acorn 6 user’s manualhomepage.ntu.edu.tw/~choying/acorn_mu.pdfacorn also works on areas where...

ACORN 6 User’s Manual

© 2004-08 ImSpec LLC. All rights reserved. http://www.imspec.com ACORN is an ImSpec LLC product with MODTRAN licensed technology. [email protected] ENVI is a registered trademark of Research Systems Inc. Fax: 206-666-3098 Version: 080101

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Contents Chapter 1: ACORN Overview ......................................................................................... 4 Chapter 2: Using ACORN ............................................................................................... 12 Chapter 3: Mode 1. Atmospheric Correction of Calibrated Hyperspectral Data ................................................................... 15 Chapter 4: Mode 1pb. Mode 1 for pushbroom imaging spectrometers with cross-track spectral calibration variation……………………..………. 24 Chapter 5: Mode 1.5. Atmospheric Correction of Hyperspectral Data with Water Vapor and Liquid Water Spectral Fitting………….…...................... 33 Chapter 6: Mode 1.5pb Atmospheric Correction of Hyperspectral Data with Water Vapor and Liquid Water Spectral Fitting for PushBroom Sensors………………………………………………………….… 42 Chapter 7: Mode 2. Single Spectrum Enhancement of a Hyperspectral Atmospheric Correction ..................................................... 51 Chapter 8: Mode 3. Atmospheric Correction of Hyperspectral Data Using the Empirical Line Method …………..……….. 57 Chapter 9: Mode 4: Convolution of Hyperspectral Data to Multispectral Data .................................................. 64

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Chapter 10: Mode 5. Atmospheric Correction of Calibrated Multispectral Data ..................................................................... 70 Chapter 11: Mode 5.5. Atmospheric Correction of Calibrated Multispectral Data with an Independent Water Vapor Image……….…… 77 Chapter 12: Mode 6. Single Spectrum Enhancement of a Multispectral Atmospheric Correction ...................................................... 84 Chapter 13: Mode 7. Atmospheric Correction by the Empirical Line Method for Multispectral Data ........................................... 90 Appendix A: Example Input Files for all ACORN Modes ................................................ 97 Appendix B: Hyperspectral File Formats ........................................................................ 109 Appendix C: Multispectral File Formats........................................................................... 117

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Chapter 1:

ACORN Overview The following topics are covered in this chapter:

Description………………………………………………………………………………………... 5 ACORN Methodology……………………………………………………………………...….… 8 Input Data Requirements…………………………………………………………………..….… 8 Software and Hardware Requirements…………………………...…………………………… 10 Cautions……………………………………………………………………………………...….... 10 Trouble Shooting……………………………………………………………………………..….. 10 ACORN Technical Support………………………………………………………………...…… 11

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Description The Atmospheric COrrection Now (ACORN) software offers a range of options for atmospheric correction of

hyperspectral and multispectral remote sensing data sets. In a subset of the modes of operation, ACORN uses

radiative transfer calculations and the measured, calibrated hyperspectral data to deduce a subset of the

atmospheric properties present in the hyperspectral data set. These derived atmospheric properties are used in

conjunction with modeled atmospheric properties to correct for the atmosphere in the hyperspectral data set. With

an input of calibrated hyperspectral radiance data, ACORN produces an output of apparent surface reflectance.

The Atmospheric CORrection Now (ACORN) software has been developed to offer a range of atmospheric

correction capabilities:

Mode 1 Radiative transfer atmospheric correction of calibrated hyperspectral data.

Mode 1pb Mode 1 for pushbroom imaging spectrometer with cross-track spectral calibration variation.

Mode 1.5 Radiative transfer atmospheric correction of calibrated hyperspectral data with water vapor and

liquid water spectral fitting

Mode 1.5pb Mode 1.5 for pushbroom imaging spectrometer with cross-track spectral calibration variation.

Mode 2 Single spectrum enhancement of a hyperspectral atmospheric correction.

Mode 3 Atmospheric correction using the empirical line method for hyperspectral data.

Mode 4 Convolution of hyperspectral data to multispectral data.

Mode 5 Radiative transfer atmospheric correction of calibrated multispectral data.

Mode 5.5 Radiative transfer atmospheric correction of calibrated multispectral data with independently

know water vapor image for spatially varying water vapor correction

Mode 6 Single spectrum enhancement of a multispectral atmospheric correction.

Mode 7 Atmospheric correction by the empirical line method for multispectral data.

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As an example of ACORN atmospheric correction, Figure 1-1 shows an image from the AVIRIS hyperspectral

instrument acquired over Cuprite, Nevada, USA. Figure 1-2 shows four calibrated radiance spectra and the

apparent reflectance spectra that result from using ACORN with the Cuprite, Nevada, USA data set. The

atmosphere is suppressed and mineral absorption features near 900, 2200, and 2300 nm are clearly identifiable.

Figure 1-1: Image cube of the AVIRIS hyperspectral data set acquired of the geologically diverse area of Cuprite Nevada, USA.

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Figure 1-1: Left: calibrated measured AVIRIS radiance spectra from Cuprite, Nevada, USA. Right: the

same spectra after ACORN atmospheric correction

ACORN also works on areas where vegetation and man-made infrastructure materials dominate. Figure 1-3

shows an AVIRIS image acquired over the Jasper Ridge Ecological Preserve, Stanford, CA, USA and adjacent

urban area. Figure 1-4 shows calibrated radiance spectra from the AVIRIS hyperspectral instrument from 5 target

areas as well as derived reflectance spectra after use of ACORN. After atmospheric correction the spectral

absorption feature inherent to the vegetation and man-made surface materials are revealed.

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Figure 1-3: Image cube of the AVIRIS hyperspectral data set acquired of the area including the Jasper Ridge Ecological Preserve, Stanford, CA, USA.

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Figure 1-2: Left: calibrated measured AVIRIS radiance spectra from Jasper Ridge Ecological Preserve,

Stanford, CA, USA. Right: the same spectra after ACORN atmospheric correction

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ACORN Methodology The most advanced form of atmospheric correction offered in ACORN is radiative transfer based. Radiative

transfer atmospheric correction of calibrated data uses both the calibrated data and provided parameters to derive

and model the absorption and scattering characteristics of the atmosphere. These atmospheric characteristics are

then used to invert the radiance to apparent surface reflectance.

The approach for atmospheric correction is based in the following equations that can be found or derived from the

information in the text Radiative Transfer by Chandrasekhar (December 1960, Dover, ISBN: 0486605906). In

simplified terms, Equation 1-1-1 gives the relationship between contributions between the source, atmosphere,

and surface to the radiance measured by an earth-looking sensor for a homogeneous plane parallel atmosphere.

Lt(λ) = F0(λ){ρa(λ) + Td(λ)ρ(λ)Tu(λ)/(1-s(λ)ρ(λ))}/π Equation 1-1-1

Where Lt is the total radiance arriving at the sensor. F0 is the top of the atmospheric solar irradiance.

ρa is the upward reflectance of the atmosphere. Td is the downward transmittance of the atmosphere. ρ is the spectral reflectance of the surface. Tu is the upward transmittance of the atmosphere; s is the downward

reflectance of the atmosphere. λ is spectral wavelength. The solution of this equation for apparent surface reflectance is given in Equation 1-1-2.

ρ(λ) = 1/[{F0(λ)Td(λ)Tu(λ)/π)/(Lt(λ)-F0(λ)ρa(λ)/π)}+s(λ)] Equation 1-1-2

Radiative transfer atmospheric correction of calibrated data uses both the calibrated data and provided parameters

to derive and model the absorption and scattering characteristics of the atmosphere. These atmospheric

characteristics are then used to invert the radiance to apparent surface reflectance. As an example over a

geologically interesting region, calibrated hyperspectral radiance data are shown in

Figure 1-1 for targets from a Cuprite, Nevada, USA data set. For an ecologically and urban example,

Figure 1-2 show the calibrated hyperspectral radiance and atmospherically corrected reflectance for targets from

the Jasper Ridge Ecological Preserve, Stanford, CA, USA.

Input Data Requirements

The quality of the ACORN atmospheric correction is closely tied to the quality of the calibration of the image

data. For all of the modes of ACORN, the spectral and radiometric calibration of the data must be accurate. Partial

exceptions to this rule exist and are indicated in the description of each mode.

At present, perfect calibration and perfect knowledge of the atmosphere are not achievable. Some artifacts will be

present in every atmospheric correction. The strength of the artifacts will be related to the quality of the

calibration, the knowledge of the atmosphere, and the ability to model the atmosphere. Several options and modes

are offered in ACORN to help suppress artifacts in the atmospheric correction.

Supporting Data Files ACORN requires supporting files in specific formats. For atmospheric correction these include a calibrated

radiance image file, a spectral calibration file (wavelength and FWHM), a gain file, and an offset file. These files

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must be prepared in advance of the ACORN run and must be obtained from the hyperspectral instrument data

provider, built from scratch, or developed from existing ACORN files.

Calibrated Image Data File ACORN only works with image files that are stored as 16 bit integers in either BIP or BIL format. The format of

the integers may be big endian (NETWORK) or little endian (HOST or INTEL). The image data must be 16-bit

integer format. The integer format little endian or big endian must be known and specified by the user at runtime.

Data written by PCs are often little endian integer format.

The image interleave must be Band Interleaved by Pixel (BIP) or Band Interleaved by Line (BIL) and known. If

the input radiance image has an ENVI header, ACORN copies the ENVI header information to an output ENVI

header to allow easy use of the reflectance corrected output file in ENVI.

Spectral Calibration files The ACORN spectral calibration file must be an ASCII files. Spectral calibration files describe how the

electromagnetic radiation is measured spectrally by the instrument of interest. Different modes of ACORN

require different spectral calibration input.

For example, for non-pushbroom hyperspectral, the first column is the wavelength position of each band in units

of nanometers. The second column is the full-width-half-maximum (FWHM) of the Gaussian function that

describes the spectral response of each band. The spectral calibration files or information to create them must

come from the data provider.

Gain Files Several of the modes of ACORN require input gain files that convert the stored integer numbers of the image data

to units of radiance (W/m^2 /µm/sr). To make the appropriate input gain file you must begin with knowledge of

the units of the image integers stored on disk. You must then produce the ASCII input gain file that has a value

for each image band that converts that band to radiance (W/m^2/µm/sr). A conversion example is given in Table

1-1.

Table 1-1: Conversion values between radiance units ________________________________________________________________________________________

10 Watts/meter^2 /micron/steradian = 1 microWatt/centimeter^2/nanometer/steradian

___________________________________________________________________________________________

Offset File The ACORN offset file is an ASCII file with one column with a value for each image band. The values

in this offset file are the real numbers that are added to the image radiance values after the gain file has

been applied. The units of the offset file are (W/m^2/µm/sr).

For most data sets the offset file values will be 0.0.

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Software and Hardware Requirements

ACORN is not an image processing software package. Independent file editing and image processing capabilities

are required to create ACORN support files and to view and assess ACORN results

Image processing software should provide image display, image reformatting and spectrum extraction capability.

Additionally some form of spreadsheet capability will likely be required to prepare spectral calibration, input

gain, and offset ASCII files necessary for running ACORN.

Image Processing Software To prepare files for ACORN atmospheric correction and to view the results an imaging processing software

package is required. There are many to choose from.

ACORN6 operates primarily in a stand-alone mode called from the Windows program interface. The ACORN6

output files include ENVI (“Environment for Visualizing Images, RSI Inc.) compatible header files for image

content description.

ACORN6 may be configured as an ENVI menu item.

System Requirements Currently ACORN is only supported on Windows platforms. Required is a 100 Mhz Pentium or faster,

running Windows 95,98, ME, NT, 2000, or XP.

Cautions ACORN is designed to work with data acquired under typical remote sensing conditions. If the atmosphere is

very hazy or smoky, some of the modes of ACORN may not succeed in fully correcting for the atmosphere.

ACORN can be applied to water targets such as lakes, rivers, and oceans, however the quality of the atmospheric

correction will be a function of the quality of the calibration and the quality of the MODTRAN calculations and

their implementation in ACORN. Atmospheric calibration over water targets is extremely challenging.

Trouble Shooting

The ACORN software is designed to be simple and straight forward, however the atmosphere correction modes of

ACORN requires a number of parameters and input files. All these parameters and input files are critical. The

formats and scales must be correct in order for ACORN to function.

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If the ACORN mode did not complete properly, please review all the input files and parameters to make sure they

are in the correct locations and in the correct format. Example of file formats for all modes of ACORN can be

found in the appendices of the Users Guide and throughout the Tutorial.

You may also want to look and the .eco file. This file will be in the same folder as the control file and have the

same name as the control file with a .eco appended (for example: default.in and default.in.eco). The .eco file will

indicate if there was difficulty with any of the input files or parameters.

Runtime Diagnostic Files If ACORN is not functioning as expected a series of echo and diagnostic files are available for each mode. The

echo and diagnostic files are generated to help identify the problem in parameter and file formats and scales.

The first file to look at is the eco file. This will be in the same folder as the ACORN input file. The name of the

file will be the same as the ACORN input file with a .eco extension added. For example if the control file is

named cup1.in the echo file will be named cup1.in.eco. This is an ASCII file and may be opened with

most editing and word processing software. The eco file should reflect the line for line the contents of the

ACORN input file. If the format or scale of any input parameters or files were detected to be incorrect there will

be an error comment in the eco file. If an error is indicated, it will need to be corrected before ACORN can run

successfully.

The second file to look at is the diag1 file. This will be in the same folder as the ACORN output reflectance file.

The name of the file will be the same as the ACORN output reflectance file with a .diag1 extension added. For

example if the control file is named cup1rfl the diag1 file will be named cup1rfl.diag1. This is an ASCII

file and may be opened with most editing and word processing software. In this file will be a summary of the

parameters used in the mode. If a problem is detected with any of these parameters a warning or error message

will be printed in the diag1 file. If an error is indicated, it will need to be corrected before ACORN can run

successfully.

The third file to look at is the diag2 file. This will be in the same folder as the ACORN output reflectance file.

The name of the file will be the same as the ACORN output reflectance file with a .diag2 added. For example if

the control file is named cup1rfl the diag1 file will be named cup1rfl.diag2. This is an ASCII file and

may be opened with most spreadsheet software. The file should be opened as space delimited. In this file will be

most of the spectral parameters entered for the given mode of ACORN. Also some of the calculated spectra will

be present. These spectral parameters can be examined to look for problems.

ACORN Technical Support ACORN technical support is available via e-mail only. Users will need to provide the 3 diagnostic files described

above, specify the operating system and possibly provide their data sets. E-mail questions to

[email protected]

We are also interested in you suggestions for improvements to ACORN. Please send them to

[email protected]

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Chapter 2:

Using ACORN The following topics are covered in this chapter:

Starting ACORN……………………………………………………………………………..…… 13 Selecting the ACORN Mode……………………………………………………………….…… 14

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Starting ACORN ACORN is started in Windows by selecting Start > Program > ACORN6 > ACORN6. The main ACORN Control Panel will open as shown in Figure 2-1. From this control panel the mode of atmospheric correction is selected.

Figure 2-1: Initial ACORN software user interface

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Selecting the ACORN Mode

The Atmospheric CORection Now (ACORN) software has been developed to offer a range of atmospheric

correction capabilities. From the user software interface select the desired ACORN mode.

Mode 1 Radiative transfer atmospheric correction of calibrated hyperspectral data.

Mode 1pb Mode 1 for pushbroom imaging spectrometer with cross-track spectral calibration variation.

Mode 1.5 Radiative transfer atmospheric correction of calibrated hyperspectral data with water vapor and

liquid water spectral fitting

Mode 1.5pb Mode 1.5 for pushbroom imaging spectrometer with cross-track spectral calibration variation.

Mode 2 Single spectrum enhancement of a hyperspectral atmospheric correction.

Mode 3 Atmospheric correction using the empirical line method for hyperspectral data.

Mode 4 Convolution of hyperspectral data to multispectral data.

Mode 5 Radiative transfer atmospheric correction of calibrated multispectral data.

Mode 5.5 Radiative transfer atmospheric correction of calibrated multispectral data with independently

know water vapor image for spatially varying water vapor correction

Mode 6 Single spectrum enhancement of a multispectral atmospheric correction.

Mode 7 Atmospheric correction by the empirical line method for multispectral data.

The following chapters describe how to enter the required parameters and files and run ACORN in each of the

modes of operation.

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Chapter 3:

Mode 1. Atmospheric Correction of Calibrated Hyperspectral Data The following topics are covered in this chapter:

Description.......................................................................................................................... 16 The Control File.................................................................................................................. 16 Editing the Control File…………………………………………………………………...……… 17 Completed Control File………………………………………………………………………..… 22 Saving the Control File and Running ACORN………………………………………………… 23 Trouble Shooting…………………………………………………………………………………. 23

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Description ACORN Mode 1 uses radiative transfer calculations and the measured, calibrated hyperspectral radiance data to

deduce a subset of the atmospheric effects present in the hyperspectral data. These derived atmospheric properties

are used in conjunction with modeled atmospheric properties to correct for the atmosphere in the hyperspectral

data set. With an input of spectrally and radiometrically calibrated hyperspectral radiance data, ACORN produces

an output of apparent surface reflectance. The output 0-1 apparent surface reflectance data is scaled to 0-10,000

integer data type.

The Control File To operate ACORN in Mode 1 a control file must be created. To access the control file editor select Mode 1 from

the software user interface. Figure 3-1 shows the control file entry dialog form for ACORN Mode 1. The control

file dialog form must be accurate and complete in order to create a control file and run ACORN.

If you have a pre existing control file or are running one of the tutorials you may open the pre existing control file

with the Open button.

If you are creating a new control file you should use the Save As button to choose the name and location to save

the control file. Save As may also be used to save an edited control file at any time to the same file name.

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Figure 3-1: ACORN Edit Control File entry dialog for Mode 1

Editing the Control File Input, Output and Calibration Names A set of files are required to run ACORN Mode 1. The names and locations of these files must be entered.

TIP: Use the search button to browse for these files.

- Enter the input image filename.

Note: The input image file must be stored as 16bit integer data and the format known. It is preferable if

there is no embedded header in the data.

- Enter an output filename.

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The output file will have the same dimensions and format as the input file.

- Enter the filename of the spectral calibration file.

This file is an ASCII file with two columns containing the wavelengths and full width half maximum

(FWHM) values for the input hyperspectral data set. The first column is the wavelength position of each band in

units of nanometers. The second column is the full-width-half-maximum FWHM of the Gaussian function that

describes the spectral response of each band. See Appendix B, “File Formats” for an example of the format of this

spectral calibration file.

- Enter the filename of the gain file.

The values in the gain file are the real numbers that convert the image integer values to radiance in units of

Watts/meter^2/micron/steradian (W/m^2/µm/sr). The gain file is an ASCII file of one column with a value for

each image band. Typically, some form of gain file is provided with the image data set to give the correct

conversion of image integer values to radiance in units of (W/m^2/µm/sr). See Appendix B, “File Formats” for an

example of the format of this gain file.

- Enter the filename of the offset file.

The values in this offset file are the real numbers that are added to the image radiance values after the gain file has

been used to convert the values into radiance in units of (W/m^2/µm/sr). The offset file is an ASCII file of one

column with a value for each image band. For most data sets the offset file values will be 0.0. See Appendix B,

“File Formats” for an example of the format of this offset file.

Image Dimensions

- Enter the image data dimensions, including the number of bands, lines and samples, and

header offset (in bytes).

The “offset” parameter is set, in bytes, to the offset from the beginning of the file to the start of

the actual data. This offset is used to skip imbedded headers.

Image Integer Format - Select the input file integer byte order format by clicking either the “host” or “network” button.

This varies by platform with PC systems usually using “host” or little-endian byte order and other platforms using

“network” or big-endian byte order. The output file will be in the same integer format as the input file.

Image File Format

- Select the image file format by clicking either the “bip” or “bil” button.

This parameter describes the input file storage format. This may be either band-interleaved-by-pixel

(bip) or band-interleaved-by-line (bil). The output file will be in the same format.

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Image Center Location

- Enter the image center latitude in degrees, minutes, seconds.

ACORN uses the convention of + for North and - for South.

Tip: you may use decimal degrees and enter 0 for minutes and seconds if you wish.

- Enter the image longitude in degrees, minutes, and seconds.

ACORN uses the convention of - for West and + for East.

Image Acquisition Time

- Enter the image acquisition date as year, month, day.

- Enter the image acquisition time as hour, minute, second.

Time is Greenwich Mean Time (GMT) or (UTC).

Tip: you may enter decimal hours and enter 0 for minutes and seconds if you wish.

Average surface elevation

- Enter the image average or nominal elevation in units of meters.

Acquisition Altitude

- Enter the image average or nominal acquisition altitude in units of kilometers.

Atmospheric Model Three atmospheric model are offered for use in the atmospheric correction: mid-latitude-summer, mid-latitude-

winter and tropical.

- Select the atmospheric model that is appropriate for the acquisition conditions of your data set.

Water Vapor Selections Differing water vapor derivation and constraint are possible. If the hyperspectral data set measures the region

between 780 and 1250 nm at 5 to 20 nm spectral resolution then ACORN should be able to derive the water vapor

from the calibrated hyperspectral data set. In this case, the water vapor can be estimated from the 820, 940 or the

1140 nm water vapor bands. The water vapor is derived on a pixel-by-pixel basis. If the data does not cover the

necessary spectral range, then a fixed water vapor amount must be used.

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- Select which spectral water vapor band, 820, 940, 1140, both 940 and 1140 nm to use for the water vapor

derivation by clicking in the appropriate button under “Derive Water Vapor.” If a fixed water vapor amount is to

be used, select the “No” button under “Derive Water Vapor.”

- Enter a fixed water vapor amount, in units of precipitable mm.

If the hyperspectral data set does not cover the 780 to 1250 nm spectral region, or if the water vapor amount

cannot be derived, then a fixed water vapor amount will be used. A typical water vapor amount for dry region data

sets is 15 mm and for humid data sets is 25 mm.

Visibility Options

Atmospheric visibility specifies the haziness of the atmosphere. For clear sky conditions, a typical

visibility is 100 km. For somewhat hazy conditions, a visibility of 20 km is often appropriate.

- Enter the image atmosphere visibility in kilometers.

- Click in the “Yes” box under “ACORN Estimated Visibility” to have ACORN attempt to

improve upon the provided visibility value.

With this option, ACORN attempts to estimate the visibility by analysis of the spatial and spectral content of the

hyperspectral data in the region from 400 to 1000 nm. An algorithm is employed to attempt to estimate the

visibility based on this analysis. If the algorithm generates an internally consistent result then the estimated

visibility will be used in the atmospheric correction. If the estimate is not found to be internally consistent with

the algorithm, then the user entered visibility will be used in the atmospheric correction. Figure 3-4 shows the

result of ACORN atmospheric correction with a fixed visibility that is too low. The result of this fixed excessively

low visibility is to generate negative reflectance values for dark targets. Figure 3-4 also shows the ACORN result

with the same low fixed visibility, but with the ACORN visibility estimation turned on. In this case, ACORN

successfully estimated a visibility that does not result in negative reflectance for the dark target. The visibility

algorithm is not simply a dark target algorithm and it is possible for extremely dark targets to cause negative

reflectance values. If ACORN does estimate a visibility, it will be stored in an ASCII diagnostic file with the

same location and name as the output reflectance file plus .diag1.

Artifact Suppression Options To reduce the residual artifacts in the atmospherically corrected data, ACORN has three types of artifact

suppression. Figure 3-2a shows the Mode 1 reflectance spectra without any artifact suppression applied and with

all three of the artifact suppression techniques (described below) applied.

- Select the desired type(s) of artifact suppression by clicking in the appropriate check boxes.

ACORN offers complete flexibility in applying the artifact suppression types. They may be applied in any

combination. If it appears the artifact suppression is not improving the quality of the atmospheric correction, all

three artifact suppressions may be turned off. Selection of artifact suppression will slow the speed of the

processing.

Type 1

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Artifact suppression Type 1 attempts to assess and correct for any mismatch in the spectral calibration of the

hyperspectral data set and the spectral radiative transfer calculations. This suppresses the artifacts (sharp spikes)

near the strong atmospheric absorption features at 760, 940, 1150, 2000 nm. Figure 3-2b shows the result of

artifact suppression type 1.

Type 2

There are often some other small artifacts across the spectral range due to errors in the absolute radiometric

calibration and/or errors in the radiative transfer calculations. Artifact suppression type 2 attempts to suppress

these. Figure 3-2c shows that the spectra are considerably smoother when both

Type 1 and 2 artifact suppression is used.

Type 3 The portions of the spectrum across the 1400 and 1900 nm water vapor bands typically give very noisy

reflectance results. These noisy values result from the low radiance values in these portions of the spectrum.

ACORN artifact suppression type 3 assesses the signal levels of the calibrated radiance and suppresses the lowest

signal portions where erroneous reflectance calculations may occur. The result is that low signal portions of the

spectrum are set to zero on the reflectance output. Figure 3-2d shows the result of ACORN artifact suppression

type 3. These spectra are close to the quality that would be measured on the ground.

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Figure 3-2. a: Result of ACORN Mode 1 atmospheric correction with no artifact suppression. b: ACORN Mode 1 atmospheric correction with Type 1 artifact suppression. c: ACORN Mode 1 atmospheric correction with Type 1 and Type 2 artifact suppression enabled. d: ACORN Mode 1 atmospheric

correction with Type 1, Type 2, and Type 3 artifact suppression

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a b

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Completed Control file A complete control file has all the files and parameters necessary to run an ACORN Mode 1 atmospheric

correction. Figure 3-3 shows a completed control file for the cuprite tutorial example provided with ACORN.

Figure 3-3. Example of a completed control file entry for ACORN Mode 1.

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Saving the Control File and Running ACORN To save the control file click the Save As button and confirm or rename the control file.

To run the specified ACORN Mode 1 atmospheric correction click the Save & Run button.

A progress bar will indicate the progress. At completion a message box will report the time required. After

completion you may run another ACORN Mode 1 atmospheric correction or exit to the primary ACORN user

interface.

Trouble Shooting







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Chapter 4:

Mode 1pb. Mode 1 for pushbroom imaging spectrometers with cross-track spectral calibration variation.

The following topics are covered in this chapter:

Description.......................................................................................................................... 25 The Control File.................................................................................................................. 25 Editing the Control File………………………………………………………………………….. 27 Completed Control File……………………………………………………………………..…… 30 Saving the Control File and Running ACORN…………………………………………..……. 31 Trouble Shooting…………………………………………………………………………………. 32

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Description ACORN Mode 1pb uses radiative transfer calculations and the measured, calibrated hyperspectral radiance data to

deduce a subset of the atmospheric effects present in the hyperspectral data. These derived atmospheric properties

are used in conjunction with modeled atmospheric properties to correct for the atmosphere in the hyperspectral

data set. With an input of spectrally and radiometrically calibrated hyperspectral radiance data, ACORN produces

an output of apparent surface reflectance. The output 0-1 apparent surface reflectance data is scaled to 0-10,000

integer data type.

ACORN Mode 1pb allows correct accounting for the cross-track variation in spectral calibration common to

many pushbroom imaging spectrometers such as Hyperion. Figure 4-1 shows the variation in cross-track spectral

calibration for Hyperion in channel 40.

Note: Because considerable file reformatting is required to utilize the full cross-track spectral calibration

this Mode requires longer computation time that the non-pushbroom Mode.

749

750

751

752

753

754

0 32 64 96 128 160 192 224 256

Cross-Track Sample (#)

Wav

elen

gth

(n

m)

Channel 40

Figure 4-1. Cross-track spectral calibration variation of the Hyperion pushbroom imaging spectrometer.

The Control File To operate ACORN in Mode 1pb a control file must be created. From the ACORN software user interface select

Mode 1pb to access the ACORN control file editor. Figure 4-2 shows the control file entry dialog form for

ACORN Mode 1pb. The control file dialog form must be accurate and complete in order to create a control file

and run ACORN.

26





Figure 4-2: ACORN Edit Control File entry dialog for Mode 1pb.

27

Editing the Control File Input, Output and Calibration Names A set of files are required to run ACORN Mode 1pb. The names and locations of these files must be entered.




- Enter the filename of the cross-track wavelength calibration file.

This file is a 2 dimensional ASCII file with the array of spectral channel position for every cross-track sample of

the instrument. For example, row one in the file would contain the spectral wavelengths for sample one. See

Appendix B, “File Formats” for an example of the format of this spectral calibration file.

- Enter the filename of the cross-track spectral response calibration file.

This file is a 2 dimensional ASCII file with the array of full-width-half-maximum FWHM of the Gaussian

function that describes the spectral response of each band. For example, row one in the file would contain the

FWHM for sample one. See Appendix B, “File Formats” for an example of the format of this FWHM calibration

file.













Image Dimensions

- Enter the image data dimensions, including the number of bands, samples, and lines, and

header offset ( in bytes).



28

Image Integer Format

- Select the input file integer byte order format by clicking either the “host” or “network” button.



Image File Format






ACORN uses the convention of + for North and - for South.



ACORN uses the convention of - for West and + for East.










29






from the calibrated hyperspectral data set. In this case, the water vapor can be estimated from the 820, 940 or the

1140 nm water vapor bands. The water vapor is derived on a pixel-by-pixel basis. If the data does not cover the

necessary spectral range, then a fixed water vapor amount must be used.

- Select which spectral water vapor band, 820, 940, 1140, both 940 and 1140 nm to use for the water vapor

derivation by clicking in the appropriate button under “Derive Water Vapor.” If a fixed water vapor amount is to

be used, select the “No” button under “Derive Water Vapor.”

- Enter a fixed water vapor amount, in units of precipitable mm.

If the hyperspectral data set does not cover the 780 to 1250 nm spectral region, or if the water vapor amount

cannot be derived, then a fixed water vapor amount will be used. A typical water vapor amount for dry region data

sets is 15 mm and for humid data sets is 25 mm.

Visibility Options









visibility will be used in the atmospheric correction. If the estimate is not found to be internally consistent with

the algorithm, then the user entered visibility will be used in the atmospheric correction. The visibility algorithm

is not simply a dark target algorithm and it is possible for extremely dark targets to cause negative reflectance

values. If ACORN successfully estimates a visibility, it will be stored in an ASCII diagnostic file with the same

location and name as the output reflectance file plus .diag1.

30


suppression.





processing.

Type 1



near the strong atmospheric absorption features at 760, 940, 1150, 2000 nm.

Type 2



these. Spectra are considerably smoother when both

Type 1 and 2 artifact suppression is used.





spectrum are set to zero on the reflectance output.

Completed Control file A complete control file has all the files and parameters necessary to run an ACORN Mode 1pb atmospheric

correction. Figure 4-2 shows a completed control file for the Stanford tutorial example provided with ACORN.

31

Figure 4-2. Example of a completed control file entry for ACORN Mode 1pb.

Saving the Control File and Running ACORN To save the control file click the Save As button and confirm or rename the control file.

To run the specified ACORN Mode 1pb atmospheric correction, click the Save & Run button.

A progress bar will indicate the progress. At completion a message box will report the time required. After

completion you may run another ACORN Mode 1pb atmospheric correction or exit to the primary ACORN user

interface.

32

Trouble Shooting







33

Chapter 5:

Mode 1.5 Atmospheric Correction of Hyperspectral Data with Water Vapor and Liquid Water Spectral Fitting The following topics are covered in this chapter:

Description......................................................................................................................... 34 The Control File.................................................................................................................. 35 Editing the Control File………………………………………………………………………….. 36 Completed Control File…………………………………………………………………......…… 39 Saving the Control File and Running ACORN…………………..……………………………. 40 Trouble Shooting…………………………………………………………………………………. 41

34

Description ACORN Mode 1.5 is similar to Mode 1, but uses spectral fitting to estimate water vapor and suppress effects of

liquid water on the surface. Liquid water is most commonly found on the surface in the leaves of vegetation. If

ignored water vapor may be over estimated over vegetation covered areas in the atmospheric correction. Figure

5-1 shows a set of radiance spectra from the AVIRIS data set acquired over the Jasper Ridge Ecological Preserve,

Stanford, CA, USA and the ACORN Mode 1.5 atmospherically corrected reflectance spectra. Figure 5-2 shows

the corresponding water vapor image and liquid water image derived in ACORN Mode 1.5 for the atmospheric

correction. Some surface features are subtly evident in the water vapor image due to sensor calibration and

radiative transfer calculation imperfections. The liquid water image is a function of the expressed strength of the

liquid water absorption feature in the spectrum. A multiple scattering model of the surface in question is required

to interpret the liquid water image in terms of absolute liquid water amount.

0

20

40

60

80

100

120

140

400 700 1000 1300 1600 1900 2200 2500

Wavelength(nm)

Rad

ian

ce (

W/m

^2/u

m/s

r).

Target 1

Target 2

Target 3

Target 4

0

2000

4000

6000

8000

10000

12000

400 700 1000 1300 1600 1900 2200 2500

Wavelength(nm)

Ref

lect

ance

/10

00

0.

Grassland

Forest

Water

Soil

Figure 5-1: Left: calibrated measured AVIRIS radiance spectra from Jasper Ridge Ecological Preserve, Stanford, CA, USA. Right: the same spectra after ACORN Mode 1.5 atmospheric correction

Figure 5-2: Left: water vapor image in precipitable microns from Jasper Ridge Ecological Preserve, Stanford, CA, USA. Right: liquid water image in microns absorption.

35

The Control File To operate ACORN in Mode 1.5 a control file must be created. To access the control file editor select Mode 1.5

from the ACORN software user interface. Figure 5-3 shows the control file entry dialog form for ACORN MODE

1.5. The control file dialog form must be accurate and complete in order to create a control file and run ACORN.





Figure 5-3: ACORN Edit Control File entry dialog for Mode 1.5

36

Editing the Control File Input, Output and Calibration File Names A set of files are required to run ACORN Mode 1.5. The names and locations of these files must be entered.






















Image Dimensions





37





Image File Format






ACORN uses the convention of (+) for North and (-) for South.



ACORN uses the convention of (-) for West and (+) for East.










38






from the calibrated hyperspectral data set. In this case, the water vapor can be estimated from the 940 or the 1140

nm water vapor band or both. The water vapor is derived on a pixel-by-pixel basis.

- Select which spectral water vapor band, 940, 1140 nm, or both to use for the water vapor derivation by clicking

in the appropriate button under “Derive Water Vapor.”

Path Radiance in Water Fit Because the derived water vapor is very sensitive to the atmospheric path radiance in the water vapor bands an

option is offered to use a path radiance parameter in the water vapor and liquid water spectral fit. This parameter

attempts to account for errors in the path radiance and may help give a result with fewer surface features

expressed in the derived water vapor image from ACORN Mode 1.5.

Visibility Options









visibility will be used in the atmospheric correction. If the algorithm fails, the user entered visibility will be used

in the atmospheric correction. If ACORN does estimate a visibility, it will be stored in an ASCII diagnostic file

with the same location and name as the output reflectance file plus .diag1.

39


suppression.





processing.

Type 1




Type 2



these. The spectra are considerably smoother when both Type 1 and 2 artifact suppression is used.





spectrum are set to zero on the reflectance output. These spectra are close to the quality that would be measured

on the ground.

Completed Control file A complete control file has all the files and parameters necessary to run an ACORN Mode 1.5 atmospheric

correction. Figure 5-4 shows a completed control file for the Jasper Ridge tutorial example provided with

ACORN.

40

Figure 5-4. Example of a completed control file entry for ACORN Mode 1.5.

Saving the Control File and Running ACORN To save the control file click the Save As button and confirm or rename the control file name.

To run the specified ACORN Mode 1.5 atmospheric correction click the Save & Run button.

A progress bar will indicate the progress. At completion a message box will report the time elapsed. After

completion you may run another ACORN Mode 1.5 atmospheric correction or exit to the primary ACORN user

interface.

41

Trouble Shooting







42

Chapter 6:

Mode 1.5pb Atmospheric Correction of Hyperspectral Data with Water Vapor and Liquid Water Spectral Fitting for PushBroom Sensors The following topics are covered in this chapter:

Description.......................................................................................................................... 43 The Control File.................................................................................................................. 43 Editing the Control File………………………………………………………………………….. 44 Completed Control File……………………………………………………………...………… 48 Saving the Control File and Running ACORN………………………………………………… 49 Trouble Shooting…………………………………………………………………………………. 50

43

Description ACORN Mode 1.5pb is similar to Mode 1.5, but is designed for data from pushbroom sensors with cross-track

spectral calibration variation. Cross-track variation in spectral calibration common to many pushbroom imaging

spectrometers such as Hyperion. Figure 6-1 shows the variation in cross-track spectral calibration for Hyperion in

channel 40.

Note: Because considerable file reformatting is required to utilize the full cross-track spectral calibration

this Mode requires longer computation time that the non-pushbroom Mode.

749

750

751

752

753

754

0 32 64 96 128 160 192 224 256

Cross-Track Sample (#)

Wav

elen

gth

(n

m)

Channel 40

Figure 6-1. Cross-track spectral calibration variation of the Hyperion pushbroom imaging spectrometer.

The Control File To operate ACORN in Mode 1.5pb a control file must be created. From the ACORN software user interface

select Mode 1.5pb to access the ACORN control file editor. Figure 6-2 shows the control file entry dialog form

for ACORN Mode 1.5pb. The control file dialog form must be accurate and complete in order to create a control

file and run ACORN.





44

Figure 6-2: ACORN Edit Control File entry dialog for Mode 1.5pb

Editing the Control File Input, Output and Calibration File Names A set of input, output and calibration files are required to run ACORN Mode 1.5pb. The names and locations of

these files must be entered.




- Enter the filename of the cross-track wavelength calibration file.

45

This file is a 2 dimensional ASCII file with the array of spectral channel position for every cross-track sample of

the instrument. For example, row one in the file would contain the spectral wavelengths for sample one. See

Appendix B, “File Formats” for an example of the format of this spectral calibration file.

- Enter the filename of the cross-track spectral response calibration file.

This file is a 2 dimensional ASCII file with the array of full-width-half-maximum FWHM of the Gaussian

function that describes the spectral response of each band. For example, row one in the file would contain the

FWHM for sample one. See Appendix B, “File Formats” for an example of the format of this FWHM calibration

file.













Image Dimensions









46

Image File Format






ACORN uses the convention of (+) for North and (-) for South.



ACORN uses the convention of (-) for West and (+) for East.













47



from the calibrated hyperspectral data set. In this case, the water vapor can be estimated from the 940 or the 1140

nm water vapor band or both. The water vapor is derived on a pixel-by-pixel basis.

- Select which spectral water vapor band, 940, 1140 nm, or both to use for the water vapor derivation by clicking

in the appropriate button under “Derive Water Vapor.”

Path Radiance in Water Fit Because the derived water vapor is very sensitive to the atmospheric path radiance in the water vapor bands an

option is offered to use a path radiance parameter in the water vapor and liquid water spectral fit. This parameter

attempts to account for errors in the path radiance and may help give a result with fewer surface features

expressed in the derived water vapor image from ACORN Mode 1.5pb.

Visibility Options









visibility will be used in the atmospheric correction. If the algorithm fails, the user entered visibility will be used

in the atmospheric correction. If ACORN does estimate a visibility, it will be stored in an ASCII diagnostic file

with the same location and name as the output reflectance file plus .diag1.


suppression.





processing.

48

Type 1




Type 2



these. The spectra are considerably smoother when both Type 1 and 2 artifact suppression is used.





spectrum are set to zero on the reflectance output. These spectra are close to the quality that would be measured

on the ground.

Completed Control file A complete control file has all the files and parameters necessary to run an ACORN Mode 1.5pb atmospheric

correction. Figure 6-3 shows a completed control file for the Stanford tutorial example provided with ACORN.

49

Figure 6-3. Example of a completed control file entry for ACORN Mode 1.5pb.


To run the specified ACORN Mode 1.5pb atmospheric correction click the Save & Run button.


completion you may run another ACORN Mode 1.5pb atmospheric correction or exit to the primary ACORN user

interface.

50

Trouble Shooting







51

Chapter 7:

Mode 2. Single Spectrum Enhancement of a Hyperspectral Atmospheric Correction The following topics are covered in this chapter:

Description.......................................................................................................................... 52 The Control File.................................................................................................................. 53 Editng the Control File……………………………………………………………….………….. 54 Completed Control File……………………………………………………..…………………… 55 Saving the Control File and Running ACORN………..………………………………………. 56 Trouble Shooting…………………………………………………………………………………. 56

52

Description

For single spectrum enhancement of a hyperspectral atmospheric correction, ACORN uses a spectrum extracted

from an atmospherically corrected hyperspectral data set and an accurately known independently measured

spectrum for the same target. With these two spectra, the full atmospherically corrected hyperspectral data set is

then corrected to the accuracy of the known spectrum. ACORN accurately and automatically convolves the

known spectrum to the spectral characteristics of the hyperspectral data set for this atmospheric correction

enhancement.

Single spectrum enhancement begins with the output of a radiative transfer atmospheric correction.

Figure 7-1 shows four spectra from various parts of the Cuprite, Nevada hyperspectral data set after using

ACORN Mode 1 atmospheric correction. For this example, no types of ACORN artifact suppression have been

used.

0

2000

4000

6000

8000

10000

12000

400 700 1000 1300 1600 1900 2200 2500

Wavelength (nm)

Refl

ecta

nce

/100

00.

Alunite

Kaolinite,

Iron Oxide

Carbonate

Offset for claity

Figure 7-1: Spectra extracted from an ACORN Mode 1 atmospherically corrected data set with no artifact suppression applied

To implement ACORN single spectrum enhancement a known measured reflectance spectrum from an area in the

atmospherically corrected data set is required. The known measured spectrum must have equal to or better

spectral resolution than the hyperspectral data. The spectral range of the measured spectrum must span that of the

hyperspectral data set. Figure 7-2 shows a measured reflectance spectrum from the Cuprite data set and the

extracted spectrum for the corresponding area in the radiative transfer atmospherically corrected data set. This

spectrum must be extracted from the hyperspectral data set using image processing software. With these two

spectra and the spectral calibration parameters of the hyperspectral data set ACORN performs a single spectrum

enhancement.

53

0

2000

4000

6000

8000

10000

12000

400 700 1000 1300 1600 1900 2200 2500

Wavelength (nm)

Ref

lect

ance

/1000

0. Bright Target

0

2000

4000

6000

8000

10000

12000

400 700 1000 1300 1600 1900 2200 2500

Wavelength (nm)

Ref

lect

ance

/10

00

0. Extracted

Figure 7-2: Left: measured spectrum for a target in the Cuprite area. Right: spectrum extracted from the ACORN corrected data for the same target

The result of the single spectrum enhancement are shown in Figure 7-3. These are the same spectra shown in

Figure 7-3. ACORN single spectrum enhancement has suppressed the majority of the artifacts present in the

original atmospheric correction.

0

2000

4000

6000

8000

10000

12000

400 700 1000 1300 1600 1900 2200 2500

Wavelength (nm)

Ref

lect

ance

/10

00

0.

Alunite

Kaolinite,

Iron Oxide

Carbonate

Offset for claity

Figure 7-3: Result of ACORN Mode 2, single spectrum enhancement, for the Cuprite hyperspectral data set

The Control File

From the primary ACORN software user interface select Mode 2. Figure 7-4 shows the control file entry dialog

form for ACORN Mode 2. The control file dialog form must be complete in order to create a control file run

ACORN.





54

Figure 7-4: Control file entry window for ACORN Mode 2

Editing the Control File Input, output and supporting files A set of input, output and supporting files are required to run ACORN Mode 2. The names and locations of these

files must be entered in the control file entry window.



Note: The input image file must be stored as 16bit integer data and the format known. It is preferable if

there is no embedded header in the data.









- Enter the filename of the image target reflectance spectrum extracted from the ACORN Mode 1 results.

This file is an ASCII file with one column containing the average values extracted for a known target from the

reflectance image generated in ACORN Mode 1. There is one value for each band in the image. The units are

reflectance *10000. See Appendix B, “File Formats” for an example of the format of this file.

55

- Enter the filename of the measured target reflectance spectrum.

This is a two column ASCII file containing the spectrum used to correct the ACORN Mode 1 data. The first

column is the wavelength in nanometers and the second column is the reflectance value for each wavelength

position in the first column. The reflectance values must be at the same scale as the Image Reflectance Spectrum

File values, reflectance*10000. The spectral sampling of this file must be equal-to or higher than the target image

reflectance spectrum and must cover the entire spectral range. See Appendix B, “File Formats” for an example of

the format of this file.

Image Dimensions









Image File Format




Completed Control file A complete control file has all the files and parameters necessary to run an ACORN Mode 2 single spectrum

enhancement. Figure 7-5 shows a completed control file for the Cuprite tutorial example provided with ACORN.

56

Figure 7-5. Example of a completed control file entry for ACORN Mode 2.


To run the specified ACORN Mode 2 atmospheric correction click the Save & Run button.


completion you may run another ACORN Mode 2 or exit to the primary ACORN user interface.

Trouble Shooting







57

Chapter 8:

Mode 3. Atmospheric Correction of Hyperspectral Data Using the Empirical Line Method The following topics are covered in this chapter:

Description.......................................................................................................................... 58 The Control File.................................................................................................................. 59 Editing the Control File…………………………�

acorn 6 user’s manualhomepage.ntu.edu.tw/~choying/acorn_mu.pdfacorn also works on areas where...

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