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

2. ©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

3. ©2014 Sea-Bird Scientific Inc. 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

4. ©2014 Sea-Bird Scientific Inc. 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

5. ©2014 Sea-Bird Scientific Inc. 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

6. ©2014 Sea-Bird Scientific Inc. 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)

7. ©2014 Sea-Bird Scientific Inc. Setup Computer Sun Cable Mechanical Termination Power supply MDU-200 + - Research Vessel RadianceIrradiance Profiler II in free-fall configuration

8. ©2014 Sea-Bird Scientific Inc. Deployment

9. ©2014 Sea-Bird Scientific Inc. Software Data logging Real-time graphical display Data processing 3D plotting of derived parameters SatView 2.9.5 ProSoft 7.7

10. ©2014 Sea-Bird Scientific Inc. 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

11. ©2014 Sea-Bird Scientific Inc. 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

12. ©2014 Sea-Bird Scientific Inc. SatView display

13. ©2014 Sea-Bird Scientific Inc. 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

14. ©2014 Sea-Bird Scientific Inc. 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

15. ©2014 Sea-Bird Scientific Inc. 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

16. ©2014 Sea-Bird Scientific Inc. 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

17. ©2014 Sea-Bird Scientific Inc. Current instrument To create new instrument context:  click on ‘New’  Browse to folder with SIP files

18. ©2014 Sea-Bird Scientific Inc. Load SIP files Note: SIP file = zip file with all cal files

19. ©2014 Sea-Bird Scientific Inc. 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

20. ©2014 Sea-Bird Scientific Inc. Calibration file parameters Cal File Prefix SensorsInstrument Type Immersion Coefficients Measureme nt Mode Frame Type HEDEsReference/SASAirSurfaceShutterDark HSEEsReference/SASAirSurfaceShutterLight MPR*Tilt Press TProfiler/AncillaryWaterFreeFallLightAncCombi ned/ Anc HPEEdProfilerWaterFreeFallShutterLight PEDEdProfilerWaterFreeFallShutterDark HPLLuProfilerWaterFreeFallShutterLight PLDLuProfilerWaterFreeFallShutterDark BB2FFluorECO Series IOPNot Required[FreeFall Surface]Not Required

21. ©2014 Sea-Bird Scientific Inc. 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

22. ©2014 Sea-Bird Scientific Inc. 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)

23. ©2014 Sea-Bird Scientific Inc. Sensor position measurements Lu distance to surface Sea surface Lu sensor Ed sensor Atmospheric pressure Pressure Tare Ed 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

24. ©2014 Sea-Bird Scientific Inc. Sensor position measurements 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 IIEdLuECO Distance to Surface0.00.3160.264 Distance to Pressure0.7860.0

25. ©2014 Sea-Bird Scientific Inc. Sensor position measurements

26. ©2014 Sea-Bird Scientific Inc. Sensor position example Pressure Tare = pressure tare value from SatView + Ed distance to pressure Pressure Ed = measured pressure – Pressure Tare Pressure Lu = measured pressure – Pressure Tare + distance to surface Uncorrected pressure sensor reading = 10.886 m Atmospheric pressure = 10.1 m Ed distance to pressure = 0.786 Ed sensor is therefore at: 10.886 m – (10.1 m + 0.786 m) = 0 m Lu sensor is therefore at: 10.886 m – (10.1 m + 0.786 m) + 0.316 m = 0.316 m

27. ©2014 Sea-Bird Scientific Inc. 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

28. ©2014 Sea-Bird Scientific Inc. New parameters context Setup processing parameters Profile editing Dark correction Averaging Data filtering Level 4 settings

29. ©2014 Sea-Bird Scientific Inc. 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

30. ©2014 Sea-Bird Scientific Inc. Load raw data files

31. ©2014 Sea-Bird Scientific Inc. Processing complete!

32. ©2014 Sea-Bird Scientific Inc. 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

33. ©2014 Sea-Bird Scientific Inc. HDF viewer

34. ©2014 Sea-Bird Scientific Inc. Surface reference

35. ©2014 Sea-Bird Scientific Inc. Downwelling irradiance Save plot as image File -> Save As ->.png

36. ©2014 Sea-Bird Scientific Inc. Water leaving radiance

37. ©2014 Sea-Bird Scientific Inc. Chlorophyll a

38. ©2014 Sea-Bird Scientific Inc. Turbidity

39. ©2014 Sea-Bird Scientific Inc. PAR

40. ©2014 Sea-Bird Scientific Inc. 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

41. ©2014 Sea-Bird Scientific Inc. Questions Thank you