Fix code indentation. Also fix bug in MATLAB display of two different types of...

Fix code indentation. Also fix bug in MATLAB display of two different types of plot (e.g. patch and plot) by setting the renderer to OpenGL.

utilities/show_sigma.m

@@ -10,7 +10,7 @@ function show_sigma(meshfile,bathfile,sigmafile,varargin)
 %    meshfile:   fvcom grid file
 %    bathfile:   fvcom bathymetry file
 %    sigmafile:  fvcom sigma distribution file
-%    spoints:    number of points in the user-selected line (optional,
+%    npts:       number of points in the user-selected line (optional,
 %                defaults to 25).
 %
 % OUTPUT:
@@ -28,22 +28,20 @@ function show_sigma(meshfile,bathfile,sigmafile,varargin)
 %   argument to increase the profile sampling frequency.
 %   
 %==============================================================================
-% meshfile = 'tst_grd.dat';
-% bathfile = 'tst_dep.dat';
-% sigmafile = 'sigma.dat';
+
 close all
 
 if nargin == 4
-    spoints = varargin{1}
+    npts = varargin{1};
 else
-    spoints = 25;
+    npts = 25;
 end
 
-% read the mesh 
+% read the mesh
 fid = fopen(meshfile,'r');
 if(fid  < 0)
-  error(['file: ' meshfile ' does not exist']);
-end;
+    error(['file: ' meshfile ' does not exist']);
+end
 C = textscan(fid, '%s %s %s %d', 1);
 Nverts = C{4};
 C = textscan(fid, '%s %s %s %d', 1);
@@ -52,28 +50,28 @@ x = zeros(Nverts,3);
 tri = zeros(Nelems,3);
 fprintf('Nverts: %d\n',Nverts)
 fprintf('Nelems: %d\n',Nelems)
-for i=1:Nelems 
-  C = textscan(fid, '%d %d %d %d %d', 1);
-  tri(i,1) = C{2}; 
-  tri(i,2) = C{3}; 
-  tri(i,3) = C{4}; 
-end;
-for i=1:Nverts 
-  C = textscan(fid, '%d %f %f %f ', 1);
-  x(i,1) = C{2}; 
-  x(i,2) = C{3}; 
-end;
-
-% read the bathy 
+for i=1:Nelems
+    C = textscan(fid, '%d %d %d %d %d', 1);
+    tri(i,1) = C{2};
+    tri(i,2) = C{3};
+    tri(i,3) = C{4};
+end
+for i=1:Nverts
+    C = textscan(fid, '%d %f %f %f ', 1);
+    x(i,1) = C{2};
+    x(i,2) = C{3};
+end
+
+% read the bathy
 fid = fopen(bathfile,'r');
 if(fid  < 0)
-  error(['file: ' bathfile ' does not exist']);
-end;
+    error(['file: ' bathfile ' does not exist']);
+end
 C = textscan(fid, '%s %s %s %d', 1);
 for i=1:Nverts
-  C = textscan(fid, '%f %f %f ', 1);
-  x(i,3) = C{3};
-end;
+    C = textscan(fid, '%f %f %f ', 1);
+    x(i,3) = C{3};
+end
 
 fprintf('min topography %f\n',min(x(:,3)));
 fprintf('max topography %f\n',max(x(:,3)));
@@ -81,7 +79,7 @@ fprintf('max topography %f\n',max(x(:,3)));
 % read the sigma file
 fid = fopen(sigmafile,'r');
 if(fid  < 0)
-  error(['file: ' sigmafile ' does not exist']);
+    error(['file: ' sigmafile ' does not exist']);
 end
 
 while ~feof(fid)
@@ -133,37 +131,42 @@ fprintf('zkl %d\n',zkl)
 
 
 % generate the sigma coordinates
-fprintf('select two endpoints of a transect')
+
+% fix "java.lang.IllegalArgumentException: adding a container to a container
+% on a different GraphicsDevice" error. See
+% http://www.mathworks.co.uk/matlabcentral/newsreader/view_thread/169024.
+set(0,'DefaultFigureRenderer','OpenGL')
+
 figure(1)
 patch('Vertices',[x(:,1),x(:,2)],'Faces',tri,...
-       'Cdata',x(:,3),'edgecolor','interp','facecolor','interp');
+    'Cdata',x(:,3),'edgecolor','interp','facecolor','interp');
 axis equal
 
 % plot to get a line
-%fprintf('select two end points of a transect with your mouse');
+fprintf('select two end points of a transect with your mouse');
 [xt,yt] = ginput(2);
 hold on
 
-npts = 25;
 ds = (xt(2)-xt(1))/(npts-1);
 xline = xt(1):ds:xt(2);
 ds = (yt(2)-yt(1))/(npts-1);
 yline = yt(1):ds:yt(2);
-plot(xline,yline,'w+')
+plot(xline, yline, 'r+')
 sline = zeros(1, npts);
 for i=2:npts
-  sline(i) = sline(i-1) + sqrt(   (xline(i)-xline(i-1))^2 + (yline(i)-yline(i-1))^2);
+    sline(i) = sline(i-1) + sqrt((xline(i)-xline(i-1))^2 + (yline(i)-yline(i-1))^2);
 end
 
 % interpolate the bathymetry along the line
-zline = griddata(x(:,1),x(:,2),x(:,3),xline,yline);
+zline = griddata(x(:,1), x(:,2), x(:,3), xline, yline);
 
-figure
-plot(sline,-zline)
+figure(2)
+plot(sline, -zline)
 
 % generate the sigma coordinates along the line
 xslice = zeros(npts,nlev);
 yslice = zeros(npts,nlev);
+z = nan(npts, nlev);
 
 % calculate the sigma distributions along the transect
 switch lower(sigtype)
@@ -180,19 +183,17 @@ switch lower(sigtype)
 end
 
 for i=1:npts
-  xslice(i,1:nlev) = sline(i);
-  yslice(i,1:nlev) = z(i,1:nlev)*zline(i);
-end;
+    xslice(i,1:nlev) = sline(i);
+    yslice(i,1:nlev) = z(i,1:nlev)*zline(i);
+end
 
 
 % plot the mesh along the transect
 for k=1:nlev
-  plot(xslice(:,k),yslice(:,k),'k'); hold on;
-end;
+    plot(xslice(:,k),yslice(:,k),'k'); hold on;
+end
 for k=1:npts
-  plot(xslice(k,:),yslice(k,:),'k'); hold on;
-end;
+    plot(xslice(k,:),yslice(k,:),'k'); hold on;
+end
 axis([xslice(1,1),xslice(end,1),min(yslice(:,end)),5])
 title('sigma distribution along the transect');
-
-