estimating primary productivity with wim/wam · 2010-12-13 · validating primary productivity...

Estimating Primary Productivity with WIM/WAM

•Please see \Course\4\Tutorial_Primary_Productivity.pdf on DVD or

•http://www.wimsoft.com/Tutorial_Primary_Productivity.pdf

•Ocean primary production (PP) is a crucial component of the Earth’s biogeochemical cycles of carbon and other major chemical elements. Net primary production (NPP, g C m-2 d-1), i.e. total primary production minus the losses due to respiration of the phytoplankton, provides the upper bound for production at higher trophic levels. In situ measurement of PP or NPP is extremely time-consuming and not representative of a larger area due to high spatial and temporal variability. Obtaining estimates of PP at regional and global scales are therefore very difficult to make without the quasi-synoptic view provided by satellite data or numerical models. In this tutorial we try several ways of estimating NPP with WIM/WAM.

© Wimsoft 2008 12/12/2010

http://www.wimsoft.com/Tutorial_Primary_Productivity.pdf

Primary Production MeasurementBiomass (Chl or Carbon)

↓

Rate of Carbon Fixed

（14C or 13C Incubation Method)In situ Method

SimulatedIn SituMethod

Photos by J. Ishizaka

12/12/2010 © Wimsoft 2008

12/12/2010 © Wimsoft 2008

Other NPP models may use different input, e.g. CbPM uses bb, K490, PAR,

GSM-Chl-a, MLD

Typical Satellite Primary Production Model, e.g.

Behrenfeld-Falkowski, 1997

Other NPP models may use different input, e.g. CbPM uses bb, K490, PAR,

GSM-Chl, MLD

Modified from J. Ishizaka

Chl.a(0)

Day Length (DL)

PA

R

Euphotic

Zone

(Zeu)

Integrated

Chl.a

Surface

Zeu

Dep

th

PP/Chl.a

PBopt

IPP

VGPM (Vertically Generalized Production Model)Behrenfeld & Falkowski (1997)

IPP : Integrated Primary

Production

・Behrenfeld&Falkowski(1997)

→Pbopt (7th Order Polynomial

of SST)

IPP = PBopt・ f[PAR(0)] ・ DL ・ Zeu ・ Chl.a(0)

J. Ishizaka12/12/2010 © Wimsoft 2008

Modified Behrenfeld and Falkowski (1997)

Two-Phytoplankton-Community Model

(Kameda and Ishizaka, JO-2005)

PPeu =

0.66125 PBopt [E0 / (E0 + 4.1)] Zeu Cz0 Dirr

PBopt = g (SST) B&F 7th order polynomial

PBopt = g (SST, CHL) K&I

CHL = CHLS + CHLL

Prod = ProdS CHLS + ProdLCHLL

J. Ishizaka12/12/2010 © Wimsoft 2008

Maximum Photosynthetic Rate per Chl-a (PBopt)

Temp. Dependent (Behrenfeld and Falkowski, 1997)

Temp. and Chl. Dependent (Kameda and Ishizaka, 2005)

12/12/2010 © Wimsoft 2008

GLI (April-June 2004)Chl-a – SST – PAR - Primary Production

12/12/2010 © Wimsoft 2008

Validating Primary Productivity measurements•Please see \Course\4\Tutorial_Primary_Productivity.pdf on DVD or

•http://www.wimsoft.com/Tutorial_Primary_Productivity.pdf

• Can use wam_match with NPP images but it’s an overkill to create global NPP datasets to validate some point measurements

•Copy \Sat folder from DVD to C:\

•Need input data:

• in situ NPP file qProdoPoint_2007.csv in\Sat\Merged\L4 with Lon, Lat, Date, Time, NPP (this is CalCOFI 2007 simulated on-deck NPP )

•List file list_calc_NPP_VGPM_L3_Merged.txt that specifies directories of satellite data and the in situ NPP file

• Satellite data corresponding to the list file

© Wimsoft 2008 12/12/2010

http://www.wimsoft.com/Tutorial_Primary_Productivity.pdf

Validating Primary Productivity cont.•If you have not done it yet, create Merged Daily Chl-a from corresponding SeaWiFS and MODISA daily datasets. Daily datasets typically miss lots of data due to clouds and swath coverage. As test, we can use Monthly data.

•Use data in SeaWiFS\L3\Daily\CHL_9 and MODISA\L3\Daily\CHL_9 or SeaWiFS\L3\Monthly\CHL_9 and MODISA\L3\Monthly\CHL_9 as inputcd C:\Sat

wam_composite_2sensors SeaWiFS\L3\Monthly\CHL_9\S2007*.hdf MODISA\L3\Monthly\CHL_9\A2007*.hdf

mkdir Merged\L3\Monthly\CHL_9

move M*.hdf Merged\L3\Monthly\CHL_9

**************************

wam_composite_2sensors SeaWiFS\L3\Daily\CHL_9\S2007*.hdf MODISA\L3\Daily\CHL_9\A2007*.hdf

mkdir Merged\L3\Daily\CHL_9

move *.hdf Merged\L3\Daily\CHL_9

© Wimsoft 2008 12/12/2010

Validating Primary Productivity cont.

•Contents of the list file (explain the naming of the file!) list_CalCOFI_VGPM_L3_2007_SWFAQU1_SWF1_MOD8.txt :

# 1 - Chl

C:\Sat\Merged\L3\Daily\CHL_9,?2007*9km.hdf

# 2 - PAR

C:\Sat\SeaWiFS\L3\Daily\PAR_9,S2007*9km.hdf

# 3 - SST

C:\Sat\Merged\L3\8day\SST_9,M2007*.hdf

# 4 - Points

C:\Sat\Merged\L4\qProdoPoint_2007.csv

--------------------------------------------------------------------------------------------

# means comment

Each line has path and matching filename pattern separated by comma

© Wimsoft 2008 12/12/2010

Validating Primary Productivity, cont.•Open command prompt, cd to C:\Sat\Merged\L4

• We will use:

• Aqua-SeaWiFS merged daily Chl-a - merged data has better coverage!

•SeaWiFS daily PAR - PAR can change rapidly due to clouds!

•Merged Terra-Aqua 8-day SST – will use 8-day to improve coverage as SST influence is rather weak

•Run:

wam_npp_point list_calc_NPP_VGPM_L3_Merged.txt VGPM

•Explain the number of files used: 364, 355, 46, 1

•Explain the output to screen

•Out file name will be list file name + _out.csv

•Rename the output file *.txt_out.csv to*.VGPM.csv

© Wimsoft 2008 12/12/2010

Validating Primary Productivity cont.

•Load output file into Excel, create new variables: LogInsitu and LogSat as LOG() of respective column

•Make plots of NPP-Sat versus NPP-in situ like in Tutorial

•Load output into wam_match, try to eliminate a few outliers

•You can try other NPP models; type wam_npp_point without arguments to see all available options

© Wimsoft 2008 12/12/2010

y = 0.5368x + 1.467R² = 0.5445

2.0

2.5

3.0

3.5

2 2.2 2.4 2.6 2.8 3 3.2 3.4 3.6 3.8

Log 1

0o

f N

PP

-Sat

Log10 of NPP-in situ, mg C m-2 d-1

Calculating Primary Productivity (images!)•Calculating Monthly NPP data; can be global or local at any resolution depending on the component satellite data• Earlier versions used exact list of images; now using a list file that specifies only the paths and patterns of component data•1st component image (e.g. Chl-a) is the primary image that specifies the outpoutresolution, wam_npp itself will find the best corresponding matching images in time, will remap if necessary•Contents of a sample list file list_calc_NPP_VGPM_L3_Merged.txt :

# path for Chl files, matching pattern#C:\Sat\Merged\L3\Monthly\CHL_9,*CHLO*.hdf# path for PAR files, matching patternC:\Sat\SeaWiFS\L3\Month\PAR_9,S*PAR*.hdf# path for SST files, matching patternC:\Sat\Merged\L3\Month\SST_9,M*.hdf

# means commentEach line has path and matching filename pattern separated by comma

© Wimsoft 2008 12/12/2010

Calculating Primary Productivity, cont.

• Open command prompt, cd C:\Sat\L4, run:

wam_npp list_calc_NPP_VGPM_L3_Merged.txt

•This will create 12 monthly NPP images of 2007 using VGPM model

•Type wam_npp without arguments to see available options

•Explain how to calculate NPP, based on OCTS Chl-a, SeaWiFS PAR and AVHRR Pathfinder SST

© Wimsoft 2008 12/12/2010

estimating primary productivity with wim/wam · 2010-12-13 · validating primary productivity...

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