making svmc matlab demos compatible with Octave 5

fangq · Nov 4, 2021 · 2585471 · 2585471
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commit 2585471
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Showing 7 changed files with 21 additions and 29 deletions.
diff --git a/mcxlab/examples/demo_diffuse_reflectance_validation.m b/mcxlab/examples/demo_diffuse_reflectance_validation.m
@@ -15,9 +15,8 @@
 %
 % This file is part of Monte Carlo eXtreme (MCX) URL:http://mcx.sf.net
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clc
-clear
-close all
+
+clear cfg
 
 %% Monte Carlo
 cfg.nphoton=1e8; % photon number

diff --git a/mcxlab/examples/demo_fullhead_atlas.m b/mcxlab/examples/demo_fullhead_atlas.m
@@ -16,8 +16,6 @@
 % This file is part of Monte Carlo eXtreme (MCX) URL:http://mcx.sf.net
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-clc
-clear
 load('fullhead_atlas.mat');
 %% prepare cfg for MCX simulation
 clear cfg

diff --git a/mcxlab/examples/demo_label_continous_hybrid.m b/mcxlab/examples/demo_label_continous_hybrid.m
@@ -1,5 +1,3 @@
-clear
-clc
 
 %% case 1: homogenous media, update the refractive index from n_old to n_new for all voxels
 clear cfg1

diff --git a/mcxlab/examples/demo_svmc_brain19_5.m b/mcxlab/examples/demo_svmc_brain19_5.m
@@ -20,9 +20,8 @@
 %
 % This file is part of Monte Carlo eXtreme (MCX) URL:http://mcx.sf.net
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clc
-clear
-close all
+
+clear cfg cfg_svmc
 
 %% common MC setup
 cfg.nphoton=1e8;
@@ -103,15 +102,15 @@
 figure;
 clines=-20:0.5:0;
 contourf(xx-0.5,zz-0.5,log10(abs(phi_svmc_interp')),clines,'linestyle','-',...
-    'color','k','linewidth',2,'DisplayName','SVMC');
+    'linecolor','k','linewidth',2,'DisplayName','SVMC');
 hold on;
 contour(xx,zz,log10(abs(squeeze(phi_vmc(:,ceil(y_plane),:))')),clines,'linestyle','--',...
-    'color','w','linewidth',2,'DisplayName','VMC');
+    'linecolor','w','linewidth',2,'DisplayName','VMC');
 colorbar('EastOutside');
 
 % plot tissue boundaries
 contour(squeeze(USC_atlas(:,ceil(y_plane),:))','linestyle','--',...
-    'color',[0.5 0.5 0.5],'linewidth',1.5,'HandleVisibility','off');
+    'linecolor',[0.5 0.5 0.5],'linewidth',1.5,'HandleVisibility','off');
 
 axis equal;
 lg=legend;

diff --git a/mcxlab/examples/demo_svmc_cubesph.m b/mcxlab/examples/demo_svmc_cubesph.m
@@ -10,9 +10,8 @@
 %
 % This file is part of Monte Carlo eXtreme (MCX) URL:http://mcx.sf.net
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clc
-clear
-close all
+
+clear cfg cfg_svmc
 
 %% common MC setup
 cfg.nphoton=1e8;
@@ -90,14 +89,14 @@
 figure;
 clines=-10:0.5:10;
 contourf(yy_svmc,zz_svmc,log10(abs(squeeze(phi_svmc(31,:,:)))),clines,'linestyle','-',...
-    'color','k','linewidth',2,'DisplayName','SVMC');
+    'linecolor','k','linewidth',2,'DisplayName','SVMC');
 hold on;
 contour(yy_vmc,zz_vmc,log10(abs(squeeze(phi_vmc(61,:,:)))),clines,'linestyle','--',...
-    'color','w','linewidth',2,'DisplayName','VMC');
+    'linecolor','w','linewidth',2,'DisplayName','VMC');
 colorbar('EastOutside');
 
 % plot media boundaries
-[xcirc,ycirc] = cylinder(25,200);
+[xcirc,ycirc] = cylinder([25,25],200);
 xcirc=xcirc(1,:)+30.5;
 ycirc=ycirc(1,:)+30.5;
 plot(xcirc,ycirc,'--','linewidth',1.5,'color',[.5 .5 .5],'HandleVisibility','off');

diff --git a/mcxlab/examples/demo_svmc_sphshells.m b/mcxlab/examples/demo_svmc_sphshells.m
@@ -14,9 +14,8 @@
 %
 % This file is part of Monte Carlo eXtreme (MCX) URL:http://mcx.sf.net
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clc
-clear
-close all
+
+clear cfg cfg_svmc
 
 %% common MC setup
 cfg.nphoton=1e8;
@@ -94,24 +93,24 @@
 figure;
 clines=-10:0.5:10;
 contourf(log10(abs(squeeze(phi_svmc(31,:,:))')),clines,'linestyle','-',...
-    'color','k','linewidth',2,'DisplayName','SVMC');
+    'linecolor','k','linewidth',2,'DisplayName','SVMC');
 hold on;
 contour(log10(abs(squeeze(phi_vmc(31,:,:))')),clines,'linestyle','--',...
-    'color','w','linewidth',2,'DisplayName','VMC');
+    'linecolor','w','linewidth',2,'DisplayName','VMC');
 colorbar('EastOutside');
 
 % plot media boundaries
-[xcirc,ycirc] = cylinder(10,200);
+[xcirc,ycirc] = cylinder([10,10],200);
 xcirc=xcirc(1,:)+31;
 ycirc=ycirc(1,:)+31;
 plot(xcirc,ycirc,'--','linewidth',1.5,'color',[.5 .5 .5],'HandleVisibility','off');
 
-[xcirc,ycirc] = cylinder(23,200);
+[xcirc,ycirc] = cylinder([23,23],200);
 xcirc=xcirc(1,:)+31;
 ycirc=ycirc(1,:)+31;
 plot(xcirc,ycirc,'--','linewidth',1.5,'color',[.5 .5 .5],'HandleVisibility','off');
 
-[xcirc,ycirc] = cylinder(25,200);
+[xcirc,ycirc] = cylinder([25,25],200);
 xcirc=xcirc(1,:)+31;
 ycirc=ycirc(1,:)+31;
 plot(xcirc,ycirc,'--','linewidth',1.5,'color',[.5 .5 .5],'HandleVisibility','off');

diff --git a/utils/mcxsvmc.m b/utils/mcxsvmc.m
@@ -95,7 +95,7 @@
     % convert each label into a binary mask, smooth it, then extract the
     % isosurface using marching cube algorithm (matlab builtin)
     if(dosmooth)
-        volsmooth=smooth3(vol==labels(i),'g',ksize,kstd);
+        volsmooth=smooth3(double(vol==labels(i)),'g',ksize,kstd);
     else
         volsmooth=(vol==labels(i));
     end
@@ -203,7 +203,7 @@
 
 nc=nc-floor(nc);
 nc=floor(nc*255);
-nn=floor((nn+1)*255/2);
+nn=min(floor((nn+1)*255/2),254);
 
 %% assemble the final volume
 if(nargout==1)