This branch post cruise JR17001 created by DAS 14/8/18 before push to gitlab

On branch JR17001_post_cruise
 Changes to be committed:
	modified:   source/mextras/mcontr_plotlines.m
	modified:   source/mscs/msload.m
	modified:   source/mscs/msposinfo.m
	modified:   source/mscs/mtranslate_varnames.m
	modified:   source/mscs/scs_to_mstar2.m
	modified:   source/msubs/m_add_variable_name.m
	modified:   source/msubs/m_write_variable.m
	modified:   source/unfinished/m_remove_outside_spaces.m
	modified:   source/unfinished/m_verson.m
	modified:   source/unfinished/mavmed.m
	modified:   source/unfinished/mcontr.m
	modified:   source/unfinished/mcontrnew.m
	modified:   source/unfinished/mgetdir.m
	modified:   source/unfinished/mheadr.m
	modified:   source/unfinished/mlisth.m
	modified:   source/unfinished/mplxyed.m
	modified:   source/unfinished/msmoothnav.m

Untracked files:
	source/unfinished/mavmed.m~

source/mextras/mcontr_plotlines.m

@@ -42,7 +42,6 @@ while cdim > 0
     cdim = size(posall,2);
 end
 hold on
-% keyboard
 % plot each contour line
 % first switch off lines in base contour plot
 set(hplot,'linestyle','none');
@@ -150,7 +149,6 @@ for kcont = 1:numcontour
     end
 
 end
-% keyboard
 % % % % % % % clabelall = get(hclabel);
 % % % % % % % clall = clabelall;
 % % % % % % % nstring = length(clabelall);

source/mscs/msload.m

@@ -58,7 +58,7 @@ nv = length(vars);
 if ~exist('varlist','var'); varlist = '/'; end
 th.fldnam = vars;
 th.noflds = nv; % create a structure equivalent to the mstar headers to parse for var names
-% keyboard
+
 varnums = m_getvlist(varlist,th);
 % time always seems to be last in the scs list; put it first if it is
 % in the load list.
@@ -75,7 +75,6 @@ end
 dc1 = nan+ones(nf,1); dc2 = dc1; totdc = 0;
 m = 'Counting data cycles';
 if ~MEXEC_G.quiet; fprintf(MEXEC_A.Mfidterm,'%s\n',m); end
-end
 
 for kf = 1:nf
     fn = fnames{kf};

source/mscs/msposinfo.m

@@ -25,7 +25,7 @@ function [lat lon] = msposinfo(dn1,navstream)
 
 m_common
 
-if ~exist('navstream','var'); navstream = MEXEC_G.uway_default_navstream; end  % use default nav stream name
+if ~exist('navstream','var'); navstream = MEXEC_G.default_navstream; end  % use default nav stream name
 
 instream = navstream; % mexec stream short name
 tstream = msresolve_stream(instream);

source/mscs/mtranslate_varnames.m

@@ -34,8 +34,8 @@ tunder(strfind(tunder,'-')) = '_';
 tunder(strfind(tunder,'.')) = '_';
 
 root_template = mgetdir('M_TEMPLATES');
-fntemplatein = [root_template '/' MEXEC_G.Mshipdatasystem '_' MEXEC_G.MSCRIPT_CRUISE_STRING '_renamelist_' tunder '.csv'];
-fntemplateot = [root_template '/' MEXEC_G.Mshipdatasystem '_' MEXEC_G.MSCRIPT_CRUISE_STRING '_renamelist_' tunder '_out.csv'];
+fntemplatein = [root_template '/' MEXEC_G.Mshipdatasystem '_renamelist_' tunder '.csv'];
+fntemplateot = [root_template '/' MEXEC_G.Mshipdatasystem '_renamelist_' tunder '_out.csv'];
 
 % clean up the translation table if needed. This code was lifted from
 % another script but should not be needed for this application.
@@ -48,6 +48,7 @@ for kline = 1:length(cellall)
     snamesin{kline} = m_remove_outside_spaces(cellrow{1});
     snamesot{kline} = m_remove_outside_spaces(cellrow{2});
     sunits{kline} = m_remove_outside_spaces(cellrow{3});
+    if length(sunits{kline})==0; sunits{kline} = ' '; end
 end
 snamesin = snamesin(:);
 snamesot = snamesot(:);
@@ -77,6 +78,7 @@ for k = 1:numvar
     end
 end
 snames_units = snames_units(:);
+
 %--------------------------------
 % 2009-01-26 07:48:13
 % mheadr

source/mscs/scs_to_mstar2.m

 function scs_to_mstar2
-% function techsas_to_mstar(tstream,dn1,dn2)
-% function ncfile = techsas_to_mstar(techsas_in,ncfile,dataname)
+% function scs_to_mstar2(tstream,dn1,dn2)
+% function ncfile = scs_to_mstar2(scs_in,ncfile,dataname)
 
-% load techsas file into mstar file
+% load scs file into mstar file
 %
 % 8 Sep 2009: SCS version of original techsas script, for JR195
 % The searched directory is MEXEC_G.uway_root, which for example can be
@@ -10,13 +10,14 @@ function scs_to_mstar2
 % The var names and units are taken from ascii file
 % seatex-gga.TPL
 % for example.
+%
 
 m_common
 m_margslocal
 m_varargs
 
 MEXEC_A.Mprog = 'scs_to_mstar2';
-m_proghd;
+if ~MEXEC_G.quiet; m_proghd; end
 
 
 instream = m_getinput('Type scs stream name or mexec short name eg gyro_s or gyro : ','s');
@@ -71,6 +72,7 @@ if isempty(tdata.time) % no data cycles found
 end
 
 ncfile.name = mstar_fn;
+
 ncfile = m_openot(ncfile); %check it is not an open mstar file
 % techsas_in.name = techsas_fn;
 
@@ -127,7 +129,6 @@ m_add_comment(ncfile,tstream);
 m_add_comment(ncfile,['at ' nowstring]);
 m_add_comment(ncfile,['Time converted from matlab day number to seconds after mstar time origin']);
     
-
 m_finis(ncfile);
 
 h = m_read_header(ncfile);
@@ -145,4 +146,5 @@ histin.version = [];
 histin.mstar_site = [];
 MEXEC_A.Mhistory_in{1} = histin;
 m_write_history;
+
 return

source/msubs/m_add_variable_name.m

@@ -24,7 +24,6 @@ ncfile.metadata = metadata;
 dimnames = m_unpack_dimnames(ncfile);
 varnames = m_unpack_varnames(ncfile);
 
-
 %test to see if a variable already exists with correct dimensions; if not, add it.
 
 kmatch = strmatch(string_var_name,varnames,'exact');
@@ -76,8 +75,7 @@ if ~isempty(kmatch) % It exists; check dimensions match;
     return
 end
 
- % Variable doesn't exist so we will add it; First, check each requested dimension exists in file
-
+% Variable doesn't exist so we will add it; First, check each requested dimension exists in file
 for k = 1:length(dims_array)
 
     kmatch = strmatch(dims_array{k},dimnames,'exact');
@@ -106,6 +104,7 @@ end
 v.Name = string_var_name;
 v.Dimension = dims_array;
 v.Nctype = datatype;
+%keyboard
 nc_addvar(ncfile.name,v);
 
 % % metadata = nc_info(ncfile.name); %refresh metadata

source/msubs/m_write_variable.m

@@ -41,7 +41,6 @@ for k = 1:length(krmatch)
     collength(k) = metadata.Dimension(kcmatch(k)).Length;
 end
 
-
 if length(krmatch) ~= length(kcmatch)
     error('m_write_variable weird mismatch of dimension names - investigate further')
 end

source/unfinished/m_remove_outside_spaces.m

@@ -2,19 +2,24 @@ function sot = m_remove_outside_spaces(sin)
 % function sot = m_remove_outside_spaces(sin)
 %
 % remove any outside spaces from a string
+% YLF edit jr17001: unless the string is just a single space
 
-s = [ ' ' sin ' '];
+if length(sin)==1 & ~strncmp(sin, ' ', 1)
+    sot = sin;
+else
+    s = [ ' ' sin ' '];
 
-while strcmp(s(1),' ') == 1
-    s(1) = [];
-    if isempty(s); break; end
-end
+    while strcmp(s(1),' ') == 1
+        s(1) = [];
+        if isempty(s); break; end
+    end
 
-s = [s ' '];
-while strcmp(s(end),' ') == 1
-    s(end) = [];
-    if isempty(s); break; end
-end
+    s = [s ' '];
+    while strcmp(s(end),' ') == 1
+        s(end) = [];
+        if isempty(s); break; end
+    end
 
-sot = s;
+    sot = s;
+end
 return
\ No newline at end of file

source/unfinished/m_verson.m

@@ -106,7 +106,6 @@ else
 %     new_version = increment+max(versions(index),file_version);
     new_version = increment+versions(index);
 end
-% keyboard
 versions(index) = new_version;
 save(MEXEC.versfile,'datanames','versions');
 if ~isnan(Mversionlock) % reset lock file

source/unfinished/mavmed.m

@@ -78,6 +78,7 @@ while copylistok == 0
             fprintf(MEXEC_A.Mfider,'\n%s\n','You must reply r or c : ');
             reply = m_getinput(' ','s');
         end
+        rc0 = rc;
     end
     copylistok = 1;
 end
@@ -149,6 +150,7 @@ step = lims(3);
 % do the truncation first.
 
 cvar = nc_varget(ncfile_in.name,h.fldnam{vcontrol});
+if ~exist('rc0'); [crows, ccols] = size(cvar); if size(cvar,2)==1; rc = 1; elseif size(cvar,1)==1; rc = 2; end; end %YLF added jr17001 because underway nc file header is incorrect about dims
 if rc == 1
     x = cvar(:,1);
 elseif rc == 2
@@ -219,8 +221,8 @@ for k = 1:length(kmat)
     z = nc_varget(ncfile_in.name,h.fldnam{kmat(k)});
     % rearrange data according to sort of control variable
     lenav = length(klo);
-    if rc == 1; zsort = z(ksort,:); zav = nan+zeros(lenav,ncols(kmat(k))); end
-    if rc == 2; zsort = z(:,ksort); zav = nan+zeros(nrows(kmat(k)),lenav); end
+    if rc == 1; zsort = z(ksort,:); zav = nan+zeros(lenav,size(z,2)); end
+    if rc == 2; zsort = z(:,ksort); zav = nan+zeros(size(z,1),lenav); end
 
     if(fullstats == 1)
         zn = zav; zstd = zav;

source/unfinished/mcontr.m

@@ -524,7 +524,6 @@ caxis(ha,colorbar_limits-1e-5)
 ca = caxis;
 % cdfot.cmap = cmap;
 
-% keyboard
 ha = gca;
 % set(ha,'position',[.1 .15 .7 .7]);
 axis([0 1 0 1]);
@@ -714,7 +713,6 @@ set(hh,'interpreter','none');
 % % % % % set(hh,'HorizontalAlignment','center')
 % % % % % set(hh,'VerticalAlignment','top')
 % % % % % set(hh,'interpreter','none');
-% keyboard
 
 % string for y variable
 xlaby = [-t1-tw]; % put first two ylabels at left of axis; remainder below axis
@@ -745,7 +743,6 @@ set(hh,'interpreter','none');
 % need xtick labels
 
 cdfot.mainplot_gca_handle = gca;
-% keyboard
 %plot colorbar as contourf
 pos = get(gca,'position');
 
@@ -774,7 +771,6 @@ yc = clev;
 [xcg,ycg]= meshgrid(xc,yc);
 zc = ycg;
 
-% keyboard
 [c2,h2] = contourf(xc,1:length(clev),zc,clev,'k-');
 % set(h2,'linestyle','none')
 for k = 1:length(clev)

source/unfinished/mcontrnew.m

@@ -637,7 +637,6 @@ ca = caxis;
 
 handles = hplot; m_recolor % jc032
 % return
-% keyboard
 ha = gca;
 % set(ha,'position',[.1 .15 .7 .7]);
 axis([0 1 0 1]);
@@ -876,8 +875,7 @@ while 1
     % % % % % set(hh,'HorizontalAlignment','center')
     % % % % % set(hh,'VerticalAlignment','top')
     % % % % % set(hh,'interpreter','none');
-    % keyboard
-    if isfield(cdfin,'xlabelset')
+        if isfield(cdfin,'xlabelset')
         if ~isempty(cdfin.xlabelset)
             cmd = ['set(hh,' cdfin.xlabelset ');']; eval(cmd);
         end
@@ -929,7 +927,6 @@ if isfield(cdfin,'colorbarset')
     if strcmp(cdfin.ylabelset,'none'); return; end
 end
 
-% keyboard
 %plot colorbar as contourf
 pos = get(gca,'position');
 
@@ -958,7 +955,6 @@ yc = clev;
 [xcg,ycg]= meshgrid(xc,yc);
 zc = ycg;
 
-% keyboard
 [c2,h2] = contourf(xc,1:length(clev),zc,clev,'k-');
 
 handles = h2; m_recolor ; % jc032
@@ -982,7 +978,6 @@ caxis(gca,ca)
 % cdfot.ca = ca; % jc032
 cdfot.colorbar_gca_handle = gca;
 
-% keyboard
 
 return
 

source/unfinished/mgetdir.m

@@ -17,5 +17,6 @@ ii = find(strcmp(M_ABBREV, MEXEC_G.MDIRLIST(:,1)));
 if length(ii)==1
    mpath = [MEXEC_G.MEXEC_DATA_ROOT '/' MEXEC_G.MDIRLIST{ii,2}];
 else
-   error([M_ABBREV ' set ' num2str(length(ii)) ' times in m_setup'])
+   warning([M_ABBREV ' set ' num2str(length(ii)) ' times in m_setup'])
+   mpath = '';
 end

source/unfinished/mheadr.m

@@ -28,7 +28,6 @@ hist = h;
 hist.filename = ncfile.name;
 MEXEC_A.Mhistory_in{1} = hist;
 
-
 % --------------------
 % Now do something with the data
 h = m_editheader(h,ncfile);

source/unfinished/mlisth.m

@@ -8,6 +8,6 @@ fn = m_getfilename; % this uses the optional argument if there is one
 ncfile.name = fn;
 
 h = m_read_header(ncfile);
-if ~MEXEC_G.quiet; m_print_header(h); end
+m_print_header(h)
 
 return
\ No newline at end of file

source/unfinished/mplxyed.m

@@ -207,7 +207,7 @@ if kedit > 0
     motsave = MEXEC_A.MARGS_OT;
     % cludge MEXEC_A.MARGS_OT to use the write_history feature
     nowtime = datestr(now,'yyyymmdd_HHMMSS');
-    editfn = ['mplxyed_' nowtime '_' h.dataname];
+    editfn = [mgetdir('M_CTD') '/mplxyed_' nowtime '_' h.dataname];
     % bak jc069 put more detailed information about source and output files in edit record file
     mess_4 = ['ot_file     : ' hist.filename];
     mess_5 = ['ot_dataname : ' hist.dataname];

source/unfinished/msmoothnav.m

@@ -151,7 +151,7 @@ cvar = nc_varget(ncfile_in.name,h.fldnam{vcontrol});
 if rc == 1
     x = cvar(:,1);
 elseif rc == 2
-    x = cvar(1,:);
+    x = cvar(1,:)';
 end
 
 if trunc == 2 | trunc == 4
@@ -219,7 +219,7 @@ for k = 1:length(kmat)
     % rearrange data according to sort of control variable
     lenav = length(klo);
     if rc == 1; zsort = z(ksort,:); zav = nan+zeros(lenav,ncols(kmat(k))); end
-    if rc == 2; zsort = z(:,ksort); zav = nan+zeros(nrows(kmat(k)),lenav); end
+    if rc == 2; zsort = z(:,ksort)'; zav = nan+zeros(lenav,nrows(kmat(k))); end
 
     if(fullstats == 1)
         zn = zav; zstd = zav;
@@ -227,49 +227,35 @@ for k = 1:length(kmat)
 
     for k2 = 1:lenav
         if ~isnan(klo(k2)) & ~isnan(khi(k2))
-            if rc == 1;
-                m = 'This code branch not operational yet';
-                fprintf(MEXEC_A.Mfider,'%s\n',m);
-                error('exiting');
-                return
-                zsub = zsort(klo(k2):khi(k2),:);
-                zav(k2,:) = m_nanmean(zsub,rc); % average in direction controlled by rc
-                if fullstats == 1
-                    ok = isfinite(zsub);
-                    zn(k2,:) = sum(ok,rc);
-                    zstd(k2,:) = m_nanstd(zsub,rc);
-                end
-            else
-                zsub = zsort(:,klo(k2):khi(k2));
-                xsub = xsort(:,klo(k2):khi(k2));
-                xsub = xsub';
-                zsub = zsub';
-                %                 keyboard
-                for ky = 1:size(zsub,2);
-                    y = zsub(:,ky);
-                    kok = find(~isnan(xsub+y));
-%                     keyboard
-                    if length(kok) > 1
-                        xoff = xsub(kok(1));
-                        p = polyfit(xsub(kok)-xoff,y(kok),1);
-                        zav(1,k2) = polyval(p,xc(k2)-xoff);
-                    end
-                end
-                xsub = xsub';
-                zsub = zsub';
-
-%                 zav(1,k2) = interp1(xsub,zsub,xc(k2));
-%                 zav(:,k2) = m_nanmean(zsub,rc); % average in direction controlled by rc
-                if fullstats == 1
-                    ok = isfinite(zsub);
-                    zn(:,k2) = sum(ok,rc);
-                    zstd(:,k2) = m_nanstd(zsub,rc);
+            
+            zsub = zsort(klo(k2):khi(k2),:);
+            xsub = xsort(klo(k2):khi(k2));
+            for ky = 1:size(zsub,2);
+                y = zsub(:,ky);
+                kok = find(~isnan(xsub+y));
+                if length(kok) > 1
+                    xoff = xsub(kok(1));
+                    p = polyfit(xsub(kok)-xoff,y(kok),1);
+                    zav(k2,:) = polyval(p,xc(k2)-xoff);
                 end
+            end
 
+            if fullstats == 1
+                ok = isfinite(zsub);
+                zn(k2,:) = sum(ok,rc);
+                zstd(k2,:) = m_nanstd(zsub);
             end
+
         end
     end
-
+    if rc==2
+        zav = zav';
+        if fullstats
+            zn = zn';
+            zstd = zstd';
+        end
+    end
+    
     vname = h.fldnam{kmat(k)};
     vname1 = vname;
     if kmat(k) == vcontrol; vname1 = [vname1 '_bin_average']; end