Bottle Specific =============== Exchange Bottle files follow all the common format specifications for their structure. The :ref:`File Identification Stamp` of an exchange bottle file starts with ``BOTTLE``. Each :ref:`data line ` in an exchange bottle file represents a single bottle closure. When ctd parameters are encountered within exchange bottle files (e.g. :ref:`CTDPRS`) they represent the corrected values being read by the CTD at the time of bottle closure, usually averaged over some interval. In bottle files, specific parameters are REQUIRED to be present and have non fill values. .. _bottle required headers: Required Bottle Parameters -------------------------- The following parameters are REQUIRED to be present in exchange bottle files where the parameter name occurs within the :ref:`parameter and unit lines` and their values be present in the :ref:`data lines`. * :ref:`EXPOCODE` * :ref:`STNNBR` * :ref:`CASTNO` * :ref:`DATE` * :ref:`LATITUDE` * :ref:`LONGITUDE` * :ref:`CTDPRS` * :ref:`SAMPNO` .. versionchanged:: 1.3 Removed :ref:`BTLNBR` as being one of two options for required columns. Unique Line Identification -------------------------- Since each :ref:`data line ` of an exchange bottle file represents a single bottle closure, enough information must be present on each line to uniquely identify closure event. This is to allow the integration of all the measurements of samples taken from that bottle at a later time. The identification is done by requiring a combination of values from specific parameters to be unique throughout the file. The following combination of parameters must have unique values: * :ref:`EXPOCODE` * :ref:`STNNBR` * :ref:`CASTNO` * :ref:`SAMPNO` .. versionchanged:: 1.3 Removed :ref:`BTLNBR` as a being a valid identifier for samples. Unique Line Identification Examples ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ In these examples, the long parameter, unit, and data lines truncated by ``[...]``. The following example exchange bottle data is all from the same cruise indicated by the expocode: ``33RO20131223``, the same station: ``1``, the same cast ``2``, but the bottle number and sample numbers differ (``24`` and ``23``). .. code-block:: none :linenos: BOTTLE,20150327CCHSIORJL # From submitted file a16s_2013_final_discrete_o2.csv: # Merged parameters: OXYGEN_FLAG_W EXPOCODE,STNNBR,CASTNO,SAMPNO,BTLNBR[...] ,,,,[...] 33RO20131223, 1, 2, 24, 24[...] 33RO20131223, 1, 2, 23, 23[...] END_DATA The following example shows an example of duplicated unique identification parameter values. More than one line contains the exact same values for :ref:`EXPOCODE`, :ref:`STNNBR`, :ref:`CASTNO`, and :ref:`SAMPNO`. .. code-block:: none :linenos: BOTTLE,20150327CCHSIORJL # From submitted file a16s_2013_final_discrete_o2.csv: # Merged parameters: OXYGEN_FLAG_W EXPOCODE,STNNBR,CASTNO,SAMPNO,BTLNBR[...] ,,,,[...] 33RO20131223, 1, 2, 24, 24[...] 33RO20131223, 1, 2, 24, 23[...] END_DATA .. _example bottle data: Example Bottle Data ------------------- .. only:: latex An example bottle exchange file is provided on the next page. .. raw:: latex \begin{landscape} \tiny \begin{verbatim} BOTTLE,20150327CCHSIORJL # From submitted file a16s_2013_final_discrete_o2.csv: # Merged parameters: OXYGEN_FLAG_W #| #| #| Analysis Institution Principal Investigator email #| ____________________________________________________________________________________ #| Chief Scientist AOML Rik Wanninkhof rik.wanninkhof@noaa.gov #| Co-Chief Scientist AOML/CIMAS Leticia Barbero leticia.barbero@noaa.gov #| CTDO NOAA/PMEL Gregory Johnson Gregory.C.Johnson@noaa.gov #| NOAA/AOML Molly Baringer Molly.Baringer@noaa.gov #| Salinity NOAA/AOML Molly Baringer Molly.Baringer@noaa.gov #| UW & Discrete pCO2 NOAA/AOML Rik Wanninkhof Rik.Wanninkhof@noaa.gov #| Total CO2 (DIC) NOAA/PMEL Richard Feely Richard.A.Feely@noaa.gov #| NOAA/AOML Rik Wanninkhof Rik.Wanninkhof@noaa.gov #| Nutrients NOAA/AOML Jia-Zhong Zhang Jia-Zhong.Zhang@noaa.gov #| NOAA/PMEL Calvin Mordy Calvin.W.Mordy@noaa.gov #| Dissolved O2 NOAA/AOML Molly Baringer Molly.Baringer@noaa.gov #| RSMAS Chris Langdon clangdon@rsmas.miami.edu #| Total Alkalinity/pH RSMAS Frank Millero fmillero@rsmas.miami.edu #| CFCs/SF6 NOAA/PMEL John Bullister John.L.Bullister@noaa.gov #| 3He/Tritium LDEO Peter Schlosser peters@ldeo.columbia.edu #| WHOI William Jenkins wjenkins@whoi.edu #| CDOM UCSB/MSI Craig Carlson carlson@lifesci.ucsb.edu #| Chipod OSU Jonathan Nash nash@coas.oregonstate.edu #| ADCP/Lowered ADCP U Hawaii Eric Firing efiring@hawaii.edu #| Trace Metals FSU William Landing wlanding@fsu.edu #| UH Chris Measures measures@hawaii.edu #| 14C/DIC WHOI Ann McNichols amcnichol@whoi.edu #| PU Robert Key key@princeton.edu #| DOC RSMAS Dennis Hansell dhansell@rsmas.miami.edu #| Data Management SIO James Swift jswift@ucsd.edu #| SIO Susan Becker sbecker@ucsd.edu #| #| Following American Geophysical Union recommendations, the data should be #| cited as: "data provider(s), cruise name or cruise ID, data file name(s), #| CLIVAR and Carbon Hydrographic Data Office, La Jolla, CA, USA, and data #| file date." For further information, please contact one of the parties #| listed above or cchdo@ucsd.edu. Users are also requested to acknowledge #| the NSF/NOAA-funded U.S. Repeat Hydrography Program in publications resulting #| from their use. #| # EXPOCODE,SECT_ID,STNNBR,CASTNO,SAMPNO,BTLNBR,BTLNBR_FLAG_W,DATE,TIME,LATITUDE,LONGITUDE,DEPTH,CTDPRS,CTDTMP,CTDSAL,CTDSAL_FLAG_W,SALNTY,SALNTY_FLAG_W,CTDOXY,CTDOXY_FLAG_W,OXYGEN,OXYGEN_FLAG_W ,,,,,,,,,,,METERS,DBAR,ITS-90,PSS-78,,PSS-78,,UMOL/KG,,UMOL/KG, 33RO20131223, A16S, 1, 2, 24, 24,2,20131226, 0706, -6.0016, -24.9998, 5809, 3.9, 26.2239, 36.3097,2, 36.3082,2, 199.1,2, 201.2,2 33RO20131223, A16S, 1, 2, 23, 23,2,20131226, 0704, -6.0016, -24.9998, 5809, 22.5, 26.2331, 36.3090,2, 36.3171,2, 199.4,2, 201.3,2 33RO20131223, A16S, 1, 2, 22, 22,2,20131226, 0702, -6.0016, -24.9998, 5809, 47.4, 26.2335, 36.3078,2, 36.3080,2, 200,2, 201.9,2 33RO20131223, A16S, 1, 2, 21, 21,2,20131226, 0700, -6.0016, -24.9998, 5809, 72.1, 26.2112, 36.3044,2, 36.3055,2, 200.6,2, 201,2 33RO20131223, A16S, 1, 2, 20, 20,2,20131226, 0658, -6.0016, -24.9998, 5809, 97.5, 24.2160, 36.1165,2, 36.1258,2, 193.2,2, 190.1,2 33RO20131223, A16S, 1, 2, 19, 19,2,20131226, 0656, -6.0016, -24.9998, 5809, 147.3, 15.5167, 35.6384,2, 35.6247,2, 104.9,2, 103.3,2 33RO20131223, A16S, 1, 2, 18, 18,2,20131226, 0654, -6.0016, -24.9998, 5809, 222.8, 12.0808, 35.1686,2, 35.1586,2, 109.3,2, 108.6,2 33RO20131223, A16S, 1, 2, 17, 17,2,20131226, 0651, -6.0016, -24.9998, 5809, 296.4, 9.8716, 34.8809,2, 34.8809,2, 124,2, 125,2 33RO20131223, A16S, 1, 2, 16, 16,2,20131226, 0648, -6.0016, -24.9998, 5809, 406.5, 8.4675, 34.7567,2, 34.7520,2, 83.8,2, 81.4,2 33RO20131223, A16S, 1, 2, 15, 15,2,20131226, 0645, -6.0016, -24.9998, 5809, 517.9, 7.1433, 34.6371,2, 34.6366,2, 93.8,2, 88.6,2 33RO20131223, A16S, 1, 2, 14, 14,2,20131226, 0642, -6.0016, -24.9998, 5809, 647.7, 5.5545, 34.5066,2, 34.5046,2, 139.4,2, 130.5,2 33RO20131223, A16S, 1, 2, 13, 13,2,20131226, 0638, -6.0016, -24.9998, 5809, 791.9, 4.6390, 34.4845,2, 34.4826,2, 158.6,2, 148.5,2 33RO20131223, A16S, 1, 2, 12, 12,2,20131226, 0633, -6.0016, -24.9998, 5809, 1047.4, 4.2414, 34.6431,2, 34.6429,2, 163.9,2, 163.7,2 33RO20131223, A16S, 1, 2, 11, 11,2,20131226, 0627, -6.0016, -24.9998, 5809, 1347.9, 4.3278, 34.8700,2, 34.8698,2, 197.4,2, 197.1,2 33RO20131223, A16S, 1, 2, 10, 10,2,20131226, 0619, -6.0016, -24.9998, 5809, 1747.8, 3.8921, 34.9665,2, 34.9664,2, 238.6,2, 238.3,2 33RO20131223, A16S, 1, 2, 9, 9,2,20131226, 0611, -6.0016, -24.9998, 5809, 2147.8, 3.2522, 34.9412,2, 34.9420,2, 242.7,2, 243.6,2 33RO20131223, A16S, 1, 2, 8, 8,2,20131226, 0602, -6.0016, -24.9998, 5809, 2597.5, 2.8568, 34.9202,2, 34.9188,2, 242.6,2, 242.3,2 33RO20131223, A16S, 1, 2, 7, 7,3,20131226, 0553, -6.0016, -24.9998, 5809, 3097.5, 2.6784, 34.9194,2, 34.9176,2, 251.1,2, 251.7,2 33RO20131223, A16S, 1, 2, 6, 6,3,20131226, 0544, -6.0016, -24.9998, 5809, 3598.4, 2.4902, 34.9073,2, 34.9727,4, 255.1,2, 235.6,4 33RO20131223, A16S, 1, 2, 5, 5,2,20131226, 0534, -6.0016, -24.9998, 5809, 4098.5, 1.8197, 34.8364,2, 34.8340,2, 242.3,2, 243.2,2 33RO20131223, A16S, 1, 2, 4, 4,2,20131226, 0524, -6.0016, -24.9998, 5809, 4598, 0.9865, 34.7443,2, 34.7432,2, 225.6,2, 226.4,2 33RO20131223, A16S, 1, 2, 3, 3,2,20131226, 0515, -6.0016, -24.9998, 5809, 5097.2, 0.7993, 34.7170,2, 34.7167,2, 220.1,2, 221.9,2 33RO20131223, A16S, 1, 2, 2, 2,2,20131226, 0505, -6.0016, -24.9998, 5809, 5597.3, 0.7292, 34.7031,2, 34.7024,2, 219.8,2, 219.9,2 33RO20131223, A16S, 1, 2, 1, 1,3,20131226, 0459, -6.0016, -24.9998, 5809, 5904.3, 0.7651, 34.7023,2, 34.7049,2, 219.9,2, 220.9,2 33RO20131223, A16S, 2, 1, 24, 24,2,20131226, 1421, -6.4977, -24.9999, 5628, 3.1, 26.2387, 36.2430,2, 36.2424,2, 201.5,2, 202.1,2 33RO20131223, A16S, 2, 1, 23, 23,2,20131226, 1419, -6.4977, -24.9999, 5628, 27.9, 26.1705, 36.2402,2, 36.2394,2, 202.2,2, 202.2,2 33RO20131223, A16S, 2, 1, 22, 22,3,20131226, 1417, -6.4977, -24.9999, 5628, 67.9, 26.1326, 36.2369,2, 36.2353,2, 201.5,2, 202.3,2 33RO20131223, A16S, 2, 1, 21, 21,2,20131226, 1415, -6.4977, -24.9999, 5628, 107.1, 22.8199, 36.1452,2, 36.1454,2, 168.2,2, 170.3,2 33RO20131223, A16S, 2, 1, 20, 20,2,20131226, 1412, -6.4977, -24.9999, 5628, 172.4, 15.2580, 35.6092,2, 35.6393,4, 112,2, 112.6,2 33RO20131223, A16S, 2, 1, 19, 19,2,20131226, 1410, -6.4977, -24.9999, 5628, 257.5, 10.8796, 35.0258,2, 35.0261,2, 92.4,2, 92.3,2 33RO20131223, A16S, 2, 1, 18, 18,2,20131226, 1407, -6.4977, -24.9999, 5628, 367.8, 9.2106, 34.8337,2, 34.8338,2, 75.2,2, 75.6,2 END_DATA \end{verbatim} \end{landscape} .. only:: html .. code-block:: none :linenos: BOTTLE,20150327CCHSIORJL # From submitted file a16s_2013_final_discrete_o2.csv: # Merged parameters: OXYGEN_FLAG_W EXPOCODE,SECT_ID,STNNBR,CASTNO,SAMPNO,BTLNBR,BTLNBR_FLAG_W,DATE,TIME,LATITUDE,LONGITUDE,DEPTH,CTDPRS,CTDTMP,CTDSAL,CTDSAL_FLAG_W,SALNTY,SALNTY_FLAG_W,CTDOXY,CTDOXY_FLAG_W,OXYGEN,OXYGEN_FLAG_W ,,,,,,,,,,,METERS,DBAR,ITS-90,PSS-78,,PSS-78,,UMOL/KG,,UMOL/KG, 33RO20131223, A16S, 1, 2, 24, 24,2,20131226, 0706, -6.0016, -24.9998, 5809, 3.9, 26.2239, 36.3097,2, 36.3082,2, 199.1,2, 201.2,2 33RO20131223, A16S, 1, 2, 23, 23,2,20131226, 0704, -6.0016, -24.9998, 5809, 22.5, 26.2331, 36.3090,2, 36.3171,2, 199.4,2, 201.3,2 33RO20131223, A16S, 1, 2, 22, 22,2,20131226, 0702, -6.0016, -24.9998, 5809, 47.4, 26.2335, 36.3078,2, 36.3080,2, 200,2, 201.9,2 33RO20131223, A16S, 1, 2, 21, 21,2,20131226, 0700, -6.0016, -24.9998, 5809, 72.1, 26.2112, 36.3044,2, 36.3055,2, 200.6,2, 201,2 33RO20131223, A16S, 1, 2, 20, 20,2,20131226, 0658, -6.0016, -24.9998, 5809, 97.5, 24.2160, 36.1165,2, 36.1258,2, 193.2,2, 190.1,2 END_DATA The basic strucutre is: * Line 1: :ref:`File Identification Stamp` starting with ``BOTTLE`` * Line 2, 3: :ref:`comment line(s)` * Lines 3, 4: :ref:`parameter and unit lines` * Lines 6-11: :ref:`data lines`.