AC-9 processing instructions

NOTE: Processing is geared for unit 0184. Accommodations were made for unit 0159. Changes will need to be made for other instruments to ac9cal, device and par files, and merge files.

New processing protocol: Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.

    your_workspace/HYDROSCAT/pb#/
             dat (processed from WETview)
             final (processed from MATLAB)
             from_DH4 (raw)
    your_workspace/AC-9/pb#/
             final (processed from MATLAB)
             processing (processed from WETview)
             raw

With these directory structures, MATLAB processing will take place in the HYDROSCAT/pb# and AC-9/pb#/processing directories. Go to these directories in UNIX, making sure you have X window forwarding or VNC viewer for MATLAB graphical piping. Once in the directory, type "MATLAB" to start the program.

Processing files end to end requires corresponding CTD files to be present in your home processing directory structure. AC9 and HS6 SeaBASS files cannot be generated until CTD SeaBASS files are created.

AC9 files are extracted from the DH4, and then run through WETLabs software on a PC (or via Virtual Machine on the Mac).

Processing Steps:

1) Open WETLabs, WETview program

2) Select 'File' -> 'Open Device...' and then select the device file from the /home/oceancolor/calibrations/Wetlabs/AC-9/Factory_Calibrations directory.

3) Choose to process .RAW files and select the appropriate folder and .raw file. This needs to be done with every station. Output files from WETLabs will have .dat extension. Put these in the raw folder of your working directory.

4) Move into the "processing" directory and start MATLAB with graphics.

5) Type "process_ac9('pb###')or process_hs6('pb###')

6) You will be instructed to identify the "steps" of the up-cast at station-4 where the CTD stops at designated depths (75, 50, 30, 20, 10, 5, 0m). You will need to mark the (two) points at each step where the CTD stops and where it continues upward.

6) You will be instructed to pick the tops and bottoms of BOTH the down-casts AND up-casts. This is different than that radiometer processing where only down-casts are picked. Be sure to pick the points in the following order: 1) top of the down-cast, 2) bottom of the down-cast, 3) bottom of the up-cast, 4) top of the up-cast. MATLAB will prompt you to save the points and again to ask if you'd like to pick points for another cast. Select "yes" to save the points and "yes" again to select points for the up-cast. Then select "yes" to save the points but "no" to continue to the next cast.

Additional Notes:

- Assumptions are made when upused.txt is generated. Make sure the list is accurate to the amount of files. Edit and rerun if needed.

- goac9.par is used in a critical ac9 temp correction script. It contains information on indexes for merged ac9 to CTD files.

- Parameters specified to merge to ctd files are in:

=> /home/data65/pb/AC9/LIST/list_ac9merge_ac9

=> upused.txt which is put in your local processing directory

=> ctd2strip_v2 strips headers from CTD.HDR files. Headers to be taken are specified inside ctd2strip_v2

=> reviewing AC9 files there are several "a" correction methods applied in goac9_tiho to look at in "plot_ac9_final.m" correction 1, 2, 3.

- Method 1 subtracting a715 baseline

- Method 2 .16 * c - a channels

- Method 3 a - (a/c -a)*(c-a)

Example pb231

offset.iop [25 34 43 51] look in merged file for this info

25 m-d-d-a412(the start of AC data) 34 m-d-d-c412 43 a412ref 51 c412ref

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pnb.offset.itemp[60] temp

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pnb.offset.rac9depth[61] 1depth

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offset.phys [2 8 7 13 20 23] 2 timeJ 8 wetstarflour 7 wetBtrans 13 t068 19 sigmat-00 23 sal00