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.

Processing should be done in your workspace - not in the Plumes and Blooms data directories.

NOTE: Processing requires corresponding CTD files to be available. The processing steps cannot be completed until CTD SeaBASS files have been 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) Start MATLAB on your desktop and make sure you have mapped a path to your working directory. For example, connect your desktop to the server by selecting: "GO" -> "Connect to Server" -> "smb://smb://smb.eri.ucsb.edu/user". Then, once at the MATLAB prompt, type: 'cd /Volumes/user/OCEANCOLOR/Plumes_and_Blooms/workspace/user/AC9/pb###/raw/. You'll also need to map-out the path to the processing scripts. Type: "addpath /Volumes/user/OCEANCOLOR/Plumes_and_Blooms/processing_scripts/PnB_AC9_Matlab. Or go to the processing directory in the UNIX environment, making sure you have X-Windows forwarding so MATLAB graphics appear on your screen. If you're having problems, try typing "xhost +" in your desktop window first and then ssh -X "server" to get to the UNIX environment. Once in the processing directory, type "MATLAB" to start the program.

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

6) You will be prompted to identify the CTD files for station-4 and the necessary AC-9 files built by the processing script. Just follow the instructions on the command line.

7) 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.

8) 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