26-02-2013

Hyperspectral Remote Sensing Applications for Vegetation

(with special emphasis on Agriculture)

Shibendu S. Ray
Mahalanobis National Crop Forecast Centre, DAC, New Delhi 110 012 Space Applications Centre, ISRO, Ahmedabad 380 015 Email: shibendu.ncfc@nic.in
DST Sponsored Training Programme Hyperspectral Remote Sensing for Agriculture, February 1827, 2013, IARI, New Delhi

Introduction

Hyperspectral remote sensing deals with large number of narrow spectral bands over a contiguous spectral range Because of its ability to detect narrow absorption features hyperspectral data are related to specific vegetation physico-chemical characteristics, ocean biological constituents, soil physical and chemical properties, mineral composition and snow characteristics Because of presence of large number of bands, hyperspectral data needs different analysis approach

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Why Hyperspectral?
Absorption Spectra of Plant Pigments

Chlorophyll

Carotene

Why Hyperspectral?
Hyperion Data for Different Landcovers
0.50 0.40
Crops Habitation Plantation Soil Water

Reflectance

0.30 0.20 0.10 0.00 425 725 1025 1325 1625 1925 2225

Modipuram (U. P.)

Wavelength(nm)

~10 nm bandwidth
0.5 0.4 Crops Habitation Plantation 0.2 0.1 0 425 Soil Water 925 1425 1925

(As per IRS Bands)

0.3

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Data Sources
Hyperion Field Spectroradiometer
224 bands 400-2500 nm range Spectral Resol. 10/11 nm Spatial Resol. 30 m Swath 7.5 km

HySi/IMS-1
64 bands 400-950 nm range Spectral separation 8 nm Spatial Resol. 505.6 m Swath 129.5 km

350-1075 (2500) nm range Resol. 3nm (350-1000nm) 10 nm (100-2500 nm)

(Airborne Hyperspectral Imager)

AHYSI

Spatial Resolution : 3.5 m Spectral Range : 420-950 nm Number of Bands: 512 Spectral sampling interval: 1.2 nm

AIMS
Average Altitude: 6.473 km Spatial Resolution: 4.4 m Swath : ~1.6 km Spectral Range: 456-889 nm Number of Bands: 143 Band Width: 3.3-4.1 nm

CHRIS/PROBAVarious data set:

Land set has 18 bands 438-1035 nm range 6-10 nm bandwidth Spatial Resol. 17m Swath 14 km Multi-angular (5 angles)

Causes of leaf spectral characteristics

(from Jensen, 2000)

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Absorption features in vegetation reflectance spectra

Wavelength [nm] 430 460 640 660 910 1020 1510 1690 1940 Cause of absorption Electron transition Electron transition Electron transition Electron transition C-H stretch, 3rd overtone N-H stretch N-H stretch, 1st overtone C-H stretch, 1st overtone O-H stretch, O-H deformation Chemicals Chlorophyll a Chlorophyll b Chlorophyll b Chlorophyll a Protein Protein Protein, Nitrogen Lignin, Starch, Protein, Nitrogen Water, Lignin, Protein, Nitrogen, Starch, Cellulose Protein Protein, Nitrogen Protein Protein, Nitrogen

1980 N-H asymmetry 2060 N-H bend, 2nd overtone / N-H bend / N-H stretch 2130 N-H stretch 2180 N-H bend, 2nd overtone / C-H stretch / C-O stretch C-O stretch / C-N stretch 2240 C-H stretch 2300 N-H stretch / C-H stretch / C-H bend, 2nd overtone 2350 CH2 bend, 2nd overtone / C-H deformation, 2nd overtone

Protein Protein, Nitrogen Cellulose, Protein, Nitrogen

(Adapted from Curran, 1989; Lucas & Curran, 1999)

Canopy Spectral Profile

Spectral Profile of Vraious Kharif Season Crops
Paddy Sorghum 0.700 0.600 0.500 Maize Finger millet Cluster bean Lady finger Green gram Horse gram 0.400 0.300 0.200 0.100 0.000 300 Cowpea Dhaincha Sugarcane Cotton Pigeon pea Groundnut Soybean Sesamum 600 900 1200 1500 1800 2100 2400 Sunflower Castor

Reflectance

Wavelength (nm)

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Vegetation Indices

Vegetation Indices

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Red Edge

The red edge position (REP), also known as the red edge inflection point (REIP), is defined as the wavelength around 720 nm at which the first derivative of the spectral reflectance curve reaches its maximum value. When a plant is healthy with high chlorophyll content and high leaf area index (LAI), the red edge position shifts towards longer wavelengths (red shifts) while the shift is towards shorter wavelengths (blue shift) when the plant suffers from disease or chlorosis and hence low LAI.

show the spectral curves before and after this analysis is done using the software.

Continuum Removal

Figure 8.3 Spectral curve before and after continuum removal

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Hyperspectral Study of Pulse Crop

Objective: discrimination of pulse crop using hyperspectral data Area: Patha village, Mahrouni taluk, Lalitpur-Jhansi, UP (IFGRI)
Spectral profiles of Rabi crops - Lalitpur, UP

Chickpea Branching

LENTIL
0.7

PEA-FLOWERING

PEA-FLOW/POD

CHICKPEA-POD

CHICKPEA-BRANCHING

0.6

Chickpea Pod

0.5
Reflectance (%)

0.4

0.3

0.2

Lentil

0.1

0.0 325

375

425

475

525

575

625

675

725

775

825

875

925

975

1025

1075

Wavelength (nm)

Discriminant Analysis
Step 1 2 3 4 5 6 7 Wavelength Wilks F-Value 800 0.305 45.6 750,800 0.014 144.6 750,800,960 0.002 149.1 750,800,940,960 0.001 149.9 450,750,800,940,960 0.000 162.7 450,490,750,800,940,960 0.000 187.1 450,490,670,750,800,940,960 0.000 188.3

Pea Flowering

Pea Pod Formation

Crop Stage Discrimination

FCC Classified Simulated LISS IV

Data: Airborne HySI Crop: Sorghum 3 Stages Location: Visalpur Village near Ahmedabad

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Crop Stress Detection (Nitrogen)

0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 300 N0 N50 N100 N150 N200 N250 N300

Reflectance

400

500

600

700 Wavelength (nm)

800

900

1000

1100

7 levels of nitrogen applied to potato crop Lower level of nitrogen had low NIR reflectance and high red reflectance

Crop Stress Detection (Nitrogen)

1.6 1.5 N0 N50 N100 N150 N200 N250 N300

Red edge 740/720

1.4 1.3 1.2 1.1 1 0.65

0.7

0.75 SIPI

0.8

0.85

0.9

Best Bands were selected using Stepwise Discriminant Analysis, Principal Component Analysis and Band-Band Correlation (560, 650, 730 and 760nm) Many Narrowband indices evaluated for discrimination Red edge ratio and SIPI((R800 - R445)/(R800 + R680)) best for discrimination Similar analysis for disease detection and water stress discrimination

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Crop Parameter Estimation

(Development of Indices: Chlorophyll)
0.2 0.1

Chl a

Chl b

Total Chlorophyll
Indices Chl a Chl b Total Chl 0.53** 0.41* 0.33 Ratio based indices 0.63** 0.45* 0.51** 0.33 0.42* 0.25

Correlation coefficient

0 -0.1 -0.2 -0.3 -0.4 -0.5 -0.6 300

R750/R700 R750/R610 R750/R420

First derivative based ratios D740/D690 0.69** 0.50* 0.59** Second derivative based ratios Dd720/Dd680 0.63** 0.45* 0.53** Dd720/Dd750 -0.66** -0.47* -0.55**

500

700

900

1100

Wavelength (nm)

Correlation curves generated for potato leaf chlorophyll with reflectance & derivatives Bands selected for ratio, using peaks and troughs of correlation curves Red-edge importance was shown in derivative based indices

Crop Parameter Estimation

(Development of Indices)
1000

Leaf Nitrogen
0.75 0.7

900

800

0.65 0.6

700 0 -0.6 -0.65 500 -0.7 -0.75 400

600

400

500

600

700

800

900

1000

Correlation map of ratio based (all possible band combinations) indices with leaf nutrients Selection of ratios with high correlation Stepwise regression for best fit model (-0.373+2.634 r750/710; R2 = 0.551, F=31.9**)

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Canopy Reflectance Model

PROSPECT+SAIL
LEAF CHARACTERISTICS N, Cab, Cw PROSPECT Canopy Structure LAI, LAD Leaf Reflectance Transmittance Soil Reflectance

SAIL CANOPY REFLECTANCE

Measurement Characteristics (View & Sun Angle)

1.

2.

PROSPECT (leaf optical properties model) requires the leaf structure parameter N, the chlorophyll a,b content Cab (g/cm2), the equivalent water thickness Cw (g/cm2), and dry matter content (g/cm2) to simulate leaf reflectance and transmittance spectra in the optical domain. SAIL (Scattering by Arbitrary Inclined Leaves) is the canopy reflectance model, which computes canopy reflectance coupled with PROSPECT and using leaf area index (LAI) and leaf angle distribution (LAD), soil background reflectance.

PROSAIL Model Calibration & LAI Estimation

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PROSAIL Inversion Software (PRIS)

Hierarchical Calibration Inversion using GA

Neural Network Training

Inversion using NN

HySi/IMS-1
Specifications
64 bands; 400-950 nm range; Spectral separation 8 nm; Spatial Resol. 505.6 m; Swath 129.5 km

Crop Classification using HySI Data

Soil Parameter Estimation using HySI Data, PLSR Model and Ground Observation
Soil Parameter N P K SOC Sand Silt Clay RMSE 11.058 2.872 7.049 0.101 6.877 5.403 3.282 R2 0.838 0.963 0.862 0.830 0.848 0.833 0.801 RPD 10.509 6.809 4.062 6.730 6.234 5.252 9.532

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Remote Sensing of Crop Residue

Soil

Straw

Matured Wheat
Residue

LCA
7 6 5 4 3 2 1 0 RESIDUE STRAW MATURED SOIL

CAI
5 4 3 2 1 0 -1 -2 RESIDUE STRAW MATURED SOIL

LCA =100[2*R2.2 (R2.1 + R2.3)]

LCA: Lignin Cellulose Absorption Index CAI: Cellulose Absorption Index

Forest Species Classification

Study Area: Shoolpaneswar Forest Data Used: Hyperion Data of October Approach: Band Selection using PLSR technique, Different Classifiers

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Discrimination of Different Forest Classes

Forest Research Institute (FRI)

Isodata: 6 classes

FRI map

SAM: 6 classes

Mangrove Study
Avicennia alba Avicennia alba
1 0.9 0.8 0.7

Sonneratia caseolaris Sonneratia caseolaris

1 0.9 0.8

Reflectance

0.6 0.5 0.4 0.3 0.2 0.1

1130 1150
Adaxial surface Abaxial surface

Reflectance

0.7 0.6 0.5 0.4 0.3 0.2

Adaxial surface Abaxial surface

L = 0.001

L = 0.044

420

0.1 440 0 400

1440 470
600 800

2050

0 400

600

800

1000 1200 1400 1600 1800 2000 2200

1000 1200 1400 1600 1800 2000 2200

Wavelength (nm)
0.05

Wanelength (nm)

Rhizophora mucronata
Rhizophora mucronata
1 0.9 0.8 0.7

0.045
0.8 0.04 0.7 0.035

Leaf reflectance spectra Random leaves

95% confidence level

0.05 0.05 0.050.05 Aa random leaves 0.045 0.045 0.045 0.045 Rm random leaves Sc random leaves0.040.04 0.04 0.04 0.035 0.035 0.035 0.035

920

Reflectance

0.6 0.03

p-value p-value

Reflectance

0.5 0.025 0.4 0.02

0.03 0.03 0.030.03

0.025 0.025 0.025

p-value

p-value

0.6 0.5 0.4 0.3 0.2 0.1 400 0 400 600 800 1000 1200 1400 1600 1800 2000 2200
Adaxial surface Abaxial surface

550, 720, 1630, 1750 nm

1620

1640

L = 0.000

0.3 0.015 0.2 0.01

L = 0.003
99% confidence level

0.020.02 0.02

0.015 0.015 0.015

0.010.01 0.01 0.005 0.005 0.005
600 600 800 800 1000 1000 1200 1200 1400 1400 1600 1600 1800 1800 2000 2000

2070

2320

0.1 0.005 0 0 400 400

0 0 0 0 0 2200 400 400 600 8001000 1000 1200 1400 1600 1800 2000 1200 1400 1600 1800 2000 2200 1000 1200 1400 1600 1800 2000 2200 400600 800 600800 800 1000 1200 1400 1600 1800 200

Wavelength (nm)

Wavelength (nm)

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Mangrove Study
Avicennia officinalis vs. A. alba Canopies of Avicennia officinalis vs Avicennia alba
0.7 0.6

Sonneratia apetala vs. S. caseolaris Canopies of Sonneratia apetal vs Sonneratia caseolaris

0.7

L = 0.03

L = 0.004
0.6 0.5

Reflectance

Reflectance

0.5 0.4 0.3 0.2

A. officinalis A. alba

0.4 0.3 0.2

S. apetala S. caseolaris

400
0.1 0 400

2310

1540 580 550

600 800 1000 1200 1400 1600 1800 2000 2200

0.1 400 0 400

2080 2150

600

800

1000 1200 1400 1600 1800 2000 2200

Wavelength (nm)

Wavelength (nm)

Xylocarpus mekingensis vs. X. granatum

Canopies of Xylocarpus mekongensis vs Xylocarpus granatum
0.8 0.7 0.6

Nypa fruticans vs. Phoenix paludosa Canopies of Nypa fruticans and Phoenix paludosa
0.7 0.6

L = 0.011
1000 960

L = 0.019
1000

0.5

Reflectance

Reflectance

0.5 0.4 0.3 0.2

X. mekongensis X. granatum

0.4 0.3 0.2

970
N. fruticans P. paludosa

720

430
0.1 0 400

0.1

690
0 400
600 800 1000 1200 1400 1600 1800 2000 2200

600

800

1000 1200 1400 1600 1800 2000 2200

Wavelength (nm)

Wavelength (nm)

Mangrove Classification: Bhitarkanika

Overall accuracy (%) Decrease in accuracy (%)

100 90 80 70 60 50 40 30 20 10 0 196 148 98 96 88 79 63 56 39 23 8

30

Class 1
Decrease in accuracy (%)

Overall accuracy (%)

25 20 15 10 5 0

Pure/ dominant communities of Heritiera fomes Mixed communities of H. fomes (with Cynometra ramiflora, Aegiceras corniculatum, Rhizophora mucronata, etc.) Mixed communities Excoecaria agallocha Avicennia sp.) of (with

Class 2

Class 3

Class 4

Number of bands

Fringing stands of mixed Sonneratia apetala (with other landward species) Mixed communities of mangrove associates & salt tolerant grasses

Class 5

FCC

Minimum Distance

Spectral Angle Mapper

Support Vector Machine

Class 1 Class 2 Class 3 Class 4 Overall Accuracy = 65.39% Kappa Coefficient () = 0.59 75.28% = 0.69 97.97% = 0.97 Class 5 Others

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Wetland Vegetation Discrimination & Water Quality

In situ spectra of various wetland plant species 0.80 0.70 0.60
A E

Reflectance

0.50 0.40 0.30 0.20 0.10 0.00 325 375 425 475 525 575 625 675 725 775 825 875 925 975 1025 1075 Wavelength (nm) Phragmites Ipomoea Typha Cheda Nelumbo Nympheae Chara
A: Phragmites karka B: Typha angustata C: Cheda (local name) D: Ipomoea aquatica E: Nelumbo nucifera F: Nympheae stellata G: Chara sp.

AVERAGE SPECTRA OF WATER, CHILIKA LAGOON

0.80 0.70

Site-1
0.60

Site-2 Site-3 Site-4 Site-5 Site-6 Site-7 Site-8 Site-9 Site-10 Site-11

REFLECTANCE

0.50 0.40 0.30 0.20 0.10 0.00 -0.10 300

Site-1

Site-8

400

500

600

700

800

900

1000

1100

WAVELENGTH (nm)

Site-10

Site-6

Best Reflectance Ratio for Chlorophyll Estimation R713/R680 Correlation coefficient for Chlorophyll-a (0.659) and Chlorophyll-a+ Pheophytine (0.677)

Analysis of CHRIS/PROBA Data

Angular effects on Vegetation Indices
CVof Indices CV Indices
NDVI SR NDVI705 mSR705 mNDVI705 SAVI MSAVI2 OSAVI MCARI TCARI NPCI MCARI2 RdEdg ZTM PRI SIPI ARVI EVI RGRI
3

40 35 30
Percentage

25 20 15 10 5 0
1 2

Stages Of Wheat

Least anisotropy- SIPI and RGRI CV <5%. They are ratios of bands with similar angular effects and hence tend to cancel out the common effects. Maximum anisotropy for Red Edge, ARVI, MSAVI, MCARI etc Other indices showing less anisotropy- ZTM,NPCI and mSR705

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Analysis of CHRIS/PROBA Data

(a )
180 160 140 120 100 80 60 40 20 0 -20 -55.37 -36.77 +32.64 View angle () +53.31
442.2 660.6 751.3 490 674.1 780.2 529.8 696.9 871.4 551 705.9 894.6 569.6 712 909 630.9 741.1 1018

Earhead~Grain Formation

% Change in dnorm

LAI Vs VI
0.8

0.6

(b )
40 35 30 25 20 15 10 5 0 -5 -55.37
442.2 660.6 751.3

Earhead~Milking Stage
0.4
490 674.1 780.2 529.8 696.9 871.4 551 705.9 894.6 569.6 712 909 630.9 741.1 1018

% Change in dnorm

0.2

mNDVI705

NDVI705

MSAVI2

OSAV I

MCARI2

MCARI

NDVI

TCARI

mSR705

RdEdg

-36.77 View angle ()

+32.64

+53.31

-0.2

-0.4

(c )
60 50

Grain Formation~ Milking Stage

-0.6
442.2 660.6 751.3 490 674.1 780.2 529.8 696.9 871.4 551 705.9 894.6 569.6 712 909 630.9 741.1 1018

Vegetation Indices

% Change in dnorm

40 30 20 10 0 -10 -55.37

Graph showing correlation of LAI and vegetation indices computed using CHRIS/PROBA data.
-36.77 +32.64 +53.31 View angle ()

The Percent change in normalized distance from nadir between the reflectance of wheat crop in different stages, for non- nadir view angles

Spectral Analysis Software

An In-house developed software to analyze spectral profiles derived from spectroradiometer

Spectral Analysis

View Chart

Derivative Spectra

Data Smoothing

Continuum Removal

Red Edge Analysis

Averaging

Vegetation Indices

Chart

Chart

Chart

Simple Averaging

Broadband Conversion

Predefined Indices

Index Calculator

Chart

Chart

Chart

RGR I

NPCI

ARVI

SAVI

SIPI

ZTM

PRI

EVI

SR

-55 -36 0 55

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Development of Spectral Library

Plant Info displayed on GUI on the basis of Users Request

User
Send Request
1 7 Send request for Plant List of Natural Veg. Send req. for Plant List of Plantation Natural 3

SAC.mdb
6

Send Request

Vegetation Plantation Ornamental Plants

Vegetation Spectral Library GUI

Send req. for Plant List of Crops Send req. for Plant List of Ornamental

Plant List displayed

5

Spectral View General Info Vegetatio n Analysis

Spectral Details Observation Details Plant photograph

Select Plant name

Fig. 4. Graphic User Interface (GUI) and query modules of spectral Library

Optimum Band Selection

SOURCE OF WAVELENGTHS SELECTED VARIATION Rabi Season Crops 400,450, 480, 550, 660, 680 nm (4) Kharif Season Crops 400, 420, 450, 500, 550, 590, 600, (5) 610, 670, 660, 710, 730, 740, 760, 830, 940 nm Wheat Varieties (15) 370, 940, 770, 750, 1030 nm Mustard Stages (2) 400, 430, 480, 610 nm Cotton- Dates of 560,700 nm Sowing (2) Rice: Nitrogen 400, 440, 570, 710, 740, 760, 770, Treatments (5) 800, 930, 970 nm Rice: Phosphorus 640, 680 nm Treatments (5) Potato: Irrigation 540, 610, 630, 700,1000 nm Treatments (3) Soil Types (4) 420, 720, 770, 790, 850 nm WILKS F VALUE LAMBDA 0.000 85.5 0.001 86.3

6.32E-05 0.065 0.001 0.001 0.701 0.172 0.000

53.9 1568.2 22.5 3.4 8.16 319.6

Large Dataset Stepwise discriminant analysis

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Selected Narrowbands
Frequency of Bands

Frequency

0
370 400 420 430 440 450 480 500 540 550 560 570 590 600 610 630 640 660 670 680 700 710 720 730 740 750 760 770 790 800 830 850 940 970 1000 1030

Wavelelength (nm)

Integration of all outputs, Bands selected on the basis of frequency of occurrence 13 optimum bands in VNIR (400-1050 nm) region These included bands in violet (2), blue (2), green (1), red (3), red edge (2), NIR (2) and moisture sensitive NIR (1) region.

Optimum Bandwidth
1st Derivative of Reflectance at Different Bandwidth with offset First Derivative Spectra
0.04 0.03

First derivative (offset)

0.02 0.01 0 -0.01

3-nm 5-nm 15nm 25nm

-0.02 -0.03 400

10nm 20nm 30nm

500

600

700 Wavelength (nm)

800

900

1000

Data from nitrogen treatment of rice crop Original spectral resolution 3 nm, resampled to 1 nm Comparison of reflectance and derivative Integrated to 3, 5, 10, 15, 20, 25, 30 nm

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Optimum Bandwidth
Reflectance difference at peaks
Reflectance (%); Bandwidth (nm) Difference from 3 nm 3 5 10 15 20 Green Reflectance 13.0 13. 12.8 12.5 12 Maximum Difference -0 -0.2 -0.5 -1 Red Reflectance 2.5 2.5 2.6 2.7 2.5 Minimum Difference -0 0.1 0.2 0 NIR Reflectance 58.0 57.0 56.0 55.0 52.0 maximum Difference RMSE -- at varying -1.0 Bandwidth -2.0 -3.0 -6.0
0.2

25 11.8 -1.2 2.75 0.25 52.0 -6.0

0.06

30 11.3 -1.7 2.9 0.4 53.0 -5.0

RMSE(400-500,700-800,900-1000)

400-500 500-600
0.15

700-800 600-700

900-1000 800-900
0.05

0.04

RMSE at varying Bandwidth

0.1

0.03

0.02 0.05 0.01

0
5 10 15 20 25 30

Bandwidth

Optimum bandwidth required differed for different wavelength regions 700-800 nm region: ~5 nm, 600-700 & 800-900 nm: upto 15 nm; 400-500nm and 9001000nm: upto 25

Conclusion
All these studies have been carried out under Hyperspectral Remote Sensing Applications project of Space Applications Centre, in collaboration with large number of organizations including IARI. Narrowband data have shown higher potential in assessing crop stresses, vegetation type discrimination, and so on. It was also found suitable for more accurate bio-chemical and biophysical parameter retrieval

Various software and database have been developed for better interpretation of hyperspectral data.
Methodologies have been developed for selection of optimum bands and bandwidth for vegetation studies.

RMSE(500-600, 600-700, 800-900)

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