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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.
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