function  retained_elements_plot (inc_e, inc_p, row) %CL
%b function  retained_elements_plot (inc_e, inc_p)
% Copyright 2000, J.E. Akin.  All rights reserved.
%  ------------------------------------------------------
%             bare minimum borders
%  Matlab program to calculate & plot 2-D FE meshes
%  ------------------------------------------------------

% c_x    = x coordinates of nod_per_el line polygon
% c_y    = y coordinates of nod_per_el line polygon
% inc_e  = increment in element numbers on plot, if > 0
% inc_p  = increment in node numbers on plot, if > 0
% msh_typ_nodes   = connectivity list for elements, nt x nod_per_el
% loop   = corners for nod_per_el line polygon
% lab_p  = 1, if node points are circled
  lab_p  = 0;
% nod_per_el = Nodes per element
% np     = Number of Points
% nt     = Number of elements
% pre_e  = Element items before type & connectivity list
% pre_p  = Nodal items before coordinates
% row    = row number where cord & connectivity start, 1 or 2 %CL
% msh_bc_xyz = Nodal coordinates (with preceeding data)
% t_x    = x coordinates of nod_per_el corners
% t_y    = y coordinates of nod_per_el corners
% x_bar  = x-centroid of each element
% xy     = Coordinates of points, np x 2
% y_bar  = y-centroid of each element

pre_e  = 0  ;
pre_p = 1;
if ( nargin == 0 )
  inc_e = 0
  inc_p = 0
  row = 1 ; %CL
elseif ( nargin == 1 )
  inc_p = 0
  row = 1 ; %CL
elseif ( nargin == 2 ) %CL
  row = 1; %CL
elseif ( nargin == 3 ) % Chad's data %CL
  pre_e =  0; %CL
  %b row = 2 ; pre_e =  0; %CL
end %if
less = row - 1 ; %CL

%    Read coordinate file and connectivity file
%    integer bc code, real xy pairs for np points (pre_p = 1)

%    Set control data: number of points
  load msh_bc_xyz.tmp ;  
  np = size (msh_bc_xyz,1) ;   % number of nodal points  
  np = np - less ;   %CL
  ns = size (msh_bc_xyz,2) - pre_p ;   % dimension of space
  if ( np == 0 )
    error ('Error missing file msh_bc_xyz.tmp')
  end % if error
  fprintf ('Read %g mesh coordinate pairs \n', np)
  % fprintf ('       x        y \n')

  x (np)      = 0.       ;       % pre-allocate array x
  y (np)      = 0.       ;       % pre-allocate array y

  % msh_bc_xyz has: pre_p items then: x, y
  %b x = msh_bc_xyz (1:np, (pre_p+1)) ; % extract x column of xy
  x = msh_bc_xyz (row:(np+less), (pre_p+1)) ; % extract x  %CL
  if ( ns >= 2)
    %b y = msh_bc_xyz (1:np, (pre_p+2)) ; % extract y column
    y = msh_bc_xyz (row:(np+less), (pre_p+2)) ; % extract y %CL
  else
    y (1:np) = 0. ;
  end % if 1D
  
%    Set control data: number elements & nodes_per_element
  load  msh_typ_nodes.tmp ; % nod_per_el nodes per element
  nt = size (msh_typ_nodes,1);           % number of elements 
  nt = nt - less ; %CL
  if ( nt == 0 )
    error ('Error missing file msh_typ_nodes.tmp')
  end % if error
  nod_per_el = size (msh_typ_nodes,2) - pre_e -1 ; % nodes per element
  fprintf ('Read %g elements with %g nodes each \n', nt,nod_per_el)
  Col_1 = pre_e+2 ; %CL
  Col_2 = nod_per_el+pre_e+1 ; %CL
  Types = msh_typ_nodes(:,pre_e+1) ;
  n_type = max(Types) ;
  if ( n_type > 1 )
    fprintf ('WARNING: Plotting multiple element types, \n')
  end % if multiple types

%   Read the list of deleted elements
% ****************************************************************
% *** in msh_deleted.tmp global substitute 1 for T and 0 for F ***
% ****************************************************************

  load msh_deleted.tmp ; % element number, 1 or 0 for T or F
  nt_check = size (msh_deleted,1);  % number of elements, fibers, segments
  if ( nt_check == 0 )
    error ('Error missing file msh_deleted.tmp')
  end % if error
  if ( nt_check < nt )
    error ('Error deleted list shorter than mesh list')
  end % if error
  n_del = sum ( msh_deleted (:, 2) == 1 );
  fprintf ('Number of deleted elements = %i \n', n_del)

  %b [M_min, J_min] = min ( msh_typ_nodes ) ; ????
  [M_min, J_min] = min ( msh_typ_nodes (row:less+nt, Col_1:Col_2) ); %CL
  if any ( M_min < 1 )
    fprintf ('Mesh seems to have mixed element types, \n')
    fprintf ('use element_type_mesh_plot instead \n')     
  end % if

  x_bar (nt)  = 0.       ;       % pre-allocate array x_bar
  y_bar (nt)  = 0.       ;       % pre-allocate array y_bar
  t_nodes (nod_per_el) = 0 ;    % Optional pre-allocation
  t_x (nod_per_el) = 0 ;        % Optional pre-allocation
  t_y (nod_per_el) = 0 ;        % Optional pre-allocation
  c_x (nod_per_el + 1) = 0 ;    % Optional pre-allocation
  c_y (nod_per_el + 1) = 0 ;    % Optional pre-allocation
  loop (nod_per_el + 1) = 0 ;   % Optional pre-allocation
 
%                set constants
  [loop] = get_El_Loop (nod_per_el) ;
  %b fprintf ('Begin element plots:')

%    Initialize plots
  xmax = max (x)      ; xmin = min (x) ;
  ymax = max (y)      ; ymin = min (y) ;
  xdiff = xmax - xmin ; ydiff = ymax - ymin ;
  if ( ydiff == 0.0 )
    ydiff = 0.1 * xdiff ; % allow for 1-D mesh (with y == 0)
    ymax = ymin + ydiff ;
  end % if no y coordinates
  % xmax = xmax + xdiff/10; ymax = ymax + ydiff/10;
  % xmin = xmin - xdiff/10; ymin = ymin - ydiff/10;
  clf                               % clear graphics
  axis ([xmin, xmax, ymin, ymax])   % set axes
  axis ('equal')                    % true shape style
  hold on                           % hold image for plots
  grid                              % add grid dots
  xlabel ('X')                      % add label
  ylabel ('Y')                      % add label
if ( n_type == 1 )
  title  (['FE Retained Elements: ', int2str(nt), ...
           ' Elements (',int2str(n_del), ' deleted), ',  int2str(np), ...
           ' Nodes'])
else
  title  (['FE Retained Elements: ', int2str(nt), ...
           ' Elements (',int2str(n_del), ' deleted), ',  int2str(np), ...
           ' Nodes, ', int2str(n_type), ' Types'])
end % if multiple types
 
%      Plot input mesh points & label them
  if (lab_p == 1)                   % plot all points
    plot (x, y, 'b.')               % mark each node
  end % if show labels

  if ( nargin == 0 ) % select increments
%    Show 20 nodes and 10 elements, or all for small mesh
    inc_p = floor(np/20) ; inc_e = floor(nt/10) ;
    if (inc_p == 0 ) 
      inc_p = np - 1 ;
    end % if inc_p
    if (inc_e == 0 ) 
      inc_e = nt - 1 ;
    end % if inc_e
%    Show all if a small mesh
    if ( np <= 20 )
      inc_p = 1 ;
    end % if np
    if ( nt <= 10 )
      inc_e = 1 ;
    end % if nt
  end % if no arguments

  if (inc_p > 0)      % plot node numbers, if node in mesh
   in_mesh (1:np) = 0 ;               % default to missing
   for i = 1:nt                       % loop all elements
     for j = 1:nod_per_el             % loop its nodes
       %b I_J =  msh_typ_nodes(i, j + (pre_e + 1)) ;
       I_J =  msh_typ_nodes(i+less, j + (pre_e + 1)) ; %CL
       if ( I_J > 0 )
         in_mesh ( I_J ) = 1; % flag as present
       end % if a non-zero node
       % in_mesh (msh_typ_nodes(i, j)) = 1; % flag as present
     end % for its nodes
   end % for all elements
%b in_mesh (1:np) = 1 ; %b ???
   % disp (in_mesh)

   for i = 1:inc_p:np                 % convert to string
     if ( in_mesh (i) > 0 )           % it is present
      p_text = sprintf ('  %g', i);   % offset # from pt
      text (x(i), y(i), p_text)       % plot pt number
     end % if present
   end % for all points
  end % if show labels
  disp (' ')

%b size(msh_typ_nodes)
%    Loop over all elements
  for it = 1:nt  ;
    if ( msh_deleted (it, 2) == 0 ) % then it was retained

%      Extract corner connectivity 
      %b t_nodes = msh_typ_nodes (it, (pre_e+2):(nod_per_el+pre_e+1)); 
      %b t_nodes =msh_typ_nodes((it+less),(pre_e+2):(nod_per_el+pre_e+1));
      t_nodes = msh_typ_nodes ((it+less), Col_1:Col_2 ) ; %CL
      [N_min, I_min] = min ( t_nodes ) ;
      if ( N_min < 1 )
        fprintf ('Element %g connectivity corrected \n', it)
        t_nodes ( I_min:nod_per_el ) = t_nodes ( I_min - 1 ) ;
        % repeat the last non-zero node
      end % if

%      Extract corner coordinates
      t_x  = x (t_nodes) ;         % x at those nodes, only
      t_y  = y (t_nodes) ;         % y at those nodes, only

%      Get the centroid
      x_bar (it) = sum (t_x' )/nod_per_el ;
      y_bar (it) = sum (t_y' )/nod_per_el ;

%      Plot this polygon
      c_x  = t_x (loop) ;       % x for nod_per_el line polygon
      c_y  = t_y (loop) ;       % y for nod_per_el line polygon
      plot (c_x, c_y)           % plot nod_per_el lines
    end % if retained
  end % for over all elements
 
%    Finish the plots with polygon numbers
  if (inc_e > 0)                     % plot elem number, inclined
    plot (x_bar, y_bar, 'g.')        % centroid of each element
    for i = 1:inc_e:nt               % convert to string
      t_text = sprintf ('   %g', i);  % offset # from pt
      text (x_bar(i), y_bar(i), t_text, 'Rotation', 45) % incline
    end % for all polygons
  end % if show labels
%       -depsc -tiff            % for an eps version
  %bprint -dpsc retained_elements_plot
  % print -deps2 mesh_plot
  hold off
  %bfprintf ('Created file retained_elements_plot.ps \n')
% end of retained_elements_plot