data processing of iop packages attenuation, absorption and backscattering c, a, b b ian walsh,...

Data Processing of IOP Packages

Attenuation, Absorption and Backscattering

c, a, bbIan Walsh, Ph.D.

Director of Science, Sea-Bird Scientific

• Review of IOP theory • Description of ac-s in-situ spectrophotometer

• ac meter protocol• Calibration overview

• Collecting data with WETview• Scattering• Correcting absorption data• Backscattering• NTU to Backscattering calibration conversion

I = I0 e-cz

Beer’s Law

particle

scatteredINCIDENT

absorbed

dissolved materials and water

scattered

particle

scatteredINCIDENT

absorbed

dissolved materials and water

scattered

c, attenuation coefficient (m-1)a, absorption coefficient (m-1)b, scattering coefficient (m-1)

Relationships:

c = a + bct = cpart + cdiss + cw

at = apart + adiss + aw

bt = bpart + bw

Components of Light Attenuation: Absorption and

Scattering

Measuring a and c: WET Labs ac-s

•Measures absorption (a) and attenuation (c)• Dual flow path design•Wavelengths from 400-730 nm with 4 nm resolution• 10 and 25 cm path lengths • 4 Hz sampling rate• 500 or 5000 m depth rating

filter wheel

Linear Variable Filters (LVFs)

Transmissometer

Collimatingoptics

Reflective tube

Air gap or reflective surfaceFlow cell cover

adapted from Zaneveld et al. 1992

Forward scattered light from ~0 to 41.7 degrees is included in the signal measured by the detector

Reflective Tube Absorption Meter

Design

ac-s Cross-Section

• Theoretical Uncertainty• ~0.0001 m-1 in waters with low attenuation

• Estimated Effective Uncertainty• ~0.002 to 0.005 m-1 in waters with low attenuation

• Wavelength dependent • nm needs longer integration time to achieve high

precision

ac-s Performance

LEGENDt - totalw - water - phytoplanktond - non-algal particlesp – particulate materialg – dissolved material

Clean Water:

Field and lab calibrations track instrument changes between factory services.

Follow WET Labs protocol document available on WET Labs website:http://www.wetlabs.com/sites/default/files/documents/acprotq.pdf

)()()()()()()()( gddwwt abababac

Calibrating ac-s:

Factory calibration defines cw

Water calibrations

Optically clean water

• Pre-use (lab) and regularly during field use

• Record values for ~30 s and average to obtain calibration values

• Replicate and track over time

For the most accurate measurements, calibrations are required to compensate for drift, i.e., scaling factors (F) vary over time.

Use deep or clean water to establish nominal cw:

Assume clean water values for particle components are low and constant in space and time

Use clean water values as additional offset in post processing

Field Calibration of ac-s

cmeasured

Define minimum at depth z

cmeasured

Adjust all profiles

Filter All Particles out of the Water

Use a 0.2 um or 0.4 um filterAssume absorption due to dissolved species is a constantWorks very well with underway systems

Calibrating with filtered water

cmeasured

“Dissolved” measurement

•0.2 micron pore-size filter on intake.

•High flow rates

•Pall Suporcap/Maxi-cap

•Pre-soak or flush with deionized water

•a and/or c, as bg = 0.0, cg = ag

•2 ac’s, or consecutive casts

•Results in reduced flow rate

•Mixing in filter smears gradients in ag

•Profiling: slow decent rate

•Must lag correct profile data

WETview Data Acquisition System

Click to OpenDevice File

ac-s should be connected and powered

Open Device File

Click to OpenDevice File

Device files are:

.dev for water

.cal for air

Open Device File

Directory will open at programlocation

Change location folder,e.g. calibration tracking or cruise data folder

Select Communication Port

Start Acquiring Data

Click to start collecting data

Data files are saved when you are done collecting data

Data View

Save Data

Directory will open at programlocation

Save Data

Change location folder,e.g. calibration tracking or cruise data folder

WETview Calibration

To start a calibration,Select Configure in the File menu

Start process after data variance is minimized. Save Data Set, then Configure

WETview Calibration

1. Stabilize signal2. Save data3. Auto Cal

WETview Calibration

1. Data Collection Counting

2. Save New Device File

WETview Calibration

Recommend using a date in the file name for tracking purposes

Note, do not overwriting the previous .cal or .dev files!

.cal files for air calibrations

.dev files for water calibrations

WETview Calibration

Data after the .cal file is used

Device File

Annotated Calibration File

ACS Meter 53000067 ; Serial number

3; structure version number tcal: 20.4 C, ical: 21.3 C. The offsets were saved to this file on 10/21/11.

0 0 ; Depth calibration 115200 ; Baud rate

0.25 ; Path length (meters) 79 ; output wavelengths 36 ; number of temperature bins

3.5823 4.381364 5.47061 6.492 7.472203C398.9 A400.9 8 1.76514 0.556434 -0.053294 -0.042208 -0.037851 -0.035375C403.7 A405.0 10 1.715154 0.680489 -0.048162 -0.037653 -0.031775 -0.031118C407.6 A408.9 11 1.655814 0.766596 -0.040607 -0.030697 -0.025398 -0.024145C412.1 A412.6 12 1.59409 0.819793 -0.035592 -0.026248 -0.021001 -0.019391C416.2 A416.9 13 1.524738 0.851991 -0.03086 -0.024106 -0.019847 -0.018846C421.0 A421.7 15 1.464843 0.872155 -0.024519 -0.018606 -0.015533 -0.014885C425.8 A426.3 16 1.418302 0.890925 -0.02176 -0.016814 -0.014411 -0.013019C430.4 A431.1 17 1.373411 0.907548 -0.018204 -0.014427 -0.012378 -0.012059C434.7 A435.2 18 1.327319 0.924527 -0.014153 -0.010815 -0.009802 -0.009154C438.9 A439.6 20 1.292539 0.940059 -0.01463 -0.010965 -0.009792 -0.008929C443.9 A444.2 21 1.262959 0.956568 -0.013204 -0.010061 -0.008488 -0.007745C448.6 A449.2 22 1.237 0.973888 -0.013317 -0.0099 -0.008602 -0.007673C453.8 A454.1 23 1.212657 0.991515 -0.013188 -0.009598 -0.008143 -0.007092C458.5 A458.9 LtBlue 1.187795 1.010199 -0.012065 -0.008582 -0.00727 -0.006473C463.3 A463.4 26 1.16446 1.029494 -0.011997 -0.008543 -0.006866 -0.006195C468.0 A468.4 27 1.150793 1.047945 -0.011844 -0.008555 -0.007142 -0.006498

NTU Calibration to Backscattering

The bead to formazin calibration relationship has been linked and conversion coefficients produced.

Wavelength NTU to Beta412 0.0099378440 0.0105935470 0.0097312488 0.0087152510 0.0073748532 0.0062665595 0.0041454650 0.0032033676 0.0029309700 0.0027272715 0.0026079720 0.0025677730 0.0024849880 0.0020546

Backscattering instruments with wide ranges for inland waters were supplied with NTU calibrations

Caution: these coefficients are only for ECO backscattering sensors, they do not apply to any other turbidity sensors

To convert the NTU scale factor to backscattering scale factor:

• NTU Scale Factor from characterization sheet:

NTU SF = 0.2427 NTU/count

For 700 nm

Multiply NTU SF by Beta conversion factor:

Beta SF = 0.027272 (m-1 sr -1 )/NTU * 0.2427 NTU/count

= 0.00662 m-1 sr -1

Wavelength NTU to Beta412 0.0099378440 0.0105935470 0.0097312488 0.0087152510 0.0073748532 0.0062665595 0.0041454650 0.0032033676 0.0029309700 0.0027272715 0.0026079720 0.0025677730 0.0024849880 0.0020546

Scattering correction of absorption

Pegau, et al., 2003, Ocean Optics Protocols for satellite ocean color sensor validation, Revision 4, Volume IV, NASA/TM-2003

•Error in reflective tube due to incomplete capture of scattered light

•Filtered absorption measurement correction not needed (bg = 0.0 )

• Methods

1. aTSm(715 nm) subtraction: null wavelength

2. Assume constant proportion of scattering (14% of b)

3. Variable proportion of scattering

• Iterative process

• Dependent on good calibrations

• Noisy data must be smoothed

• Compare between methods

• Use of dissolved ag to compute ap to check corrections

Method 1 – subtraction of NIR null wavelength

apg(l) = aTSm(l) – aTS

m(NIR) NIR ~ 710 750 nm

Assumptions:

•The shape and magnitude of the VSF is independent of l

•No absorption by any materials in NIR

•Scattering error the same for all wavelengths

Advantages:

•Allows for changes as a function depth and particle type

•Uses data from the a side only

Method 2 – Constant proportion of b

apg(l) = aTSm(l) – Y [cTS

m(l) - aTSm(l)]

Assumptions:

•The shape of the VSF is independent of l and type of particles

•Scattering error the same for all wavelengths

Advantages:

•Allows for changes as a function of depth, but not particle type

•If NIR channel is unavailable, or if no TS data available

varies from ~ 0.14 for predominately biological particles (open ocean) to 0.18 in waters where scattering dominated by suspended particles (Case 2).

Smooth b before correcting

Method 3 – varying proportion of b

apg() = aTSm() – NIR [cTS

m() - aTSm()]

Assumptions:

•Shape of VSF independent of

Advantages:

•Allows for changes as a function of depth and particle type

Disadvantage:

•Requires multiple measurements, thus easy to induce noise in absorption data. Smooth and b before correcting.

NIR should be between 0.07 and 0.35

NIR = aTSm(NIR) / [cTS

m(NIR) - aTSm(NIR)]

Data collection

•Strongly recommended to collect CTD data

•Provides hydrographic information for interpretation

•Needed for temperature and salinity corrections of ac data

•Data acquisition system – multiple instruments

•Control sampling and power

•Store, integrate, and real-time output of data

Processing steps

1. Apply instrument calibration

a. Factory Calibration

b. Field Calibration

2. Profiling: Lag offset

3. Apply temperature and salinity corrections

4. Scattering correction of total absorption data

5. Binning

6. Derived parameters

7. Quality control

Merge with CTD data

Profiling:

•Interpolation to ac-s resolution

•Time stamps of instruments

•Depth adjustment – pressure

•Binning or averaging?

•Depends on resolution you want

•Reduces the variability

Lag corrections• Profiling systems

• Lag between hydrographic data and ac data

• Flushing time of flow tube volume

• Function of tubing length, pump speed, flow rate

• Filter reduces flow rate, increases the lag

• Approaches to correct data

1. Direct: Measure flow rate in ac using flow meter

• Requires estimating the volume of the intake tubing, and the relative position of the intakes to the ac sample tubes.

2. Indirect:

• NIR dependence on temperature

• Multiple casts with different decent rates.

Temperature & salinity correction

Pegau & Zaneveld 1993

~0.003 m-1 deg-1

At 715 nm

-0.008

-0.006

-0.004

-0.002

400 500 600 700

Wavelength (nm)

~ -0.0002 m-1 PSU-1

Absorption and beam attenuation properties of pure water vary as a function of temperature and salinity. Must correct in relation to the properties of pure water at the time of calibration

SalinityTemperature

Temperature affects absorption NOT scattering (minimal)

Thus same affects on a and c

Salinity affects absorption AND scattering differently

Thus different affects on a and c

Temperature & salinity correction

•Calibration Temperature (Tt): pure water in flow tubes during calibration.

•Provided in device file from WET Labs

•Must measure the temperature during your pure water calibration

•Salinity (S): (recall that pure water = 0.0 PSU).

•Coefficients in:

Pegau, et al., 1997, Absorption and attenuation of visible and near-infrared light in water: dependence on temperature and salinity, Appl. Opt., 36(24): 6035-6046.

Binning

•Depends on application and desired resolution•You may want to bin BEFORE processing to simplify. •Independence of samples:

•Flow in ac not laminar. Takes one complete flushing time to obtain an independent sample. Increased flushing time with filtered measurements.•Between flow tubes (a and c). Two separate sample volumes. Occurrence of rare large particles in one tube and not the other.•At typical pump speeds, best resolution 0.3 m, or at least 2 seconds of data.

•Binning•Median: minimize the influence of rare particles, especially when using a and c measurements together.•Average: check sample distribution, normal?

data processing of iop packages attenuation, absorption and backscattering c, a, b b ian walsh,...

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