Re: basic implementation for isosurface, isocolors, isonormals

[Thomas Treichl]

David Bateman schrieb:
> Martin Helm wrote:
> > First of all,
> >
> > thank you for your effort David. I can confirm the errors reported by 
> > Thomas. To be precise they happen with the first two examples in the 
> > "subplot" example group which use the syntax
> > patch ("Faces", f, "Vertices", v, "EdgeColor", whatever)
> >
> > The other two examples which use "FaceVertexCData" and facecoloring 
> > work well.
> >
> > If I simply add the "FaceColor" attribute with some value to the 
> > failing patch command, the problem disappears, so the bug seems to be 
> > trivial (a misssing default value for "FaceColor")
> >
> > e.g.
> >
> > patch ("Faces", f, "Vertices", v, "FaceColor", "blue","EdgeColor", 
> > "none")
> >
> > works well. I'll look through the code.
> >
> > - mh
> >   
> The old 3.0.x behavior was that the default facecolor was [0,1,0]. I 
> presume that is the compatible behavior and so re-established that as 
> the default with the attached patch. The demo in the help string then 
> works correctly for the gnuplot CVS. But there appear to be some issue 
> with colormap with gnuplot 4.2.4 and the x11 terminal in a multiplot 
> environment.. I suppose I should try 4.2.5 and see if that works
>
> D.

Hi David, Martin,

thanks again for this work. I'd say that this is really a very cool new feature 
that then comes with 3.2...

Some time ago I also was working on the help text of isonormals.m and 
__marching_cubes__.m (Martin already knows because I wrote him an email some 
time ago offside the lists to preserve double-work ;) David, can you please 
apply the attached changeset?

Thanks and best regards,

  Thomas

# HG changeset patch
# User Thomas Treichl <address@hidden>
# Date 1239739325 -7200
# Node ID 3b810beddfa64d947c1fe399b17f325d70e0eac1
# Parent  308311b642b2be2c4e171e15b9e8f35ea4615975
Added help texts and tests.

diff --git a/scripts/ChangeLog b/scripts/ChangeLog
--- a/scripts/ChangeLog
+++ b/scripts/ChangeLog
@@ -1,4 +1,9 @@
-2009-04-11  David Bateman  <address@hidden>
+2009-04-14  Thomas Treichl  <address@hidden>
+
+       * plot/__marching_cube__.m: Add help text.
+       * plot/isonormals.m: Add help text and tests.
+
+2009-04-14  David Bateman  <address@hidden>
 
        * plot/__patch__.m: Set default facecolor to [0,1,0].
        
diff --git a/scripts/plot/__marching_cube__.m b/scripts/plot/__marching_cube__.m
--- a/scripts/plot/__marching_cube__.m
+++ b/scripts/plot/__marching_cube__.m
@@ -12,52 +12,63 @@
 ##
 ## You should have received a copy of the GNU General Public License
 ## along with this program; if not, see http://www.gnu.org/licenses/gpl.html.
+
+## -*- texinfo -*-
+## @deftypefn  {Function File} address@hidden, @var{p}] =} __marching_cube__ 
(@var{x}, @var{y}, @var{z}, @var{val}, @var{iso})
+## @deftypefn  {Function File} address@hidden, @var{p}, @var{c}] =} 
__marching_cube__ (@var{x}, @var{y}, @var{z}, @var{val}, @var{iso}, @var{col})
 ##
+## Return the triangulation information @var{t} at points @var{p} for
+## the isosurface values resp. the volume data @var{val} and the iso
+## level @var{iso}.  It is considered that the volume data @var{val} is
+## given at the points @var{x}, @var{y} and @var{z} which are of type
+## three--dimensional numeric arrays.  The orientation of the triangles
+## is choosen such that the normals point from the higher values to the
+## lower values.
+##
+## Optionally the color data @var{col} can be passed to this function
+## whereas computed vertices color data @var{c} is returned as third
+## argument.
+##
+## The marching cube algorithm is well known and described eg. at
+## Wikipedia. The triangulation lookup table and the edge table used
+## here are based on Cory Gene Bloyd's implementation and can be found
+## beyond other surface and geometry stuff at Paul Bourke's website
+## @uref{http://local.wasp.uwa.edu.au/~pbourke/geometry/polygonise}.
+##
+## For example,
+## @example
+## N = 20;
+## lin = linspace(0, 2, N);
+## [x, y, z] = meshgrid (lin, lin, lin);
+##
+## c = (x-.5).^2 + (y-.5).^2 + (z-.5).^2;
+## [t, p] = __marching_cube__ (x, y, z, c, .5);
+##
+## figure ();
+## trimesh (t, p(:,1), p(:,2), p(:,3));
+## @end example
+##
+## Instead of the @command{trimesh} function the @command{patch}
+## function can be used to visualize the geometry. For example,
+##
+## @example
+## figure (); view (-38, 20);
+## pa = patch ("Faces", t, "Vertices", p, "FaceVertexCData", p, \
+##             "FaceColor", "interp", "EdgeColor", "none");
+##
+## ## Revert normals
+## set (pa, "VertexNormals", -get(pa, "VertexNormals"));
+##
+## ## Set lightning (available with the JHandles package)
+## # set (pa, "FaceLighting", "gouraud");
+## # light( "Position", [1 1 5]);
+## @end example
+##
+## @end deftypefn
+
 ## Author: Martin Helm <address@hidden>
 
-## -*- texinfo -*-
-## @deftypefn {Function File} address@hidden, @var{p}, @var{col}] =} 
__marching_cube__ (@var{x}, @var{y}, @var{z}, @var{c}, @var{iso}, @var{color})
-## Undocumented internal function.
-## @end deftypefn
-
-## usage: [T, P] = marching_cube( XX, YY, ZZ, C, ISO)
-## usage: [T, P, COL] = marching_cube( XX, YY, ZZ, C, ISO, COLOR)
-##
-## Calculates the triangulation T with points P for the isosurface
-## with level ISO. XX, YY, ZZ are meshgrid like values for the
-## cube and C holds the scalar values of the field,
-## COLOR holds additinal scalar values for coloring the surface.
-## The orientation of the triangles is choosen such that the
-## normals point from the lower values to the higher values.
-##
-## edgeTable and triTable are taken from Paul Bourke
-## (http://local.wasp.uwa.edu.au/~pbourke/geometry/polygonise/)
-## Based on tables by Cory Gene Bloyd
-##
-## Example:
-##
-## x = linspace(0, 2, 20);
-## y = linspace(0, 2, 20);
-## z = linspace(0, 2, 20);
-##
-## [ xx, yy, zz ] = meshgrid(x, y, z);
-##
-## c = (xx-.5).^2 + (yy-.5).^2 + (zz-.5).^2;
-## [T, p] = marching_cube(xx, yy, zz, c, 0.5);
-## trimesh(T, p(:, 1), p(:, 2), p(:, 3));
-##
-## with jhandles you can also use the patch function to visualize
-## 
-## clf
-## pa = patch('Faces',T,'Vertices',p,'FaceVertexCData',p, ...
-## 'FaceColor','interp', 'EdgeColor', 'none');
-## set(pa, "VertexNormals", -get(pa, "VertexNormals")) # revert normals
-## view(-30, 30)
-## set(pa, "FaceLighting", "gouraud")
-## light( "Position", [1 1 5])
-##
-
-function [T, p, col] = __marching_cube__( xx, yy, zz, c, iso, colors)
+function [T, p, col] = __marching_cube__ (xx, yy, zz, c, iso, colors)
   
   persistent edge_table=[];
   persistent tri_table=[];
@@ -502,4 +513,4 @@
   0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1;
   0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1;
   -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 ] + 1;
-endfunction
\ No newline at end of file
+endfunction
diff --git a/scripts/plot/isonormals.m b/scripts/plot/isonormals.m
--- a/scripts/plot/isonormals.m
+++ b/scripts/plot/isonormals.m
@@ -12,17 +12,83 @@
 ##
 ## You should have received a copy of the GNU General Public License
 ## along with this program; if not, see http://www.gnu.org/licenses/gpl.html.
+
+## -*- texinfo -*-
+## @deftypefn  {Function File} address@hidden =} isonormals (@var{val}, 
@var{v})
+## @deftypefnx {Function File} address@hidden =} isonormals (@var{val}, 
@var{p})
+## @deftypefnx {Function File} address@hidden =} isonormals (@var{x}, @var{y}, 
@var{z}, @var{val}, @var{v})
+## @deftypefnx {Function File} address@hidden =} isonormals (@var{x}, @var{y}, 
@var{z}, @var{val}, @var{p})
+## @deftypefnx {Function File} address@hidden =} isonormals (@dots{}, "negate")
+## @deftypefnx {Function File} isonormals (@dots{}, @var{p})
 ##
+## If called with one output argument and the first input argument
+## @var{val} is a three--dimensional array that contains the data for an
+## isosurface geometry and the second input argument @var{v} keeps the
+## vertices of an isosurface then return the normals @var{n} in form of
+## a matrix with the same size than @var{v} at computed points
+## @command{[x, y, z] = meshgrid (1:l, 1:m, 1:n)}.  The output argument
+## @var{n} can be taken to manually set @var{VertexNormals} of a patch.
+##
+## If called with further input arguments @var{x}, @var{y} and @var{z}
+## which are three--dimensional arrays with the same size than @var{val}
+## then the volume data is taken at those given points.  Instead of the
+## vertices data @var{v} a patch handle @var{p} can be passed to this
+## function.
+##
+## If given the string input argument "negate" as last input argument
+## then compute the reverse vector normals of an isosurface geometry.
+##
+## If no output argument is given then directly redraw the patch that is
+## given by the patch handle @var{p}.
+##
+## For example,
+## @example
+## function [] = isofinish (p)
+##   set (gca, "DataAspectRatioMode","manual","DataAspectRatio",[1 1 1]);
+##   set (p, "VertexNormals", -get(p,"VertexNormals")); ## Revert normals
+##   set (p, "FaceColor", "interp");
+##   ## set (p, "FaceLighting", "phong");
+##   ## light ("Position", [1 1 5]); ## Available with JHandles
+## endfunction
+##
+## N = 15;    ## Increase number of vertices in each direction
+## iso = .4;  ## Change isovalue to .1 to display a sphere
+## lin = linspace (0, 2, N);
+## [x, y, z] = meshgrid (lin, lin, lin);
+## c = abs ((x-.5).^2 + (y-.5).^2 + (z-.5).^2);
+## figure (); ## Open another figure window
+##
+## subplot (2, 2, 1); view (-38, 20);
+## [f, v, cdat] = isosurface (x, y, z, c, iso, y);
+## p = patch ("Faces", f, "Vertices", v, "FaceVertexCData", cdat, \
+##        "FaceColor", "interp", "EdgeColor", "none");
+## isofinish (p); ## Call user function isofinish
+##
+## subplot (2, 2, 2); view (-38, 20);
+## p = patch ("Faces", f, "Vertices", v, "FaceVertexCData", cdat, \
+##        "FaceColor", "interp", "EdgeColor", "none");
+## isonormals (x, y, z, c, p); ## Directly modify patch
+## isofinish (p);
+##
+## subplot (2, 2, 3); view (-38, 20);
+## p = patch ("Faces", f, "Vertices", v, "FaceVertexCData", cdat, \
+##        "FaceColor", "interp", "EdgeColor", "none");
+## n = isonormals (x, y, z, c, v); ## Compute normals of isosurface
+## set (p, "VertexNormals", n);    ## Manually set vertex normals
+## isofinish (p);
+##
+## subplot (2, 2, 4); view (-38, 20);
+## p = patch ("Faces", f, "Vertices", v, "FaceVertexCData", cdat, \
+##        "FaceColor", "interp", "EdgeColor", "none");
+## isonormals (x, y, z, c, v, "negate"); ## Use reverse directly
+## isofinish (p);
+## @end example
+##
+## @seealso {isosurface, isocolors, isocaps, marching_cube}
+##
+## @end deftypefn
+
 ## Author: Martin Helm <address@hidden>
-
-## usage: NORMALS = isonormals(X,Y,Z,V,VERT)
-## usage: NORMALS = isonormals(V,VERT)
-## usage: NORMALS = isonormals(V,P)
-## usage: NORMALS = isonormals(X,Y,Z,V,P)
-## usage: NORMALS = isonormals(...,'negate')
-## usage: isonormals(V,P)
-## usage: isonormals(X,Y,Z,V,P)
-##
 
 function varargout = isonormals(varargin)
   na = nargin;
@@ -75,4 +141,18 @@
     otherwise
       print_usage ();
   endswitch
-endfunction
\ No newline at end of file
+endfunction
+
+%!test
+%!  [x, y, z] = meshgrid (0:.5:2, 0:.5:2, 0:.5:2);
+%!  c = abs ((x-.5).^2 + (y-.5).^2 + (z-.5).^2); 
+%!  [f, v, cdat] = isosurface (x, y, z, c, .4, y);
+%!  n = isonormals (x, y, z, c, v);
+%!  assert (size (v), size (n));
+%!test
+%!  [x, y, z] = meshgrid (0:.5:2, 0:.5:2, 0:.5:2);
+%!  c = abs ((x-.5).^2 + (y-.5).^2 + (z-.5).^2); 
+%!  [f, v, cdat] = isosurface (x, y, z, c, .4, y);
+%!  np = isonormals (x, y, z, c, v);
+%!  nn = isonormals (x, y, z, c, v, "negate");
+%!  assert (all (np == -nn));