Chi hooks

Code/CTD.json

@@ -200,6 +200,11 @@
 			"long_name": "Turbidity",
 			"standard_name": "sea_water_turbidity",
 			"coverage_content_type": "physicalMeasurement"
+		},
+		"sn": {
+			"units": "",
+			"long_name": "Serial Number",
+			"coverage_content_type": "auxiliaryInformation"
 		}
 	},
 

Code/Combo.json

@@ -546,6 +546,11 @@
 			"units": "",
 			"long_name": "ODAS Library Version",
 			"coverage_content_type": "auxiliaryInformation"
+		},
+		"sn": {
+			"units": "",
+			"long_name": "Serial Number",
+			"coverage_content_type": "auxiliaryInformation"
 		}
 	},
 

Code/calc_chi.m

@@ -0,0 +1,35 @@
+%
+% Calculate chi from temperature gradients given an already calculated epsilon
+%
+% Aug-2024, Pat Welch, pat@mousebrains.com
+
+function [dInfo, tbl] = calc_chi(diss, dInfo)
+arguments (Input)
+    diss table % Profile information
+    dInfo (1,:) table % Summary information about the profile
+end % arguments Input
+arguments (Output)
+    dInfo (1,:) table % pInfo with extra fields
+    tbl table % Tabular form of diss struct
+end % arguments Output
+
+kappa_T = 1.4e-7; % thermal diffusivity [m^2/s]
+
+tbl = table();
+tbl.t = diss.t;
+tbl.depth = diss.depth;
+
+names = string(diss.Properties.VariableNames);
+
+for name = names(startsWith(names, "gradT"))
+    gradT = diss.(name);
+    gradT2 = gradT.^2;
+    % gradT2(gradT <= 0) = NaN;
+    index = extractAfter(name, "gradT");
+    tbl.(name) = gradT;
+    tbl.(sprintf("chi_dT%s_mean", index)) = 2 * kappa_T * diss.N2 .* diss.epsilonMean ./ gradT2;
+    for j = 1:size(diss.e,2)
+        tbl.(sprintf("chi_dT%s_e%d", index, j)) = 2 * kappa_T * diss.N2 .* diss.e(:,j) ./ gradT2;
+    end % for j
+end % for name
+end % calc_chi

Code/chi2binned.m

@@ -19,86 +19,73 @@
     return;
 end % if ~row.qProfileOkay
 
-warning("Chi binning not implemented");
-
-% fnChi = row.fnChi;
-% fnBin = fullfile(pars.chi_binned_root, append(row.name, ".mat"));
-% row.fnChiBin = fnBin;
-% 
-% if isnewer(fnBin, fnChi)
-%     retval = {fnBin, []}; % We want this for combining
-%     fprintf("%s: %s is newer than %s\n", row.name, row.fnBin, row.fnChi);
-%     return;
-% end % if isnewer
-% 
-% if isempty(a)
-%     fprintf("Loading %s\n", row.fnChi);
-%     a = load(row.fnChi);
-% end % if isempty
-% 
-% %% Bin the data into depth bins
-% 
-% pInfo = a.info;
-% profiles = a.profiles;
-% 
-% fprintf("%s: Binning %d profiles\n", row.name, numel(profiles));
-% 
-% if pars.profile_direction == "time" % Bin in time
-%     binSize = seconds(pars.binChi_width); % Bin stepsize in (sec)
-%     keyName = "t";
-%     binFunc = @bin_by_time;
-%     glueFunc = @glue_lengthwise;
-% else % Bin by depth
-%     binSize = pars.binChi_width; % Bin stepsize (m)
-%     keyName = pars.binChi_variable; % Variable to bin by
-%     binFunc = @bin_by_real;
-%     glueFunc = @glue_widthwise;
-% end % if profile_direction
-% 
-% casts = cell(numel(profiles),1);
-% for index = 1:numel(profiles)
-%     profile = profiles{index};
-%     nE = size(profile.e, 2);
-%     prof2 = table();
-%     for name = string(profile.Properties.VariableNames)
-%         sz = size(profile.(name),2);
-%         if ~ismatrix(profile.(name)), continue; end
-%         if sz == 1
-%             prof2.(name) = profile.(name);
-%         elseif sz == nE
-%             for j = 1:sz
-%                 prof2.(append(name, "_", string(j))) = profile.(name)(:,j);
-%             end % for j;
-%         end % if sz
-%     end % for name
-% 
-%     casts{index} = binFunc(binSize, keyName, prof2, pars.binChi_method);
-% end % for index
-% 
-% qDrop = cellfun(@isempty, casts); % This shouldn't happend
-% 
-% if any(qDrop)
-%     casts = casts(~qDrop);
-%     pInfo = pInfo(~qDrop,:);
-% end % any qDrop
-% 
-% if isempty(casts)
-%     row.qProfileOkay = false;
-%     fprintf("%s: No usable casts found in %s\n", row.name, row.fnProf);
-%     return;
-% end
-% 
-% tbl = glueFunc("bin", casts);
-% 
-% binned = struct ( ...
-%     "tbl", tbl, ...
-%     "info", pInfo);
-% if isfield(a, "fp07")
-%     binned.fp07 = a.fp07;
-% end % if isfield
-% 
-% my_mk_directory(fnBin);
-% save(fnBin, "-struct", "binned", pars.matlab_file_format);
-% fprintf("%s: Saving %d profiles to %s\n", row.name, size(binned.info,1), fnBin);
-% retval = {fnBin, binned};
+fnChi = row.fnChi;
+fnBin = fullfile(pars.chi_binned_root, append(row.name, ".mat"));
+row.fnChiBin = fnBin;
+
+if isnewer(fnBin, fnChi)
+    retval = {fnBin, []}; % We want this for combining
+    fprintf("%s: %s is newer than %s\n", row.name, row.fnBin, row.fnChi);
+    return;
+end % if isnewer
+
+if isempty(a)
+    fprintf("Loading %s\n", row.fnChi);
+    a = load(row.fnChi);
+end % if isempty
+
+%% Bin the data into depth bins
+
+pInfo = a.info;
+profiles = a.profiles;
+
+fprintf("%s: Binning %d profiles\n", row.name, numel(profiles));
+
+if pars.profile_direction == "time" % Bin in time
+    binSize = seconds(pars.binChi_width); % Bin stepsize in (sec)
+    keyName = "t";
+    binFunc = @bin_by_time;
+    glueFunc = @glue_lengthwise;
+else % Bin by depth
+    binSize = pars.binChi_width; % Bin stepsize (m)
+    keyName = pars.binChi_variable; % Variable to bin by
+    binFunc = @bin_by_real;
+    glueFunc = @glue_widthwise;
+end % if profile_direction
+
+casts = cell(numel(profiles),1);
+for index = 1:numel(profiles)
+    profile = profiles{index};
+    prof2 = table();
+    for name = string(profile.Properties.VariableNames)
+        if ~ismatrix(profile.(name)), continue; end
+        prof2.(name) = profile.(name);
+    end % for name
+
+    casts{index} = binFunc(binSize, keyName, prof2, pars.binChi_method);
+end % for index
+
+qDrop = cellfun(@isempty, casts); % This shouldn't happend
+
+if any(qDrop)
+    casts = casts(~qDrop);
+    pInfo = pInfo(~qDrop,:);
+end % any qDrop
+
+if isempty(casts)
+    row.qProfileOkay = false;
+    fprintf("%s: No usable casts found in %s\n", row.name, row.fnProf);
+    return;
+end
+
+tbl = glueFunc("bin", casts);
+
+binned = struct ( ...
+    "tbl", tbl, ...
+    "info", pInfo);
+
+my_mk_directory(fnBin);
+save(fnBin, "-struct", "binned", pars.matlab_file_format);
+fprintf("%s: Saving %d profiles to %s\n", row.name, size(binned.info,1), fnBin);
+retval = {fnBin, binned};
 end % chi2binned

Code/convert2mat.m

@@ -36,6 +36,14 @@
     a = odas_p2mat(char(row.fn), p2args{:}); % extract P file contents
     my_mk_directory(row.fnMat);
     save(row.fnMat, "-struct", "a", pars.matlab_file_format); % save into a mat file
+
+    row.sn = setupstr(a.setupfilestr, 'instrument_info', 'sn'); % Get the serial number in the instrument_info stanza
+    if isempty(row.sn)
+        row.sn = missing;
+    else
+        row.sn = string(row.sn{1});
+    end % if isempty
+
     row.qMatOkay = true;
     fprintf("Took %.2f seconds to convert %s\n", toc(stime), row.name);
 catch ME

Code/ctd2binned.m

@@ -144,7 +144,7 @@
 fnCTD = fullfile(pars.ctd_root, append(row.name, ".mat"));
 row.fnCTD = fnCTD;
 
-cInfo = row(:,["name", "t0", "tEnd"]);
+cInfo = row(:,["name", "t0", "tEnd", "sn"]);
 cInfo = renamevars(cInfo, "tEnd", "t1"); % For NetCDF time range
 
 binned = struct("tbl", tbl, "info", cInfo);
@@ -216,4 +216,4 @@
     ctd.lon(q) = gps.lon(t) - dLondt .* dt;
     ctd.lat(q) = gps.lat(t) - dLatdt .* dt;
 end
-end % addGPS
+end % addGPS

Code/mat2profile.m

@@ -157,7 +157,7 @@
 
 profilesInfo = struct();
 profilesInfo.profiles = profiles;
-profilesInfo.row = row(1,["name", "date", "fClock" "t0", "t1", "tEnd"]);
+profilesInfo.row = row(1,["name", "date", "fClock" "t0", "t1", "tEnd", "sn"]);
 profilesInfo.pInfo = profileInfo;
 if qFP07
     profilesInfo.fp07Lags = fp07_lags;
@@ -181,6 +181,7 @@
 tbl = table();
 tbl.name = repmat(row.name, nProfiles, 1);
 tbl.index = (1:nProfiles)';
+tbl.sn = repmat(row.sn, nProfiles,1);
 tbl.t0 = NaT(nProfiles,1);
 tbl.t1 = NaT(nProfiles,1);
 tbl.n_slow = nan(nProfiles,1);