AC-9 processing instructions - Revision history

Dcourt at 16:55, 24 August 2016

2016-08-24T16:55:52Z

Dcourt at 20:29, 23 August 2016

2016-08-23T20:29:54Z

Dcourt at 20:29, 23 August 2016

2016-08-23T20:29:29Z

Dcourt at 20:27, 23 August 2016

2016-08-23T20:27:09Z

Dcourt at 20:20, 23 August 2016

2016-08-23T20:20:10Z

Dcourt at 20:18, 23 August 2016

2016-08-23T20:18:00Z

Dcourt at 20:16, 23 August 2016

2016-08-23T20:16:39Z

Dcourt at 20:08, 23 August 2016

2016-08-23T20:08:26Z

Dcourt at 20:06, 23 August 2016

2016-08-23T20:06:21Z

Dcourt at 23:47, 17 August 2016

2016-08-17T23:47:31Z

@@ Line 1: / Line 1: @@
 '''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.'''
-Files to be processed from the AC9 must be placed in their appropriate respective processing folders in UNIX.
+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).
@@ Line 20: / Line 15: @@
 ) 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.
-) 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.
+) 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.
 ) Type "'''process_ac9('pb###')'''

← Older revision		Revision as of 20:29, 23 August 2016
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	4) 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.		4) 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###')'''		5) Type "'''process_ac9('pb###')'''

@@ Line 1: / Line 1: @@
 '''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.'''
-Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.
+Files to be processed from the AC9 must be placed in their appropriate respective processing folders in UNIX.
       your_workspace/AC-9/pb#/
                final (processed from MATLAB)
-               processing
+               processing (working environment)
                raw (raw files from AC-9 plus processed files from WETview)
 '''NOTE:''' Processing requires corresponding CTD files to be present.  The processing steps cannot be completed until CTD SeaBASS files are created.
@@ Line 27: / Line 20: @@
 ) 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.
-) Move into the "processing" directory and start MATLAB with graphics.
+) 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.
-) Type "process_ac9('pb###')or process_hs6('pb###')
+) Type "'''process_ac9('pb###')'''
 ) 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.

@@ Line 1: / Line 1: @@
 '''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.'''
 Files to be processed from the AC9 and HS6 must be placed in their appropriate respective processing folders in UNIX.
       your_workspace/HYDROSCAT/pb#/
@@ Line 12: / Line 11: @@
                raw (raw files from AC-9 plus processed files from WETview)
-With these directory structures, MATLAB processing will take place in the HYDROSCAT/pb# and AC-9/pb#/processing directories.
+Go to these directories 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.
-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.
+Once in the processing directory, type "MATLAB" to start the program.
 AC9 files are extracted from the DH4, and then run through WETLabs software on a PC (or via Virtual Machine on the Mac).

@@ Line 32: / Line 32: @@
 ) Type "process_ac9('pb###')or process_hs6('pb###')
-) 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.
+) 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.
-) 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.
+) 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.

← Older revision		Revision as of 20:16, 23 August 2016
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	5) Type "process_ac9('pb###')or process_hs6('pb###')		5) Type "process_ac9('pb###')or process_hs6('pb###')

−	6) You will be instructed to pick the tops and bottoms of ~~the~~ '''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.'''	+	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.

← Older revision		Revision as of 20:08, 23 August 2016
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	5) Type "process_ac9('pb###')or process_hs6('pb###')		5) Type "process_ac9('pb###')or process_hs6('pb###')

−	6) You will be instructed to pick the tops and bottoms of the '''BOTH the down AND up''' ~~casts~~. ~~'''~~This is different than that radiometer processing where only ~~downcasts~~ are picked.~~'''~~ Be sure to pick the points in the following order: 1) top of the ~~downcast~~, 2) bottom of the ~~downcast~~, 3) bottom of the ~~upcast~~, 4) top of the ~~upcast~~.	+	6) You will be instructed to pick the tops and bottoms of the '''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.'''

← Older revision		Revision as of 20:06, 23 August 2016
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	5) Type "process_ac9('pb###')or process_hs6('pb###')		5) Type "process_ac9('pb###')or process_hs6('pb###')

−	6) You will be instructed to pick the bottoms ~~and tops~~ of the '''up ~~and down~~''' casts. '''This is different than that radiometer processing where only downcasts are picked.'''	+	6) You will be instructed to pick the tops and bottoms of the '''BOTH the down AND up''' casts. '''This is different than that radiometer processing where only downcasts are picked.''' Be sure to pick the points in the following order: 1) top of the downcast, 2) bottom of the downcast, 3) bottom of the upcast, 4) top of the upcast.

@@ Line 24: / Line 24: @@
 ) Open WETLabs, WETview program
-) Select tab -> open device file and then select device file from the /home/oceancolor/calibrations/...Factory_Calibrations directory.
+) Select 'File' -> 'Open Device...' and then select the device file from the /home/oceancolor/calibrations/Wetlabs/AC-9/Factory_Calibrations directory.
 ) 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.