Code change to handle case of missing prof files

Normally, all floats have *_prof.nc files on the GDAC. BGC floats
also have *_Sprof.nc files. In early February 2023, JMA was
reprocessing some older float files, and temporarily, only
Sprof files were present on the GDAC, not the corresponding
prof files.

This fix handles this case.

Author: hfrenzel-noaa

auxil/initialize_sprof.m

@@ -37,7 +37,7 @@ function initialize_sprof(file_name)
 Sprof.lat  = H{3};
 Sprof.lon  = H{4};
 Sprof.ocean = H{5};
-% Sprof.profiler = H{6}; % profiler type; not yet used
+Sprof.profiler = H{6}; % profiler type
 % column 7: institution
 Sprof.sens = H{8};
 Sprof.split_sens = cellfun(@split, Sprof.sens, 'UniformOutput', false);

initialize_argo.m

@@ -164,6 +164,7 @@ function initialize_argo()
 
 % Extract unique BGC floats
 [uwmo_sprof,ia] = unique(Sprof.wmo,'stable'); % keep list order
+Sprof_wmo = Sprof.wmo; % needed later if sprof_only is not empty
 Sprof.wmo = str2double(Sprof.wmo);
 ia(end+1) = length(Sprof.urls) + 1;
 bgc_prof_idx1 = ia(1:end-1);
@@ -185,13 +186,50 @@ function initialize_argo()
 % Extract unique floats
 % note that older floats have 5-digit IDs
 [uwmo_prof,ia2] = unique(Prof.wmo,'stable'); % keep list order
+Prof_wmo = Prof.wmo; % needed later if sprof_only is not empty
 Prof.wmo = str2double(Prof.wmo);
 ulist = Prof.urls(ia2);
-dacs = regexp(ulist(:,1),'^\w+','once','match');
+dacs = regexp(ulist(:),'^\w+','once','match');
 prof_fnames = regexprep(uwmo_prof,'\d+','$0_prof.nc');
-tmp = regexprep(ulist(:,1),'profiles.+','');
+tmp = regexprep(ulist(:),'profiles.+','');
 prof_fp = strcat(tmp,prof_fnames);
 
+% are there any floats that have only Sprof files, but not prof files?
+sprof_only = setdiff(uwmo_sprof, uwmo_prof);
+if ~isempty(sprof_only)
+    n_sprof_only = length(sprof_only);
+    fprintf('The following %d floats have only Sprof files, not prof files:\n', ...
+        n_sprof_only)
+    disp(cell2mat(sprof_only))
+    disp('') % empty line in command window
+    idx_sprof_only = cellfun(@(x) find(strcmp(Sprof_wmo, x), 1), sprof_only);
+    add_dacs = regexp(Sprof.urls(idx_sprof_only),'^\w+','once','match');
+    % since the float type is 'bgc', prof will be replaced by Sprof later
+    add_fnames = regexprep(sprof_only,'\d+','$0_prof.nc');
+    tmp = regexprep(Sprof.urls(idx_sprof_only),'profiles.+','');
+    add_fp = strcat(tmp, add_fnames);
+    % add them to other variables so Float structure will have them
+    prof_fp = [prof_fp; add_fp];
+    prof_fnames = [prof_fnames; add_fnames];
+    dacs = [dacs; add_dacs];
+    wmo_sprof_only = str2double(sprof_only);
+    idx_in_sprof = cell2mat(arrayfun(@(x) find(Sprof.wmo == x), ...
+        wmo_sprof_only, 'UniformOutput', false));
+    % add all fields from the "special" floats into the Prof structure
+    Prof.urls = [Prof.urls; Sprof.urls(idx_in_sprof)];
+    Prof.date = [Prof.date; Sprof.date(idx_in_sprof)];
+    Prof.lat = [Prof.lat; Sprof.lat(idx_in_sprof)];
+    Prof.lon = [Prof.lon; Sprof.lon(idx_in_sprof)];
+    Prof.ocean = [Prof.ocean; Sprof.ocean(idx_in_sprof)];
+    Prof.profiler = [Prof.profiler; Sprof.profiler(idx_in_sprof)];
+    Prof.update = [Prof.update; Sprof.update(idx_in_sprof)];
+    Prof.split_sens = [Prof.split_sens; Sprof.split_sens(idx_in_sprof)];
+    Prof.wmo = [Prof.wmo; Sprof.wmo(idx_in_sprof)];
+    Prof_wmo = [Prof_wmo; Sprof_wmo(idx_in_sprof)];
+    [uwmo_prof,ia2] = unique(Prof_wmo,'stable');
+end
+
+
 % need to find out which floats are phys (in Prof only) and bgc (in Sprof)
 is_uniq_bgc = ismember(uwmo_prof,uwmo_sprof);
 nbgc = sum(is_uniq_bgc); % # of bgc floats (this may be revised later)
@@ -271,6 +309,15 @@ function initialize_argo()
 bgc_prof_idx2 = bgc_prof_idx2(is_true_bgc == 1);
 Float.bgc_prof_idx1(strcmp(Float.type, 'bgc')) = bgc_prof_idx1;
 Float.bgc_prof_idx2(strcmp(Float.type, 'bgc')) = bgc_prof_idx2;
+% add this check in case that files without prof files do not have
+% any BGC sensors, so that they will be classified as 'phys' floats
+% but Sprof files need to be read anyway
+Float.has_prof_file = ones(length(Float.type), 1);
+if ~isempty(sprof_only)
+    idx_in_float = cell2mat(arrayfun(@(x) find(Float.wmoid == x), ...
+        wmo_sprof_only, 'UniformOutput', false));
+    Float.has_prof_file(idx_in_float) = 0;
+end
 
 % for all "true" BGC floats, i.e., those that are listed in the Sprof
 % index file and have more than pTS sensors, Sprof files will be used
@@ -279,12 +326,14 @@ function initialize_argo()
 fprintf('%d "true" BGC floats were found\n', sum(idx_bgc));
 idx_phys = strcmp(Float.type, 'phys');
 fprintf('%d core and deep floats were found\n', sum(idx_phys));
-Float.file_path(strcmp(Float.type, 'bgc')) = ...
+Float.file_path(strcmp(Float.type, 'bgc') | ~Float.has_prof_file) = ...
     cellfun(@(x) strrep(x, 'prof', 'Sprof'), ...
-    Float.file_path(strcmp(Float.type, 'bgc')), 'UniformOutput', false);
-Float.file_name(strcmp(Float.type, 'bgc')) = ...
+    Float.file_path(strcmp(Float.type, 'bgc') | ~Float.has_prof_file), ...
+    'UniformOutput', false);
+Float.file_name(strcmp(Float.type, 'bgc') | ~Float.has_prof_file) = ...
     cellfun(@(x) strrep(x, 'prof', 'Sprof'), ...
-    Float.file_name(strcmp(Float.type, 'bgc')), 'UniformOutput', false);
+    Float.file_name(strcmp(Float.type, 'bgc') | ~Float.has_prof_file), ...
+    'UniformOutput', false);
 
 % use the update date of the last profile of each float
 Float.update(strcmp(Float.type, 'bgc')) = Sprof.update(bgc_prof_idx2);