BIOPHYSA PHYSICALLY-BASED CONTINUOUS

FIELDS ALGORITHMEcosystem, Climate and Carbon

ModelsFORREST G. HALL, FRED HUEMMRICHJoint Center for Earth Systems Technology (JCET)

NASA's Goddard Space Flight CenterGreenbelt, MD 20771

Derek PeddleLethbridge University

Alberta, Canada

David LandisSSAI

Lanham, MD

2005 Activities

• 2005 our first full year of activity• Initial test and development using

helicopter MMR (landsat 5 radiometer)– SNF 1983 data sets, 3 solar zenith angles

• Development of Landsat BIOPHYS• Processing of selected Landsat scenes• Biophysical structure and succession• Preliminary validation• Initiation of MODIS development and

testing

Satellites(spectral, angular, temporal)

si (Ωi)

CANOPY REFLECTANCE MODEL (LUTS)si= (LOP,BOP,Cg,LAIC,LAIb,CC)

Satellite Measurement (L2) si±∆ sii i bands, angles, dates

Table LookupLOP,BOP,Cg,LAIC,LAIb,CC k si±∆ si i

Compute Parameter Statistics<LOP,BOP, Cg ,LAIC,LAIb, CC> Ecosystem Parameters

, Fpar, gc, Zo, Pv,NPv=

F(<LOP,BOP, Cg,LAIC,LAIb, CC>)

Bio

ph

ys Fra

mew

ork

Nu

merica

l, Non-a

naly

tic

BIOPHYS CONCEPT

Band 1

Band 2

Band 3Canopy Reflectance M

odels

Zap!

Spectral Space

BioopticalParameter 1

Bio

popti

cal Para

mete

r 2

Biooptical P

aramete

r3

BiophysicalParameter

Space

BIOPHYS uses CRMs to map spectral space

Into bioopticalparameter space.

1

si (Ωi, Bi) =(LOP, BOP,Cg, h/w, LAIC, LAIb, CC)

si (Ωi, Bi) = Spectral SpaceΩi = view and illumination geometryBiooptical parameters Bi

LOP&BOP= leaf&background optical properties

Cg = Canopy geometryLAIC = Crown leaf area indexLAIb = Branch leaf area indexCC = fractional crown cover

Biophysical Parameter 1

Bio

ph

ysi

cal Para

mete

r 2

Biophysical P

aramete

r3

Carbon/Water/EnergyTransport Relations

Map Biooptical ParametersInto model Parameters, for example

Fpar = PARd – PARd*c - PAR *d τc +u*PARd*τc - *u PARd*τ2c (2) PARd

Model Parameterscanopy albedoFpar = Fraction of absorbed photosynthetically active radiationgc = bulk canopy conductancePv,NPv Fraction of photosynthetically and non-photosynthetically active vegetationLAI = Canopy leaf area index

Original GeoSail Reflectance LUT

BIOPHYS Landsat Processing Program:

Creating the “Averaged” Table

SELECT avg(green_lai),stddev(green_lai),avg(branch_lai),stddev(branch_lai),avg(fract_canopy_cover),stddev(fract_canopy_cover),avg(crown_h_w_ratio),stddev(crown_h_w_ratio) FROM boreal_gs_test2 WHERE (landsat_b2_refl_sza35 BETWEEN 1 AND 100) AND (landsat_b3_refl_sza35 BETWEEN 201 AND 300) AND (landsat_b4_refl_sza35 BETWEEN 1001 AND 1100);

SELECT avg(green_lai),stddev(green_lai),avg(branch_lai),stddev(branch_lai),avg(fract_canopy_cover),stddev(fract_canopy_cover),avg(crown_h_w_ratio),stddev(crown_h_w_ratio) FROM boreal_gs_test2 WHERE (landsat_b2_refl_sza35 BETWEEN 1 AND 100) AND (landsat_b3_refl_sza35 BETWEEN 201 AND 300) AND (landsat_b4_refl_sza35 BETWEEN 1001 AND 1100);

Sample SQL Query

New “Averaged” Reflectance LUT ASCII File

Create the Original LUTThe original data was created using the GeoSail model. The

biophysical parameters (Green LAI, Branch LAI, Fractional Canopy Cover, & Crown H/W Ratio) were

varied sequentially as input to the model. A reflectance for various SZA’s (30 to 70, in 5 steps) and Landsat Bands

(1 to 4) was then output from the model.

Create the “Averaged” LUTThe original MySQL table was then processed using a C program that runs a series of SQL commands and saves the results to a data file. These commands used SQL to

create averages and standard deviations for the biophysical parameters where the reflectance for bands 2, 3, and 4 were all within preset binned values (bin size was 100,

which is a 1% tolerance). It also creates “%counts” for the 4 cover types (aspen, spruce, ojp, yjp).This processing

took about 48 hours, but only had to be done once.

Keep the “Averaged” LUT As an ASCII FileThe resulting ASCII data file (with 15,000 records) was then

used by the image-processing program (next slide).

species green_lai branch_lai fract_cc hw_ratio r_b1_sza30 r_b2_sza30 r_b3_sza30 r_b4_sza30 r_b1_sza35 r_b2_sza35 r_b3_sza35

aspen 1 1 10 100 0.0523 0.0772 0.127 0.225 0.0523 0.0772 0.1269

aspen 1 1 20 100 0.0522 0.0772 0.1268 0.2251 0.0522 0.0772 0.1267

aspen 1 1 30 100 0.0522 0.0772 0.1266 0.2253 0.0522 0.0771 0.1265

aspen 1 1 40 100 0.0522 0.0771 0.1264 0.2255 0.0522 0.0771 0.1263

aspen 1 1 50 100 0.0522 0.0771 0.1262 0.2257 0.0522 0.0771 0.1261

aspen 1 1 60 100 0.0522 0.0771 0.1261 0.2259 0.0522 0.0771 0.126

aspen 1 1 70 100 0.0522 0.0771 0.126 0.2261 0.0522 0.0771 0.1259

aspen 1 1 80 100 0.0522 0.0772 0.1259 0.2264 0.0522 0.0771 0.1258

aspen 1 1 90 100 0.0523 0.0772 0.1258 0.2267 0.0523 0.0772 0.1258

aspen 1 1 100 100 0.0523 0.0773 0.1258 0.2271 0.0523 0.0773 0.1258

aspen 1 1 10 150 0.0522 0.0772 0.1269 0.225 0.0522 0.0772 0.1269

aspen 1 1 20 150 0.0522 0.0772 0.1267 0.2251 0.0522 0.0771 0.1266

aspen 1 1 30 150 0.0522 0.0771 0.1265 0.2252 0.0521 0.0771 0.1264

aspen 1 1 40 150 0.0522 0.0771 0.1263 0.2253 0.0521 0.077 0.1262

species green_lai branch_lai fract_cc hw_ratio r_b1_sza30 r_b2_sza30 r_b3_sza30 r_b4_sza30 r_b1_sza35 r_b2_sza35 r_b3_sza35

aspen 1 1 10 100 0.0523 0.0772 0.127 0.225 0.0523 0.0772 0.1269

aspen 1 1 20 100 0.0522 0.0772 0.1268 0.2251 0.0522 0.0772 0.1267

aspen 1 1 30 100 0.0522 0.0772 0.1266 0.2253 0.0522 0.0771 0.1265

aspen 1 1 40 100 0.0522 0.0771 0.1264 0.2255 0.0522 0.0771 0.1263

aspen 1 1 50 100 0.0522 0.0771 0.1262 0.2257 0.0522 0.0771 0.1261

aspen 1 1 60 100 0.0522 0.0771 0.1261 0.2259 0.0522 0.0771 0.126

aspen 1 1 70 100 0.0522 0.0771 0.126 0.2261 0.0522 0.0771 0.1259

aspen 1 1 80 100 0.0522 0.0772 0.1259 0.2264 0.0522 0.0771 0.1258

aspen 1 1 90 100 0.0523 0.0772 0.1258 0.2267 0.0523 0.0772 0.1258

aspen 1 1 100 100 0.0523 0.0773 0.1258 0.2271 0.0523 0.0773 0.1258

aspen 1 1 10 150 0.0522 0.0772 0.1269 0.225 0.0522 0.0772 0.1269

aspen 1 1 20 150 0.0522 0.0772 0.1267 0.2251 0.0522 0.0771 0.1266

aspen 1 1 30 150 0.0522 0.0771 0.1265 0.2252 0.0521 0.0771 0.1264

aspen 1 1 40 150 0.0522 0.0771 0.1263 0.2253 0.0521 0.077 0.1262

sza refl_bin2 refl_bin3 refl_bin4 grn_lai_av grn_lai_sd brch_lai_av brch_lai_sd frac_cc_av frac_cc_sd crwn_hw_rat_av crwn_hw_rat_sd

30 100 100 400 311 188 200 0 54 12 1558 122

30 100 100 500 354 180 184 26 68 17 1338 301

30 100 100 600 428 169 159 43 75 16 1201 378

30 100 100 700 502 144 131 53 79 16 1141 395

30 100 100 800 561 134 98 51 81 14 1169 376

30 100 100 900 590 118 64 36 84 12 1165 368

30 100 100 1000 620 108 33 24 85 9 1205 340

30 100 100 1100 635 93 8 11 87 4 1188 362

30 100 200 400 52 32 200 0 86 14 1179 386

30 100 200 500 132 78 195 14 84 18 922 424

30 100 200 600 233 156 160 29 77 19 962 428

30 100 200 700 372 73 87 26 52 9 1205 324

30 100 200 800 428 69 48 27 51 7 1200 261

30 200 100 500 276 48 196 13 56 6 1369 275

30 200 100 600 399 143 186 24 61 17 1332 384

30 200 100 700 445 150 150 43 73 19 903 496

30 200 100 800 453 152 119 46 84 15 807 478

30 200 100 900 473 147 91 41 88 13 767 444

sza refl_bin2 refl_bin3 refl_bin4 grn_lai_av grn_lai_sd brch_lai_av brch_lai_sd frac_cc_av frac_cc_sd crwn_hw_rat_av crwn_hw_rat_sd

30 100 100 400 311 188 200 0 54 12 1558 122

30 100 100 500 354 180 184 26 68 17 1338 301

30 100 100 600 428 169 159 43 75 16 1201 378

30 100 100 700 502 144 131 53 79 16 1141 395

30 100 100 800 561 134 98 51 81 14 1169 376

30 100 100 900 590 118 64 36 84 12 1165 368

30 100 100 1000 620 108 33 24 85 9 1205 340

30 100 100 1100 635 93 8 11 87 4 1188 362

30 100 200 400 52 32 200 0 86 14 1179 386

30 100 200 500 132 78 195 14 84 18 922 424

30 100 200 600 233 156 160 29 77 19 962 428

30 100 200 700 372 73 87 26 52 9 1205 324

30 100 200 800 428 69 48 27 51 7 1200 261

30 200 100 500 276 48 196 13 56 6 1369 275

30 200 100 600 399 143 186 24 61 17 1332 384

30 200 100 700 445 150 150 43 73 19 903 496

30 200 100 800 453 152 119 46 84 15 807 478

30 200 100 900 473 147 91 41 88 13 767 444

Load the Original LUT into MySQLThe GeoSail data file (with 2.5 million records) was loaded into a MySQL table. Then all values were turned into 2-byte

integers to match the Landsat file format: reflectances x 10,000 and 4 biophysical parameters x 100.

Initial Test Landsat (MMR), vis, nir 0.01)

16 Black Spruce sites3 solar angles (3 dates)

1983 Superior National Forest, MinnesotaSite Avg

DBH(cm)

SD DBH(cm)

Stems perm2

BasalFract

Avg BMI(kg/ m2)

SD BMI(kg/ m2)

Avg LAI SD LAI Tree Ht(ft)

Description

12 4.54 2.11 0.16413 0.00032 0.678 0.127 0.484 0.181 20 sparse, low black spruce

19 4.05 1.98 0.25564 0.00041 1.032 0.200 0.692 0.242 25 low black spruce

18 4.24 2.06 0.26062 0.00046 1.093 0.192 0.739 0.254 25 low black spruce

51 5.92 3.04 0.37799 0.00131 3.620 0.501 1.685 0.454 25 low density black spruce

56 8.09 4.29 0.25569 0.00168 5.280 0.345 1.834 0.329 medium density black spruce

102 5.92 2.34 0.91716 0.00292 7.246 0.736 3.670 1.228 50 high density black spruce

42 8.60 5.80 0.25863 0.00218 7.314 0.455 2.279 0.283 60 medium density black spruce

45 7.28 3.65 0.53387 0.00278 8.446 1.253 3.085 0.761 40 medium density black spruce

43 8.44 4.79 0.36305 0.00268 8.696 0.716 2.791 0.476 60 medium density black spruce

68 7.40 2.83 0.66002 0.00325 8.719 0.515 3.475 1.042 45 high density black spruce

48 9.83 3.19 0.33953 0.00285 9.149 1.665 2.700 0.795 50 medium density black spruce

52 9.92 3.91 0.35588 0.00318 10.036 0.574 3.034 0.588 60 low density black spruce

15 12.21 3.83 0.22381 0.00288 10.680 0.675 2.692 0.383 60 dense, mature black spruce

41 13.49 5.73 0.18303 0.00308 11.135 0.517 2.842 0.313 60 high density black spruce

2 14.52 4.43 0.17507 0.00317 12.378 0.830 2.884 0.340 50 dense, mature black spruce

14 13.22 4.13 0.24669 0.00372 13.643 0.587 3.266 0.427 60 dense, mature black spruce

SNF Landsat Analyses: Results• Landsat data acquired at

multiple solar view angles improved retrieval precision.

0.00

0.50

1.00

1.50

2.00

2.50

0 1000 2000 3000 4000 5000

Number of Retrieved Records

Standard Deviation Crown Green LAI

Max SZA

Min SZA

Max 2 SZA

Min 2 SZA

3 SZA

0.0

1.0

2.0

3.0

4.0

5.0

0.0 1.0 2.0 3.0 4.0 5.0

Measured LAI

Modeled Site Green LAI

• Mean of non-unique solutions appear to converge on actual mean

0

20

40

60

80

100

120

0.01 0.25 0.5 0.75 1 1.5 2 3 4 5 7

Site LAI

Counts

12

42

14

BIOPHYS Landsat Processing Program: Using the “Averaged” LUT, Logic-flow

DiagramNew “Averaged” Reflectance LUT ASCII file

repeat for each point in the 4 lines

repeat for each line in the 3 bands

Start

End

Output FilesOutput Files

Read in the file name and the SZA. Extract all records from the “averaged” ASCII LUT for

that SZA (about 1600 records) and store them in a 4D array “the_table[r2][r3][r4][c]” within

the program (the 3 major indexes are the 3 refl/100). This is the only time the program

accesses the LUT file.

Open the Landsat RAW files (bands 2, 3, & 4) and the QA file (if present).

Open 13 output files to write the results to: AV and STDEV for each of the 4 biophysical

parameters, NDVI, and 4 %cover files (aspen, spruce, ojp, yjp).

Read line Y of QA & band 2,3,4.

If no QA problem, use point X of line Y of each band (binned into values of 100, then

divided by 100) as an index number into the stored array “the_table[r2][r3][r4]” and

return the 1 unique array record that fits that combination of reflectances in those bands.

Store the 12 values from the array (AV and STDEV for the 4 biophysical parameters, 4

%counts) into the same point in the 12 output lines. Computer NDVI.

When all the values for this line Y are processed, write each of the 13

output lines to its open file.

Close all 13 output files, and the 3 input files. This processing takes

about 60 seconds total.

Landsat Image Files in RAW binary format

Landsat Image Files in RAW binary format crown_green_lai_av

RAW binary filecrown_green_lai_av

RAW binary filecrown_green_lai_sd

RAW binary filecrown_green_lai_sd

RAW binary file

crown_branch_lai_avRAW binary file

crown_branch_lai_avRAW binary file

crown_branch_lai_sdRAW binary file

crown_branch_lai_sdRAW binary file

fract_canopy_cover_avRAW binary file

fract_canopy_cover_avRAW binary file

fract_canopy_cover_sdRAW binary file

fract_canopy_cover_sdRAW binary file

crown_h_w_ratio_avRAW binary file

crown_h_w_ratio_avRAW binary file

crown_h_w_ratio_sdRAW binary file

crown_h_w_ratio_sdRAW binary file

sza refl_bin2 refl_bin3 refl_bin4 grn_lai_av grn_lai_sd brch_lai_av brch_lai_sd frac_cc_av frac_cc_sd crwn_hw_rat_av crwn_hw_rat_sd

30 100 100 400 311 188 200 0 54 12 1558 122

30 100 100 500 354 180 184 26 68 17 1338 301

30 100 100 600 428 169 159 43 75 16 1201 378

30 100 100 700 502 144 131 53 79 16 1141 395

30 100 100 800 561 134 98 51 81 14 1169 376

30 100 100 900 590 118 64 36 84 12 1165 368

30 100 100 1000 620 108 33 24 85 9 1205 340

30 100 100 1100 635 93 8 11 87 4 1188 362

30 100 200 400 52 32 200 0 86 14 1179 386

30 100 200 500 132 78 195 14 84 18 922 424

30 100 200 600 233 156 160 29 77 19 962 428

sza refl_bin2 refl_bin3 refl_bin4 grn_lai_av grn_lai_sd brch_lai_av brch_lai_sd frac_cc_av frac_cc_sd crwn_hw_rat_av crwn_hw_rat_sd

30 100 100 400 311 188 200 0 54 12 1558 122

30 100 100 500 354 180 184 26 68 17 1338 301

30 100 100 600 428 169 159 43 75 16 1201 378

30 100 100 700 502 144 131 53 79 16 1141 395

30 100 100 800 561 134 98 51 81 14 1169 376

30 100 100 900 590 118 64 36 84 12 1165 368

30 100 100 1000 620 108 33 24 85 9 1205 340

30 100 100 1100 635 93 8 11 87 4 1188 362

30 100 200 400 52 32 200 0 86 14 1179 386

30 100 200 500 132 78 195 14 84 18 922 424

30 100 200 600 233 156 160 29 77 19 962 428

%cover AspenRAW binary file%cover Aspen

RAW binary file%cover Spruce

RAW binary file%cover Spruce

RAW binary file

%cover OJPRAW binary file

%cover OJPRAW binary file

%cover YJPRAW binary file

%cover YJPRAW binary file

Computed NDVIRAW binary fileComputed NDVIRAW binary file

Check the QA bits for point X in line Y. If there is a problem, fill the LUT return array

values with “-99”.

BIOPHYS Landsat Output:Canopy Green LAI Average

BOREAS Region (p37 r22)Aug 12, 2001, SZA 45°

BIOPHYS Landsat Output:Canopy Green LAI St-Dev

BOREAS Region (p37 r22)Aug 12, 2001, SZA 45°

BIOPHYS Landsat Output:Fractional Canopy Cover Average

(%)

BOREAS Region (p37 r22)Aug 12, 2001, SZA 45°

BIOPHYS Landsat Output:Canopy Branch LAI Average

BOREAS Region (p37 r22)Aug 12, 2001, SZA 45°

BIOPHYS Landsat Output:Aspen Cover (%)

Note: this is actually the percent of retrieved solutions from the LUT that corresponded to this cover type.

Note: this is actually the percent of retrieved solutions from the LUT that corresponded to this cover type.

BOREAS Region (p37 r22)Aug 12, 2001, SZA 45°

~1990Landsat

~2000Landsat

1990-2000:

• 1.03 Mha burnt, logged (5.8% of area)• 0.89 Mha in early regrowth (4.9% of area)

LEDAPSActivity

Landsat 5Uncorrected

Landsat 5Corrected

Landsat 7Corrected

BIOPHYS AND A BOREALCHRONOSEQUENCE

0

1

2

3

4

5

6

7

0 20 40 60 80 100 120 140

Time Since Burn (Years)

Mean Crown Green LAI

0.00

0.20

0.40

0.60

0.80

1.00

0 20 40 60 80 100 120 140

Time Since Burn (Years)

Mean Fraction Canopy Cover

INITIAL MODIS INVESTIGATIONS

0

500

1000

1500

2000

2500

3000

3500

4000

4500

1 2 3 4 5

Number of Observations Used

Number of Retrieved Records

• MODIS pixels extracted from acquisitions for 16 day period during August 2001 over BOREAS Black Spruce Site

• Atmospherically corrected using MODIS aerosol product and 6s.

RESULTS• MODIS provided very

limited sample of BRDF• Retrieved parameter values

sensitive to view & illumination geometry

• Number of non-unique solutions decreased rapidly with number of angles used in retrievals

Day of Year (2001)

Overpass Time (UTC)

View Zenith Angle

Solar Zenith Angle

View Azimuth Angle from

Principle Plane

215 1825 9.6 37.3 118.4224 1820 1.2 40.1 92.8225 1905 48.2 39.5 112.3228 1755 31.3 42.5 56.1229 1840 25.5 41.0 115.3230 1745 43.5 43.9 55.1

What’s Next

• Complete exploratory work• Finalize RT Model (GOMS, GORT …) selection.• Build the LUTs• Run MODIS BIOPHYS Algorithm over selected

regions• Evaluate MODIS Products and Iterate

– PRODUCE PROVISIONAL DATA SETS WITH BIOPHYS OVER SELECTED STUDY REGIONS.

– PLACE PROVISIONAL DATA SETS ONLINE; INITIATE USER EVALUATION.