README_reprocessing.txt
                                                                 Oceanus 402 CTD data reprocessing

Reason for reprocessing: 
    Add primary and secondary SigmaT  and  secondary Salinity to datafiles; casts nedded to be reprocessed: Down and Up;
    BTL files: Calculate Secondary SigmaT instead of primary (there was a problem with Conductivity Primary sensor).
Software: Seabird Seasoft_DOS;
Bat file name:   oc402_reprocess_down_and_up.bat;
Bat file location: c:\Seasoft_DOS\.


NOTES:
 1. Seasoft_DOS works with filenames length<=7 (Seasoft_DOS feature).
   However, there is one exception for Down cast in case if one of the SPLIT options is '-nd'. It means do not add 'd' prefix to the DOWNcast output filename (this option is not available for the UPcast). 
 2. Length of oc402 CTD filenames is 8 characters (e.g. oc402001.dat) and one name is 9 characters (oc402073a.dat).
 3. Program oc402_reprocess_down_and_up.bat designated to process both UP and DOWN casts so filenames should be shorten to 7 characters before processing and renamed back after processing.
    Names e.g.: oc402001 => c402001 => Uc402001 (or Dc402001) => oc402001 with respective extension.

PROCESSING PROCEDURE:

1. RENAME RAW CTD DATA FILES on LINUX
before reprocessing with SEASOFT_DOS on PC machine. 

1.1. Copy raw datafiles from  CD =>  /home/olga/oc402/ctd_reprocessing/raw/
  Raw CTD datafiles names:
*.BL;
*.CON;
*.dat;
*.HDR.

1.2. Rename CTD datafiles on LINUX. Examples of renaming:

oc402084.BL                        - PREVIOUS name
rename oc c oc??????.*
c402084.BL                          - NEW name

od402189.BL                        - PREVIOUS name
rename od d od??????.*
d402189.BL                         - NEW name

oe402189.BL                        - PREVIOUS name
rename oe e oe??????.*
e402189.BL                         - NEW name

oc402001a.BL                      - PREVIOUS name
rename oc4 4 oc??????a.*
402001a.BL                         - NEW name

2. TRANSFER RENAMED RAW DATA FILES and oc402.con file to PC machine using WinSCP2.exe to
   c:\olga\oc402\ctd\proc\raw_renamed\.

3. COPY  RENAMED RAW DATA FILES and oc402.con file on PC:
from:
  c:\olga\oc402\ctd\proc\raw_renamed\
to:
  c:\olga\oc402\ctd\proc\  THIS IS WORKING DIRECTORY - DATA SOURCE for  processing with SEASOFT_DOS

4. PROCESS DATA using SEASOFT_DOS software and bat file for DOWN and UP casts.

4.1. Enter to Seasoft_DOS directory:
     cd c:\Seasoft_DOS;

4.2. Run test bat file to set up and save configuration for each Seasoft_DOS block used for processing:
     edit the program ctd_reprocess_down_and_up.bat: replace '-ax' in each command line with '-a', this will display setup forms while processing;
    save  as ctd_reprocess_down_and_up_test.bat;
    temporarily remove raw data from working directory c:\olga\oc402\ctd\proc\  except any one cast ;
    run ctd_reprocess_down_and_up_test.bat, check up and edit  input options in the displayed forms;
    return raw data to c:\olga\oc402\ctd\proc\.

4.3.  Run ctd_reprocess_down_and_up.bat (it takes >2hours to process ~260 files).

5. MOVE PROCESSED datafiles on PC:
  move  c:\olga\oc402\ctd\reprocessing\D*.*  c:\olga\oc402\ctd\reprocessing_down\
  move  c:\olga\oc402\ctd\reprocessing\U*.*  c:\olga\oc402\ctd\reprocessing_up\

6. TRANSFER PROCESSED DATA FILES to LINUX machine using WinSCP2.exe to:
     /home/olga/oc402/ctd_reprocessing/down_cast/
     /home/olga/oc402/ctd_reprocessing/up_cast/

7. On LINUX machine: COPY datafiles:
from /home/olga/oc402/ctd_reprocessing/up_cast/  and /home/olga/oc402/ctd_reprocessing/down_cast/ 
to  /home/olga/oc402/ctd_reprocessing

8. In the /home/olga/oc402/ctd_reprocessing/ directory RENAME DOWN casts files to RESTORE original filenames.

rename DC oc DC4?????.*
rename DD od DD4?????.*
rename DE oe DE4?????.*
rename D oc D4?????a.*

9. In the /home/olga/oc402/ctd_reprocessing/ directory  RENAME UP casts files to RESTORE original filenames.

rename UC oc UC4?????.*
rename UD od UD4?????.*
rename UE oe UE4?????.*
rename U oc U4?????A.*

10. In case if only DOWN casts or only UP casts are processing, use bat files:
oc402_reprocess_down.bat (c:\Seasoft_DOS\) or 
oc402_reprocess_up.bat (c:\Seasoft_DOS\)
See programs comments for more information.