function roms_grid_adjust(ncfile, theCommand)
%
% example usage: roms_grid_adjust('spbay_carq_grd.nc')
%
% use this to adjust bathymetry and mask values and grid lines
% !!! Grid should be orthogonal. Adjustment of grid lines will affect orthogonality.
% 
% Usage: 
% Depth toggle button on - shows bathymetry.
% Mask toggle button on - shows mask at rho points.
% Depth and mask button on - is to adjust bathy but bathy is shown 
%       only at points where mask = 1 (land).
% Lines on = adjusts grid lines.
% Need to have zoom off to change any values.
%
% Zoom in to area of interest, turn zoom off.
% Click on cell - acitve cell is outlined in magenta.
% Value of bathy or mask is shown in lower left corner.
% To change value - type new value in the edit box and hit the "set value" button.
% Dispaly will update new values.
% To save the data - you need to select "save data" button.
% There is no undo !! 
%
%jcwarner 4/27/03
%


global grid_plot outline thePointIndex ud set_value h_full_grid mask_rho_full_grid ncfile_name varr input_value
global adjust_depth_tool adjust_mask_tool adjust_lines_tool
global varr_depth varr_mask varr_lines mask_rho_full_grid_nan mouse_down xy

if nargin==1  %then we are just starting
  ncfile_name=ncfile;
  ncload(ncfile);
  nc=netcdf(ncfile);

  %create a "full grid" arrays 
  % x/y _full_grid are bounding psi points, extra rows and columns all around
  zsize=size(h);
  x_full_grid=ones(zsize+1);
  x_full_grid(2:end-1,2:end-1)=x_psi;
  x_full_grid(2:end-1,1)=x_psi(:,1)-(x_psi(:,2)-x_psi(:,1));
  x_full_grid(2:end-1,end)=x_psi(:,end)+(x_psi(:,end)-x_psi(:,end-1));
  x_full_grid(1,2:end-1)=x_psi(1,:)-(x_psi(2,:)-x_psi(1,:));
  x_full_grid(end,2:end-1)=x_psi(end,:)+(x_psi(end,:)-x_psi(end-1,:));
  x_full_grid(1,1)=x_full_grid(1,2)-(x_full_grid(1,3)-x_full_grid(1,2));
  x_full_grid(1,end)=x_full_grid(1,end-1)+(x_full_grid(1,end-1)-x_full_grid(1,end-2));;
  x_full_grid(end,1)=x_full_grid(end,2)-(x_full_grid(end,3)-x_full_grid(end,2));
  x_full_grid(end,end)=x_full_grid(end,end-1)+(x_full_grid(end,end-1)-x_full_grid(end,end-2));;
%
  y_full_grid=ones(zsize+1);
  y_full_grid(2:end-1,2:end-1)=y_psi;
  y_full_grid(2:end-1,1)=y_psi(:,1)-(y_psi(:,2)-y_psi(:,1));
  y_full_grid(2:end-1,end)=y_psi(:,end)+(y_psi(:,end)-y_psi(:,end-1));
  y_full_grid(1,2:end-1)=y_psi(1,:)-(y_psi(2,:)-y_psi(1,:));
  y_full_grid(end,2:end-1)=y_psi(end,:)+(y_psi(end,:)-y_psi(end-1,:));
  y_full_grid(1,1)=y_full_grid(1,2)-(y_full_grid(1,3)-y_full_grid(1,2));
  y_full_grid(1,end)=y_full_grid(1,end-1)+(y_full_grid(1,end-1)-y_full_grid(1,end-2));;
  y_full_grid(end,1)=y_full_grid(end,2)-(y_full_grid(end,3)-y_full_grid(end,2));
  y_full_grid(end,end)=y_full_grid(end,end-1)+(y_full_grid(end,end-1)-y_full_grid(end,end-2));;
%
% h_full_grid is one more row and column than roms grid, to account for pcolor 
  h_full_grid=zeros(zsize+1);
  h_full_grid(1:end-1,1:end-1)=h;  %pcolor does not use the right and top rows of h
% mask_rho_full_grid - same idea as h_full_grid
  mask_rho_full_grid=zeros(zsize+1);
  mask_rho_full_grid(1:end-1,1:end-1)=mask_rho;
% create array mask_rho_full_grid_nan which is mask_rho with nan's at all land points
  z_size=size(mask_rho_full_grid);
  mask_rho_full_grid_nan=mask_rho_full_grid(:);
  zz=find(mask_rho_full_grid_nan==0);
  mask_rho_full_grid_nan(zz)=nan;
  mask_rho_full_grid_nan=reshape(mask_rho_full_grid_nan,z_size);
% varr is the variable that we are plotting, default strtup is to adjust depth
   varr=h_full_grid;
%
   varr_depth=1;
   varr_mask=0;
   varr_lines=0;
%
   mouse_down=0;
%
  figure
  grid_plot=pcolor(x_full_grid,y_full_grid,varr);colorbar  %this shows the entire grid
  hold on
  ud=size(x_psi,1)+2;  %number of vertical rows
  thePointIndex=10;    %just picked 10 to start with
  %plot the magenta box to show which cell has been selected
  outline=plot([x_full_grid(thePointIndex) x_full_grid(thePointIndex+1) x_full_grid(thePointIndex+1+ud) x_full_grid(thePointIndex+ud) x_full_grid(thePointIndex)], ...
               [y_full_grid(thePointIndex) y_full_grid(thePointIndex+1) y_full_grid(thePointIndex+1+ud) y_full_grid(thePointIndex+ud) y_full_grid(thePointIndex)],'m');
  set(outline,'linewidth',2)
  set(grid_plot,'Buttondownfcn','roms_grid_adjust(1,''mouse_down'')');
  set(gcf,'toolbar','figure')
  set(gcf,'WindowButtonUpfcn','roms_grid_adjust(1, ''mouse_up'')');
  set(gcf,'WindowButtonMotionfcn','roms_grid_adjust(1, ''motion'')');


  %select to adjust depth (startup default)
   adjust_depth_tool=uicontrol('style','toggle','string','DEPTH','tag','adjust_depth_tool', 'units','normal', ...
                    'position',[0.01 0.5 0.10 0.05], 'value',[1], ...
                    'callback','roms_grid_adjust(1,''adjust_tool'')');
  %select to adjust mask
   adjust_mask_tool=uicontrol('style','toggle','string','MASK','tag','adjust_mask_tool', 'units','normal', ...
                    'position',[0.01 0.4 0.10 0.05], 'value', [0], ...
                    'callback','roms_grid_adjust(1,''adjust_tool'')');
  %select to adjust lines
   adjust_lines_tool=uicontrol('style','toggle','string','LINES','tag','adjust_lines_tool', 'units','normal', ...
                    'position',[0.01 0.3 0.10 0.05], 'value', [0], ...
                    'callback','roms_grid_adjust(1,''adjust_tool'')');
  %window to input data
   input_value=uicontrol('style','edit','string',num2str(varr(thePointIndex)),'tag','input_value', 'units','normal', ...
                    'position',[0.02 0.01 0.10 0.05]); %, 'callback','roms_grid_adjust(1,'''')');
   set_value=uicontrol('style','pushbutton','string','set value','tag','set_value', 'units','normal', ...
                    'position',[0.15 0.01 0.10 0.05], 'callback','roms_grid_adjust(1,''set_value'')');
  %setup save data tool
   save_tool=uicontrol('style','pushbutton','string','save data','tag','save_tool', 'units','normal', ...
                    'position',[0.6 0.01 0.10 0.05], 'callback','roms_grid_adjust(1,''save_data'')');
  zoom on

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% now for all the callback routines
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
else

switch theCommand

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'mouse_down'
  %get index of the point that is moving
        xy = get(gca, 'CurrentPoint');
		xlim = get(gca, 'XLim');
		ylim = get(gca, 'YLim');
        xdata=get(grid_plot,'xdata');
        xdata=xdata(:);
        ydata=get(grid_plot,'ydata');
        ydata=ydata(:);

        if (xy(1, 1) > xlim(1))
          mouse_down=1;
        end
		
% Use pixel coordinates to detect point.
       if mouse_down
          oldUnits = get(gca, 'Units');
          set(gca, 'Units', 'pixels')
		  pos = get(gca, 'Position');
		  set(gca, 'Units', oldUnits)
		
		  width = pos(3);
		  height = pos(4);

		  xdist = width * (xdata - xy(1, 1)) / diff(xlim);
		  ydist = height * (ydata - xy(1, 2)) / diff(ylim);
		
		  dist = abs(xdist + sqrt(-1) * ydist);
		  f = find(dist == min(dist));
		  thePointIndex = f(1);

          set(outline,'xdata',[xdata(thePointIndex) xdata(thePointIndex+1) xdata(thePointIndex+1+ud) xdata(thePointIndex+ud) xdata(thePointIndex)], ...
                      'ydata',[ydata(thePointIndex) ydata(thePointIndex+1) ydata(thePointIndex+1+ud) ydata(thePointIndex+ud) ydata(thePointIndex)]);
          set(input_value, 'string',num2str(varr(thePointIndex)))
       end
          set(grid_plot,'cdata',varr)
          colorbar

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'mouse_up'
        mouse_down=0;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'motion'
        if (varr_lines + mouse_down == 2)
%        if ~exist('mouse_down'); mouse_down='n'; end
	       xy = get(gca, 'CurrentPoint');
           xdata=get(grid_plot,'xdata');
           xdata_old=xdata;
           x_size=size(xdata);
           xdata=xdata(:);
           ydata=get(grid_plot,'ydata');
           ydata_old=ydata;
           y_size=size(ydata); 
           ydata=ydata(:);
% update perimeter data with the new location
          xdata(thePointIndex)=xy(1,1);
          ydata(thePointIndex)=xy(1,2);
          xdata=reshape(xdata,[x_size]);
          ydata=reshape(ydata,[y_size]);
          set(grid_plot,'xdata',xdata,'ydata',ydata)
         end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'set_value'
        varr(thePointIndex)=str2num(get(input_value,'string'));
        set(grid_plot,'cdata',varr)
        colorbar

        if varr_depth
          h_full_grid(thePointIndex)=varr(thePointIndex);
        elseif varr_mask
          mask_rho_full_grid=varr;
         % create array mask_rho_full_grid_nan which is mask_rho with nan's at all land points
          z_size=size(mask_rho_full_grid);
          mask_rho_full_grid_nan=mask_rho_full_grid(:);
          zz=find(mask_rho_full_grid_nan==0);
          mask_rho_full_grid_nan(zz)=nan;
          mask_rho_full_grid_nan=reshape(mask_rho_full_grid_nan,z_size);
        end

        save roms_grid_adjust.mat

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'save_data'

%  roms_grid_adjust_write_grid(ncfile)   %  this alos adjusts grid dimensions, may not be correct

if (1)
  nc=netcdf(ncfile_name,'write');
  nc{'h'}(:)=h_full_grid(1:end-1,1:end-1);
  LP=size(h_full_grid,2)-1;
  MP=size(h_full_grid,1)-1;
  rmask=mask_rho_full_grid(1:end-1,1:end-1);
  umask = zeros(size(rmask));
  vmask = zeros(size(rmask));
  pmask = zeros(size(rmask));

  for i = 2:LP
	for j = 1:MP
		 umask(j, i-1) = rmask(j, i) * rmask(j, i-1);
    end
  end
  for i = 1:LP
    for j = 2:MP
		 vmask(j-1, i) = rmask(j, i) * rmask(j-1, i);
    end
  end
  for i = 2:LP
	 for j = 2:MP
 		 pmask(j-1, i-1) = rmask(j, i) * rmask(j, i-1) * rmask(j-1, i) * rmask(j-1, i-1);
     end
  end
  nc{'mask_rho'}(:) = rmask;
  nc{'mask_psi'}(:) = pmask(1:end-1, 1:end-1);
  nc{'mask_u'}(:) = umask(1:end, 1:end-1);
  nc{'mask_v'}(:) = vmask(1:end-1, 1:end);

  ncclose(ncfile)
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'adjust_tool'
  zdepth=get(adjust_depth_tool,'value');
  zmask=get(adjust_mask_tool,'value');
  zlines=get(adjust_lines_tool,'value');
  if zmask & ~zdepth   %only mask tool is active
    varr=mask_rho_full_grid;
%    set(adjust_depth_tool, 'value',[0]);
    varr_depth=0;
    varr_mask=1;
%    varr_lines=0;
  end
  if ~zmask & zdepth  %only depth tool is active
    varr=h_full_grid;
    varr_depth=1;
    varr_mask=0;
 %   varr_lines=0;
  end
  if zmask & zdepth  %both depth and mask active
    varr=h_full_grid.*mask_rho_full_grid_nan;
    varr_depth=1;
    varr_mask=0;
 %   varr_lines=0;
  end
  if ~zmask & ~zdepth  %neither depth nor mask active
    varr=h_full_grid.*nan;
    varr_depth=0;
    varr_mask=0;
 %   varr_lines=0;
  end
  if zlines            %lines tool active
    varr=h_full_grid.*nan;
    varr_depth=0;
    varr_mask=0;
    varr_lines=1;
    set(outline,'visible','off')
  end
  if ~zlines            %lines tool active
%    varr=h_full_grid.*nan;
%    varr_depth=0;
%    varr_mask=0;
     varr_lines=0;
    set(outline,'visible','on')
  end
   roms_grid_adjust(1,'mouse_down');

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end %switch
end %nargin 


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%not used stuff down here
if (0)
ncload('mass_bay_ecom_grid_7.nc');
nc=netcdf('mass_bay_ecom_grid_7.nc','write');
dx_new=zeros(size(pm));
dy_new=dx_new;
dmde_new=dx_new;
dndx_new=dx_new;

dx_new(:,2:67)=sqrt(((x_rho(:,3:end)-x_rho(:,1:end-2))/2).^2 + ...
                    ((y_rho(:,3:end)-y_rho(:,1:end-2))/2).^2);
dx_new(:,1)=sqrt(((x_rho(:,2)-x_rho(:,1))).^2 + ...
                 ((y_rho(:,2)-y_rho(:,1))).^2);
dx_new(:,68)=sqrt(((x_rho(:,68)-x_rho(:,67))).^2 + ...
                 ((y_rho(:,68)-y_rho(:,67))).^2);

dy_new(2:67,:)=sqrt(((x_rho(3:end,:)-x_rho(1:end-2,:))/2).^2 + ...
                    ((y_rho(3:end,:)-y_rho(1:end-2,:))/2).^2);
dy_new(1,:)=sqrt(((x_rho(2,:)-x_rho(1,:))).^2 + ...
                 ((y_rho(2,:)-y_rho(1,:))).^2);
dy_new(68,:)=sqrt(((x_rho(68,:)-x_rho(67,:))).^2 + ...
                 ((y_rho(68,:)-y_rho(67,:))).^2);
pm_new=1./dx_new;
pn_new=1./dy_new;


dmde_new(2:end-1, :) = 0.5*(1./pm_new(3:end, :) - 1./pm_new(1:end-2, :));
dmde_new(1, :) = dmde_new(2,:);
dmde_new(end, :) = dmde_new(end-1,:);
dndx_new(:, 2:end-1) = 0.5*(1./pn_new(:, 3:end) - 1./pn_new(:, 1:end-2));
dndx_new(:,1) = dndx_new(:,2);
dndx_new(:,end) = dndx_new(:,end-1);

nc{'pm'}(:)=1./dx_new(:);
nc{'pn'}(:)=1./dy_new(:);
nc{'dmde'}(:)=dmde_new(:);
nc{'dndx'}(:)=dndx_new(:);
ncclose

end