How to fill timeseries data using interpolated data then have a nice contour plot

I have heavily edited data from an underwater glider that measures temperature, conductivity, and pressure. From that we get salinity, density and sigma (sigma = density - 1000). The instrument did not sample very well, hence the heavy editing. I need to make "pretty" contour plots for a poster. This is not for a publication so I am not worried about the amount of filtering or smoothing.

I am having trouble with the contour lines of sigma (density), please see below.

The black contour lines should trace the filled contours of sigma but they look very bad. The data was binned by 1 m before any gridding is done. here is the code used to generate the plots.

% load data
load Matlab_data
maxy = 50;

    t = 1;
    Tstep = t./24./60; % Grid data on t minute time intervals
    X1 = time(1)-Tstep:Tstep:time(end)+Tstep; 
    Y1 = 0:1:maxy; % Grid data on 1 meter depth intervals

    ygrid = [' Depth grid: ' num2str(diff(Y1(1:2)))];
    xgrid = [' Time grid: ' num2str(diff(X1(1:2)))];

    [X,Y]= meshgrid(X1,Y1);
    bad_vals = isnan(sal) .* ~isfinite(sal) .* isnan(press); % don't include NaNs or funky imaginary salinities in the contours
    vals = find(bad_vals == 0);

    Zd = griddata(time(vals),depth(vals),density(vals),X,Y);
    Zt = griddata(time(vals),depth(vals),temp(vals),X,Y);
    Zs = griddata(time(vals),depth(vals),sal(vals),X,Y);
    Zst = griddata(time(vals),depth(vals),sigmat(vals),X,Y); 

    % Interpolate over gaps
    vst = interp1gap(sigmat);
    vs = interp1gap(sal);
    % Grid interpolated salinity and sigma data
    Zst_interp = griddata(time(vals),depth(vals),vst(vals),X,Y);
    Zs_interp = griddata(time(vals),depth(vals),vs(vals),X,Y);

     %%Contour Plot
      % Set up the figure
      figure3=figure('Position', [2000, 50, 1500, 500]);
      clf
      colormap(jet);

    % Temperature
    ax1 = subplot(2, 1,1);
      [c,h] = contourf(X,Y,Zst,50,'linestyle','none'); %,[4:.5:9],'linestyle','none');
      cRange = caxis;
       hold on
      [c2,h2] = contour(X,Y,Zst,[24 24.5 25],'color','k'); %,[22:.5:26.5],'linewidth',1.5,'color','k');
      clabel(c2,h2,'fontsize',10,'labelspacing',150);
      set(h2,'linewidth',1)
      hc = colorbar;
      colormap(jet);

      datetick('x','mm/dd','keeplimits','keepticks');

      grid on;
      box on
      pos = get(gca,'position');
      set(gca,'YDir','reverse')%,'position',[pos(1) pos(2) pos(3)-.06 pos(4)]);
      set(gca,'xlim',[time(1)+.5./24 time(end)-.5./24],...
          'ylim',[0 maxy],'fontsize',8,'xminortick','on','yminortick','on');
      set(get(hc,'ylabel'),'string','Sigma-Theta (kg m^-^3)','rotation',270,'verticalalignment','bottom');
      ylabel('Ocean Depth (m)');
      xlabel('Date');
      %title(['Sigma Theta (kg m^-^3) -' strrep(tag,'_','\_')], 'fontweight', 'bold','FontSize',12)
      title(['Sigma Theta (kg m^-^3) :' ygrid xgrid ], 'fontweight', 'bold','FontSize',12)    

    ax2 = subplot(2, 1,2);
      %h=pcolor(X,Y,Zst);
      [c,h] = contourf(X,Y,Zst_interp,50,'linestyle','none'); %,[4:.5:9],'linestyle','none');
      shading interp
      hc = colorbar;
      cRange = caxis;
      hold on
      [c2,h2] = contour(X,Y,Zst,[24 24.5 25],'color','k'); %,[22:.5:26.5],'linewidth',1.5,'color','k');
      clabel(c2,h2,'fontsize',10,'labelspacing',150);
      set(h2,'linewidth',1)
      hc = colorbar;
      colormap(jet);
      caxis(cRange);

      datetick('x','mm/dd','keeplimits','keepticks');

      grid on;
      box on
      pos = get(gca,'position');
      set(gca,'YDir','reverse')%,'position',[pos(1) pos(2) pos(3)-.06 pos(4)]);
      set(gca,'xlim',[time(1)+.5./24 time(end)-.5./24],...
          'ylim',[0 maxy],'fontsize',8,'xminortick','on','yminortick','on');
      set(get(hc,'ylabel'),'string','Sigma-Theta (kg m^-^3)','rotation',270,'verticalalignment','bottom');
      ylabel('Ocean Depth (m)');
      xlabel('Date');
     % title(['Sigma Theta (kg m^-^3) -' strrep(tag,'_','\_')], 'fontweight', 'bold','FontSize',12)

      title(['Sigma Theta interp1gap (kg m^-^3) :' ygrid xgrid ], 'fontweight', 'bold','FontSize',12)

Please help! I have TWO issues... the first and most obvious is the ugly black contour lines, these should "flow" around the filled contours nicely. If anyone has experience or suggestions of how to smooth these please pass it along, with code if possible.

The second issue lies in the bottom plot, I need to fill the gaps in data (due to editing original bad data). I used the function interp1gap, available on the File exchange http://www.mathworks.com/matlabcentral/fileexchange/45842-interp1gap but it also interpolates the data to deeper depths, which I do not want. I just want the gaps to be filled in, such as by choosing their horizontal neighbors and filling in.

Please let me know if you have any suggestions for fixing this! I have attached the data (Matlab_data.mat) and it includes time, depth, sal (salinity), sigmat, press, temp, and density.

Is this an issue of gridding? Please be as specific as possible and any code and figures would be greatly appreciated if you have time to look into this.

[Nicolai von Oppeln Bronikowski]

Hi Brita,

I am also analyzing ocean glider data and was wondering if you have gotten further on this topic. I am having trouble gridding the initial vectors of depth and range/time and science measurements due to the increasing/decreasing trends in depth.. (I broke up the glider mission by completed transects).

Would love to hear from you!

Nicolai Bronikowski

email: nvob37 at mun dot ca

Answer 1

[Greg Dionne]

If you have a copy of the R2016a Signal Processing Toolbox, try fillgaps.

Seems to work okay on your density grid (I've limited it here below to using 500 points around each gap)

>> fillgaps(density,500)

The blue points are your samples and the red trace is the imputed curve.

>> fillgaps(sigmat,500)