CLASlite

The Tropical Deforestation and Forest Disturbance

Monitoring User Friendly System

USERS GUIDE VERSION 2

Carnegie Institution for Science

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Following decades of scientific development, forest monitoring
with satellites should be an everyday activity for non-experts,
thus helping to improve environmental conservation, forest
management, and resource policy development.

CLASlite Team:

Gregory P. Asner, Principal Investigator

Guayana Paez-Acosta, Project Coordinator
John K. Clark, Technical Development Lead
David E. Knapp, Senior Programmer
S.R. Aravindh Balaji, Programmer

User Guide updated July 13, 2010.

For updated information on CLASlite and software, check the CLASlite website:
http://claslite.ciw.edu/

For technical assistance, e-mail: claslite_support@ciw.edu or post your comments

on CLASlite website Users Forum.

Department of Global Ecology

Carnegie Institution for Science
260 Panama Street
Stanford, CA 94305 USA

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 CLASlite Users Guide Content

Welcome to CLASlite Users Guide ................................................................................................ 4

User Agreement .............................................................................................................................. 5
I. The Science behind CLASlite .................................................................................................. 6
I.1 The tropical forest spectral library: ................................................................................ 6
I.2 Development, Testing and Validation of CLAS and AutoMCU....................................... 7
I.3 CLASlite Analysis ............................................................................................................ 8
Eleven Novel CLASlite Outputs: ........................................................................................... 8
CLASlite Use and Dissemination ............................................................................................ 9
I.3.1 Interpreting CLASlite Output Images ........................................................................... 11
II. Running CLASlite v.2 ..................................................................................................... 13
III. Potential and Limits of CLASlite .......................................................................................... 20
IV. Frequently Asked Questions FAQs .................................................................................... 22
V. Practicing with CLASlite: Case Studies ............................................................................... 27
V.1 Timber Extraction: Brazil (multi-image analysis) ....................................................... 27
V.2 Long Term Clearing: Hawaii (single image analysis) ................................................. 30
VI. Glossary ................................................................................................................................ 32
Appendix I: CLASlite Installation and Useful Links ..................................................................... 33
Appendix II: Image Preparation and Band Analysis for CLASlite .............................................. 35
Information for example imagery provided with CLASlite ................................................. 39
Appendix III: Journal references ................................................................................................. 41

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Welcome to CLASlite Users Guide

The Carnegie Landsat Analysis System Lite (CLASlite) is a software package designed for
highly automated identification of deforestation and forest degradation from remotely sensed
satellite imagery. CLASlite incorporates state-of-the-art research in remote sensing into a
simple, user-friendly yet powerful tool specifically designed and licensed for use by non-profit
academic, non-government, and government organizations of tropical forest Nations.

This guide provides the user with information on CLASlites scientific background and steps on
how to use it, as well as keys for interpreting its outputs and for understanding its potential use
and limitations.

We hope CLASlite contributes to your organizations forest monitoring efforts, and as a result,
helps to strengthen regional forest monitoring capacities at large, which is needed for improved
global environmental management.

For further information and questions regarding CLASlite, feel free to contact us by e-mailing
claslite@ciw.edu

The CLASlite Team at the Carnegie Institution

Gregory Asner is a faculty member in the Carnegie Institutions Department of Global Ecology
and in the Environmental Earth System Science Department at Stanford University. Greg is the
original developer and lead for CLAS, CLASlite and the AutoMCU projects.

Guayana Pez-Acosta is the project coordinator for the CLASlite capacity-building program;
Guayana coordinates the design, planning, and training activities for the CLASlite user
community.

John Clark is a remote sensing technician and the CLASlite technical development lead. John
interfaces user needs with technical development and provides training and technical support to
the CLASlite community.

David Knapp is a senior staff programmer and image processing specialist; Dave leads the
algorithm implementation and satellite data processing for CLAS and CLASlite.

Aravindh Balaji is a programmer for the CLASlite project; Aravindh leads the development of
the graphical user interface and processing environment for CLASlite.

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User Agreement
Installation and use of the CLASlite software indicates that the User fully accepts all conditions
stated below:

Carnegie Landsat Analysis System lite, version 2

The Carnegie Institution of Washington (Carnegie) is a private organization that has, with private
funding, developed the Carnegie Landsat Analysis System Lite (CLASlite) for tropical forest mapping.
It is the intention of Carnegie to work with third parties in the dissemination and use of CLASlite for the
purpose of conducting environmental studies and monitoring. The purpose of this User Agreement is to
protect Carnegies Proprietary Information and to insure the proper handling of data and information in
studies involving the use of CLASlite.

Accordingly, by installing the CLASlite software, the User agrees to the following:

1. The CLASlite software, including all executable and supporting digital files and libraries, remains
the property of Carnegie, and shall not be reproduced or provided to any other party for any
reason without previous and written approval by Carnegie. Any effort to use CLASlite in an
unauthorized way or to reproduce any portion of the CLASlite software is prohibited.

2. CLASlite software, and any results obtained from the use of CLASlite, are to be used for non-
profit purposes only and shall not be used for any commercial or for-profit purposes.

3. Any reports, presentations or publications by the User containing data from a CLASlite analysis,
or resulting from such data or study, will be accompanied by an appropriate acknowledgement of
CLASlite and any involved CLASlite personnel, including, if appropriate, designation of such
personnel as co-authors.

4. Use of CLASlite results in reports or publications requires proper citation of CLASlite and the
Carnegie Institution of Washington. In addition, the following supporting organizations should
be acknowledged: The Gordon and Betty Moore Foundation and The John D. and Catherine T.
MacArthur Foundation.

5. The Carnegie Institution makes no warranty as to the quality and/or accuracy of any data obtained
by the User pursuant to any CLASlite study, or the suitability of any such data for any purpose.
The User assumes all risks and liabilities in the collection, interpretation and use of any data or
results obtained using the CLASlite program. The User will indemnify Carnegie against any
claims or damages resulting from the Users use of CLASlite as provided herein.

6. Upon Carnegies request, the User will return to Carnegie all copies of any Proprietary
Information and CLASlite materials which may have been provided to, or used by, the User in
connection with its performance of any CLASlite studies.

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 I. The Science behind CLASlite

CLASlite is the result of more than a decade of biophysical remote sensing research and
fieldwork that provides an automated satellite mapping approach to determine one of the most
important components of tropical forest structure: fractional cover of vegetation canopies, dead
vegetation, and bare surfaces. These fractional covers are core determinants of ecosystem
composition, physiology, structure, biomass, and biogeochemical processes. Fractional cover
analysis lies at the heart of CLASlite, making it a powerful, stable and biophysically-grounded
tool that allows rapid forest monitoring with error tracking.
Some of the major developments that have made CLASlite possible today are:

I.1 The tropical forest spectral library:

Until recently, there were a limited number of spectral signatures of green and senescent
vegetation and bare substrates for tropical regions. These spectral signatures are the information
needed to convert satellite image pixels to ecologically relevant information that people can
readily understand and use. The spectral library for tropical forest signatures encompasses the
general variation in canopy and soil properties, and was developed using a combination of field
spectroradiometers and specialized hyperspectral satellite imagery, both of which were collected
and analyzed during a series of field studies conducted from 1996 to 2003 (Asner et al. 2003a,
2004a, 2005).

There are three generic, nearly universal spectra libraries created for CLASlite. Live vegetation
is technically referred to as Photosynthetic Vegetation (PV) because live vegetation maintains
unique spectral properties associated with leaf photosynthetic pigments and canopy water
content. The dead or senescent vegetation fraction is termed Non-photosynthetic Vegetation
(NPV), which is expressed in the spectrum as bright surface material with spectral features
associated with dried carbon compounds. Finally, bare substrate is often dominated by exposed
mineral soil, but can also be rocks and human-made infrastructure (e.g. brick).

For the tropical forest spectral library used in CLASlite, both the bare substrate and NPV spectra
were collected via ground-based spectroscopic measurements using field spectroradiometers
(Analytical Spectral Devices, Inc., Boulder, Colorado). The bare substrate library incorporates a
diverse range of mineral soil types, surface organic matter levels and moisture conditions. The
NPV spectra library includes surface litter, senescent grass, deforestation residues (slash), and
other dry carbon constituents collected from a wide range of species and decomposition states.

In contrast to bare substrate and NPV, the PV spectra of forest canopies require overhead
viewing conditions, which is difficult with trees ranging in height from 5 meters to more than 50
meters. Spectral measurements of individual leaves, stacks of foliage, or partial canopies (e.g.,
branches) introduce major errors in spectral mixture models requiring canopy-level information
(Asner 2008). To develop a canopy-level spectral library for CLASlite, PV spectral data were
collected using the Earth Observing-1 (EO-1) Hyperion sensor (Ungar et al. 2003), which is the
first spaceborne imaging spectrometer launched by NASA for environmental applications.
Hyperion data were collected over many tropical forest control sites in Brazil in 1999-2000,

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providing more than 40,000 spectral observations made at 30-m resolution (Asner et al. 2005).
These hyperspectral data were atmospherically corrected to reflectance and convolved to the
spectral channels used by Landsat 4, 5, and 7, the Advanced Land Imager (ALI), ASTER, SPOT-
4 and -5 sensors, and MODIS in CLASlite. As a result, these data include the variable effects of
intra- and inter-crown shadowing, common in tropical forests (Asner and Warner 2003). In total,
the spectra represent more than 230,000 field and spaceborne spectrometer observations.

I.2 Development, Testing and Validation of CLAS and AutoMCU

The Carnegie Landsat Analysis System (CLAS) was developed as an expert system for national-
level mapping of tropical deforestation and forest disturbance, including selective logging (Asner
et al. 2005, 2006). CLAS includes a core sub-model called the AutoMCU, or Automated Monte
Carlo Unmixing (Asner and Heidebrecht 2002, Asner et al. 2004), that provides quantitative
analysis of the fractional or percentage cover (0-100%) of live and dead vegetation, and bare
substrate within each satellite pixel (e.g., within each 30 x 30 m pixel in a Landsat image).
The tropical forest spectral library provided the spectral reflectance bundles required by the
AutoMCU sub-model: pv( ), npv( ), and substrate( ) [Box I.1]. The AutoMCU is a probabilistic
approach based on canopy physics (Asner 1998) to deconvolve each image pixel into these three
constituent cover fractions, PV, NPV and bare substrate.

Testing and validation of CLAS Box I.1: The AutoMCU is based on an

In 2005, CLAS was used for the first time
over a large area (Asner et al. 2005),
analyzing 480 images from 1999 to 2002 of
the states of Par, Mato Grosso, Rondonia,
Roraima and Acre. In these initial studies,
CLAS was used to map selective logging,
with a conservative estimate of errors
ranging from 11-14%.
In 2007, 80% of the Peruvian Amazon was
analyzed from 1999 to 2005 using CLAS,
yielding forest cover, deforestation and
forest disturbance rates at 30 m spatial
resolution. Uncertainties in deforestation
and forest disturbance detection were 0.5%
and 9.0%, respectively, evaluated by an
independent Peruvian field team (Oliveira et
al. 2007). The core technology of the CLAS
change-detection algorithm was improved
with optimized, automated versions of the
atmospheric and haze correction and the
water- and/or cloud-masking processes of
the AutoMCU (Asner et al. 2004).
algorithm developed for forest, savanna,
woodland and shrubland ecosystems (Asner
1998, Asner and Lobell 2000, Asner and
Heidebrecht 2002), which was later modified
for tropical forests (Asner et al. 2004, 2005).
The method uses three general spectral
endmember bundles, derived from
extensive field databases and satellite
imagery, to decompose each image pixel
using the following linear equation:
pixel = Ce e] + = [Cpv pv +
Cnpv npv + Csubstrate substratel] +
where e is the reflectance endmember
library (e) at wavelength and is an error
term. Solving for each sub-pixel cover
fraction (Ce) requires that the satellite
observations ( pixel) contain sufficient
spectral information to solve a set of linear
equations, each of the form in equation (1)
but at different wavelengths ( ).

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 I.3 CLASlite Analysis

CLASlite is a subset of the larger CLAS processing system. It builds off many of the core
modules within CLAS that facilitate high-resolution forest cover analysis.
In contrast to CLAS, the CLASlite approach was redeveloped and streamlined to increase
automation and user friendliness. Two of the core sub-models continue to be the AutoMCU
(Automated Monte Carlo Unmixing) and the 6S (Second Simulation of the Satellite Signal in the
Solar Spectrum) atmospheric correction method (Vermote et al. 1997). The AutoMCU provides
sub-pixel quantitative analysis of the percentage cover of live and dead (or senescent) vegetation
and bare substrate, while the 6S is applied in a unique approach to atmospherically correct
CLASlite imagery using observations from the NASA Terra MODIS sensor.

Eleven Novel CLASlite Outputs:

Calibrated Reflectance Image, providing spectral bands calibrated from raw data to
apparent surface (top-of-canopy) reflectance. The number of bands varies by sensor (e.g.
Landsat: 6 reflectance bands; SPOT: 4 bands, etc.).
3 Fractional Cover Images, indicating the presence of live vegetation (technically, PV),
dead vegetation (technically, NPV) and bare substrate (B) at a sub-pixel level (e.g., sub-30 m
resolution in Landsat imagery or sub-20 m resolution in SPOT-4 imagery).
3 Uncertainty Images, for each image described above, another image is provided that gives
the uncertainty of the PV, NPV and B images for each one, totaling 3 more images. Here, all
values of uncertainty are given as standard deviations of the mean percentage cover from the
initial three bands described above. The higher the number, the more uncertain that
CLASlite was in estimating PV, NPV or B in that pixel. These three uncertainty images are
helpful for locating areas in the image that have suspicious results. Uncertainty can be
caused by clouds and cloud shadows, water bodies, atmospheric haze (e.g., from fires),
unique land features, extreme terrain, and other issues.
Total Error Image shows the total error for CLASlite image. Total Error is expressed as
Root Mean Square (RMS) error. A pixel with a low Total Error indicates that CLASlite
solution is probably good, whereas a high Total Error suggests that the solution was not good
and should either be discarded or used with caution. Total Error image is a final check of the
accuracy of the CLASlite results.

Forest Cover Image, mapping forest cover from a single image.

Deforestation and Forest Disturbance Image, detecting change between two or more
images taken of the same geographic area over time. This multi-image analysis is the most
accurate approach for detection of forest loss (deforestation), gain (secondary regrowth) or
degradation (areas of forest disturbance).

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CLASlite Use and Dissemination CLASlite is a sufficiently general yet
discriminatory method that identifies
In 2007 CLASlite v1.0 was developed forest changes
from super computing and programming
into a lite software package. In 2008, 1
CLASlite was ready for use by non-profit 1. It accommodates changes in forest without being
institutions, and first training sessions overly sensitive to variation in forest type, architecture

Makes maximized use of imagery

were conducted in Peru with and species composition: Auto MCU
2. It allows for correction of atmospheric effects, yet has

Is available to the broader forest

approximately 18 institutions, including, room for a degree of uncertainty in atmosphere

monitoring user community

non-governmental organizations and composition at the time of data acquisition.

available
academic institutions. CLASlite v2.0 is 3. It works with a wide variety of satellite sensors and
therefore Carnegies newest effort; the imagery: LANDSAT (4, 5, 7), MODIS, SPOT (4,5), ASTER, 2
3 ALI
tool includes new functionalities and 4. From the technology perspective: it provides
supports a wider range of satellites (for automation of method, applicable to a standard desktop
details See Table I.2) computer, and is designed to be readily learned by an
entry level technician.
Currently, the goal is to foster CLASlite 5. From the capacity building perspective: its
transference to government, academic and transference is based on a knowledge sharing process
accompanied by timely and effective technical
non-government institutions of the Andes assistance to support the understanding of the tool.
and Guiana Shield regions.
Figure I.2 The goal has been providing a rapid and reliable system for
mapping of forest cover, deforestation and degradation.

Table I. 2 Carnegies Systems for Forest Analysis

Software requirements CLASlite V.2.0 CLASlite V.1.0 CLAS

Remote sensing expertise of
Low Low High
user
Frequency of time-series for Annual time-
Selectable Single image
analysis series of images
Hours Hours
Processing time Days-to-Weeks

PC (processor
x86 (32 bits)), PC (processor
Windows XP x86 (32 bits)),
Operating system and Vista, 4 GB Windows XP, 2 Super computers
hard disc, 1 GB GB hard disc, 1
RAM). GB RAM)

Software functionalities
Image calibration and pre- Full Full Full
processing implementation implementation implementation
Image atmospheric Full Full Full
correction implementation implementation implementation
Analysis of forest cover at Full Full Full
sub-pixel resolution implementation implementation implementation
Analysis of live vs. dead Full Full Full
vegetation cover implementation implementation implementation
Cloud and cloud shadow Partial Partial Full
masking implementation implementation implementation
Pattern recognition for
Full
detailed mapped of logging No No
implementation
operations
LANDSAT 4, 5,
7, ASTER, ALI, LANDSAT 4, 5,
Satellites supported LANDSAT 5, 7
MODIS, SPOT- 7, ASTER, ALI
4, SPOT-5
Satellite images processed Several
One Hundreds
per use (up to ten)
Forest change detection Yes No Yes
Forest cover mapping Yes No Yes
Image viewer Yes No No

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Fig. I.3 CLASlite Processing System

Box I.2: The CLASlite Processing System incorporates: (i) radiometric calibration and
atmospheric correction of satellite data; (ii) deconvolution of image pixels into sub-pixel fractional
cover of live forest canopy, dead or senescent vegetation, and bare substrates; (iii) cloud and water
masking; and (iv) classification of the imagery into forest/non-forest, deforestation and forest
disturbance. See Figure I.3. These processes are arranged in 6 steps explained in Section II: Running
CLASlite.
Images sources supported: Landsat 4 and 5 Thematic Mapper (TM), Landsat 7 Enhanced Thematic
Mapper Plus (ETM+), Advanced Spaceborne Thermal Emission and Reflection Radiometer
(ASTER), Earth Observing-1 Advanced Land Imager (ALI), Satellite pour l'Observation de la Terre
4 (20 m color) and 5 (10 m color) (SPOT), and the Moderate Resolution Imaging Spectrometer
(MODIS). Along with the raw imagery, information on geographic location and basic sensor
settings is required, both of which are provided in the satellite ephemeris data often stored in the
image header information.

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I.3.1 Interpreting CLASlite Output Images

Reflectance Image Bands Analysis

After an image has been converted to apparent surface reflectance in Step 2, the image can be
viewed in Freelook to the see the reflectance profile of each pixel. In the figure below, bands 5,
4, 3 (RGB) are displayed for the reflectance of the Landsat-7 example image.

If you place your cursor over a

.
forested pixel, you can see a spectral
profile of that pixel by selecting
OptionsZ Profile.

In the spectral profile, the X axis

represents the band number and the
Y axis represents reflectance (%
times 100). In figure I.4, you can
see that the vegetation has a NIR
(band 4) reflectance of more than
30%, while the red reflectance (band
3) is only 2%. This difference
between the NIR and red reflectance
is characteristic of vibrant
vegetation. The line between these
two bands is called the red edge.

You can also see that in the visible Red Edge

bands (1, 2, and 3), this pixel is
brighter in the green (band 2) than in
Visible
the blue and red (bands 1 and 3, Bands
respectively). This is why
vegetation looks green to the human
eye
Fig. I. 4 Band Analysis pixel reflectance profile
In a pixel that has little to no
vegetation, you can see that the NIR
reflectance is lower and the Red
reflectance is higher than in
vegetated pixels. The typical form
that we saw in the vegetation with
peaks at bands 2 and 4 does not exist
in the spectrum of this pixel,
indicating that there is less
vegetation.

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 Fractional Cover Image Bands Analysis

After the fractional cover image is produced, one can look at it in Freelook as a 3-band color
composite.

CLASlite Team typically displays

band 1 (Bare) in red, band 2 (PV) in
green, and band 3 (NPV) in blue.

If we select Options Cursor

Location/Value, we can see the values
of the 3 fractions in percent. In the
example below, the pixel has 4%
.
Bare, 96% PV, and 0% NPV. The
sum of these percentages will be close
to 100, but because of rounding, they
might not sum to exactly 100. These
This indicates
three values that wefractions
are the mean can be
from theconfident in the
30 iterations thatability of the
were run on
fractions
this pixel. to reproduce the
Fig. I. 5 Band Analysis pixel fractional cover profile
reflectance of the pixels specit
In the next example pixel, which is
much redder in appearance, the
fractions are 35% Bare, 40% PV, and
27% NPV. The next 3 bands in the
image (bands 4, 5, 6) contain the
standard deviation of the respective
fractions. If we look at a Z profile of
the pixel, we can see a plot of the
values of all 7 bands of the fractional
cover image. In this example, bands
1, 2, and 3 are the values that we saw
earlier from the cursor value/location.
We can see that the standard
deviations of the fractions (bands 4, 5,
and 6, respectively) show that the
deviation from the mean was very
small for the 30 iterations, indicating This indicates that we can be confident in the ability of
that the solution for the 3 fractions the fractions to reproduce the reflectance of the pixels
was very consistent. spectra. If the RMSE were high, as it typically is for
The RMSE (band 7) is also relatively clouds and other features for which CLASlite was not
low, indicating that the spectral profile intended, then we should be suspicious of the fractions
that was created from the AutoMCU for that pixel. For this reason, the RMSE is used to mask
analysis was very close to the actual out pixels that are contaminated by water, clouds, and
spectra of the pixel. other undesirable features.

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 Fractional Cover Image, Compiled Deforestation and Forest Disturbance Maps, and
Forest Cover Map

Images below show the fractional cover (Fig. I.6) of the three components of tropical forest
structure, which depending on percentages (Table I.3) indicate forest condition. Further analysis
based on decision three criteria (Table I.4) allows identifying deforestation and disturbance via the
multi image mode (Step 4) and forest cover via the single image mode (Step 5) (Figures I.7 and
I.8, respectively)
Table I. 3 % of Fractional Cover and relation to
forest condition
Primary Disturbed
forest or forest or Deforested
Fractional cover
late woody area
image
secondary areas
forest
Live vegetation 90%-
0-80% 0-10%
(LV or PV) 100%
Dead vegetation
0-10% 60-70% >80%
(DV or NPV)
Bare substrate 0-5% 0-20% >10%
Fractional cover
~ 100% ~ 100% ~ 100%
at sub-pixel level

Fig. I.6 Fractional Cover Image

Table I. 4 Fractional cover value in % of PV, NPV, S

(X0 X1 before and after images)
- Used to generate Deforestation and Forest Disturbance
(Multi-image mode) & Forest Cover Mapping (Single-
image mode) -
Fig. I.7 Deforestation (left) and Disturbance (right) Images - Multi-
Deforestation - Multi Image Mode image mode

((PV0 > 60%) AND

((-100% < PV1-PV0 < -40%) and (NPV1-NPV0 > 4%))) OR
((NPV0 < 30% and S0 < 15%) and (PV1 80% and NPV1 > 20% and S1 0%)
and (PV1-PV0 < -9% and NPV1-NPV0 > 15% and S1-S0 > -99.9%))
Disturbance - Multi Image Mode

(PV1-PV0 -40%) AND

(PV0 > 80% and NPV0 < 25% and S0 < 15%) AND
(PV1 < 85% and NPV1 > 15% and S1 < 7%) AND
((PV1-PV0 < -6% and 7% < NPV1-NPV0 < 14% and S1-S0 -1%) or
(PV1-PV0 < -7% and NPV1-NPV0 > 13% and S1-S0 < -1%))

Forest cover - Single Image Mode

Fig. I.8 Forest cover mapping. Single
PV 80% image mode

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II. Running CLASlite v.2

Before running CLASlite, the user should have completed task 1 CLASlite Installation and
task 2 Image Preparation, as referred in Appendix 1 (CLASlite Installation), and Appendix 2
(Image Preparation), respectively.

To start CLASlite, click on the shortcut for the

CLASlite_v2 on your desktop. The IDL Virtual Machine
panel will appear. Click Continue. The CLASlite welcome
panel will then appear followed by the main CLASlite
work panel.

After the image data have been formatted properly, the data
could be run through either a single step procedure (Auto
Run Image Analysis) or a double step procedure (Calibrate
Satellite Images and Generate Fractional Cover Map).
Both options are equipped with processing multiple images
at the same time.

In addition to this, CLASlite v.2 is loaded with two

additional steps to determine the forest cover (Map Forest
Cover) and change in the forest cover (Map Forest
Change). All of these steps could be accessed from the
main panel of CLASlite v.2 as shown to the left.
Figure II.1 Main panel of CLASlite v.2

Step 1 would initially calibrate the satellite images based on the metadata; perform atmospheric
correction followed by masking of clouds and water bodies. It also has an option of correcting
haze present in the image. After pre-processing of the image, a spectral mixture analysis is
performed on it to determine the soil, live vegetation and dead vegetation content. This would
help the user to deduce the amount of vegetation present in the given image sample.

To perform only the calibration of satellite images, step 2 could be chosen with raw geolocated
satellite images. Similarly, in order to perform only the spectral mixture analysis of reflectance
images, step 3 could be run.

Step 4, Map Forest Change, is provided to determine the scale of deforestation and disturbance
that has occurred over a given region through the years. This step comes along with the option
for mapping the magnitude of deforestation and disturbance that has occurred over time. For
users having just a single image, step 5 provides a quick approach to estimating the amount of
forest present in a given region. Both steps 4 and 5 require images that have been processed by
CLASlite.

Step 6 is an option to provide the users with an additional masking in order to minimize the
problems caused by clouds, atmospheric haze, water bodies and other artifacts common to
satellite imagery.

14
In steps 1, 2 and 3 we also provide the user an option to populate the parameters with the
predefined values. This option would be helpful mainly in the case when the user has more than
one image to process at the same time. Instead of entering the data values individually for each
image, the user could load a predefined table with all the necessary values. Examples of such
tables are provided in the example data folder on the CLASlite ftpwith the names book_autorun,
book_refl, book_frac. The values in the table should be comma separated and arranged in a
specific order. The first line in the table should be the label name. In the following lines the user
enters the data values.

For all steps, except 5, the user would be

required to enter the directory of his/her input
file and output files. In step 5, the user would be
required to enter the input image file and the
output image will be automatically placed in the
directory where the input file is.

Each of these steps is described in detail in the

following pages. The output of these steps is
also shown, using an example Landsat7 image
from the Peruvian Amazon (Figure 2.1).

Step 1: AutoRun Image Analysis

This step is essentially a combination of the
satellite image calibration and the fractional
cover map generation. The user is expected to Figure II.2 Typical Landsat-7 image showing Peruvian
provide the input data file along with its forest in greens and cloud contamination in white
metadata and an output file to which the
fractional cover map would be written into. The reflectance image would be given the input
filename with _refl appended to it at the end. The AutoRun Image Analysis comes along with
the options like:
Process multiple files.
Store the fractional cover image file in ENVI / TIFF format.
Haze correction.
Supports LANDSAT 4,5,7, ALI, ASTER, MODIS, SPOT

In the case of MODIS, the input image would be the reflectance image.

On choosing the AutoRun Image Analysis option, the user would be asked to choose the number
of images to be processed. This step comes with a maximum option of 4 images. The user is
then expected to enter the input filename and its corresponding metadata for each image.

Input Image File: Enter the raw image that you prepared for use in CLASlite v.2. This file
can be in ENVI or GeoTIFF format. The input file must have geo-referencing information
in a UTM projection, WGS-84 ellipsoid. (Note: MODIS data is usually an 8 day composite
reflectance image. Hence the input image file would be the corresponding reflectance
image)

15
 Center Latitude: Enter the center latitude of the image, in decimal degrees. Use positive
values to indicate Northern hemisphere and negative values to indicate Southern
hemisphere.

Center Longitude: Enter the center longitude of the image, in decimal degrees. Use
positive values to indicate Eastern hemisphere and negative values to indicate Western
hemisphere.

Scene Center Date: Enter the date of the image acquisition. Enter the day, month, and year
using leading zeros when necessary. For example, to indicate February 1, 2007, enter
01022007.

Scene Center Time: Enter the time of the scene acquisition (UTC), entering hours and
minutes, without any separator. For example, to enter 21:03 UTC, simply enter 2103.
UTC is Universal Time Coordinated, which is the same as Greenwich Mean Time (GMT).

Scene Center Elevation: Enter an approximation of the elevation of the land in the image,
or the elevation of the part of the image in which you are primarily interested. The value
entered should be in units of meters above mean sea level.

Satellite: Select the satellite that collected the image. Choices are: Landsat 4, Landsat 5,
Landsat 7, ALI, ASTER, SPOT-4, SPOT-5, and MODIS. See Section 3 for information on
each satellite.

Proc. System: If your input image is from Landsat 7, select the processing system that
created the input image. The choices are NLAPS or LPGS. Consult the metadata of your
image or the Landsat 7 Data Users Handbook. See the FAQs for more information.

Gain Settings: If your image was acquired by Landsat 7, you will need to select the gain
settings for bands 1-5, and 7. In order to determine the correct radiance from the image,
CLASlite needs to know if each band was collected at the low or high gain setting. Click
Gain Settings and select L or H (for low or high) for each band. Typically, all bands will
have the high gain setting, except for band 4. However, for the particular example image
from Figure 1, all bands were collected at the low gain setting.

Output Image File: Enter the desired name of your output fractional cover image.
After entering the inputs for a given image, click Save for storing the values for the
corresponding image. To change the value for any image, click on the corresponding
button and then hit Previous to load the previous values entered for the corresponding
image. After making the necessary corrections, click Save again to store the values.

Upon completion of entering the metadata for all the images click Run. CLASlite create each
reflectance image followed by applying the spectral mixture analysis on it to generate the
fractional cover image.

The following figure shows the various panels that would help the user to generate the output
image.

16
 Figure II.3 Widgets used in Auto run Image Analysis and Satellite Image Calibration

Step 2: Satellite Image Calibration

Satellite Image Calibration is an embedded step in the AutoRun Image Analysis. Like the
previous step, this also requires the user to provide the data files along with its metadata, the one
difference being that, instead of the fractional cover map, the reflectance image is written into
the output file. The following are the underlying steps in the calibration.
From the metadata and the input image file, the potential areas of clouds and water bodies
are identified.
If haze correction option is chosen, the input image is corrected for one. (This might
make the image to look a bit brighter)
The radiance image is then calculated and based on the metadata values; atmospheric
correction is performed on it using 6S.
Reflectance image is then calculated with the identified water bodies and clouds masked
out.

17
This step comes with batch processing, haze correction and it supports LANDSAT 4,5,7, ALI,
ASTER and SPOT.

Step 3: Fractional cover map generator

The second half of the AutoRun Image Analysis is the fractional cover map generator which is
based on the Automated Monte Carlo (AutoMCU) algorithm. The AutoMCU is used to
determine the photosynthetic vegetation, bare soil and the non-photosynthetic vegetation from
the reflectance image. Based on the satellite, the output from the algorithm is then suitably
scaled. In certain cases, the scaling might result in the masking of desired regions. To overcome
this limitation, the user would be required to perform an additional scaling / threshold on the
fraction cover image. To facilitate this process, an image viewer is embedded into this step
which would display the image with a certain RMS (Root Mean Squared) threshold value
applied to it. The user is expected to vary this value to obtain an acceptable representation of the
fractional cover map.

Figure II.4 Fractional Cover Map Generator

For this particular example image, when the RMS error threshold is set to 800, the resulting
image is masked more appropriately, limiting the masked areas to cloud, cloud shadows, and
water. This iterative masking approach allows the user to control the amount of cloud shadow
that is left unmasked in the image. The user may re-run the adjustment as often has he or she
likes, iteratively adjusting, viewing the results, and readjusting. After the user selects Accept,
any additional changes will need to done by re-running Step 4 from the beginning. In summary,
it is highly advantageous to minimize any cloud and cloud shadow by masking in order to get the
best final product, since the algorithms used in CLASlite are sensitive to anomalies caused by
these artifacts. This iterative masking and re-masking step allows the user to control this final
output from CLASlite.

Step 4: Forest Change Map (Multi-Image Analysis)

The forest change map is used to determine the amount of deforestation and disturbance that has
occurred over a region during a period. The user is expected to input at least two fractional
cover images sharing some common area. Compiled deforestation and disturbance maps are

18
then calculated and created, with each year of deforestation and disturbance color coded for
easier identification. While these colors are not displayed in ENVI Freelook, the raster outputs
maintain value classification corresponding to a pixels year of forest change.

Step 5: Forest Cover Map (Single Image Analysis)

The last option in the main menu is used to determine the amount of forest in a given fractional
cover image. This option might be useful to estimate the forest cover in a given region. The
output image is written into the same directory of the fractional cover image file with a filename
of the input file appended at the end with forest_cover_map.

Figure II.5 Widgets used in Map Forest Change and Map Forest Cover

Step 6: Additional LANDSAT Masking

This step is provided as an option to the user to mask out values in the reflectance image based
on the associated thermal image using data from Landsat 4, 5, or 7. In order to make it more
comfortable for the user to read in the coordinate values of a thermal image, a viewer is
provided. On selecting Step 6 enter the values as follows:

Sensor: Select the satellite sensor that collected the image.

Input Raw Image: Enter the original raw input image. This is the same file that you entered as input
in Steps 1 / 2.

Input Reflectance Image: Enter the reflectance image that was created in Step 2.

Input Thermal Image: Enter the name of the file containing the thermal image. This thermal image
must have the same number of pixels and lines as the Input Raw Image.

Cloud Thermal Threshold: Set the thermal threshold to an appropriate DN in the thermal band so
that anything below that threshold will be masked out of the data. Each image will have a different

19
thermal threshold based on the temperature of the land surface and the atmosphere. However, a
thermal threshold of 125 to 160 is advisable for better results.

Output Masked Reflectance Image: Enter the desired name of the output masked
reflectance image. This is the image that will be used to generate a fractional cover map in
Step 3.

Figure II.6 Additional LANDSAT Masking

III. Potential and Limits of CLASlite

1. The power of CLASlite rests in

its unique ability to convert
seemingly green carpets of
dense tropical forest cover found
in the basic satellite images into
highly detailed maps that can be
readily searched for
deforestation, logging and other
forest disturbance events such as
natural tree falls and storm
damage.

2. It does not provide a final map, but a set of ecologically meaningful images identifying
forest cover, deforestation and disturbance that can be readily analyzed, processed and
presented by the user.

3. Areas where clearing, logging and other forest disturbances have recently occurred are
accentuated and easily identified by CLASlites algorithms.

4. Both deforestation and secondary forest regrowth can be tracked by the CLASlite user.
Deforestation is clearly shown as a loss of forest cover, producing bare substrate and NPV.
Regrowth can be tracked by a careful accounted of forest recovery following clearing,
which must be previously mapped.

20
5. While the software alone cannot distinguish types of disturbance (anthropogenic vs.
natural), CLASlite allows the user for the first time to classify disturbance in a rapid,
automated fashion.

6. Its not a tool for direct biodiversity monitoring. It can assist in reaching conclusions
regarding biodiversity from forest presence or absence and disturbance, but it has not been
designed for the purpose of direct biodiversity (species) monitoring.

7. Field verification of CLASlite output image is recommended if forest monitoring is

conducted as basis for on-the-ground project development and execution.

8. The capability for detecting disturbance or deforestation from a single image should be
used with caution. Disturbance and deforestation are based on a change in condition from
one time period to another. Although patterns of deforestation or disturbance can be
inferred from a single image, a human interpretation of the results is necessary. Therefore
anything detected as disturbance or deforestation from a single image should be used as a
guide to further investigation and validation. Using a pair of images to detect disturbance
and deforestation is better than relying on a single image.

9. In detecting forest change, the multi image analysis should use images from the same time
of the years considered, preferably from the same month. Otherwise changes in forest
phenology might affect CLASlites capability for forest change detection.

10. The haze correction is designed to homogenize the effects of haze that may exist in parts
of the image. If haze is evenly distributed across the image, the haze correction will be less
effective. It provides the most benefit by averaging out the effects of haze across the entire
image.

11. Despite being a highly automated tool, the Box III.1: CLASlite demand from User
user needs to become familiar with CLASlite
output images. Type of disturbance Dedication Demanded

Deforestation, without
Requires little training.
subsequent secondary
Its easily identifiable
forest regrowth
Areas of selective logging
and heavy forest Requires some training
disturbance
Areas of very little Requires in-depth
disturbance, and even training and additional
small tree-fall gaps time

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IV. Frequently Asked Questions FAQs

1. I am having trouble installing CLASlite what can I do?

Start by checking that you are using Windows XP or Vista on a 32-bit machine. This is a
requirement for CLASlite. Next, send your problem to the claslite_support@ciw.edu e-
mail; we will answer as soon as possible.

2. How does variable terrain affect the CLASlite analysis?

In general, there is little effect of varying terrain on CLASlite results unless shadows are
cast by mountains or hill slopes onto the forest canopy. At that point, CLASlite results
can be unreliable. Fortunately, the error images provides in standard CLASlite output
provide a means to easily locate, assess and discard areas where mountain shadows have
created uncertain results. However, in varying terrain where the terrain remains generally
well illuminated, the Monte Carlo Unmixing (AutoMCU) core module is able to soak
up or accommodate terrain variability, allowing for a good result.

3. How would riverine forests vs. inland forests be shown in the CLASlite output
image, would there be any clearly identifiable difference?

Riverine forests often have higher bare substrate or NPV fractions because river
inundation either damages the forest or deposits sediments in these forests. It is typical to
see yellow colors in a bare-PV-NPV composite image from the fractional cover mapping
step yellow indicates mixtures of bare and PV. In addition, the pattern of forest canopy
cover (PV) is usually visually distinct from upload terra firme forests: the riverine
forests often have a striated appearance due to fluvial dynamics.

4. I dont have the metadata what can I do?

In some cases, the metadata for an image may be unavailable or incomplete. A common
type of metadata that may be lacking for Landsat-7 imagey is the gain settings. In most
cases for tropical forest, the only two gain settings for Landsat-7 will be with all 6 bands
having the high gain setting (i.e., HHHHHH) or with only band 4 having the low setting
(e.g., HHHLHH). The option for different processing systems (NLAPS or LPGS) for
Landsat data is not critical, but knowing this can produce a slightly better reflectance
image. Please refer to the webpage http://landsathandbook.gsfc.nasa.gov/handbook/
handbook_htmls/chapter12/htmls/level1_differences.html for more information. If you
cannot find the processing system, we recommend using the default, NLAPS.

For further information about metadata and image preparation, please review the
document, Pre-CLASlite Preparation, available on the CLASlite website.

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5. How many bits per pixel are supported by CLASlite?

The type of data required of the input to CLASlite varies, depending on the satellite. For
example, for Landsat data, the values should be 1 byte per pixel. Please refer to
Appendix II (Data Preparation) for details of how the data for the various types of
satellite data should be formatted for CLASlite.

6. How is the atmospheric correction done to CLASlite images?

CLASlite ingests raw satellite imagery and applies sensor gains and offsets to derive exo-
atmospheric radiance for each image band. The radiance data are then passed to a fully
automated version of the 6S atmospheric radiative transfer model (Vermote et al. 1997)
to derive apparent surface reflectance for each spectral band. The 6S model requires a
number of inputs which include an estimate of aerosol and water vapor. These
parameters are held in geographic look-up tables derived from the NASA MODIS 1-
degree atmospheric products. Coordinating the MODIS aerosol and water vapor data
with the high resolution satellite being processed by CLASlite is done on an automated
basis. CLASlite uses the latest version of 6S (http://6s.ltdri.org/) which supports
Landsat-4, 5, and 7, as well as ASTER, ALI, and SPOT. CLASlite does not do
atmospheric correction on MODIS land imagery because those data are already processed
to surface reflectance in the 8-day composite product (MOD09A1).

7. For what years does CLASlite have atmospheric data available for atmospheric
correction? What happens if I process an image from a year for which CLASlite
does not have atmospheric data? Will this affect my results?

CLASlite contains MODIS aerosol and water vapor data from 2000-present.
Atmospheric data is updated and made available to CLASlite users monthly. If you
process an image from a year in which CLASlite does not have atmospheric data,
CLASlite will automatically select the closest, previous data set for use in atmospheric
correction. Because aerosol and water vapor data are derived from monthly means,
atmospheric correction with data from a different year creates a sufficiently accurate
reflectance image for application of the Auto-MCU, a robust, probabilistic approach.

8. What file formats does CLASlite support?

CLASlite supports files in both ENVI format and GeoTIFF. Files in either format can be
processed by the tool in any step. Additionally, the user has the option to save any
resulting file in either format. The default file format for CLASlite results is ENVI.
ENVI images consist of two files, one without an extension, the image file, and a second
with the extension .hdr, an ancillary information file containing necessary spatial
information about the image. Both files are necessary, but the file without an extension is
the file that is loaded into CLASlite or ENVI Freelook. ENVI files can be opened in both
ENVI and ERDAS, while GeoTIFFs are a more universal format.

23
 When saving a CLASlite result in GeoTIFF format, it is important that the user defines
the output filename without an extension. Selecting the option, "Save result as
GeoTIFF," will add the appropriate extension to the resulting file. If the user adds an
extension to the output filename, CLASlite will not recognize the output file and will
show an error at the end of the process.

9. Is it possible to use CLASlite for UTM zone 17S?

CLASlite now supports all imagery in the UTM projection.

10. I have an ASTER image that is not working well. What should I do?

Its possible that the radiance and reflectance images were not created with the the correct
gains and offsets. ASTER images have a number of different gain settings that require the
user to apply them using his or her own image processing software (ENVI, ERDAS, etc.).
Please refer to Appendix II to see how to find the gain settings of your data and apply
them before using the imagery in CLASlite.

11. Would CLASlite explain common errors?

Most of the error messages are displayed during their occurrence. In most cases, the user
would be brought back to the stage previous to the error occurrence for them to rectify
their errors. However, there might be cases wherein error messages would be displayed
and on accepting those, CLASlite would shut down. In such cases the user would have to
rerun the process again. Some of the common error messages that occur are:

"Attempt to subscript CUMU_TOTAL with MAXINDEX is out of range"

This error occurs when the user chooses to apply Linear 2% stretching on a piece of
chosen area which has more zero valued pixels. The linear 2% stretching depends on the
histogram and since most of the values are zero, histogram stretching would not be
performed. The users are advised to avoid selecting areas with more zero valued pixels
and apply linear 2% stretch on it.

Number of bands does not match the requirement. The different satellite/sensor images
used in CLASlite depend on the number of bands in each. Refer to Appendix II: Image
Preparation and Band Analysis for CLASlite Use for further information.

12. Is it possible to perform the multi image analysis combining images from different
satellites?

You can perform multi image analysis on images from different satellites as long as the
pixel resolution is the same.

24
13. What should be the overlap area between images in order to perform a multi-image
analysis? When would the non-overlapped area be too large as to make the analysis
non-acceptable?

In order to perform multi-image analysis on a set of MCU images, there is no specified

maximum limit but all the images to be compared must at the least have one pixel in
common.

14. When in multi-image mode, what happens if I have variation in the amount of time
between images?

You can input as many images as you wish. If the timestep is annual or more frequently,
then your deforestation and disturbance maps produced by CLASlite will be closer to
gross rates of change. If your images were collected more than a year apart from one
another, then the deforestation and disturbance maps produced by CLASlite will
represent longer-term, net rates of change. It is up to you to interpret the forest changes
mapped by CLASlite you need to consider if you are seeing gross or net changes. Net
forest change can miss forest regrowth, canopy recovery, disturbance, and other
processes that may occur between image dates. Gross forest change resolves all forest
gains and losses as they occur.

15. Why does CLASlite not support Landsat MSS?

In the past, we have decided not to support Landsat MSS since the instrument is noisy.
However, if there is overwhelming demand for MSS data, we will consider supporting it
in an updated version of CLASlite.

16. How much error in the image-to-image registration is allowable by CLASlite?

Currently, the multi-image analysis feature in CLASlite requires the user to co-register
his/her imagery during the image preparation step to one (1) pixel uncertainty.

17. Does CLASlite v.2 support 64-bit Windows?

Yes, but you must install IDL for 32-bit machines first so that CLASlite can run in the
32-bit IDL environment.

18. How did the CLASlite team decide on the decision criteria for forest cover,
deforestation and disturbance?

These criteria are based on practical experience with CLASlite in humid tropical forest
settings in Brazil, Peru, Madagascar, Borneo and Hawaii. However, we provide the
fractional cover values (from Step 3) to the user so that he/she can create decision criteria
that best suite his/her needs. Personalized decision criteria can be implemented using
third-party software such as ENVI, ERDAS Imagine, or ArcGIS.

25
19. Can CLASlite run mosaics of satellite imagery?

Yes, you can process a mosaic, but you must have enough computer memory to allow it.
It is generally advisable to run CLASlite on individual images and then mosaic the MCU
results.

For other error messages specific to certain conditions, refer to our website
http://claslite.ciw.edu or mail us at claslite_support@ciw.edu

26
 V. Practicing with CLASlite: Case Studies
V.1 Timber Extraction: Brazil (multi-image analysis)

I. Problem Statement
Many forested landscapes in the Amazon are undergoing rapid changes from industrial and
illegal logging activities, clearing for cattle pasture and crops, and biofuels development.
Tracking these changes through time is challenging, but CLASlite provides an easy approach to
monitor forest cover loss and recovery from both deforestation and forest degradation.

The eastern Brazilian Amazon is considered one of the oldest frontiers for land-use change. A
region south of Belm in the State of Par, known as Fazenda Cauaxi, is located along the Rio
Capim. Cauaxi has a history of light deforestation, but major logging activities moved into the
region in the late 1990s, opening this area up for increased human activities. Here, we focus an
exercise on how to use CLASlite to monitor selective logging and forest degradation in the
region.

II. Analysis
This exercise involves processing four Landsat-7 (ETM+) images through CLASlite and creating
image output that identifies deforestation and disturbance. The four images that we will use in
the exercise are from the following dates and Landsat path/row coordinates:

Path/Row Date
223/063 13-July-1999
223/063 31-July-2000
223/063 03-August-2001
223/063 07-September-2002

1. Image Preparation
Before running CLASlite, you must first prepare your images. Using the image processing or
GIS software of your choice, co-register the images so that they match up to within +/- 1 pixel of
one another. This ensures that any observed changes in forest cover and disturbance between the
images are the result of an actual change in the forest from one image to the next, are not an error
resulting from misregistration between images. We have already done this step for you, but it
should be emphasized that the image-to-image registration is critical to any multi-data analysis
for forest change, be it using CLASlite or any other mapping software. As discussed in the Data
Preparation section, prepare the images so that bands 1, 2, 3, 4, 5, and 7 from each image are in a
GeoTIFF or ENVI format. The thermal band from each image should be in a separate file, with
the same pixel size and extent as the corresponding file containing the other bands (e.g., 30 meter
spatial resolution).
223/063 13-Jul-99 223/063 31-Jul-00 223/063 03-Aug-01 223/063 07-Sep-02
Bands 1,2,3,4,5,7 Bands 1,2,3,4,5,7 Bands 1,2,3,4,5,7 Bands 1,2,3,4,5,7

223/063 13-Jul-99 223/063 31-Jul-00 223/063 03-Aug-01 223/063 07-Sep-02

Thermal Band Thermal Band Thermal Band Thermal Band

27
 2. Surface Reflectance- Step 2 of CLASlite
Your next step is to process the images to apparent surface reflectance. Enter the metadata
information for each image. If you do not have this information with your image, you should be
able to find it online on one of the websites where satellite data are distributed. Please consult
the FAQs for more information for this particular set of images. After you have saved the
information for the four images, click Run. Each image will take approximately 5 minutes to
create a calibrated reflectance image. You have just completed a step that normally can take
many hours!

3. Cloud Masking-Step 3 of CLASlite

After the reflectance images are created, you have the option of using the thermal bands of the
Landsat images to mask out clouds in the imagery. This step is not required, but it can help to
reduce the amount of data that will be processed in subsequent steps, thus saving you time.

For the purposes of this tutorial, perform the cloud masking on the 1999 image. Enter the raw
image, reflectance image, and thermal image. Enter an output file name that will contain the
masked reflectance image. Click View to see the thermal image to determine a thermal
threshold value to mask out clouds. Remember, clouds in this image will appear dark, because
they are colder than the land surface. Do not select a threshold that is too high or you might
mask out good pixels that are not cloudy. When you have set the thermal threshold value, click
Run to generate a masked reflectance image.

4. Fractional Cover (AutoMCU)- Step 3 of CLASlite

When you have the masked reflectance images that you want to convert to fractional cover, enter
them into Step 3. For each image, enter the name of the input reflectance file and the name of
the fractional cover image that will be generated from it. After youve entered the information
for each image, click Run to start the batch process.

After the batch process finishes, you will be prompted to determine a threshold to scale the
preliminary results into a final image. You should first click Adjust to perform the first
adjustment. When Pass 1 and Pass 2 are completed, click on the View button to see the output
fraction cover image. An image viewer will appear and you can draw a box to see an area at full
resolution. You can also use the Stretch feature to enhance the contrast of the colors
representing the PV (green), NPV (blue), and Bare Substrate (Red). You may find that the initial
adjustment has masked out too much of the image. Reduce the threshold so that less of the
image is masked and click Adjust again.

After the image is readjusted, click View again to inspect the image. Continue this until the
image appears with cloudy and other problem pixels masked out. When the image appears to be
adjusted properly, select Accept to dismiss the scaling window for that image. If there are
other images to process, perform the scaling process for the other images.

Congratulations! You have completed a task that used to take weeks to months to accomplish!
We encourage you to view the images in Freelook or your favorite image visualization package.

28
 5. Deforestation and Disturbance Maps- Step 4 of CLASlite
Your next step is to use the fractional cover images to determine deforestation and disturbance
over the time period covered by the images (1999-2002). Select step 4 from the menu and enter
the names of the 4 images, in sequence, from the earliest to the latest. Click on Run to create the
deforestation and disturbance images for the time series of images. CLASlite will place files
called Compiled_deforestation and Compiled_disturbance on your Desktop. Based on the
differences between the four images, the program will classify a pixel in up to three classes of
deforestation and three classes of disturbance, depending on the interval of when the change
occurred. The figure below depicts the interval in which the various disturbance and
deforestation classes occurred.
13-Jul-99 31-Jul-00 03-Aug-01 07-Sep-02

disturb_year_1 disturb_year_2 disturb_year_3

deforest_year_1 deforest_year_2 deforest_year_3

Now that you have time sequences of deforestation and forest disturbance, you can view them in
Freelook or your favorite image visualization software. You will notice that a large amount of
forest disturbance occurred in the years between 1999 and 2002 in this region of the Brazilian
Amazon. During these years, the Carnegie field team, along with collaborators from the
Brazilian federal agricultural agency (EMBRAPA) and the Tropical Forest Foundation,
determined that nearly all of the forest disturbance patterns shown in these images were caused
by selective logging. In 2004, they showed that not only could logging be monitored, but the
intensity of logging, the amount of canopy loss, could be tracked. They were able to correlate
logging intensity, defined here as the fractional change in PV, NPV and bare substrate, with the
amount of carbon removed from the forest in tree bole wood.

III. Interpretation of Results

The compiled deforestation can be viewed in

ENVI as a classification image. Each year of
deforestation is coded with a different color.
Deforestation
The deforestation in the first year is shown in
orange (pixel value 1), the second year in
yellow-green (pixel value 2), and the third
year in gray (pixel value 3). If you view this
image using other software, you may be able
to assign a color table to the image.

The deforestation image is associated with

areas in which the PV fraction decreased
significantly between two images. Figure V.1 Fractional Cover and Deforestation Images

29
 Similarly, the compiled disturbance image
can be viewed with the same color coding
assigned to the different years of
disturbance. Disturbance is more subtle,
and so you will see many isolated pixels
associated with possible disturbance. You
will notice, however, that clumps of pixels Selective logging
in a single year (color) can generally be
associated with selective logging activity,
as identified in Figure V.2.

Figure V.2 Disturbance Image

V.2 Long Term Clearing: Hawaii (single image analysis)

I. Problem Statement
Many forested landscapes in Hawaii have been undergoing continuous long-term change due to
sugar cane agriculture and cattle ranching.
The northeastern region of the Big Island of Hawaii, while containing vast amounts of forest,
have been slowly encroached upon over time. For this single image analysis, we will see how to
identify the amount of forested area in an image.

II. Analysis
This exercise involves processing one Landsat-7 (ETM+) image through CLASlite and creating
image output that identifies the forested area. The image that we will use in the exercise is from
December 30, 2000, Path/Row 062/046.

1. Image Preparation
Your image should be in ENVI or GeoTIFF format with the spectral bands ordered 1, 2, 3, 4, 5,
and 7. Make sure that the image is properly georeferenced. Since there are hardly any clouds in
the subset provided for this case study, we will not need the thermal band.

2. Surface Reflectance- Step 2 of CLASlite

Your next step is to process the images to apparent surface reflectance. This is performed in
Step 2 of CLASlite. Enter the metadata information for each image. If you do not have this
information with your image, you should be able to find it online on one of the websites where
satellite data are distributed. Please consult the FAQs for more information for this particular set
of images.

30
After you have saved the information for the image, click Run. It will take approximately 5
minutes to create a calibrated reflectance image. You have just completed a step that normally
can take many hours!

3. Fractional Cover (AutoMCU) - Step 3 of CLASlite

Now that you have a reflectance image, you want to convert it to fractional cover. In Step 3 of
CLASlite, enter the name of the reflectance image and the name of the fractional cover image
that will be generated from it. After youve entered the information for the image, click Run
to start the process.
After the process finishes, you will be prompted to determine a threshold to scale the preliminary
results into a final image. You should first click Adjust to perform the first adjustment. When
Pass 1 and Pass 2 are completed, click on the View button to see the output fraction cover
image. An image viewer will appear and you can draw a box to see an area at full resolution.
You can also use the Stretch feature to enhance the contrast of the colors representing the PV
(green), NPV (blue), and Bare Substrate (Red). You may find that the initial adjustment has
masked out too much of the image. Reduce the threshold so that less of the image is masked and
click Adjust again.
After the image is readjusted, click View again to inspect the image. When the image appears
to be adjusted properly, select Accept to dismiss the scaling window for that image.
Congratulations! You have completed a task that used to take weeks to months to accomplish!
We encourage you to view the images in Freelook or your favorite image visualization package.

4. Forest Map - Step 5 of CLASlite

Your next step is to use the fractional cover image to determine forested versus non-forested
areas. Select step 5 to map the forest cover. Enter the name of the fractional cover image and
click on Load. An output file will be created with the same name as the input file with
forest_cover_map appended to it.

III. Interpretation of Results

The image of forest cover can be viewed as a single band grayscale image. Any areas that are
forested will have the pixel value 0 (zero) and all non-forested areas will have a value of 4.
Caution should be used when interpreting these results. The forest cover is determined based on
the amount of photosynthetic vegetation (PV), but it is possible that there is confusion with non-
forest vegetation. Furthermore,
because we are only using a single
image in this case study, we cannot
infer when a particular area changed
from forest to non-forest. A multi-
image analysis is preferable for
making that kind of determination.
In Figure 3 you can see how the red
and yellow areas in the fractional
cover image correspond to areas
where development has encroached
Fig. V.3 Fractional cover and Forest-No forest image (Step 6
on the forested areas shown in green. Output Image)

31
 VI. Glossary

Calibration: process performed by CLASlite that includes: identification of regions to be

masked, calculation of the radiance image, atmospheric correction and calculation of the
reflectance image.
Deforestation: Direct human-caused conversion of forest to less than 10-30% tree cover (UN
Framework Convention on Climate Change).
Degradation: A human interpretation of forest disturbance, when the disturbance reaches a level
that suppresses carbon storage and other ecosystem services.
Disturbance: Partial removal of forest canopies, with the remaining forest canopy generally
exceeding 30%.
Forest canopy gap: In logged areas, canopy gaps are created by tree falls and skid trails,
resulting in damage or death of standing trees.
Forest Monitoring: Mapping forests in a consistent manner that allows detection and
quantification of changes in forest cover over time.
Forest Regrowth: Increases in forest cover and biomass following forest clearing and
abandonment.
Gain: A general term used to denote a change in signal power.
Intact forest: Patches of forest that are not damaged, surrounded by small clearings or
dominated by canopy gaps associated with human activity (GOFC-GOLD 2006).
Masking out: Removing certain image pixels from an analysis.
Non-photosynthetic vegetation: Dead or senescent vegetation.
Photosynthetic vegetation: Live, green vegetation.
Regeneration: Previously damaged forest can recover, resulting in biomass sequestration
(GOFC-GOLD 2006).
IPCC: Intergovernmental Panel on Climate Change

32
Appendix I: CLASlite Installation and Useful Links
System Requirements: Additional Software Installed:

3 GB of disk space. IDL 7.0.6 (32 bit version)

2GB RAM Freelook: Software for viewing images.

Installation Instructions

1. Go to the ftp and download the installer zip file from software_installer/english and save it
onto your desktop. Double click the zip file, and enter the password provided to you. The
executable will then install CLASlite, Freelook and IDL 7.0.6 onto your system.

You will see a welcome screen similar to the one shown below. On the welcome screen click
next. Accept the user agreement of CLASlite. Click next. You will be notified of the
minimum space requirements for the installation of CLASlite 2.0 onto your system.

CLASlite will then be installed in your machine under C:\claslite. The basic support files and
additional software packages (IDL VM and Freelook) will also be installed along with it. 32
bit IDL VM is necessary for running CLASlite 2.0.

2. Go to the ftp and download the license.exe file from software_installer onto your desktop.
Double click on the .exe file. This action will create a system logfile which will be
automatically placed onto your desktop. Email the logfile to claslite_support@ciw.edu
writing the word environment in the subject line.

33
3. Go to the ftp and click on continent_files. Navigate to the corresponding continent of
interest. Download the zip file and extract its contents to C:\claslite\support_files

4. Go to the ftp site and download the zip file under modis_atmosphere. Extract the contents of
the compressed folder and place them under C:\claslite\support_files

Note: without the corresponding continent (step 3) and atmosphere files (step 4) CLASlite
would not function.

Useful Links
Global Land Cover Facility
Landsat.org
Instituto Nacional de Pesquisas Espaciais
Tropical Rain Forest Information Center
USGS Global Visualization Viewer
TerraServer Online Imagery
Warehouse Inventory Search Tool
SPOT Image
ENVI
ERDAS
http://glcf.umiacs.umd.edu/portal/geocover/
http://landsat.org/
http://www.dgi.inpe.br/CDSR/
http://www.trfic.msu.edu/
http://glovis.usgs.gov/
http://www.terraserver.com/
http://wist.echo.nasa.gov/
http://www.spot.com/
http://www.ittvis.com/
http://www.erdas.com/

34
Appendix II: Image Preparation and Band Analysis for CLASlite

Processing data through CLASlite is simple but first requires that the data be prepared for input
to the software. It is important to do each step correctly in order to get the best result. The
satellite data supplied to CLASlite must be in the correct format and have the correct number of
bands. The expected formats and characteristics of the data vary by sensor. Common steps for
preparing CLASlite input from any satellite are:

1. Geo-referencing the image to a UTM projection (WGS-84 ellipsoid)

2. In the case of LANDSAT, resampling thermal band to the same resolution in image size
to the spectral data
3. Reordering bands, if necessary
4. Saving the image to GeoTIFF or ENVI format

The data requirements for each satellite sensor are listed in this section. You can use almost any
image processing package to prepare your image. Popular image processing packages include
ENVI and ERDAS. It may also be possible to the Grid module of ArcGIS to prepare the imagery
for CLASlite.

1. Landsat Thematic Mapper (TM) 4, 5, and Enhanced Thematic Mapper+ (ETM+) 7

CLASlite has the capability to process images from the Landsat 4, 5 and 7 satellites. The image
data must be in two files. One file must contain the data for Landsat bands 1-5 and band 7
(ordered 1,2,3,4,5,7). If you also have the thermal band for masking clouds (band 6, high gain),
it must be in a separate file, and must cover the exact same area and have the same pixel size as
the other file. Therefore, it may be necessary to resample the thermal band from its original
resolution to the pixel size of the other bands, prior to use with CLASlite. When you resample
the imagery, use the nearest neighbor resampling kernel. The pixel values in all Landsat imagery
used in CLASlite must be 1-byte values and must not have any atmospheric corrections applied
to them.

2. Earth Observing-1 (EO-1) Advanced Land Imager (ALI)

CLASlite can process images from the Earth Observing-1 satellite, which carries the Advanced
Land Imager (ALI) sensor. Only ALI level-1G data are supported in CLASlite.

ALI does not have a thermal band. Only the 9 visible, near-infrared and shortwave-infrared
bands must be contained in one file with the original 16-bit integer values for each pixel. The
bands should be in the order shown below. The 9 bands of ALI data are:
MS-1: 433 453 nm
MS-1: 450 515 nm
MS-2: 525 605 nm
MS-3: 630 690 nm
MS-4: 775 805 nm
MS-4: 845 890 nm
MS-5: 1200 1300 nm
MS-5: 1550 1750 nm
MS-7: 2080 2350 nm

35
 3. Advanced Spaceborne Thermal Emission & Reflection Radiometer (ASTER)

CLASlite can process ASTER Level-1B imagery acquired by the NASA Terra satellite. ASTER
images come in different resolutions. The visible/near-infrared (VNIR) imagery has 15-meter
pixels, while the shortwave-infrared (SWIR) imagery has 30-meter pixels. Since these bands
come in different resolutions, it is recommended that all of the bands be resampled using the
nearest neighbor kernel to the lowest (30-meter) resolution of the 9 VNIR and SWIR bands. The
thermal bands of ASTER have 90-meter pixels, but they are not used in CLASlite.

One potential problem with ASTER data is that the VNIR and SWIR images are collected from
two different telescopes, making it possible for the two sets of bands to be misaligned.
Misalignment is more likely to occur in areas with large variations in elevation. When
misalignment is a problem, the best thing to do is to geo-reference the images separately, then
combine them using image-to-image registration.

CLASlite requires that the radiance conversion coefficients be applied before using CLASlite.
ASTER Level 1B data have various gain settings which should be provided in the *.met file that
accompanies the data. In that file, look for a line that contains ASTERGains. A few lines
after that line, you should see a line that contains the ASTER gain settings. The following
example is used to illustrate how to identify the gain settings.

Value = ("01 HGH, 02 HGH, 3N NOR, 3B NOR, 04 NOR, 05 NOR, 06 NOR, 07 NOR, 08 NOR, 09 NOR")

In this particular example, the gain settings are High (HGH) for bands 1 and 2, while bands
3N, 4, 5, 6, 7, 8, and 9 use the Normal (NOR) gain settings. The 3B band is not used in
CLASlite and should not be included in the image file that you prepare.

Band No. Coefficients Coefficients Coefficients Coefficients

High Gain Normal Gain Low Gain 1 Low Gain 2
1 0.676 1.688 2.25 N/A
2 0.708 1.415 1.89 N/A
3N 0.423 0.862 1.15 N/A
4 0.1087 0.2174 0.290 0.290
5 0.0348 0.0696 0.0925 0.409
6 0.0313 0.0625 0.0830 0.390
7 0.0299 0.0597 0.0795 0.332
8 0.0209 0.0417 0.0556 0.245
9 0.0159 0.0318 0.0424 0.265

The coefficients should be applied to the data according to the following equation:
Radiance = (DN value -1) x coefficient

When these coefficients are applied, the data should be written out as floating point values with
the bands ordered 1, 2, 3N, 4, 5, 6, 7, 8, 9.

36
 4. Systme Pour l'Observation de la Terre (SPOT) 4 and 5

The CAP and DIMAP formats are supported for SPOT-4 (HRVIR) and 5 (HRG) in CLASlite.
The 4 spectral bands should be organized into a single GeoTIFF or ENVI file with a 20-meter
pixel size. In order for CLASlite to convert the image to reflectance, it will need to read the
LEADXX.DAT file for CAP formatted images and the .DIM or .XML for DIMAP formatted
images. This file should be included on the original media on which the SPOT image was
received and contains gain parameters that are needed to convert the image to radiance and
reflectance.

As in the case of Landsat data, the input file should be 1-byte per pixel.

Bands of SPOT-4 (HRVIR) and SPOT-5 (HRG)

Band 1: 490-610 nm
Band 2: 610-680 nm
Band 3: 780-890 nm
Band 4: 1580-1750 nm

5. Moderate Resolution Imaging Spectroradiometer (MODIS)

The MODIS 8-day composited surface reflectance (MOD09A1) product is supported in

CLASlite. Unlike the other satellite data supported in CLASlite, this MODIS product is already
provided in reflectance and is georeferenced. Thus, it does not need to be run in the reflectance
generation step of CLASlite. Bands 1 and 2 come in a resolution which is twice that of the other
five bands. Therefore, it is necessary to resample the data to match the spatial resolution of the
other bands. Because bands 1 and 2 will be resampled to a coarser resolution, you can use a
pixel aggregation kernel to combine each 2-by-2 matrix of pixels to a single pixel. If your
software does not provide this capability, a nearest neighbor kernel should be acceptable.
Band 3: 459-479 nm
The data file that you provide CLASlite needs to be in a GeoTIFF or Band 4: 545-565 nm
ENVI file with the bands in the following order 3, 4, 1, 2, 5, 6, 7. Band 1: 620-670 nm
Band 2: 841-876 nm
Although this may seem odd, it is the order of the bands based on their Band 5: 1230-1250 nm
spectral wavelength, which is what CLASlite expects. Band 6: 1628-1652 nm
Band 7: 2105-2155 nm

37
 Satellite specifications for CLASlite

Satellites Supported
Landsat
SPOT 4 &
TM & ASTER ALI MODIS
5
ETM+
Thermal
Yes No No No No
Band Used
Number of
Spectral 6 9 9 4 7
Bands Used
MS-1, MS-
1, MS-2,
1,2,3N,4
1,2,3,4,5, MS-3, MS- 3,4,1,2,5,
Band Order ,5,6, 1,2,3,4
7 4, MS-4, 6,7
7,8,9
MS-5, MS-
5, MS-7
Reflectance
Determined Yes Yes Yes Yes No
in CLASlite
32-bit 16-bit 16-bit
Input Date
8-bit floating short 8-bit short
Type
point integer integer
Level of Data Level HRVIR or MOD09A
N/A Level 1G
Supported 1B HRG 1

38
 Information for example imagery provided with CLASlite

Cauaxi, Para', Brazil (Selective Logging) Peru (Landsat 5 & 7, Path/Row 003/068) All images
---------------------------------------------- were processed using LPGS
Landsat-7 (4 images, Path/Row 223/063) --------------------------------------------------------------------------
--------
File: cauaxi_071399 Date: 12081999 (Landsat 7)
Date: 13071999 Time: 1439
Time: 1317 Latitude: -11.19
Latitude: -3.80 Longitude: -69.57
Longitude: -48.39 Elev: 320
Elev: 50 Gain Settings: HHHHHH
Gain Settings: HHHHHH
Proc. System: LPGS Date: 26072000 (Landsat 7)
Time: 1437
File: cauaxi_073100 Latitude: -11.19
Date: 31072000 Longitude: -69.57
Latitude: -3.80 Gain Settings: HHHLHH
Longitude: -48.39
Time: 1315 Date: 29072001 (Landsat 7)
Elev: 50 Time: 1435
Gain Settings: HHHLHH Latitude: -11.19
Proc. System: LPGS Longitude: -69.57
Elev: 320
File: cauaxi_080301 Gain Settings: HHHLHH
Date: 03082001
Time: 1313 Date: 16072002 (Landsat 7)
Latitude: -3.80 Time: 1434
Longitude: -48.39 Latitude: -11.19
Elev: 50 Longitude: -69.57
Gain Settings: HHHLHH Elev: 320
Proc. System: LPGS Gain Settings: HHHLHH

File: cauaxi_090702 Date: 15082003 (Landsat 5)

Date: 07092002 Time: 1424
Time: 1312 Latitude: -11.19
Latitude: -3.80 Longitude: -69.57
Longitude: -48.39 Elev: 320
Elev: 50 Gain Settings: N/A
Gain Settings: HHHLHH
Proc. System: LPGS Date: 15092004 (Landsat 5)
Time: 1430
Generic Example of Landsat-7 image (Peru) Latitude: -11.19
---------------------------------- Longitude: -69.57
Image File: landsat7.tif Elev: 320
Sensor: Landsat-7 Gain Settings: N/A
Acquisition Date: 07092002
Acquisition Time (UTC): 1451 Date: 18092005 (Landsat 5)
Latitude: -8.7 Time: 1434
Longitude: -74.7 Latitude: -11.19
Elevation (meters): 175 Longitude: -69.57
Gain Settings (Bands 1-5, 7): LLLLLL Elev: 320
Processing System: LPGS Gain Settings: N/A

39
Generic Example of Landsat-5 image (Peru) Date: 04082006 (Landsat 5)
---------------------------------- Time: 1439
Image File: landsat5.tif Latitude: -11.19
Sensor: Landsat-5 Longitude: -69.57
Acquisition Date: 20102003 Elev: 320
Acquisition Time (UTC): 1442 Gain Settings: N/A
Latitude: -8.6
Longitude: -74.2 Date: 23082007 (Landsat 5)
Elevation (meters): 160 Time: 1439
Gain Settings (Bands 1-5, 7): Not required Latitude: -11.19
Processing System: LPGS Longitude: -69.57
Elev: 320
Gain Settings: N/A

Generic Example of ASTER imagery
**(Suriname)
----------------------------------
Image File: ASTER.tif
Sensor: ASTER
Acquisition Date: 04092000
Acquisition Time (UTC): 1424
Latitude: 4.3
Longitude: -54.5
Elevation (meters): 200
Gain Settings (Bands 1-5, 7): Not required
Processing System: Not required
Generic Example of Landsat-7 image with clouds
(Peru)
-----------------------------------------------
Image File: landsat7_clouds.tif
Sensor: Landsat-7
Acquisition Date: 16082000
Acquisition Time (UTC): 1455
Latitude: -9.7
Longitude: -74.8
Elevation (meters): 300
Gain Settings (Bands 1-5, 7): HHHLHH
Processing System: LPGS

Generic Example of ALI imagery **(Colombia)

--------------------------------
Image File: ALI.tif
Sensor: ALI
Acquisition Date: 28122002
Acquisition Time (UTC): 1450
Latitude: 1.3
Longitude: -71.8
Elevation (meters): 225
Gain Settings (Bands 1-5, 7): Not required
Processing System: Not required

**Updated July 13, 2010

40
Appendix III: Journal references
Primary papers:
1. Asner, G.P., M. Keller, R. Pereira, J.C. Zweede, and J.N.M. Silva. 2004. Canopy damage and
recovery following selective logging in an Amazon forest: Integrating field and satellite studies.
Ecological Applications 14(4):280-298.
2. Asner, G.P., D.E. Knapp, A.N. Cooper, M.C.C. Bustamante, and L.O. Olander. 2005. Ecosystem
structure throughout the Brazilian Amazon. Earth Interactions 9(7):1-31.
3. Asner, G.P., D.E. Knapp, E.N. Broadbent, P.J.C. Oliveira, M. Keller, and J.N. Silva. 2005. Selective
logging in the Brazilian Amazon. Science 310:480-482.
4. Asner, G.P., E.N. Broadbent, P.J.C. Oliveira, D.E. Knapp, M. Keller, and J.N. Silva. 2006. Condition
and fate of logged forests in the Brazilian Amazon. Proceedings of the National Academy of Sciences.
103(34):12947-12950.
5. Asner, G.P., D.E. Knapp, A. Balaji, G. Pez-Acosta. 2009. Automated mapping of tropical
deforestation and forest degradation: CLASlite. Journal of Applied Remote Sensing, vol. 3
(033543), 24pp. [doi:10.1117/1.3223675]

Supporting papers:
6. Asner, G.P. and K.B. Heidebrecht. 2002. Spectral unmixing of vegetation, soil and dry carbon in arid
regions: Comparing multi-spectral and hyperspectral observations. International Journal of Remote
Sensing 23:3,939-3,958.
7. Asner, G.P., M.M.C. Bustamante, and A.R. Townsend. 2003. Scale dependence of biophysical
structure in deforested lands bordering the Tapajs National Forest, Central Amazon. Remote Sensing
of Environment 87:507-520.
8. Asner, G.P., M. Keller, and J.N.M. Silva. 2004. Spatial and temporal dynamics of forest canopy gaps
following selective logging in the eastern Amazon. Global Change Biology 10(5):765-783.
9. DeFries, R., G.P. Asner, F. Achard, C. Justice, N. Laporte, K. Price, C. Small, and J. Townshend.
2005. Monitoring tropical deforestation for emerging carbon markets. Tropical Deforestation and
Climate Change. P. Moutinho and S. Schwartzman (eds.) Amazon Institute for Environmental
Research, Belm, Brazil.
10. Broadbent, E.N., D.J. Zarin, G.P. Asner, M. Pena-Claros, A. Cooper, and R. Littell. 2006. Forest
structure and spectral properties after selective logging in Bolivia. Ecological Applications 16:1148-
1163.
11. Oliveira, P.J., G.P. Asner, D.E. Knapp, A. Almeyda, R. Galvan-Gildemeister, S. Keene, R.F. Raybin,
and R.C. Smith. 2007. Land-use allocation protects the Peruvian Amazon. Science 317:1233-1236.
12. Davidson, E.A., G.P. Asner, T.A. Stone, C. Neill, and R. de O. Figueiredo. 2008. Objective indicators
of pasture degradation from spectral mixture analysis of Landsat imagery. Journal of Geophysical
Research 133, G00B03, doi: 10.1029/2007JG000622.
13. Broadbent, E.N., G.P. Asner, P.J.C. Oliveira, D.E. Knapp, M. Keller, and J.N. Silva. 2008. Forest
fragmentation from deforestation and selective logging in the Brazilian Amazon. Biological
Conservation 141:1745-1757.

41