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# Data processing after Poseidon cruise POS519
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All data can be found on GEOMAR's data portal. Some data are open access, some are restricted. PLease contact me in case the access is restricted.

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- [CTD data](#ctd-data)
- [underway data](#underway-data)
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## CTD data 
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The CTD data (temperature, salinity, oxygen) were processed and calibrated by Gerd Krahmann. The single casts are found
in the zip folder [pos_519_1_ctd_rel1.zip (access is restricted to GEOMAR)](https://portal.geomar.de/metadata/download/agree/346718).
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all data measured from the niskin bottles can be found in the file ["POS519_niskin_data.txt"](https://portal.geomar.de/metadata/download/agree/349226). I used quality flags according to 
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WOCE standards:
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flag | 2 | 3 | 4 | 5 
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:--- | :---: | :---: | :---: | :---:
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meaning | good | questionable | bad | unknown/raw

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The file will be updated as new data come available. The content is:
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variable | unit | description | additional notes
:--- | :--- | :--- | :---
profile no. |	| number of CTD cast |
niskin no.	| | niskin bottle number |
sample no. | | sample identifier as used on board |
latitude | deg N | |
longitude | deg E | |
Date  | UTC | |
Time  | UTC | |
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pressure | dbar | CTD pressure reading in dbar | [info](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/pos_519_1_report.txt)
temperature | degC | CTD temperature reading | [info](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/pos_519_1_report.txt)
salinity | | calculated CTD salinity | [info](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/pos_519_1_report.txt)
oxygen sensor | µmol/kg | Oxygen concantration as recorded by the CTD sensor. The data are calibrated with Winkler titrated samples. | [info](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/pos_519_1_report.txt)
chl2_raw | | flourescence from Wetlabs Fluorometer (serial # FLNTURTD-2928) | [info](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/pos_519_1_report.txt)
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chlorophyll a | µg/L |	calculated chlorophyll concentration using calibration coefficients from Wetlabs| [calibration coefficents from Wetlabs](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/FLNTURTD-2928.Charsheet-1.pdf)
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potential density | kg/m3 | | [info](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/pos_519_1_report.txt)
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oxygen titrated | µmol/kg | oxygen concebtration determined by Winkler titration on board |
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turb_raw | | turbidity data raw from Wetlabs fluorometer  | [info](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/docs/pos_519_1_report.txt)
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NO3 | µmol/kg |	nitrate concentration, calibration solution was too low, so some samples are off scale -> QF=3 |
NO2 corr. | µmol/kg | nitrite concentration  |
PO4 | µmol/kg| phospate concentration, calibration solution was too low, so some samples are off scale -> QF=3  |
SiO2 | µmol/kg | silicate concentration	 |
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## Underway data
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The underway data are stored in a matlab file called uw_data_pos519.mat and uw_data_pos519.txt.

The data in the matlab file are grouped into structures but they are all on the same time grid. The data in teh text file are structured accordingly:
the first row corresponds to the first structure level and the second row to the second.
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The following tabel gives an overview. It will grow with more data being added. The data for each structure are described below.
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1st level|2nd level | unit | description  
:--- | :--- | :--- | :---
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mtime | | | Matlab time
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lat | | deg N | Latitude
lon | | den E | Longitude
dship. | course | deg | course over ground
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 | heading | deg | ship's heading
 | sal | PSU | salinity calculated from conductivity with ship's thermosalinograph [SBE21](https://www.seabird.com/)
 | sst_ship | degC | seawater temperature at water intake, SBE38. There were problems with the data recording, so there are data gaps.
 | tsg_temp | degC | seawater temperature inside SBE21
 | wind_dir_t | deg | true wind direction
 | wind_speed_t | m/s | true wind speed
 | air_press | mbar | air pressure
 | rh | % | humidity
 | wind_dir_r | deg | wind direction, relative to the ship
 | wind_speed_r | m/s | wind speed, relative to the ship
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In order to convert the .mat file into .txt file I used teh following Matlab code:
´´´
% mat2text.m
% converts the .mat file with structures into text file

[file,path_in]=uigetfile(cd,'choose file ','*.mat');
cd(path_in)

load(file);
clear path_in file
txtdata=[datevec(mtime), lat,lon];
clear mtime lat lon
s1=' \t \t \t \t \t \t \t \t';
s2='Year\tMonth\tDay\tHour\tMinute\tSecond\tLatitude\tLongitude\t';
s3='%d\t %d\t %d\t %d\t %d\t %d\t %8.5f\t %8.5f\t'; 

w=whos;
names=char(w.name);
matches= strcmp({w.class}, 'struct');
for i=1:size(matches,2)
    if matches(i)==1
    st=names(i,:);
    eval(['sa=table2array(struct2table(',st,'));'])
    eval(['saf=fieldnames(',st,');'])
    txtdata=[txtdata, sa];
    saf=char(saf); 
        for j=1:size(saf,1)
            s1=[s1,st,'\t'];
            s2=[s2, saf(j,:),'\t'];
            s3=[s3, ' %8.2f\t'];
        end
    end
end

s1(end)='n';
s2(end)='n';
s3(end)='n';
outname='uw_data_pos519.txt';
fid=fopen(outname,'wt');
fprintf(fid,s1);
fprintf(fid,s2);
fprintf(fid,s3,txtdata');
fclose(fid);
clear
´´´



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### import dship data

Downloaded data from shipd DSHIP system in 30 s interval ([POS519_UW_dship.dat](https://git.geomar.de/tobias-steinhoff/Poseidon-POS519/blob/master/data%20processing/data/POS519_UW_dship.dat):
). The dship data were imported into matlab using the following script:
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```Matlab
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% import_dship.m
[file,path_in]=uigetfile(cd,'choose file ','*.dat');
cd(path_in)
an=dlmread(file,'\t',3,0);

mtime=an(:,2);
dship.course=an(:,3);
dship.heading=an(:,4);
lat=an(:,5);
lon=an(:,6);
dship.sal=an(:,7);
dship.sst_ship=an(:,8);
dship.tsg_temp=an(:,9);
dship.wind_dir_t=an(:,10);
dship.wind_speed_t=an(:,11);
dship.air_press=an(:,12);
dship.rh=an(:,13);
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dship.wind_dir_r=an(:,14);
dship.wind_speed_r=an(:,15);    
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clear an file path_in
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```
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[top](#data-processing-after-poseidon-cruise-pos519)
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