From db834f9b73bbdfe5bdd762ffb051aa11bd492409 Mon Sep 17 00:00:00 2001
From: dlegland <david.legland@inra.fr>
Date: Thu, 26 Sep 2019 10:17:21 +0200
Subject: [PATCH] various code cleanup

---
 CHANGELOG.md                            |  7 ++++---
 matGeom/geom2d/crackPattern.m           | 13 +++++++------
 matGeom/geom2d/crackPattern2.m          |  4 ++--
 matGeom/geom2d/hexagonalGrid.m          | 23 +++++++++++------------
 matGeom/geom3d/rotation3dAxisAndAngle.m |  4 ++--
 matGeom/meshes3d/cutMeshByPlane.m       |  4 +++-
 6 files changed, 29 insertions(+), 26 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be7460ae..b5608dce 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,10 +8,11 @@ and finally by module.
 ## [Unreleased]
 
 
-## MatGeom 1.2.0 - 2018-06-07
+## MatGeom 1.2.1 - 2019-09-26
 
-Main changes are new functions for processing 3D meshes, and renaming of 
-inertia ellipse/ellipsoid into equivalent ellipse/ellipsoid.
+Main changes are new functions for processing 3D meshes (repairing, 
+simplification), and renaming of inertia ellipse/ellipsoid into equivalent 
+ellipse/ellipsoid.
 
 ### Added
 
diff --git a/matGeom/geom2d/crackPattern.m b/matGeom/geom2d/crackPattern.m
index b1a62845..4d288512 100644
--- a/matGeom/geom2d/crackPattern.m
+++ b/matGeom/geom2d/crackPattern.m
@@ -19,8 +19,10 @@
 %     figure;
 %     drawEdge(E);
 %
-%   See also drawEdge
+%   See also 
+%     drawEdge
 %
+
 %   ---------
 %
 %   author : David Legland 
@@ -94,7 +96,7 @@
                 end
             else
                  if abs(pos2)<abs(posr(i2)) && abs(pos2)<lines(il, 6)
-                    if lines(i, 5) ~= posr(i2);
+                    if lines(i, 5) ~= posr(i2)
                         edges(i, 3:4) = pi(il,:);
                         lines(i, 5) = posr(i2);
                         modif = 1;
@@ -106,13 +108,12 @@
         end   % end processing of right points of the line
             
         
-        
          % consider points to the left (negative position), and sort them
         indl = find(pos<=0 && pos~=Inf);
         [posl, indl2] = sort(abs(pos(indl)));        
 
         % look for the closest intersection to the right
-        for i2=1:length(indl2)
+        for i2 = 1:length(indl2)
             % index of intersected line
             il = indl(indl2(i2));
             
@@ -123,7 +124,7 @@
             % stop the current line, or if it was stopped before
             if pos2>0
                 if pos2<abs(posl(i2)) && pos2<lines(il, 5)
-                    if lines(i, 6) ~= abs(posl(i2));
+                    if lines(i, 6) ~= abs(posl(i2))
                         edges(i, 1:2) = pi(il, :);
                         lines(i, 6) = abs(posl(i2));
                         modif = 1;
@@ -132,7 +133,7 @@
                 end
             else
                  if abs(pos2)<abs(posl(i2)) && abs(pos2)<lines(il, 6)
-                    if lines(i, 6) ~= abs(posl(i2));
+                    if lines(i, 6) ~= abs(posl(i2))
                         edges(i, 1:2) = pi(il, :);
                         lines(i, 6) = abs(posl(i2));
                         modif = 1;
diff --git a/matGeom/geom2d/crackPattern2.m b/matGeom/geom2d/crackPattern2.m
index 026a78c5..ba8fe39e 100644
--- a/matGeom/geom2d/crackPattern2.m
+++ b/matGeom/geom2d/crackPattern2.m
@@ -44,8 +44,8 @@
 % reach the intersection point.
 NP = size(points, 1);
 lines = zeros(0, 5);
-for i=1:size(alpha, 2)    
-    lines = [lines; points speed.*cos(alpha(:,i)) speed.*sin(alpha(:,i)) Inf*ones(NP, 1)];
+for i = 1:size(alpha, 2)
+    lines = [lines; points speed.*cos(alpha(:,i)) speed.*sin(alpha(:,i)) Inf*ones(NP, 1)]; %#ok<AGROW>
 end
 NL = size(lines, 1);
 
diff --git a/matGeom/geom2d/hexagonalGrid.m b/matGeom/geom2d/hexagonalGrid.m
index ad111941..d7020d5c 100644
--- a/matGeom/geom2d/hexagonalGrid.m
+++ b/matGeom/geom2d/hexagonalGrid.m
@@ -1,7 +1,7 @@
 function varargout = hexagonalGrid(bounds, origin, size, varargin)
 %HEXAGONALGRID Generate hexagonal grid of points in the plane.
 %
-%   usage
+%   usage:
 %   PTS = hexagonalGrid(BOUNDS, ORIGIN, SIZE)
 %   generate points, lying in the window defined by BOUNDS (=[xmin ymin
 %   xmax ymax]), starting from origin with a constant step equal to size.
@@ -10,18 +10,18 @@
 %
 %   TODO: add possibility to use rotated grid
 %
+
 %   ---------
 %
 %   author : David Legland 
 %   INRA - TPV URPOI - BIA IMASTE
 %   created the 06/08/2005.
 %
+
 size = size(1);
 dx = 3*size;
 dy = size*sqrt(3);
 
-
-
 % consider two square grids with different centers
 pts1 = squareGrid(bounds, origin + [0 0],        [dx dy], varargin{:});
 pts2 = squareGrid(bounds, origin + [dx/3 0],     [dx dy], varargin{:});
@@ -32,11 +32,9 @@
 pts = [pts1;pts2;pts3;pts4];
 
 
-
-
 % eventually compute also edges, clipped by bounds
 % TODO : manage generation of edges 
-if nargout>1
+if nargout > 1
     edges = zeros([0 4]);
     x0 = origin(1);
     y0 = origin(2);
@@ -55,11 +53,11 @@
     ny = length(ly);
     nx = length(lx);
  
-    if bounds(1)-x1+dx<size
+    if bounds(1)-x1+dx < size
         disp('intersect bounding box');
     end
     
-    if bounds(3)-x2<size
+    if bounds(3)-x2 < size
         disp('intersect 2');
         edges = [edges;repmat(x2, [ny 1]) ly repmat(bounds(3), [ny 1]) ly];
         x2 = x2-dx;
@@ -67,22 +65,23 @@
         nx = length(lx);
     end
   
-    for i=1:length(ly)
+    for i = 1:length(ly)
         ind = (1:nx)';
+        tmpEdges = zeros(length(ind), 4);
         tmpEdges(ind, 1) = lx;
         tmpEdges(ind, 2) = ly(i);
         tmpEdges(ind, 3) = lx+size;
         tmpEdges(ind, 4) = ly(i);
-        edges = [edges; tmpEdges];
+        edges = [edges; tmpEdges]; %#ok<AGROW>
     end
     
 end
 
 % process output arguments
-if nargout>0
+if nargout > 0
     varargout{1} = pts;
     
-    if nargout>1
+    if nargout > 1
         varargout{2} = edges;
     end
 end
\ No newline at end of file
diff --git a/matGeom/geom3d/rotation3dAxisAndAngle.m b/matGeom/geom3d/rotation3dAxisAndAngle.m
index b77ea0c0..ca89c6e6 100644
--- a/matGeom/geom3d/rotation3dAxisAndAngle.m
+++ b/matGeom/geom3d/rotation3dAxisAndAngle.m
@@ -1,5 +1,5 @@
 function [axis, theta] = rotation3dAxisAndAngle(mat)
-%ROTATION3DAXISANDANGLE Determine axis and angle of a 3D rotation matrix.
+%ROTATION3DAXISANDANGLE Determine axis and angle of a 3D rotation matrix.
 %
 %   [AXIS, ANGLE] = rotation3dAxisAndAngle(MAT)
 %   Where MAT is a 4-by-4 matrix representing a rotation, computes the
@@ -58,7 +58,7 @@
 
 % try to get a point on the line
 % seems to work, but not sure about stability
-[V, D] = eig(mat-eye(4)); %#ok<NASGU>
+[V, D] = eig(mat-eye(4)); %#ok<ASGLU>
 origin = V(1:3,4)'/V(4, 4);
 
 % create line corresponding to rotation axis
diff --git a/matGeom/meshes3d/cutMeshByPlane.m b/matGeom/meshes3d/cutMeshByPlane.m
index 08ffd74b..54663b1f 100644
--- a/matGeom/meshes3d/cutMeshByPlane.m
+++ b/matGeom/meshes3d/cutMeshByPlane.m
@@ -1,5 +1,6 @@
 function varargout = cutMeshByPlane(v, f, plane, varargin)
 %CUTMESHBYPLANE Cut a mesh by a plane.
+%
 %   [ABOVE, IN, BELOW] = cutMeshByPlane(MESH, PLANE)
 %   where MESH, ABOVE, IN, BELOW are structs with the fields vertices and
 %   faces, and PLANE is given as a row containing initial point and 2
@@ -20,6 +21,7 @@
 %   [BELOW_V, BELOW_F] = cutMeshByPlane(MESH, PLANE, 'part', 'below') is
 %   possible, too.
 %
+
 % ---------
 % Authors: oqilipo, David Legland
 % Created: 2017-07-09
@@ -33,7 +35,7 @@
 % If first argument is a struct
 if nargin == 2 || nargin == 4
     if ~isempty(varargin)
-        varargin={plane, varargin{:}};
+        varargin = [{plane}, varargin(:)'];
     end
     plane = f;
     [v, f] = parseMeshData(v);