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profiles_SA.m
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%% South Atlantic
% 2005
clear
pack
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_QC_SA.mat
t1 = datenum(2005,01,01);
t2 = datenum(2006,01,01);
ind = find(time >= t1 & time <= t2);
temp = temp(:,ind); pres = pres(:,ind); psal = psal(:,ind);
latitude = latitude(ind); longitude = longitude(ind); time = time(ind);
fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(ind,:); pres_qc = pres_qc(ind,:); psal_qc = psal_qc(ind,:);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
temp_qc_adj = temp_qc_adj(ind,:); pres_qc_adj = pres_qc_adj(ind,:); psal_qc_adj = psal_qc_adj(ind,:);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_2005.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat
t1 = datenum(2005,01,01);
t2 = datenum(2006,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind); time_adj = time_adj(ind);
datamode = datamode(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_adj_2005.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_err_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat time_adj
t1 = datenum(2005,01,01);
t2 = datenum(2006,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind); time_adj = time_adj(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_err_2005.mat');
% 2006
clear
pack
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_QC_SA.mat
t1 = datenum(2006,01,01);
t2 = datenum(2007,01,01);
ind = find(time >= t1 & time <= t2);
temp = temp(:,ind); pres = pres(:,ind); psal = psal(:,ind);
latitude = latitude(ind); longitude = longitude(ind); time = time(ind);
fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(ind,:); pres_qc = pres_qc(ind,:); psal_qc = psal_qc(ind,:);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
temp_qc_adj = temp_qc_adj(ind,:); pres_qc_adj = pres_qc_adj(ind,:); psal_qc_adj = psal_qc_adj(ind,:);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_2006.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat
t1 = datenum(2006,01,01);
t2 = datenum(2007,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind); time_adj = time_adj(ind);
datamode = datamode(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_adj_2006.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_err_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat time_adj
t1 = datenum(2006,01,01);
t2 = datenum(2007,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind); time_adj = time_adj(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_err_2006.mat');
% 2007
clear
pack
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_QC_SA.mat
t1 = datenum(2007,01,01);
t2 = datenum(2008,01,01);
ind = find(time >= t1 & time <= t2);
temp = temp(:,ind); pres = pres(:,ind); psal = psal(:,ind);
latitude = latitude(ind); longitude = longitude(ind); time = time(ind);
fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(ind,:); pres_qc = pres_qc(ind,:); psal_qc = psal_qc(ind,:);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
temp_qc_adj = temp_qc_adj(ind,:); pres_qc_adj = pres_qc_adj(ind,:); psal_qc_adj = psal_qc_adj(ind,:);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_2007.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat
t1 = datenum(2007,01,01);
t2 = datenum(2008,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind); time_adj = time_adj(ind);
datamode = datamode(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_adj_2007.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_err_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat time_adj
t1 = datenum(2007,01,01);
t2 = datenum(2008,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind); time_adj = time_adj(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_err_2007.mat');
% 2008
clear
pack
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_QC_SA.mat
t1 = datenum(2008,01,01);
t2 = datenum(2009,01,01);
ind = find(time >= t1 & time <= t2);
temp = temp(:,ind); pres = pres(:,ind); psal = psal(:,ind);
latitude = latitude(ind); longitude = longitude(ind); time = time(ind);
fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(ind,:); pres_qc = pres_qc(ind,:); psal_qc = psal_qc(ind,:);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
temp_qc_adj = temp_qc_adj(ind,:); pres_qc_adj = pres_qc_adj(ind,:); psal_qc_adj = psal_qc_adj(ind,:);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_2008.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat
t1 = datenum(2008,01,01);
t2 = datenum(2009,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind); time_adj = time_adj(ind);
datamode = datamode(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_adj_2008.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_err_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat time_adj
t1 = datenum(2008,01,01);
t2 = datenum(2009,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind); time_adj = time_adj(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_err_2008.mat');
% 2009
clear
pack
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_QC_SA.mat
t1 = datenum(2009,01,01);
t2 = datenum(2010,01,01);
ind = find(time >= t1 & time <= t2);
temp = temp(:,ind); pres = pres(:,ind); psal = psal(:,ind);
latitude = latitude(ind); longitude = longitude(ind); time = time(ind);
fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(ind,:); pres_qc = pres_qc(ind,:); psal_qc = psal_qc(ind,:);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
temp_qc_adj = temp_qc_adj(ind,:); pres_qc_adj = pres_qc_adj(ind,:); psal_qc_adj = psal_qc_adj(ind,:);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_2009.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat
t1 = datenum(2009,01,01);
t2 = datenum(2010,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind); time_adj = time_adj(ind);
datamode = datamode(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_adj_2009.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_err_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat time_adj
t1 = datenum(2009,01,01);
t2 = datenum(2010,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind); time_adj = time_adj(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_err_2009.mat');
% 2010
clear
pack
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_QC_SA.mat
t1 = datenum(2010,01,01);
t2 = datenum(2011,01,01);
ind = find(time >= t1 & time <= t2);
temp = temp(:,ind); pres = pres(:,ind); psal = psal(:,ind);
latitude = latitude(ind); longitude = longitude(ind); time = time(ind);
fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(ind,:); pres_qc = pres_qc(ind,:); psal_qc = psal_qc(ind,:);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
temp_qc_adj = temp_qc_adj(ind,:); pres_qc_adj = pres_qc_adj(ind,:); psal_qc_adj = psal_qc_adj(ind,:);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_2010.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat
t1 = datenum(2010,01,01);
t2 = datenum(2011,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind); time_adj = time_adj(ind);
datamode = datamode(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_adj_2010.mat');
clear; pack;
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_err_SA.mat
load /home/alison/Matlab/Mat' files'/Global' Mapping 2'/South' Atlantic'/profiles_adj_SA.mat time_adj
t1 = datenum(2010,01,01);
t2 = datenum(2011,01,01);
ind = find(time_adj >= t1 & time_adj <= t2);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind); time_adj = time_adj(ind);
clear t1 t2 dir_name ind float_num
save('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/prof_err_2010.mat');
%% quality control
% 2005
clear; pack
load /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/prof_2005.mat;
load /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/prof_adj_2005.mat;
load /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/prof_err_2005.mat;
pres_qc = pres_qc';
psal_qc = psal_qc';
temp_qc = temp_qc';
pres_qc_adj = pres_qc_adj';
psal_qc_adj = psal_qc_adj';
temp_qc_adj = temp_qc_adj';
% plot locations of data
figure(1); clf
axesm('mercator','MapLatLimit',[-85 5],'MapLonLimit',[-100 50])
plotm(latitude,longitude,'.');
geoshow('landareas.shp','FaceColor',[.9 .9 .9])
setm(gca, 'grid','on','meridianlabel','on','parallellabel','on','plinelocation',5,'mlinelocation',5,'plabellocation',5,'mlabellocation',5)
axis tight
figure(2); clf
plot(longitude,latitude,'.'); grid on;
% lat/lon range
ind = find(longitude <= 30 & longitude >= -75 & latitude <= 0 & latitude >= -80);
temp = temp(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres = pres(:,ind);
psal = psal(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(:,ind); pres_qc = pres_qc(:,ind); psal_qc = psal_qc(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
datamode = datamode(ind); time_adj = time_adj(ind);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind);
temp_qc_adj = temp_qc_adj(:,ind); pres_qc_adj = pres_qc_adj(:,ind); psal_qc_adj = psal_qc_adj(:,ind);
% plot locations of data
figure(1); clf
axesm('mercator','MapLatLimit',[-85 5],'MapLonLimit',[-100 50])
plotm(latitude,longitude,'.');
geoshow('landareas.shp','FaceColor',[.9 .9 .9])
setm(gca, 'grid','on','meridianlabel','on','parallellabel','on','plinelocation',10,'mlinelocation',10,'plabellocation',10,'mlabellocation',10)
axis tight
% look at maximum pressures
maxp = (max(abs(pres),[],1))';
% find & remove profiles with maxp < 800 db
indp = find(maxp < 800);
per800 = 100*length(indp)/length(maxp) %#ok<*NOPTS,*NASGU>
num_800 = [fnum(indp) time(indp)];
ind = find(maxp >= 800);
temp = temp(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres = pres(:,ind);
psal = psal(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(:,ind); pres_qc = pres_qc(:,ind); psal_qc = psal_qc(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
datamode = datamode(ind); time_adj = time_adj(ind);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind);
temp_qc_adj = temp_qc_adj(:,ind); pres_qc_adj = pres_qc_adj(:,ind); psal_qc_adj = psal_qc_adj(:,ind);
clear ans ind indp per800 t2
save /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/bad_floats.mat num_800
clear num_800 maxp
% delete all Nan profiles
clear ind; k = 1;
for i = 1:length(fnum)
t = temp(:,i); s = psal(:,i); p = pres(:,i);
ss = sum(~isnan(s)); tt = sum(~isnan(t)); pp = sum(~isnan(p));
if ~(tt == 0 || ss == 0 || pp == 0)
ind(k) = i; k = k+1; %#ok<SAGROW>
end
end
clear t s p ss tt pp k i
ind = ind';
temp = temp(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres = pres(:,ind);
psal = psal(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(:,ind); pres_qc = pres_qc(:,ind); psal_qc = psal_qc(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
datamode = datamode(ind); time_adj = time_adj(ind);
temp_adj = temp_adj(:,ind); pres_adj = pres_adj(:,ind); psal_adj = psal_adj(:,ind);
temp_err = temp_err(:,ind); pres_err = pres_err(:,ind); psal_err = psal_err(:,ind);
temp_qc_adj = temp_qc_adj(:,ind); pres_qc_adj = pres_qc_adj(:,ind); psal_qc_adj = psal_qc_adj(:,ind);
indt = find(sum(~isnan(temp),2) == 0); %#ok<MXFND>
indp = find(sum(~isnan(pres),2) == 0); %#ok<MXFND>
inds = find(sum(~isnan(psal),2) == 0); %#ok<MXFND>
ind = max([min(indt) min(indp) min(inds)]);
temp = temp(1:ind,:); psal = psal(1:ind,:); pres = pres(1:ind,:);
temp_qc = temp_qc(1:ind,:); pres_qc = pres_qc(1:ind,:); psal_qc = psal_qc(1:ind,:);
temp_adj = temp_adj(1:ind,:); psal_adj = psal_adj(1:ind,:); pres_adj = pres_adj(1:ind,:);
temp_qc_adj = temp_qc_adj(1:ind,:); pres_qc_adj = pres_qc_adj(1:ind,:); psal_qc_adj = psal_qc_adj(1:ind,:);
temp_err = temp_err(1:ind,:); psal_err = psal_err(1:ind,:); pres_err = pres_err(1:ind,:);
clear indt indp inds ind
save /home/alison/Matlab/M'at files'/Global' Mapping 2'/South' Atlantic'/tmp.mat
% graylist floats
cd('/home/alison/Matlab/M files/Global Mapping 2/');
[grayfloat,~,start_date,end_date,errtype] = graylist('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/');
%% %%%% quality control flags %%%%
% examine flags on temperature data
[mm,nn] = size(temp);
tqc = NaN(size(temp));
for j = 1:nn
for i = 1:mm
if ~isnan(temp(i,j))
if (strcmp(temp_qc_adj(i,j),'1') || strcmp(temp_qc_adj(i,j),'0') || strcmp(temp_qc_adj(i,j),'2') || strcmp(temp_qc_adj(i,j),' ') || double(temp_qc_adj(i,j))==0)
tqc(i,j) = 1;
else
tqc(i,j) = 0;
end
end
end
end
% examine flags on salinity data
[mm,nn] = size(psal);
sqc = NaN(size(psal));
for j = 1:nn
for i = 1:mm
if ~isnan(psal(i,j))
if (strcmp(psal_qc_adj(i,j),'1') || strcmp(psal_qc_adj(i,j),'0') || strcmp(psal_qc_adj(i,j),'2') || strcmp(psal_qc_adj(i,j),' ') || double(psal_qc_adj(i,j))==0)
sqc(i,j) = 1;
else
sqc(i,j) = 0;
end
end
end
end
% examine flags on pressure data
[mm,nn] = size(pres);
pqc = NaN(size(pres));
for j = 1:nn
for i = 1:mm
if ~isnan(pres(i,j))
if (strcmp(pres_qc_adj(i,j),'1') || strcmp(pres_qc_adj(i,j),'0') || strcmp(pres_qc_adj(i,j),'2') || strcmp(pres_qc_adj(i,j),' ') || double(pres_qc_adj(i,j))==0)
pqc(i,j) = 1;
else
pqc(i,j) = 0;
end
end
end
end
clear mm nn i j
% display number of profiles with one or more bad qc flag
num_bad_temp = length(find(sum(tqc == 0,1) > 0))
num_bad_pres = length(find(sum(pqc == 0,1) > 0))
num_bad_psal = length(find(sum(sqc == 0,1) > 0))
clear num_bad_*
% make 2nd variable set with data with qc ~= 0,1,2,' ' set to NaN
temp2 = temp_adj; temp2(tqc == 0) = NaN;
psal2 = psal_adj; psal2(sqc == 0) = NaN;
pres2 = pres_adj; pres2(pqc == 0) = NaN;
% need t, s, and p at every point - make NaN's consistent across all data
ind = find(isnan(pres2));
temp2(ind) = NaN;
psal2(ind) = NaN;
ind = find(isnan(psal2));
temp2(ind) = NaN;
pres2(ind) = NaN;
ind = find(isnan(temp2));
pres2(ind) = NaN;
psal2(ind) = NaN;
% delete profiles that are all NaNs
clear ind indb; k = 1; l = 1;
for i = 1:length(fnum)
t = temp2(:,i); s = psal2(:,i); p = pres2(:,i);
ss = sum(~isnan(s)); tt = sum(~isnan(t)); pp = sum(~isnan(p));
if ~(tt == 0 || ss == 0 || pp == 0)
ind(k) = i; k = k+1; %#ok<SAGROW>
else
indb(l) = i; l = l+1; %#ok<SAGROW>
end
end
clear t s p ss tt pp k i l
ind = ind'; indb = indb';
num_badQC = [fnum(indb) time(indb)];
save /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/bad_floats.mat num_badQC -APPEND
clear indb num_badQC
temp2 = temp2(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres2 = pres2(:,ind);
psal2 = psal2(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc_adj = temp_qc_adj(:,ind); pres_qc_adj = pres_qc_adj(:,ind); psal_qc_adj = psal_qc_adj(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
pqc = pqc(:,ind); pres = pres(:,ind); psal = psal(:,ind); sqc = sqc(:,ind); temp = temp(:,ind); tqc = tqc(:,ind);
pres_adj = pres_adj(:,ind); pres_err = pres_err(:,ind); pres_qc = pres_qc(:,ind);
psal_adj = psal_adj(:,ind); psal_err = psal_err(:,ind); psal_qc = psal_qc(:,ind);
temp_adj = temp_adj(:,ind); temp_err = temp_err(:,ind); temp_qc = temp_qc(:,ind);
datamode = datamode(ind); time_adj = time_adj(ind);
clear ind
% find & remove profiles with maxp < 800 db
maxp = (max(abs(pres2),[],1))';
indp = find(maxp < 800);
per800 = 100*length(indp)/length(maxp) %#ok<*NOPTS,*NASGU>
num_800_2 = [fnum(indp) time(indp)];
ind = find(maxp >= 800);
temp2 = temp2(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres2 = pres2(:,ind);
psal2 = psal2(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc_adj = temp_qc_adj(:,ind); pres_qc_adj = pres_qc_adj(:,ind); psal_qc_adj = psal_qc_adj(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
pqc = pqc(:,ind); pres = pres(:,ind); psal = psal(:,ind); sqc = sqc(:,ind); temp = temp(:,ind); tqc = tqc(:,ind);
pres_adj = pres_adj(:,ind); pres_err = pres_err(:,ind); pres_qc = pres_qc(:,ind);
psal_adj = psal_adj(:,ind); psal_err = psal_err(:,ind); psal_qc = psal_qc(:,ind);
temp_adj = temp_adj(:,ind); temp_err = temp_err(:,ind); temp_qc = temp_qc(:,ind);
datamode = datamode(ind); time_adj = time_adj(ind);
clear ind
clear ans ind indp per800 t2
save /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/bad_floats.mat num_800_2
clear num_800_2 maxp
% % compute percentage of good values in each profile
% [~,nn] = size(pres2);
% percentNaN = NaN(nn,3);
% for i = 1:nn
% p = pqc(:,i); t = tqc(:,i); s = sqc(:,i);
% np = sum(p == 0); nt = sum(t == 0); ns = sum(s == 0);
% npp = sum(~isnan(p)); ntt = sum(~isnan(t)); nss = sum(~isnan(s));
% percentNaN(i,:) = 100*[np./npp nt/ntt ns/nss];
% end
% clear i p np lastp mm nn npp t nt ntt s ns nss
%
% ind = find(percentNaN(:,1) > 25 | percentNaN(:,2) > 25 | percentNaN(:,3) > 25);
% for ii = 1:length(ind)
% fnum(ind(ii))
% figure(1); clf
% plot(temp(:,ind(ii)),-pres(:,ind(ii)),'m.-'); hold on;
% plot(temp2(:,ind(ii)),-pres2(:,ind(ii)),'r.-');
% disp(temp_qc(:,ind(ii))');
% disp(pres_qc(:,ind(ii))');
% disp(psal_qc(:,ind(ii))');
% figure(2); clf
% plot(psal(:,ind(ii)),-pres(:,ind(ii)),'c.-'); hold on;
% plot(psal2(:,ind(ii)),-pres2(:,ind(ii)),'b.-');
% pause
% end
% clear ii ans
%
% num_percentNaN = [fnum(ind) time(ind)];
% save /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/bad_floats.mat num_percentNaN -APPEND
% clear num_percentNaN
%
% temp2(:,ind) = NaN; pres2(:,ind) = NaN; psal2(:,ind) = NaN;
%
% % delete profiles that are all NaNs
% clear ind indb; k = 1; l = 1;
% for i = 1:length(fnum)
% t = temp2(:,i); s = psal2(:,i); p = pres2(:,i);
% ss = sum(~isnan(s)); tt = sum(~isnan(t)); pp = sum(~isnan(p));
%
% if ~(tt == 0 || ss == 0 || pp == 0)
% ind(k) = i; k = k+1; %#ok<SAGROW>
% else
% indb(l) = i; l = l+1; %#ok<SAGROW>
% end
% end
% clear t s p ss tt pp k i l
% ind = ind'; indb = indb';
%
% temp2 = temp2(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres2 = pres2(:,ind);
% psal2 = psal2(:,ind); fnum = fnum(ind); type = type(ind);
% temp_qc = temp_qc(:,ind); pres_qc = pres_qc(:,ind); psal_qc = psal_qc(:,ind);
% position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
% prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
% pqc = pqc(:,ind); pres = pres(:,ind); psal = psal(:,ind); sqc = sqc(:,ind); temp = temp(:,ind); tqc = tqc(:,ind);
% clear ind indb percentNaN
% find & delete short profiles
n = sum(~isnan(temp2),1)';
for i = 1:10
disp(i); ind = find(n == i); length(ind)
% figure(1); clf
% plot(temp2(:,ind),-pres2(:,ind),'.-');
% pause
end
ind = find(n <= 10 & n > 0); length(ind)
num_shortprof = [fnum(ind) time(ind)];
save /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/bad_floats.mat num_shortprof -APPEND
clear num_shortprof
temp2(:,ind) = NaN; pres2(:,ind) = NaN; psal2(:,ind) = NaN;
clear n i ind ans
% delete profiles that are all NaNs
clear ind indb; k = 1; l = 1;
for i = 1:length(fnum)
t = temp2(:,i); s = psal2(:,i); p = pres2(:,i);
ss = sum(~isnan(s)); tt = sum(~isnan(t)); pp = sum(~isnan(p));
if ~(tt == 0 || ss == 0 || pp == 0)
ind(k) = i; k = k+1; %#ok<SAGROW>
else
indb(l) = i; l = l+1; %#ok<SAGROW>
end
end
clear t s p ss tt pp k i l
ind = ind'; indb = indb';
temp2 = temp2(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres2 = pres2(:,ind);
psal2 = psal2(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc_adj = temp_qc_adj(:,ind); pres_qc_adj = pres_qc_adj(:,ind); psal_qc_adj = psal_qc_adj(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
pqc = pqc(:,ind); pres = pres(:,ind); psal = psal(:,ind); sqc = sqc(:,ind); temp = temp(:,ind); tqc = tqc(:,ind);
pres_adj = pres_adj(:,ind); pres_err = pres_err(:,ind); pres_qc = pres_qc(:,ind);
psal_adj = psal_adj(:,ind); psal_err = psal_err(:,ind); psal_qc = psal_qc(:,ind);
temp_adj = temp_adj(:,ind); temp_err = temp_err(:,ind); temp_qc = temp_qc(:,ind);
datamode = datamode(ind); time_adj = time_adj(ind);
clear ind indb
save /home/alison/Matlab/M'at files'/Global' Mapping 2'/South' Atlantic'/tmp.mat
%% remove greylist floats
k = 1;
badfloats = 0; type_err = cell(1,1); bad_start = 0; bad_end = 0;
for i = 1:length(grayfloat)
if sum(grayfloat(i) == fnum) > 0
if grayfloat(i) ~= badfloats
badfloats(k,1) = grayfloat(i); %#ok<SAGROW>
type_err(k,1) = errtype(i);
bad_start(k,1) = start_date(i); %#ok<SAGROW>
bad_end(k,1) = end_date(i); %#ok<SAGROW>
k = k+1;
end
end
end
clear k i
ind = find(~strcmp(type_err,'potential problem with bin assignment'));
badfloats = badfloats(ind);
type_err = type_err(ind);
bad_start = bad_start(ind);
bad_end = bad_end(ind);
badstart = cellstr(num2str(bad_start));
badend = cellstr(num2str(bad_end));
for i = 1:length(badstart)
bs = char(badstart(i));
bs = datenum([sscanf(bs(1:4),'%f'),sscanf(bs(5:6),'%f'),sscanf(bs(7:8),'%f')]);
bad_st(i,1) = bs; %#ok<SAGROW>
be = char(badend(i));
if ~strcmp(be,' NaN') && ~strcmp(be,'NaN')
be = datenum([sscanf(be(1:4),'%f'),sscanf(be(5:6),'%f'),sscanf(be(7:8),'%f')]);
bad_end(i) = be;
else
bad_end(i) = NaN;
end
end
fnumb = []; timeb = [];
for j = 1:length(badfloats)
if isnan(bad_end(j))
ind = find(~((fnum == badfloats(j))&(time > bad_st(j))));
indb = find((fnum == badfloats(j)) & (time > bad_st(j)));
else
ind = find(~(fnum == badfloats(j) & time > bad_st(j) & time < bad_end(j)));
indb = find(fnum == badfloats(j) & time > bad_st(j) & time < bad_end(j));
end
fnumb = [fnumb; fnum(indb)]; %#ok<AGROW>
timeb = [timeb; time(indb)]; %#ok<AGROW>
temp2 = temp2(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres2 = pres2(:,ind);
psal2 = psal2(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc_adj = temp_qc_adj(:,ind); pres_qc_adj = pres_qc_adj(:,ind); psal_qc_adj = psal_qc_adj(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
pqc = pqc(:,ind); pres = pres(:,ind); psal = psal(:,ind); sqc = sqc(:,ind); temp = temp(:,ind); tqc = tqc(:,ind);
pres_adj = pres_adj(:,ind); pres_err = pres_err(:,ind); pres_qc = pres_qc(:,ind);
psal_adj = psal_adj(:,ind); psal_err = psal_err(:,ind); psal_qc = psal_qc(:,ind);
temp_adj = temp_adj(:,ind); temp_err = temp_err(:,ind); temp_qc = temp_qc(:,ind);
datamode = datamode(ind); time_adj = time_adj(ind);
end
num_gray = [fnumb timeb];
save /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/bad_floats.mat num_gray -APPEND
clear num_gray fnumb timeb indb ind
clear bad* end_date j ind param start_date be bs i
clear ans errtype grayfloat ii percentNaN type_err
% graylist floats
cd('/home/alison/Matlab/M files/Global Mapping 2/');
[grayfloat,param,start_date,end_date,errtype] = graylist('/home/alison/Matlab/Mat files/Global Mapping 2/South Atlantic/');
save /home/alison/Matlab/M'at files'/Global' Mapping 2'/South' Atlantic'/tmp.mat
%% look for out-of-range pressures
figure(1); clf; imagesc(pres); colorbar;
figure(2); clf; imagesc(pres2); colorbar
outofrangenum = [];
ind = find(pres > 2100); length(ind)
[i,j] = find(pres2 > 2100); length(i)
tempnum = fnum(j);
presnum = 0; k = 1;
for ii = 1:length(tempnum)
if tempnum(ii) ~= presnum
presnum(k,1) = tempnum(ii); %#ok<SAGROW>
k = k+1;
end
end
outofrangenum = [outofrangenum; presnum];
ind = find(pres < 0); length(ind)
[~,j] = find(pres2 < 0); length(j)
tempnum = fnum(j);
presnum = 0; k = 1;
for ii = 1:length(tempnum)
if tempnum(ii) ~= presnum
presnum(k,1) = tempnum(ii); %#ok<SAGROW>
k = k+1;
end
end
outofrangenum = [outofrangenum; presnum];
% look for out-of-range temperatures
figure(1); clf; imagesc(temp); colorbar;
figure(2); clf; imagesc(temp2); colorbar
ind = find(temp > 40); length(ind)
[~,j] = find(temp2 > 40); length(j)
tempnum = fnum(j);
tmpnum = 0; k = 1;
for ii = 1:length(tempnum)
if tempnum(ii) ~= tmpnum
tmpnum(k,1) = tempnum(ii); %#ok<SAGROW>
k = k+1;
end
end
outofrangenum = [outofrangenum; tmpnum];
ind = find(temp <= -3); length(ind)
[~,j] = find(temp2 <= -3); length(j)
tempnum = fnum(j);
tmpnum = 0; k = 1;
for ii = 1:length(tempnum)
if tempnum(ii) ~= tmpnum
tmpnum(k,1) = tempnum(ii); %#ok<SAGROW>
k = k+1;
end
end
outofrangenum = [outofrangenum; tmpnum];
% look for out-of-range salinities
figure(1); clf; imagesc(psal); colorbar;
figure(2); clf; imagesc(psal2); colorbar
ind = find(psal > 39); length(ind)
[~,j] = find(psal2 > 39); length(j)
tempnum = fnum(j);
psalnum = 0; k = 1;
for ii = 1:length(tempnum)
if tempnum(ii) ~= psalnum
psalnum(k,1) = tempnum(ii); %#ok<SAGROW>
k = k+1;
end
end
outofrangenum = [outofrangenum; psalnum];
ind = find(psal <= 20); length(ind)
[~,j] = find(psal2 <= 20); length(j)
tempnum = fnum(j);
psalnum = 0; k = 1;
for ii = 1:length(tempnum)
if tempnum(ii) ~= psalnum
psalnum(k,1) = tempnum(ii); %#ok<SAGROW>
k = k+1;
end
end
outofrangenum = [outofrangenum; psalnum];
badnum = sort(outofrangenum);
clear psalnum tmpnum tempnum presnum i ii ind j k outofrangenum NaNnum ans
fnumb = []; timeb = [];
% badnum = badnum(5:end)
%
% badnum(i)
% ind = find(fnum == badnum(i));
% figure(1); clf; plot(temp2(:,ind),-pres2(:,ind),'.-'); grid on;
% figure(2); clf; plot(psal2(:,ind),-pres2(:,ind),'.-'); grid on;
% tmpt = temp2(:,ind); tmps = psal2(:,ind); tmpp = pres2(:,ind); tmpj = datestr(time(ind));
% if sum(badnum(i) == grayfloat) > 0
% disp('greylisted');
% ii = find(badnum(i) == grayfloat);
% disp(param(ii)); disp(errtype(ii)); disp(start_date(ii)); disp(end_date(ii));
% end
%
% i = 1;
% % set bad values to Nan
% pres2(1,ind(8:10)) = NaN;
% fnumb = [fnumb; fnum(ind(8:10))];
% timeb = [timeb; time(ind(8:10))];
%
% i = 2;
% pres2(1,ind(4)) = NaN;
% pres2(1,ind(10)) = NaN;
% pres2(1,ind(12)) = NaN;
% pres2(1,ind(15)) = NaN;
% fnumb = [fnumb; fnum(ind(4))];
% timeb = [timeb; time(ind(4))];
% fnumb = [fnumb; fnum(ind(10))];
% timeb = [timeb; time(ind(10))];
% fnumb = [fnumb; fnum(ind(12))];
% timeb = [timeb; time(ind(12))];
% fnumb = [fnumb; fnum(ind(15))];
% timeb = [timeb; time(ind(15))];
num_lowS = [fnumb timeb];
save /home/alison/Matlab/Ma't files'/Global' Mapping 2'/South' Atlantic'/bad_floats.mat num_lowS -APPEND
clear num_lowS fnumb timeb indb ind ans i ii tmpj tmpp tmps tmpt
% need t, s, and p at every point - make NaN's consistent across all data
ind = find(isnan(pres2));
temp2(ind) = NaN;
psal2(ind) = NaN;
ind = find(isnan(psal2));
temp2(ind) = NaN;
pres2(ind) = NaN;
ind = find(isnan(temp2));
pres2(ind) = NaN;
psal2(ind) = NaN;
% delete profiles that are all NaNs
clear ind indb; k = 1; l = 1;
for i = 1:length(fnum)
t = temp2(:,i); s = psal2(:,i); p = pres2(:,i);
ss = sum(~isnan(s)); tt = sum(~isnan(t)); pp = sum(~isnan(p));
if ~(tt == 0 || ss == 0 || pp == 0)
ind(k) = i; k = k+1; %#ok<SAGROW>
else
indb(l) = i; l = l+1; %#ok<SAGROW>
end
end
clear t s p ss tt pp k i l
ind = ind'; indb = indb';
temp2 = temp2(:,ind); latitude = latitude(ind); longitude = longitude(ind); time = time(ind); pres2 = pres2(:,ind);
psal2 = psal2(:,ind); fnum = fnum(ind); type = type(ind);
temp_qc = temp_qc(:,ind); pres_qc = pres_qc(:,ind); psal_qc = psal_qc(:,ind);
position_qc = position_qc(ind); juld_qc = juld_qc(ind); prof_temp_qc = prof_temp_qc(ind);
prof_psal_qc = prof_psal_qc(ind); prof_pres_qc = prof_pres_qc(ind);
pqc = pqc(:,ind); pres = pres(:,ind); psal = psal(:,ind); sqc = sqc(:,ind); temp = temp(:,ind); tqc = tqc(:,ind);
clear ind indb badnum
%% find profiles with repeat pressures
clear ind1; k = 1;
for i = 1:length(fnum)
p = pres2(:,i);
for j = 1:length(p)
if ~isnan(p(j))
if sum(p == p(j)) > 1
ind1(k) = i; %#ok<SAGROW>
k = k+1;
end
end
end
end
clear p i j k
ind1 = ind1';
% % individual float numbers of profiles with repeat pressures
% k = 1; ind = 0;
% for i = 1:length(ind1)
% if fnum(ind1(i)) ~= ind
% ind(k) = fnum(ind1(i)); %#ok<SAGROW>
% k = k+1;
% end
% end
% ind = ind'; clear i k
% length(ind)
%
% for i = 1:length(ind)
% ii = find(fnum == ind(i));
% plot(temp2(:,ii),-pres2(:,ii),'.-');
% ind(i)
% pres2(1:2,ii)
% pause
% end
% clear ii i
%
% i = 3;
% k = 1;
% for iii = 1:length(ii)
% p = pres2(:,ii(iii));
% for j = 1:length(p)
% if ~isnan(p(j))
% if sum(p == p(j)) > 1
% ind2(k) = iii; %#ok<SAGROW>
% k = k+1;
% end
% end
% end
% end
% pres2(53,ii(8)) = NaN;
%
% ind(i)
% ii = find(fnum == ind(i));
% figure(1); clf; plot(temp2(:,ii),-pres2(:,ii),'.-'); grid on;
% figure(2); clf; plot(psal2(:,ii),-pres2(:,ii),'.-'); grid on;
% tmpt = temp2(:,ii); tmps = psal2(:,ii); tmpp = pres2(:,ii); tmpj = datestr(time(ii));
% if sum(ind(i) == grayfloat) > 0
% disp('greylisted');
% jj = find(ind(i) == grayfloat);
% disp(param(jj)); disp(errtype(jj)); disp(start_date(jj)); disp(end_date(jj));
% end
ind = find(isnan(pres2));
temp2(ind) = NaN;
psal2(ind) = NaN;
ind = find(isnan(psal2));
temp2(ind) = NaN;
pres2(ind) = NaN;
ind = find(isnan(temp2));
pres2(ind) = NaN;
psal2(ind) = NaN;
% find profiles with increasing pressures
k = 1; ind1 = [];
for i = 1:length(fnum)
p = pres2(:,i);
p = p(~isnan(p));
pd = p(2:end)-p(1:end-1);
if sum(pd < 0) > 0
ind1(k) = i; %#ok<SAGROW>
k = k+1;
end
end
clear ind i k p pd s t j
ind1 = ind1';
% individual float numbers of profiles with increasing pressures
k = 1; ind = 0;
for i = 1:length(ind1)
if fnum(ind1(i)) ~= ind
ind(k) = fnum(ind1(i)); %#ok<SAGROW>
k = k+1;
end
end
ind = ind'; clear i k
length(ind)
for i = 1:length(ind)
ii = find(fnum == ind(i));
plot(temp2(:,ii),-pres2(:,ii),'.-');
ind(i)
pres2(1:2,ii)
pause
end
clear ii i
i = 1;
k = 1; clear ind2
for iii = 1:length(ii)
p = pres2(:,ii(iii));
p = p(~isnan(p));
pd = p(2:end)-p(1:end-1);
if sum(pd < 0) > 0
ind2(k) = iii; %#ok<SAGROW>