HyperPro II Optical Profiler Deployment and data processing Geoff MacIntyre May 15, 2014

HyperPro II Optical Profiler

Deployment and data processingGeoff MacIntyre

May 15, 2014

©2014 Sea-Bird Scientific Inc.

Outline

• HyperPro II overview• Instrument setup and configuration• Deployment best practices• Data logging and real-time display software• Data processing and analysis


Applications

Measures colour of the ocean and how it varies spectrally throughout the euphotic zone

calibration / validation data for ocean colour satellites

biological and physical oceanographic research involving light in the ocean

naval research involving characterization of underwater light field


Features

Free-falling• Low tilt angle• Free of ship shadow

Hyper or multi-spectral radiometers

Buoy mode for surface measurements

Full suite of ancillary measurements• Temperature and conductivity probe

• Tw accuracy 0.01 C from -2.5 to +40• C accuracy 0.005 mS/cm

• WET Labs ECO pucks• Tilt sensor• Pressure sensor

• Depth accuracy 0.1 m (Druck 0-300 psi)

Downwelling irradiance sensor (Ed)

Upwelling radiance sensor (Lu)

WET Labs ECO puck (Chl a, CDOM, Turb)

Temperature & Conductivity probe

Pressure sensor


Surface reference

Surface reference sensor (Es)• Provides reference irradiance data

during vertical profile• Captures any changes in the

reference light field• Used to normalize in-water data for

water leaving radiance calculations


Computer and power

MDU-200

HyperPro

• Converts 12 VDC to 48 VDC• Converts RS485 to RS232

power supply

computer

Computer with SatView data logging and real-time display software

Power supply (12 VDC)


SetupComputer

Sun CableMechanical Termination

Power supplyMDU-200

+ -

ResearchVessel

Radiance Irradiance

Profiler II in free-fall configuration


Deployment


Software

• Data logging • Real-time graphical display

• Data processing

• 3D plotting of derived parameters

SatView 2.9.5 ProSoft 7.7


Data logging and display

SatView 2.9.5• Primary function is for data logging• Secondary function is for real-time display of data• Can be used with any Satlantic instrument


SatView setup

• Load instrument package file (SIP) into main window• Select COM ports• Configure settings• Setup display

windows • Depth profile• Spectral displays• Times series view• Ancillary data

• Pressure tare


SatView display


Optical data processing

ProSoft 7.7• Data processing and analysis package• Written and compiled using MatLab version 6.5.0• Automated data processing standardized to remove subjectivity• Data and metadata organization based on the Hierarchical Data Format (HDF)

Minimum requirements• Operating System: Microsoft® Windows® 2000/2003/XP/Vista Processor (CPU): 1 GHz

32-bit (x86)• Memory (RAM): 512 MB• Free Disk Space: 50 MB


ProSoft overview

Processing Context• Defines all the parameters necessary for processing

instrument data• Current Instrument context created by loading all cal/SIP

files for instrument package• Current Parameters context created by configuring

processing parameters

Multi-level processing• Enables user to process data from raw to final data products

in one step• All intermediate processing levels are automatically

processed with accompanying files (*.HDF) being produced

Single level processing• Enables user to process data over a single level


Data levels defined Level 1

• raw binary data file from the profiler• file extension is .RAW

Level 1a • binary data is extracted from raw data • extracted information is grouped along with its calibration information• file nametag is _L1a

Level 1b • level1b data is calibrated, CAL, BIN or NULL dark correction is applied• file nametag is _L1b

Level 2 • shutter dark correction is applied• profile editing is performed• file nametag is _L2


Data levels defined

Level 2s • data interpolated onto a common co-ordinates vector, which is either depth (Profiler)

or time (Reference only or SAS) • file nametag is _L2s

Level 3a • includes averaging of Level 2s data as defined by the processing parameters (e.g. time,

depth) • file nametag is _L3a

Level 4 • includes higher level data products (users choice) calculated from level 3a data• products include normalized water leaving radiance, reflectance profiles,

photosynthetically available radiation etc. • file nametag is _L4


Current instrument

To create new instrument context: click on ‘New’ Browse to folder with SIP files


Load SIP files

Note: SIP file = zip file with all cal files


Instrument configuration

Load all required cal files• Select cal files• Click >> at bottom

Setup parameters for each calibration file

• Select cal file• Set parameters

• See ref table on p14 of manual

• Set distances• See diagram on p16 of manual


Calibration file parameters

Cal File Prefix

Sensors Instrument Type

Immersion Coefficients

Measurement Mode

Frame Type

HED Es Reference/SAS Air Surface ShutterDark

HSE Es Reference/SAS Air Surface ShutterLight

MPR* Tilt Press T Profiler/Ancillary Water FreeFall LightAncCombined/ Anc

HPE Ed Profiler Water FreeFall ShutterLight

PED Ed Profiler Water FreeFall ShutterDark

HPL Lu Profiler Water FreeFall ShutterLight

PLD Lu Profiler Water FreeFall ShutterDark

BB2F Fluor ECO Series IOP Not Required [FreeFall Surface] Not Required


Sensor parameters

ProSoft references optical/ancillary data to pressure during processing

Sensors physically offset from pressure sensor

Enter sensor distance measurements

Enter Pressure Tare method

Enter Water Medium


Pressure Tare

The Pressure Tare parameter is used to adjust measured pressure values for atmospheric pressure, there are two methods

• ‘On Deck’ (recommended)• ‘In water’

The ‘On deck’ pressure tare is taken with the profiler held upright on deck of the ship

The pressure tare value is captured by SatView and added to the data file

Pressure tare is then equal to atmospheric pressure (~10.1 m)


Sensor position measurements

Lu distance to surface

Sea surface

Lu sensorEd sensor Atmospheric

pressure

Pressure TareEd distance to surface

Pressure reference

• All data referenced to depth• Must compensate for

physical offset of instruments on package• Ed sensor referenced to

pressure sensor; then all other sensors references to Ed sensor



Pressure Tare value is added to the distance from the Ed sensor to the pressure sensor reference line

Sensor distance values can be measured or looked up in table (p18 of manual)

HyperPro II Ed Lu ECO

Distance to Surface 0.0 0.316 0.264

Distance to Pressure 0.786 0.0 0.0




Sensor position example

Pressure Tare = pressure tare value from SatView + Ed distance to pressurePressure Ed = measured pressure – Pressure TarePressure Lu = measured pressure – Pressure Tare + distance to surface

Uncorrected pressure sensor reading = 10.886 mAtmospheric pressure = 10.1 mEd distance to pressure = 0.786Ed sensor is therefore at: 10.886 m – (10.1 m + 0.786 m) = 0 mLu sensor is therefore at: 10.886 m – (10.1 m + 0.786 m) + 0.316 m = 0.316 m


Current parameters

Current Parameters defines processing factors such as data filtering, averaging and interpolating

User can set up and save a few different ‘Current Parameters’ to use for processing data sets for different purposes

Can be setup independent of the specific instrument used to log the data, examples:

• HyperPro 1m bins• HyperPro tilt edit off• HyperSAS 1s averages


New parameters context

Setup processing parameters • Profile editing• Dark correction• Averaging • Data filtering • Level 4 settings


Processing

Only have to perform Current Instrument and Current Parameters set up the first time you use the instrument, unless:

• you add a new sensor• get new calibration files• want to change your processing parameters


Load raw data files


Processing complete!


Common problems

Issue: • processing locks up during conversion from Level 3 to 4• error message “Matrix dimensions must agree”• likely an incorrect setting for a cal file in ‘Instrument Context’

Solution: • check instrument context setup• check each of the cal file settings for correct:

• Instrument type• Frame type

Issue: • processing locks up during conversion from Level 1b to 2• error message “index exceeds matrix dimensions”

Solution: • wrong dark correction method selected for type of instrument• edit processing parameters


HDF viewer


Surface reference


Downwelling irradiance

Save plot as imageFile -> Save As -> .png


Water leaving radiance


Chlorophyll a


Turbidity


PAR


Export to ASCII

Export data to ASCII format for use in MS Excel • General data• Turbidity/Par data

Export data in MAT files for use with MatLab


Questions

Thank you

Documents

HyperPro II Optical Profiler Deployment and data processing Geoff MacIntyre May 15, 2014