227,6 @@
 
 
 
-Ks = [1,5];
-for kk=1:numel(Ks)
-  K = Ks(kk);
-  m = m + 1;
-  alpha = 1.1;
-  %methods(m).modelname = sprintf('mixK%d,a%2.1f', K, alpha);
-  methods(m).modelname = sprintf('mix%d', K);
-  methods(m).fitFn = @(labels) mixDiscreteFit(labels, K, 'maxIter', 30, ...
-    'verbose', false, 'alpha', 1.1);
-  methods(m).logprobFn = @(model, labels) mixDiscreteLogprob(model, labels);
-  methods(m).predictMissingFn = @(model, labels) mixDiscretePredictMissing(model, labels);
-end 
-
-
 %{
 Ks = [1,5,10,20,40];
 for kk=1:numel(Ks)
@@ -436,7 +421,7 @@
 [styles, colors, symbols, plotstr] =  plotColors();
 
 
-%{
+
 % NLL - for catFA, which cannot compute valid loglik,
 % we use NaNs
 figure;
@@ -454,7 +439,7 @@
   dataName, Nnodes, Ntrain, Ntest))
 fname = fullfile(figFolder, sprintf('negloglik-%s.png', dataName));
 print(gcf, '-dpng', fname);
-%}
+
 
 % imputation error
 figure;
@@ -486,6 +471,8 @@
   fname = fullfile(figFolder, sprintf('tree-%s', dataName))
   graphviz(tree.edge_weights, 'labels', nodeNames, 'directed', 1, 'filename', fname);
 end
+%}
+
 
 m = strfindCell('dgm', methodNames);
 if ~isempty(m)
@@ -495,6 +482,7 @@
   graphviz(dgm.G, 'labels', dgm.nodeNames, 'directed', 1, 'filename', fname);
 end
 
+%{
 m = strfindCell('mrf-L1', methodNames);
 if ~isempty(m)
   mrf = models{m};
@@ -519,8 +507,6 @@
     %title(sprintf('%5.3f', mix.mixWeight(k)))
   end
 end
-
-
 %}
 
 %{

diff --git a/demos/dtreeDemoIris.m b/demos/dtreeDemoIris.m
@@ -1,10 +1,7 @@
 % Demonstrate classification/decision tree on 2d 3class iris data
 % From http://www.mathworks.com/products/statistics/demos.html?file=/products/demos/shipping/stats/classdemo.html
 
-if  ~statsToolboxInstalled
-  fprintf('cannot run %s without stats toolbox; skipping\n', mfilename())
-  return
-end
+requireStatsToolbox
 
 
 % "Resubstitution error" is the training set error

diff --git a/demos/glmnetDemo.m b/demos/glmnetDemo.m
@@ -1,3 +1,5 @@
+
+
 if ~glmnetInstalled
     fprintf('cannot run %s without glmnet; skipping\n', mfilename());
     return;

diff --git a/demos/hclustYeastDemo.m b/demos/hclustYeastDemo.m
@@ -5,12 +5,8 @@
 
 % This file is from pmtk3.googlecode.com
 
-%requireStatsToolbox
-%requireBioinfoToolbox
-if ~bioinfoToolboxInstalled
-    fprintf('cannot run %s without bioinformatics toolbox; skipping\n', mfilename());
-    return;
-end
+requireStatsToolbox
+requireBioinfoToolbox
 loadData('yeastData310') % 'X', 'genes', 'times');
 
 corrDist = pdist(X, 'corr');

diff --git a/demos/kmeansYeastDemo.m b/demos/kmeansYeastDemo.m
@@ -1,19 +1,14 @@
 %% Cluster yeast data using Kmeans
-%PMTKneedBioToolbox redgreencmap
-%% 
 
-% This file is from pmtk3.googlecode.com
 
-%requireBioinfoToolbox
-if ~bioinfoToolboxInstalled
-    fprintf('cannot run %s without bioinformatics toolbox; skipping\n', mfilename());
-    return;
-end
-loadData('yeastData310') % 'X', 'genes', 'times');
+% This file is from pmtk3.googlecode.com
 
 
+loadData('yeastData310') % 'X', 'genes', 'times');
 
-figure;imagesc(X);colormap(redgreencmap)
+figure;imagesc(X);
+%colormap(redgreencmap) % bioinfoToolbox
+colormap(redgreenColormap)
 xlabel('time')
 set(gca,'xticklabel',times)
 ylabel('genes')

diff --git a/demos/linregRobustDemo.m b/demos/linregRobustDemo.m
@@ -5,11 +5,7 @@
 % This file is from pmtk3.googlecode.com
 
 function linregRobustDemo()
-%requireOptimToolbox
-if ~optimToolboxInstalled
-    fprintf('cannot run %s without optimization toolbox; skipping\n', mfilename());
-    return;
-end
+requireOptimToolbox
 seed = 0; setSeed(seed);
 x = sort(rand(10,1));
 y = 1+2*x + rand(size(x))-.5;

diff --git a/demos/linregStudentTest.m b/demos/linregStudentTest.m
@@ -2,12 +2,11 @@
 %PMTKauthor Yi Huang
 %%
 
+
 % This file is from pmtk3.googlecode.com
 
-if ~optimToolboxInstalled
-    fprintf('cannot run %s without optimization toolbox; skipping\n', mfilename());
-    return;
-end
+requireOptimToolbox
+
 
 seed = 0; setSeed(seed);
 x = sort(rand(10,1));

diff --git a/demos/mrfImageDenoisingApprox.m b/demos/mrfImageDenoisingApprox.m
@@ -11,10 +11,7 @@
     fprintf('cannot run %s without libdai; skipping\n', mfilename());
     return;
 end
-if ~imagesToolboxInstalled
-    fprintf('cannot run %s without image processing toolbox; skipping\n', mfilename());
-    return;
-end
+requireImageToolbox
 setSeed(0); 
 infEngine = 'libdaibp';
 sz = 32;

diff --git a/demos/qpDemo.m b/demos/qpDemo.m
@@ -3,10 +3,7 @@
 
 % This file is from pmtk3.googlecode.com
 
-if ~optimToolboxInstalled
-    fprintf('cannot run %s without optim toolbox; skipping\n', mfilename());
-    return;
-end
+requireOptimToolbox
 H = 2*eye(2);
 g = -[3,0.25];
 A = [1 1; 1 -1; -1 1; -1 -1];

diff --git a/matlabTools/graphics/graphviz.m b/matlabTools/graphics/graphviz.m
@@ -133,7 +133,12 @@ function graphviz(adj, varargin)
 
 
 if ~isempty(filename)
-  cmd = sprintf('ps2pdf %s.ps %s.pdf', filename, filename);
+  if ismac
+    str = '/usr/local/bin/ps2pdf';
+  else
+    str = 'ps2pdf';
+  end
+  cmd = sprintf('%s %s.ps %s.pdf', str, filename, filename);
   status = system(cmd);
   if status ~= 0
     error(sprintf('error executing %s', cmd));
@@ -183,8 +188,14 @@ function graphviz(adj, varargin)
     opts = strcat(opts,' -Glandscape ');
 end
 
+if ismac
+  dotstr = '/usr/local/bin/dot';
+else
+  dotstr = 'dot';
+end
 %cmd = strcat('C:\temp\graphviz-2.8\bin\dot ',opts,' -T ps -o graphVizIt.ps graphVizIt.txt ')
-cmd = sprintf('dot %s -Tps %s -o %s', opts, dotname, outname);
+cmd = sprintf('%s %s -Tps %s -o %s', dotstr, opts, dotname, outname);
+%cmd = sprintf('dot -Tps %s -o %s', dotname, outname);
 %cmd = sprintf('dot %s -Tpng %s -o %s', opts, dotname, outname);
 status = system(cmd);
 if status ~= 0

diff --git a/matlabTools/metaTools/whoCallsMe.m b/matlabTools/metaTools/whoCallsMe.m
@@ -23,10 +23,11 @@
 
 % This file is from pmtk3.googlecode.com
 
-[recache, recursive, verbose] = process_options(varargin, ...
+[recache, recursive, verbose, skipBuiltin] = process_options(varargin, ...
     'recache'  , false, ...
     'recursive', false, ...
-    'verbose',   true);
+    'verbose',   true, ...
+    'skipBuiltin', true);
 %%
 w = which(fname);
 
@@ -37,8 +38,8 @@
     end
     return
 end
-if startswith(w, matlabroot) || startswith(w, 'built-in (')
-    list = []; g = []; map = struct();
+if skipBuiltin && (startswith(w, matlabroot) || startswith(w, 'built-in ('))
+    list = []; m =[]; g = []; map = struct();
     if verbose
         fprintf('%s is a built-in matlab function.\n', fname);
     end
@@ -89,7 +90,7 @@
     else
         fprintf('The dependency graph is out of date\n\n'); 
         [list, m, g, map] = whoCallsMe(fname, 'recache', true, ...
-        'recursive', recursive, 'verbose', verbose);
+        'recursive', recursive, 'verbose', verbose, 'skipBuiltin', skipBuiltin);
     end
 end
 

diff --git a/matlabTools/stats/requireBioinfoToolbox.m → matlabTools/util/requireBioinfoToolbox.m b/matlabTools/stats/requireBioinfoToolbox.m → matlabTools/util/requireBioinfoToolbox.m
diff --git a/matlabTools/stats/requireImageToolbox.m → matlabTools/util/requireImageToolbox.m b/matlabTools/stats/requireImageToolbox.m → matlabTools/util/requireImageToolbox.m
diff --git a/matlabTools/stats/requireOptimToolbox.m → matlabTools/util/requireOptimToolbox.m b/matlabTools/stats/requireOptimToolbox.m → matlabTools/util/requireOptimToolbox.m
@@ -2,6 +2,7 @@ function requireOptimToolbox()
 % Throw an error as the calling function if the optim toolbox is not installed
 
 % This file is from pmtk3.googlecode.com
+
 
 if ~optimToolboxInstalled
     if isOctave

diff --git a/matlabTools/stats/requireStatsToolbox.m → matlabTools/util/requireStatsToolbox.m b/matlabTools/stats/requireStatsToolbox.m → matlabTools/util/requireStatsToolbox.m
diff --git a/pmtkTools/getConfigValue.m b/pmtkTools/getConfigValue.m
@@ -99,7 +99,14 @@
         end
     end
 end
-remove = cellfun(@(c)~isvarname(c) || length(c) < 5, tags); 
+%remove = cellfun(@(c)~isvarname(c) || length(c) < 5, tags); 
+remove = [];
+for i=1:numel(tags)
+  c = tags{i};
+  if ~isvarname(c) || length(c) < 5
+    remove = [remove i];
+  end
+end
 tags(remove) = [];
 lines(remove) = []; 
 end