do_transect_plot

 Function to display transect plots of FVCOM variables (i.e. temperature)

  [Plots]=do_transect_plot(plotOPTS,FVCOM)

 DESCRIPTION:
    Generates transect plots of variables

 INPUT:
   plotOPTS   = structure array with predefined options for generating the
   maps
   FVCOM  = data extracted from FVCOM NC file. See read_netCDF_FVCOM for
   details

   plotOPTS.range_lat: [50.1000 50.4000]
   plotOPTS.range_lon: [-4.5000 -3.8500]
   If the above exist, it will generate an m_map plot with transect
   position
   plotOPTS.mesh: [1x1 struct]
   plotOPTS.coastline_file: '../mat/tamar3_0coast.mat'
   plotOPTS.zone: 30
   plotOPTS.ell: 'grs80'
   plotOPTS.fig_name: 'co2_S5_slowleak'
   plotOPTS.mesh: [1x1 struct]
   plotOPTS.var_plot: 'PH'
   plotOPTS.clims: [6 8]
   plotOPTS.nz_plot: 1
   plotOPTS.figure: 1
   plotOPTS.Time_record: 7.3271e+05
   plotOPTS.data_dec: 5
   plotOPTS.vel_sca: 5
   plotOPTS.pause: 0.5000

0001 function [Plots]=do_transect_plot(plotOPTS,FVCOM)
0002 %
0003 % Function to display transect plots of FVCOM variables (i.e. temperature)
0004 %
0005 %  [Plots]=do_transect_plot(plotOPTS,FVCOM)
0006 %
0007 % DESCRIPTION:
0008 %    Generates transect plots of variables
0009 %
0010 % INPUT:
0011 %   plotOPTS   = structure array with predefined options for generating the
0012 %   maps
0013 %   FVCOM  = data extracted from FVCOM NC file. See read_netCDF_FVCOM for
0014 %   details
0015 %
0016 %   plotOPTS.range_lat: [50.1000 50.4000]
0017 %   plotOPTS.range_lon: [-4.5000 -3.8500]
0018 %   If the above exist, it will generate an m_map plot with transect
0019 %   position
0020 %   plotOPTS.mesh: [1x1 struct]
0021 %   plotOPTS.coastline_file: '../mat/tamar3_0coast.mat'
0022 %   plotOPTS.zone: 30
0023 %   plotOPTS.ell: 'grs80'
0024 %   plotOPTS.fig_name: 'co2_S5_slowleak'
0025 %   plotOPTS.mesh: [1x1 struct]
0026 %   plotOPTS.var_plot: 'PH'
0027 %   plotOPTS.clims: [6 8]
0028 %   plotOPTS.nz_plot: 1
0029 %   plotOPTS.figure: 1
0030 %   plotOPTS.Time_record: 7.3271e+05
0031 %   plotOPTS.data_dec: 5
0032 %   plotOPTS.vel_sca: 5
0033 %   plotOPTS.pause: 0.5000
0034 
0035 %
0036 % OUTPUT:
0037 %   Plots = structure array with figure handles
0038 %
0039 % EXAMPLE USAGE
0040 %    [Plots]=do_transect_plot(plotOPTS,FVCOM)
0041 %
0042 % Author(s):
0043 %    Ricardo Torres (Plymouth Marine Laboratory)
0044 %
0045 % Revision history
0046 %
0047 %==============================================================================
0048 figure(plotOPTS.figure);
0049 if ~(isfield(FVCOM,'zeta') | ~isfield(FVCOM,'h') | ~isfield(FVCOM,'siglay'))
0050     fprintf('You seem to be missing either  zeta, h, or siglay from FVCOM variable\n');
0051     fprintf(' Stoping. Try again\n');
0052     Plots=[];
0053     return
0054 end
0055 
0056 % convert sigma levels to z levels
0057 nz=size(FVCOM.(plotOPTS.var_plot),2)
0058 if isfield(plotOPTS,'Time_record')
0059     nt=length(plotOPTS.Time_record)
0060 else
0061     nt=1;
0062 end
0063 
0064 nxy=length(plotOPTS.trn_nodes.y)
0065 FVCOM.z=ones(nxy,nz,nt);
0066 for tt=1:nt
0067     z=FVCOM.h(:)+FVCOM.zeta(:,tt);
0068     for zz=1:nz
0069         FVCOM.z(:,zz,tt)=z+z.*FVCOM.siglay(:,zz);
0070     end
0071 end
0072 % plot animation of timeseries of transect
0073 XX=repmat(plotOPTS.trn_dis(:)',nz,1)';
0074 for tt=1:nt
0075     YY=squeeze(FVCOM.z(:,:,tt));
0076     ZZ=squeeze(FVCOM.(plotOPTS.var_plot)(:,:,tt));
0077     Plots(plotOPTS.figure).handles=contourf(XX/100000,-YY,(ZZ),200,'edgecolor','none');
0078     caxis(plotOPTS.clims);
0079     colorbar
0080     xlabel('Distance along Transect')
0081     ylabel('Depth m')
0082     ylim([-max(FVCOM.h(:)) 0])
0083     pause(.5)
0084 end
0085 
0086 
0087 if isfield(plotOPTS,'range_lat')
0088     m_mappath;
0089     %plot map with transect overlaid
0090     figure(plotOPTS.figure+1);clf
0091     m_proj('UTM','lon',[ plotOPTS.range_lon],'lat',[plotOPTS.range_lat],'zon',plotOPTS.zone,'ell',plotOPTS.ell)
0092     m_grid('box','fancy')
0093     % add coastline if present
0094     if (isfield(plotOPTS,'coastline_file') && ~isempty(plotOPTS.coastline_file) )
0095         m_usercoast(plotOPTS.coastline_file,'Color','k','LineWidth',3);
0096     end
0097     
0098     %plot vertices
0099     col=0.7*[1 1 1];
0100     if plotOPTS.do_mesh
0101         %plot vertices
0102         [X,Y]=m_ll2xy(plotOPTS.mesh.lon,plotOPTS.mesh.lat,'clip','on');
0103         Plots(plotOPTS.figure).mesh=patch('Vertices',[X,Y],'Faces',plotOPTS.mesh.tri,...
0104             'EdgeColor',[0.6 0.6 0.6],'FaceColor','none');hold on
0105         
0106     end
0107     % plot with matlab
0108     hold on
0109     [x,y]=m_ll2ll(plotOPTS.trn_nodes.x,plotOPTS.trn_nodes.y);
0110     [X,Y]=m_ll2xy(x+6,y,'clip','on');
0111     plot(X,Y,'r','LineWidth',2.5)
0112 end
0113