Merge branch 'master' of https://github.com/fieldsend/mo_lons

fieldsend · May 10, 2019 · 60b2509 · 60b2509
2 parents 57e4319 + 12d40ff
commit 60b2509
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diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ Note codebase is illustrative of proceedures and not optimised for speed!
 
 FUNCTION OVERVIEW
 
-regenerate_GECCO_2019_plots.m --- scriptwill regenerate all the PLON, DNON and PLOS-net plots from the paper
+generate_GECCO_2019_plots.m --- script will regenerate all the PLON, DNON and PLOS-net plots from the paper
 
 gecco_workshop_2019_problem1.m, gecco_workshop_2019_problem2.m and gecco_workshop_2019_problem3.m --- cost functions used in illustrations in the paper. The last takes an argument holding the grid for each objective (this data is stored in the two .mat files loaded in regenerate_GECCO_2019_plots.m).
 

diff --git a/gecco_workshop_2019_problem1.m b/gecco_workshop_2019_problem1.m
@@ -1,5 +1,14 @@
 function y = gecco_workshop_2019_problem1(x,S)
 
+% y = gecco_workshop_2019_problem1(x,S)
+%
+% First simple illustrative problem used in GECCO 2019 paper.
+%
+% Jonathan Fieldsend, University of Exeter, 2019
+% See license information in package, available at 
+% https://github.com/fieldsend/mo_lons
+
+
 if (sum(x<=0)>0)
     error('input variable cannot be negative');
 end

diff --git a/gecco_workshop_2019_problem2.m b/gecco_workshop_2019_problem2.m
@@ -1,5 +1,14 @@
 function y = gecco_workshop_2019_problem1(x,S)
 
+% y = gecco_workshop_2019_problem1(x,S)
+%
+% Second simple illustrative problem used in GECCO 2019 paper.
+%
+% Jonathan Fieldsend, University of Exeter, 2019
+% See license information in package, available at 
+% https://github.com/fieldsend/mo_lons
+
+
 if (sum(x<=0)>0)
     error('input variable cannot be negative');
 end

diff --git a/gecco_workshop_2019_problem3.m b/gecco_workshop_2019_problem3.m
@@ -1,5 +1,15 @@
 function y = gecco_workshop_2019_problem3(x,S)
 
+% y = gecco_workshop_2019_problem1(x,S)
+%
+% Many-objective illustrative problem used in GECCO 
+% 2019 paper. S contains extra data needed by the 
+% different problem versions, available in the repository 
+%
+% Jonathan Fieldsend, University of Exeter, 2019
+% See license information in package, available at 
+% https://github.com/fieldsend/mo_lons
+
 if (sum(x<=0)>0)
     error('input variable cannot be negative');
 end
@@ -18,5 +28,3 @@
 y(5) = S.F5(x(1),x(2)); 
 
 
-
-
diff --git a/plot_PLOS_net.m b/plot_PLOS_net.m
@@ -1,5 +1,16 @@
 function [DNO] = plot_PLOS_net(X,Y,state,neighbours,edge_weight,node_weight)
 
+% [DNO] = plot_PLOS_net(X,Y,state,neighbours,edge_weight,node_weight)
+%
+% Function plots the PLOS-net for the given parameters, outputted from the 
+% exaustive_generate_lon function. See e.g. generate_GECCO_2019_plots for 
+% example usage.
+%
+% Jonathan Fieldsend, University of Exeter, 2019
+% See license information in package, available at 
+% https://github.com/fieldsend/mo_lons
+
+
 [~,k] = size(Y);
 
 % function plots the PLOS-net for the given inputs
@@ -57,20 +68,7 @@
     highlight(H,i,'MarkerSize',node_weight,'NodeColor',0.1+abs(ones(1,3)*(Y(DNO(i),k)-min_y)/(max_y-min_y)-1)*0.5);
 end
 
-
-% if min_y==max_y
-%     for i=1:length(basin_size)
-%         highlight(H,i,'MarkerSize',node_weight*basin_size(i)/sum(basin_size),'NodeColor',[0 0 0]);
-%     end
-% else
-%     for i=1:length(basin_size)
-%             highlight(H,i,'MarkerSize',node_weight*basin_size(i)/sum(basin_size),'NodeColor',0.1+abs(ones(1,3)*(Q(i)-min_y)/(max_y-min_y)-1)*0.5);
-%     end
-% end
 set(gca,'YTick',[])
 set(gca,'XTick',[])
 
-
-
-
 end
diff --git a/process_d_lon.m b/process_d_lon.m
@@ -1,8 +1,17 @@
 function [V,B,EE,C,PO] = process_d_lon(X,Y,w,YY,state, neighbours)
 
-
+%  [V,B,EE,C,PO] = process_d_lon(X,Y,w,YY,state, neighbours)
+%
+% Processes data outputted from exaustive_generate_lon to create 
+% the matrices needed to plot the DNON
+%
+% see generate_GECCO_2019_plots for example usage
+%
 % state holds destination of all walks from the index
-
+%
+% Jonathan Fieldsend, University of Exeter, 2019
+% See license information in package, available at 
+% https://github.com/fieldsend/mo_lons
 
 V=cell(1,1);
 v_index=1;

diff --git a/process_p_lon.m b/process_p_lon.m
@@ -1,5 +1,17 @@
 function [V,B,Adj,EE,C] = process_p_lon(X,Y,state,neighbours)
 
+%  [V,B,EE,C,PO] = process_p_lon(X,Y,w,YY,state, neighbours)
+%
+% Processes data outputted from exaustive_generate_lon to create 
+% the matrices needed to plot the PLON
+%
+% see generate_GECCO_2019_plots for example usage
+%
+% state holds destination of the walk from the index
+%
+% Jonathan Fieldsend, University of Exeter, 2019
+% See license information in package, available at 
+% https://github.com/fieldsend/mo_lons
 
 min_state = cell(0);
     for j=1:length(state)
@@ -60,24 +72,13 @@
                 Z(j) = 1;
             end
         end
-        %if length(K)==length(V{j}) %if V{j} is a subset of state{i}
-        %    B(j) = B(j)+1;
-        %    Z(j) = 1;
-        %end
+
     end
     % now increase weight between vertices which all have path from ith
     Adj(Z==1,index) = Adj(Z==1,index)+1;
-%     for j=1:length(V)
-%         if (Z(j)==true)
-%             Adj(j,Z==1) =  Adj(j,Z==1) + 1;
-%             Adj(Z==1,j) =  Adj(Z==1,j) + 1;
-%         end
-%     end
+
 end
 
-%for j=1:length(V)
-%   Adj(j,j) = length(V{j}); 
-%end
 
 % now colour each vertex
 
@@ -106,9 +107,6 @@
 
 
 
-
-
-
 % add esacpe edges to links
 EE = zeros(length(B)); % matrix of edges between basins, filled with zeros initially
 for i=1:length(B) % process each vertex