testing on Mac

Aquadopp/reprocess_AQH.m

@@ -96,7 +96,7 @@
         [time,vel,amp,cor,press,pitch,roll,heading] = ...
             readSWIFTv3_AQH([bfiles(iburst).folder '\' bfiles(iburst).name]);
     else
-        load([bfiles(iburst).folder '\' bfiles(iburst).name],...
+        load([bfiles(iburst).folder slash bfiles(iburst).name],...
             'Vel','Cor','Amp','Pressure','pitch','roll','heading','time')
         if exist('Vel','var')
         vel = Vel;

GeneralTools/KZ_PostProcessing/L0_createSBD.m

@@ -11,10 +11,11 @@
 %               9/2017  add oxygen optode and sea owl fluorometer
 %               9/2019  changed time convention to use start of the burst,rather than end
 %
+%   K. Zeiden, 10/2024 overhaul to make PC compatible and catch all sensor payloads
 
 %% Experiment directory 
 
-expdir = 'S:\SEAFAC\June2024';
+expdir = '/Volumes/Data/SEAFAC/June2024';
 SBDfold = 'ProcessedSBD';
 
 %% Sampling Parameters
@@ -108,7 +109,7 @@
     end
     syscommand = [syscommand ' ' sbdfile];
     else
-        syscommand = ['!cat ' payloadfile];
+        syscommand = ['cat ' payloadfile];
         for iprc = 1:length(PRCburstfiles)
             syscommand = [syscommand ' ' PRCburstfiles(iprc).folder slash PRCburstfiles(iprc).name];
         end

GeneralTools/KZ_PostProcessing/L1_compileSWIFT.m

@@ -13,10 +13,10 @@
     %   microSWIFT - Use the time embedded within the payload 50 or 51 or 52 of the
     %     SBD file, which is the time at the end of the burst of raw data.
 
-% K. Zeiden 10/01/2024
+% K. Zeiden 10/01/2024, based on orginal compileSWIFT_SBDservertelemetry.m
 
 %% Experiment directory
-expdir = 'S:\SEAFAC\June2024';
+expdir = '/Volumes/Data/SEAFAC/June2024';
 
 % SBD folder
 SBDfold = 'ProcessedSBD';
@@ -30,7 +30,7 @@
 end
 
 % Processing parameters
-plotflag = true;  % binary flag for plotting (compiled plots, not individual plots... that flag is in the readSWIFT_SBD call)
+plotflag = false;  % binary flag for plotting (compiled plots, not individual plots... that flag is in the readSWIFT_SBD call)
 
 % List missions
 missions = dir([expdir slash 'SWIFT*']);

GeneralTools/KZ_PostProcessing/L2_pruneSWIFT.m

@@ -1,9 +1,9 @@
 % Find out-of-water bursts and prune them from the SWIFT structure
 
-% K. Zeiden 10/10/2024
+% K. Zeiden 10/10/2024... similar to SWIFT_QC.m
 
 %% Experiment Directory
-expdir = 'S:\SEAFAC\June2024';
+expdir = '/Volumes/Data/SEAFAC/June2024';
 
 %% Parameters for QC/out-of-water identification
 
@@ -14,7 +14,7 @@
 end
 
 % Processing parameters
-plotflag = true;  % binary flag for plotting (compiled plots, not individual plots... that flag is in the readSWIFT_SBD call)
+plotflag = false;  % binary flag for plotting (compiled plots, not individual plots... that flag is in the readSWIFT_SBD call)
 
 % QC Parameters
 minwaveheight = 0;% minimum wave height in data screening

GeneralTools/KZ_PostProcessing/L3_postprocessSWIFT.m

@@ -3,16 +3,16 @@
 % Master post-processing function, that calls sub-functions to reprocess
 % each different type of raw SWIFT data and create an L3 product.
 % L1 product must have been created prior to running this script,
-% by running 'compileSWIFT.m', and L2 created by running 'qcSWIFT.m';
+% by running 'compileSWIFT.m', and L2 created by running 'pruneSWIFT.m';
 
-% K. Zeiden 07/2024
+% K. Zeiden 07/2024, based on existing sensor-specific processing codes w 
 
 % Need to consider additional QC steps after processing...
 % Airmar temp, NaN out if below/above -20/50 deg C
 % Wind speed, NaN out above 30 m/s
 
 %% Experiment Directory
-expdir = ['S:' slash 'SEAFAC' slash 'June2024'];
+expdir = ['/Volumes/Data/SEAFAC/June2024'];
 
 %% Processing toggles
 
@@ -33,7 +33,7 @@
 rpAQD = true; % TKE
 
 % Plotting toggle
-plotflag = true;
+plotflag = false;
 
 % List of missions
 missions = dir([expdir slash 'SWIFT*']);

GeneralTools/plotSWIFTV3.m

@@ -8,7 +8,8 @@
 nt = length(swift.time);
 
 fh = figure('color','w');
-fullscreen(2)
+%fullscreen(2)
+h = tight_subplot(8,3,[0.035 0.05],[0.1 0.075],0.075);
 h = tight_subplot(8,3,[0.035 0.05],[0.1 0.075],0.075);
 % tight_subplot(Nh, Nw, [gap_h gap_w], [lower upper], [left right] )
 

Signature/absorption.m

@@ -0,0 +1,45 @@
+function alpha = absorption(S,T,D,f)
+
+% seawater sound absorption coefficient (alpha), in dB/m
+% Adapted from http://resource.npl.co.uk/acoustics/techguides/seaabsorption/
+
+% 	 f frequency (kHz)
+% 	 T Temperature (degC)
+% 	 S Salinity (ppt)
+% 	 D Depth (m)
+% 	 pH Acidity = 8(fixed here)
+
+% Francois R. E., Garrison G. R., "Sound absorption based on ocean measurements: Part I:Pure water and magnesium sulfate contributions", Journal of the Acoustical Society of America, 72(3), 896-907, 1982.
+% Francois R. E., Garrison G. R., "Sound absorption based on ocean measurements: Part II:Boric acid contribution and equation for total absorption", Journal of the Acoustical Society of America, 72(6), 1879-1890, 1982.
+
+% Total absorption = Boric Acid Contrib. + Magnesium Sulphate Contrib. + Pure Water Contrib.
+
+pH = 8;
+T_kel = 273 + T;
+% Calculate speed of sound (according to Francois & Garrison, JASA 72 (6) p1886)
+% c = 1412 + 3.21*T + 1.19*S + 0.0167*D;
+c = sw_svel(S,T,D);
+
+% Boric acid contribution
+A1 = (8.86 ./ c ) .* 10.^(0.78 * pH - 5);
+P1 = 1;
+f1 = 2.8 * sqrt(S / 35) .* 10.^(4 - 1245 ./ T_kel);
+Boric = (A1 .* P1 .* f1 .* f.*f)./(f.*f + f1.*f1);
+
+% MgSO4 contribution
+A2 = 21.44 * (S ./ c) .* (1 + 0.025 * T);
+P2 = 1 - 1.37e-4 * D + 6.2e-9* D.*D;
+f2 = (8.17 .* 10.^(8 - 1990./T_kel))./(1 + 0.0018 * (S - 35));
+MgSO4 = (A2 .* P2 .* f2 * f.*f)./(f.*f + f2.*f2);
+
+% Pure water contribution
+A3 = T*nan;
+i1 = (T <= 20);
+A3(i1)  = 4.937e-4 - 2.59e-5  * T(i1)  + 9.11e-7 * T(i1).*T(i1)   - 1.50e-8*T(i1).*T(i1).*T(i1);
+A3(~i1) = 3.964e-4 - 1.146e-5 * T(~i1) + 1.45e-7 * T(~i1).*T(~i1) - 6.50e-10*T(~i1).*T(~i1).*T(~i1);
+P3 = 1 - 3.83e-5 * D + 4.9e-10* D.*D;
+H2O = A3 .* P3 .* f.*f;
+
+% Total absorption
+alpha = Boric + MgSO4 + H2O;
+alpha = alpha/1e3 ; % dB/m

Winds/inertialdissipation.m

@@ -30,7 +30,7 @@
 % Window length
 twin = 256;   % Window length in seconds (should make 2^N samples)
 nwin = round(fs*twin);  % Window length in data points
-if isodd(nwin) % Enforce even number window length
+if rem(nwin,2) ~= 0 % Enforce even number window length
     nwin = nwin-1;
 end