Seabird Utiltiy for Moored and Profiling InStallations.
	 			(SUMPIS)
                    

Wendi Ruef 2006
Last revised: January 2016


Overview
========
  The design of sumpis grew out of a necessity to automatically
  process the large number of data files collected with the 
  Seabird CTD packages deployed on the ORCA mooring packages.
  At the time the Seabird data conversion software ran only in 
  a Windows operating system.  As the ORCA project server is a 
  Linux based system, we initially used a Windows emulator on 
  the server to run the software, but quickly found this to be 
  cumbersome and vulnerable to potential hang ups.
  Our solution was to write a processing software package in Perl
  that uses all the Seabird equations (published in the sensor
  manuals, calibration sheets, and application notes) and 
  calibrations, while minimizing the number of configuration files
  necessary for processing.  

Installation
============
  Dependencies:
  	Perl version: 5.8 or higher. 
             
  Unpack the distribution and place it in your path.  Test by
  running:

      make test


Manual Operations
=================

  The SUMPIS program is used to process files collected with
  a Seabird CTD.  The current version supports the following 
  CTDS:
	19
	19Plus
	19Plus_v2
  Auxiliary Sensors:
	Oxygen:
		SBE 43 
	Flurometers:
		WetLABS WetStar 
		WetLABS FLNTUS	
	Nutrients:
		SatLantic ISUS

  Sumpis may be run through the command line or packaged in 
  a shell script.  It is used to process a directory of raw HEX files.

  Here is a list of the current command line options:
	-no-align: do not automatically align auxiliary sensors 
	-format: choose the file format to print out 
	-caldir: where the raw files can be found
	
	example command line:
	./sumpis.pl -no_align -format 19Plus_compare -caldir raw -config ../configurationFiles/TORCA_conf.txt raw/201601


File Descriptions
=================
  Raw files: Raw data files output from the Seabird CTD in HEX
	- must include header obtained by running the "DS" 
          command (display status)
	  followed by the "DH" command (display header) 
 	  followed by the "DC" command (display casts)

*DS
*SeacatPlus V 1.6b  SERIAL NO. 5071    14 Jan 2016  10:50:02
*vbatt = 11.5, vlith =  8.1, ioper =  61.9 ma, ipump = 178.8 ma, 
*iext01 =   5.1 ma
*iext23 =  41.4 ma
* Temperature SN = 5071
* Conductivity SN = 5071
*status = not logging
*number of scans to average = 1
*samples = 1504, free = 440001, casts = 1
*mode = profile, minimum cond freq = 0, pump delay = 0 sec
*autorun = no, ignore magnetic switch = yes
*battery type = alkaline, battery cutoff =  7.3 volts
*pressure sensor = strain gauge, range = 508.0
*SBE 38 = no, Gas Tension Device = no
*Ext Volt 0 = yes, Ext Volt 1 = yes, Ext Volt 2 = yes, Ext Volt 3 = yes
*echo commands = yes
*output format = raw HEX
*S>DH
*cast   1 14 Jan 2016 10:43:42 samples 1 to 1504, avg = 1, stop = stop cmd
*S>DC
*END*
06CDAB157A20086F7C4FDD2B6D0003092B145C
06CDA9157A17086F7F4FDE2B6A000309FC1449
06CDA115798B086F7C4FDE2B72000409BE140F
06CCB5157BB5086F7B4FDE2B74000409CE13FA
//
S>

  Buoy Config files: config file that lists the basic buoy stats 
  (Latitude is necessary as it is used to calculate depth in meters) and 
  location of the necessary config and deployment files


#Example entries:
# name = "string of description"
# name = value, value, value
# name = value
# name = string_one_word
# name = path/to/file

Location = "ORCA buoy, Twanoh, Hood Canal....."
Latitude = 47.372
Longitude = 123.00833
sensor_deploy_history = /home/orca/bin/sumpis/configurationFiles/sensor_deployment_history_twanoh.txt
sensor_cal_history = /home/orca/bin/sumpis/configurationFiles/sensor_calibration_data.txt
discrete_cal_data = /home/orca/bin/sumpis/calibrations/discrete_O2_twanoh.txt
O2_bottle_volume_data = /home/orca/bin/sumpis/calibrations/O2_bottle_volumes.txt
output_column_order = Temp, Cond, Sal, Press

  Sensor Deployment History: deployment history of the sensors at 
  a particular buoy location.


# Format:
# [date time]
# Cast_number
# CTD_type CTD_serial_number
# Pump_type Pump_serial_number
# Volt0_sensor_type sensor_model serial_number
# Volt1_sensor_type sensor_model serial_number
# Volt2_sensor_type sensor_model serial_number
# Volt3_sensor_type sensor_model serial_number
#
# EX:
# [01/01/05 12:00]
# CAST=200510/ORCA2_CAST0002.HEX
# CTD=SBE19 SN=2835
# PUMP=5T SN=052902
# V0=O2 Model=SBE43 SN=0015
# V1=Fluor Model=WetStar SN=WS3S-586P
# V2=NA Model=NA SN=NA
# V3=NA Model=NA SN=NA
# Serial2=Currents Model=Aquadopp SN=2348  
#    

[01/19/05 10:00]
CAST=200501/ORCA1_CAST0001.HEX
CTD=SBE19 SN=2835
PUMP=5T SN=052902
V0=O2 Model=SBE43 SN=0015
V1=NA Model=NA SN=NA
V2=Fluor Model=WetStar SN=WS3S-668P
V3=NA Model=NA SN=NA
Serial2=NA Model=NA SN=NA

  Sensor calibration history: all the calibration coefficients from 
  the different sensors, as reported by Seabird.

# Format:
# Sensor_type serial_number
# sensor_cal_date=[cal_date] 
# cal_coefficients
# sensor_cal_date=[cal date]
# cal_coefficients
#
# EX:
# Sensor=SBE19 SN=2835
# CTD_cal_date=[07/08/1999]
# cond_g=-4.16533426 cond_h=4.96296919e-01 cond_i=1.54601169e-03 cond_j=-4.7723728e-05 cond_CPcor=-9.57e-08 cond_CTcor=3.25e-06
# temp_g=4.21059973e-03 temp_h=5.97017997e-04 temp_i=3.80929083e-06 temp_j=-1.85656400e-06 temp_f0=1000.00
# press_M=-6.526e-02 press_B=248.60 press_A0=248.24555 press_A1=-6.524518e-02 press_A2=5.430179e-08
#
# all numbers with a decimal point must start with a digit (0.5, 0.0, etc)
# Scientific notation is accepted (1.345e-04)
#CTD_cal_date=[//]
#cond_g= cond_h= cond_i= cond_j= cond_CPcor= cond_CTcor=
#temp_g= temp_h= temp_i= temp_j= temp_f0=
#press_M= press_B= press_A0= press_A1= press_A2=
#CTD_cal_date=[//]
#cond_g= cond_h= cond_i= cond_j= cond_CPcor= cond_CTcor=
#temp_a0= temp_a1= temp_a2= temp_a3=
#press_PA0= press_PA1= press_PA2= press_PTempPA0= press_PTempPA1= press_PTempPA2=
#press_PTCA0= press_PTCA1= press_PTCA2= press_PTCB0= press_PTCB1= press_PTCB2=

# # # # # # # # # # # # # # # #
# Data entered and verified:  # 
# 14 December 2006 -- WMR     #
#		 	      #
# # # # # # # # # # # # # # # #

Sensor=SBE19 SN=2835
CTD_cal_date=[07/08/1999]
cond_g=-4.16533426e+00 cond_h=4.96296919e-01 cond_i=1.54601169e-03 cond_j=-4.77623728e-05 cond_CPcor=-9.57e-08 cond_CTcor=3.25e-06
temp_g=4.21059973e-03 temp_h=5.97017997e-04 temp_i=3.80929083e-06 temp_j=-1.85656400e-06 temp_f0=1000.00
press_M=-0.06526 press_B=248.60 press_A0=248.24555 press_A1=-6.524518e-02 press_A2=5.430179e-08
CTD_cal_date=[12/07/2001]
cond_g=-4.09700020e+00 cond_h=4.90273419e-01 cond_i=6.58576977e-04 cond_j=-2.46017159e-06 cond_CPcor=-9.57e-08 cond_CTcor=3.25e-06
temp_g=4.20839244e-03 temp_h=5.91775059e-04 temp_i=-3.18337943e-07 temp_j=-2.92764296e-06 temp_f0=1000.00
press_M=-0.06524 press_B=248.84 press_A0=248.46950 press_A1=-6.523024e-02 press_A2=5.705084e-08


  O2 bottle volume data: file that stores bottle volumes of 
  winkler sample bottles for use in calculating discrete samples.
  The current version of the code does not use discrete samples 
  to calibrate the sensor data.

  output column order: not currently used


Known Issues
============

	- alignment algorithm cannot shift by frations of a scan 
          as is done in the Seabird software package.