Cleaned version

moored_adcp_proc/adcp_surface_fit.m

-function [zbins,zadcp1,offset,x_null]=adcp_surface_fit(zadcp,ea,surface_bins,blen,blnk,nbin);
+function [zbins,zadcp1,offset,x_null]=adcp_surface_fit(zadcp,ea,surface_bins,blen,blnk,nbin)
     
     % Bin depth matrix
-    dpt1 = repmat(zadcp,nbin,1);
+    dpt1   = repmat(zadcp,nbin,1);
     binmat = repmat((1:nbin)',1,length(dpt1));   
-    z = dpt1-(binmat-0.5)*blen-blnk; 
+    z      = dpt1-(binmat-0.5)*blen-blnk; 
     
     % Loop over time, determine bin of maximum ea in surface bin range and 
     % do quadratic fit over 2 neighbouring and center bins   
-    easurf=ea(surface_bins,:);
+    easurf = ea(surface_bins,:);
     for ii=1:length(ea)
-        [eamax,maxind]=max(easurf(:,ii));
+        [eamax,maxind] = max(easurf(:,ii));
         
-        if length(eamax)>1; maxind=maxind(1); end
+        if length(eamax)>1 
+            maxind = maxind(1); 
+        end
         
-        if maxind>1 & eamax>80
-            if surface_bins(maxind)==nbin; 
+        if maxind>1 && eamax>80
+            if surface_bins(maxind)==nbin 
                 xtofit(1:2) = easurf(maxind-1:maxind,ii);
-                xtofit(3) = 0;
+                xtofit(3)   = 0;
             else           
-                xtofit = easurf(maxind-1:maxind+1,ii);
+                xtofit      = easurf(maxind-1:maxind+1,ii);
             end
 
             for jj=1:3
-                A(jj,:)=[(surface_bins(maxind)+jj-2)^2, surface_bins(maxind)+jj-2, 1];
+                A(jj,:) = [(surface_bins(maxind)+jj-2)^2, surface_bins(maxind)+jj-2, 1];
             end 
-            coef(:,ii)= A\xtofit;
+            coef(:,ii) = A\xtofit;
         else
-            coef(:,ii)=NaN;
+            coef(:,ii) = NaN;
         end
     end
     
     % Find maximum of quadratic fit ax^2+bx+c: 2ax+b=0
     x_null = -coef(2,:)./2./coef(1,:);
-
-    %offset=-round(nmedian((x_null-0.5)*blen+blnk)-nmedian(zadcp));
-    offset=-round(((x_null)*blen+blnk)-(zadcp)); %% P. Rousselot - offset over time
+    
+    
+    %% Calculate offset
+    offset = round(((x_null-0.5)*blen+blnk)-(zadcp));     
     disp('-------------------------------');
-    disp(['Depth offset is ' num2str(nanmean(offset)) ' m']);
+    disp(['Depth offset is ' num2str(round(nanmean(offset))) ' m']);
     disp('-------------------------------');
     
+    % offset over time cleaned (median filter)
+    [offset_clean,~] = clean_median(offset,20,2.8,[0.5 5],2,NaN);
+    lin_offset       = linspace(1,length(offset),length(offset));
+    offset           = interp1(lin_offset(~isnan(offset_clean)),...
+        offset_clean(~isnan(offset_clean)),lin_offset,'linear','extrap');
+    % offset median
+    %offset = nanmedian(offset);
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     
-    % Plot histogram of differences
-    dz=((x_null)*blen+blnk)-zadcp;
-    count=[-100:1:100];
-    ncount=hist(-dz,count);
+    %% Plot histogram of differences
+    dz     = ((x_null-0.5)*blen+blnk)-zadcp;
+    count  = [-100:1:100];
+    ncount = hist(-dz,count);
     figure(1);
     bar(count,ncount);
     grid on
@@ -53,38 +64,33 @@ function [zbins,zadcp1,offset,x_null]=adcp_surface_fit(zadcp,ea,surface_bins,ble
     plot(-zadcp,'b');
     grid on
     hold on;
-    plot(-(x_null)*blen+blnk,'r');
+    plot(-((x_null-0.5)*blen+blnk),'r');
     legend('Original','Reconstructed from surface reflection');
     
-%     if abs(offset)>15
-%        reply = input('Do you want to overwrite offset? 1/0 [0]:');
-%        if isempty(reply)
-%           reply = 0;
-%        end
-%        
-%        if reply==1
-%            offset=input('Enter new offset:');
-%        end
-%     end
+    if abs(offset)>15
+       reply = input('Do you want to overwrite offset? 1/0 [0]:');
+       if isempty(reply)
+          reply = 0;
+       end
+       
+       if reply==1
+           offset=input('Enter new offset:');
+       end
+    end
     
-    disp(['Offset of ' num2str(offset) ' m is applied']);
-    offset = 19;
-    % Apply offset to get correct bin depth and instrument depth:
-    zbins=z-offset;
-    zadcp1=zadcp-offset;
+    %% Apply offset to get correct bin depth and instrument depth:
+    zbins  = z+offset;
+    zadcp1 = zadcp+offset;
     
     figure(2);
     plot(-zadcp1,'y');
     text(300, max(zadcp),['Offset applied: ' num2str(offset) ' m']);
-    %,'fonts',12,'fontw','bold','backgroundc','w');
-    legend('Original','Reconstructed from surface reflection','Offset applied');
-    
+    legend('Original','Reconstructed from surface reflection','Offset applied');   
     %print -dpng surface_fit;
     
     figure(3);
     pcolor([1:length(x_null)],-zbins,ea); shading flat;
     title('Amplitude'); colorbar; ylabel('Depth [m]');xlabel('Time index');
-    
     %print -dpng surface_ea;
 
 end
\ No newline at end of file

moored_adcp_proc/filtfilt.m

@@ -56,7 +56,7 @@
 %   Copyright 1988-2011 The MathWorks, Inc.
 %   $Revision: 1.7.4.10 $  $Date: 2012/12/25 21:34:47 $
 
-error(nargchk(3,3,nargin,'struct'))
+narginchk(3,3)
 
 % Only double precision is supported
 if ~isa(b,'double') || ~isa(a,'double') || ~isa(x,'double')