Chapter 7: Atmospheric correction
R. Richter, 'A spatially adaptive fast atmospheric correction
Chapter 7: Atmospheric
correction
Understanding atmospheric correction
The data obtained by optical satellite sensors with high
spatial resolution has become an invaluable tool for many
groups interested in studying, managing, developing, and
protecting our population, environment, and resources.
Unfortunately, satellite images are often obscured by
atmospheric effects like haze as a result of conditions in the
atmosphere at the time the image was captured. Atmospheric
correction is a process used to reduce or eliminate
atmospheric effects and reveal more accurate surface
reflectance values.
Two atmospheric correction processes are available:
ATCOR2, which is used for correcting satellite imagery
over flat terrain, and ATCOR3, which is used for correcting
satellite imagery over rugged terrain. Both are algorithms
that work with a database of atmospheric correction
functions, which are stored in lookup tables. The algorithms
have been developed mainly for satellite sensors with a small
swath angle such as Landsat and SPOT, but some wide
field-of-view (FOV) sensors such as IRS-WiFS are
supported as well.
For more information on the atmospheric correction, please
see the following articles:
algorithm' Int. J. Remote Sensing, Vol. 17, 1201-1214 (1996)
R. Richter, 'Atmospheric correction of satellite data with
haze removal including a haze/clear transition region',
Computers & Geosciences, Vol. 22, 675-681 (1996)
R. Richter, 'Correction of satellite imagery over mountainous
terrain', Applied Optics, Vol. 37, 4004-4015 (1998)
Preparing data
Before you begin setting up the atmospheric correction
process, the data must be in one PCIDSK (.pix) file with all
the channels in the same bit depth and resolution. Focus
supports 8-bit unsigned, 16-bit unsigned, 16-bit signed, and
32-bit real bit depths.
1. Transfer the data from the CD to PCIDSK (.pix) files.
2. Reproject the thermal data.
3. Assemble the data into one PCIDSK (.pix) file.
Transfer data to PCIDSK
You should import your images from the compact disk (CD)
using the appropriate CD read algorithm. Each sensor has
its own CD read algorithm. It creates a PCIDSK file, imports
the imagery channels from the CD, extracts the metadata,
and saves the satellite path information in a segment. By
preparing your imagery this way, Focus can automatically
set or calculate several parameters when you configure the
atmospheric correction.
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The number and types of bands on the CD depends on the
sensor used to capture the data. Usually, the visible, thermal,
and panchromatic bands are in different resolutions. Some
sensors may not provide thermal or panchromatic bands.
Read the bands of the same resolution at the same time into
one file.
For example, Landsat 7 data usually has eight bands: bands
1 to 5 and 7 are the visible wavelengths with a 30-meter
resolution, band 6 contains two thermal wavelengths with
a 60-meter resolution, and band 8 is the panchromatic with
a 15-meter resolution. You would use the CDLAND7
algorithm to read bands 1 to 5 and 7 into a file, then band 6
into a file, and then band 8 into a file.
If you do not intend to use the thermal or panchromatic
bands in the atmospheric correction process, then you do
not need to read those bands into a file.
The CD read algorithms are available through EASI,
Modeler, OrthoEngine, and Focus.
1. In the main menu, click Tools and then click Algorithm
Librarian.
2. Under PCI Predefined in the Data Interchange folder,
open the CD Reading/Utilities folder.
3. Click the appropriate CD read algorithm for the data.
4. Click Open.
5. Enter the required information on the Files and Input
Params 1 tabs.
6. Click Run.
7. Repeat for each set of bands with the same resolution.
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Reprojecting data
If you intend to use a thermal band in the atmospheric
correction (ATCOR) process, you need to reproject it to the
same resolution as the visible bands. For Landsat 7 data you
can use either the high gain or low gain thermal channels
with ATCOR. For ASTER data use band 13.
For example, Landsat 7 thermal bands have a 60-meter
resolution while its visible bands have 30-meter resolution.
Therefore, the thermal bands have to be reprojected to a
30-meter resolution.
1. In the main menu, click Tools and then click
Reprojection.
2. Click the Browse button beside Source file and select
the file that you want to reproject.
3. In the Destination file box, type the path and file name
for the reprojected data.
4. In the Output format box, click PIX:PCIDSK.
5. Under Reprojection Bounds, click Use bounds and
resolution in the list.
6. In the Pixel Size boxes in the X and Y boxes, type the
new resolution.
7. In the Resampling list, click the resampling method of
your choice.
• Nearest: Nearest Neighbor resampling identifies the
gray level of the pixel closest to the specified input
coordinates and assigns that value to the output
coordinates. Although this method is considered the
most efficient in terms of computation time, it
introduces small errors in the output image. The
output image may be offset spatially by up to half a
 Chapter 7: Atmospheric correction

pixel, which may cause the image to have a jagged 3. Beside Destination file click the Browse button and
appearance. select the file containing the visible bands.
• Bi-Linear: Bi-linear resampling determines the gray 4. Under Source Layers, click Select All.
level from the weighted average of the four closest 5. Click Add.
pixels to the specified input coordinates and assigns
that value to the output coordinates. This method 6. Click Transfer Layers.
generates an image with a smoother appearance than
Nearest Neighbor resampling, but the gray level
values are altered in the process, which results in
blurring or loss of image resolution. Opening the Atmospheric Correction
• Cubic: Cubic resampling determines the gray level
from the weighted average of the 16 closest pixels
Configuration dialog box
to the specified input coordinates and assigns that
Before you begin setting up the process, you should import
value to the output coordinates. The resulting image
your images from the compact disk (CD) using the
is slightly sharper than one produced by Bi-linear
appropriate CD read algorithm. For example, if you have
resampling, and it does not have the disjointed
IKONOS imagery, you would use CDIKONOS to import
appearance produced by Nearest Neighbor
your images. By preparing your imagery this way, Focus
resampling.
can automatically set or calculate several parameters. Also,
8. Under Source Layers, click Select All. the data must be in one PCIDSK (.pix) file with all the
channels in the same bit depth and resolution. For more
9. Click Add.
information, see Preparing data on page 249.
10. Click Reproject.
Once your files are prepared, you can configure the
Atmospheric Correction parameters. These parameters define
Assembling data into a file the image to be corrected, the source of the elevation, the
sensor information, the atmospheric conditions, and other
If you intend to use a thermal band in the atmospheric required parameters.
correction process, you need to add the thermal band to the
file containing the visible bands. The thermal band must be 1. In the main menu, click Analysis.
in the same resolution as the visible bands. For Landsat 7 2. Click Atmospheric Correction.
data you can use either the high gain or low gain thermal
channel with ATCOR. For ASTER data use band 13.

1. From the Files tree, right-click the thermal channel.

2. Click Export (Save As) and click To existing file.

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Setting up atmospheric correction parameters
1. In the Image file list, type the path and file name of the
file that you you want to correct or click Browse to select
a file.
2. If the image represents an area of flat terrain or if you
do not have a digital elevation model (DEM) for the
image, click Constant(ATCOR2) and in the Height
box type a value representing a constant elevation for
the area covered by the image.
3. If you do have a DEM for the image, click DEM
(ATCOR3). In the File box click the file that contains
the DEM or click Browse to select a file. In the Layer
list select the layer containing the elevation values.
4. To calculate Sky View and Shadow or to import Slope
and Aspect calculations, click Setup. For more
information, see Calculating slope, aspect, sky view, and
shadow on page 255.
5. In the Units list, click the unit of measurement used for
the elevation values.
6. In the Sensor type list, click the type of sensor used to
collect the image.
7. If you did not use a CD read algorithm to import your
images, you may need to match the sensor band numbers
to the correct image channel numbers. To set up the
channels, click Band Setup. For more information, see
Matching band numbers to channel numbers on page
256.
8. In Pixel size list, type the pixel size of the input image.
9. If the date is included in the metadata, the Date boxes
are set automatically. If not, in the Date boxes click the
month, day, and year when the image was taken.
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10. The Tilt list is available only when the sensor selected
provides the tilt capability. If the sensor was tilted when
the image was taken, click the title angle used in the Tilt
list. If the metadata describes the tilt angle in terms of
left and right, right means West and left means East.
11. In the Calibration file list click the calibration file for
the image and sensor type or click Browse to select a
file. In most cases you can use the file with  standard 
(or std) in the file name. For more information, see
Editing an existing calibration file to create a new file
on page 258.
12. In the Atmospheric definition area list, click the aerosol
type for the image. For more information see About
aerosol types on page 253.
13. In the Condition list, click the standard atmosphere
present when the image was taken. For more information
see About standard atmospheres on page 253.
14. If you also selected a thermal band to correct, in the
Thermal atmospheric definition list click the standard
atmosphere present when the image was taken.
15. If the date, time, and position are included in the
metadata, the solar zenith value will be calculated
automatically. If they are not, in the Solar zenith box
type the solar zenith value or click Calculate to calculate
the value (see Calculating the solar zenith and azimuth
on page 256).
16. (Available for ATCOR3 only) If the date, time, and
position are included in the metadata, the solar azimuth
value will be calculated automatically. If they are not,
in the Solar azimuth box type the solar azimuth value
or click Calculate to calculate the value.
17. In the Visibility box type the visibility value. For more
information, see About visibility on page 257.

18. In the Adjacency box type the adjacency value. For more
information, see About adjacency on page 257.
19. (Available for thermal bands only) In the Offset to
surface temperature list, type the value used to
compensate for a systematic error in the conversion of
radiance values to temperature values. For more
information, see Determining the offset to surface
temperature value on page 257.
20. Click OK.
About aerosol types
About standard atmospheres
The Atmospheric definition area list on the Atmospheric
Correction Configuration dialog box (see Opening the
Atmospheric Correction Configuration dialog box on page
251) contains the possible aerosol types for the image. The
aerosol type is determined by the predominant particles
present in the area at the time the image was captured, which
usually can be inferred its geographic location. Wind
direction and weather conditions in the area in the days
before the image was taken can affect the aerosol type
present.
The aerosol types are:
• Rural: The rural aerosol type is composed mostly of
dust-like and organic particles. It is predominant in
continental areas whose atmosphere is not strongly
influenced by urban or industrial centers. It is
recommended for areas such as forested, agricultural, or
snow-covered areas.
• Urban: The urban aerosol type is composed mostly of
particles such as sulfate aerosols resulting from
combustion and industrial activities. If you do not know
Chapter 7: Atmospheric correction
the composition of the atmosphere, the rural aerosol type
is recommended.
• Desert: The desert aerosol type is composed mostly of
large dust-like particles. If you do not know the
composition of the atmosphere, the rural aerosol type is
recommended.
• Maritime: The maritime aerosol type is composed
mostly of sea-salt, dust-like and organic particles. If you
do not know the composition of the atmosphere, the rural
aerosol type is recommended.
The Condition list and the Thermal atmospheric definition
list on the Atmospheric Correction Configuration dialog box
(see Opening the Atmospheric Correction Configuration
dialog box on page 251) contain the standard atmospheres
used in Atmospheric Correction. Standard atmospheres are
vertical profiles of pressure, temperature, water vapor, and
ozone density.
The water vapor content present in the area plays a key role
in determining which standard atmosphere to select when
performing an atmospheric correction. For sensors that do
not include water vapor bands, you can estimate the water
vapor content based on the season when the image was
captured and the location.
The standard atmospheres are:
• Dry or Dry Desert: A dry atmosphere has a total water
vapor content of 0.41 (g cm-2).
• Fall (spring): A fall (autumn) atmosphere has a total
water vapor content of 1.14 (g cm-2).
• Humid: A humid atmosphere has a total water vapor
content of 4.94 (g cm-2).
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• Mid-latitude summer: A midlatitude summer
atmosphere has a total water vapor content of 2.92 (g
cm-2).
• Mid-latitude winter: A midlatitude winter atmosphere
has a total water vapor content of 0.85 (g cm-2).
• Sub-Arctic summer: A sub-arctic summer atmosphere
has a total water vapor content of 2.08 (g cm-2).
• Sub-Arctic winter: A sub-arctic winter atmosphere has
a total water vapor content of 0.42 (g cm-2).
• Tropical: A tropical atmosphere has a total water vapor
content of 4.11 (cm or g cm-2).
• Arid: An arid atmosphere has a total water vapor content
of 2.15 (g cm-2).
• US standard: The 1976 US Standard atmosphere has a
total water vapor content of 1.42 (g cm-2).
Opening the elevation information setup dialog
box
In ATCOR3 a digital elevation model (DEM) is used to
calculate the effect of radiance and transmittance over rugged
terrain. The Slope and Aspect calculations are mandatory
for ATCOR3. The Sky View and Shadow calculations are
optional. These calculations can be automatically calculated
from the DEM or you can import them in the Elevation
Information Setup dialog box if you have already created a
file containing these values.
If you click Calculate for Slope, Aspect, Sky View, or
Shadow, PCIDSK files are automatically created in the user
folder where you installed Geomatica when you perform
the atmospheric correction. By default each file name is the
original input file name prefixed with 'slope_', 'aspect_',
'skyview_', or 'shadow_'.
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The Slope algorithm measures the angle of the incline for
each pixel, which is expressed as a value between 0 and 90
degrees. The value is calculated from the plane formed by
the vector connecting the left and right neighbours of the
pixel and the vector connecting the upper and lower
neighbours of the pixel.
The Aspect algorithm measures the orientation of the slope
of each pixel, which is expressed as a value between 0 and
360 degrees relative to the top of the image. The value is
calculated from the orientation of the plane formed by the
vector connecting the left and right neighbours of a pixel
and the vector connecting the upper and lower neighbours
of the pixel. The angle is measured between north (top of
image) and the projection of the normal vector of this plane
onto the horizontal plane.
The Sky View algorithm uses a ray tracing program to
determine the proportion of the sky hemisphere visible for
each pixel of the terrain.
The shadow file contains a layer that includes both self
shadowing and cast shadow effects. In the layer the shadows
are represented by a pixel value of 0 and the rest of the pixels
are given a value of 1. The self-shadowing effect is caused
by pixels from areas facing away from the sun which are on
slopes steeper than the solar elevation angle. Cast shadows
are areas in shadow due to objects blocking the sun. The
Shadow algorithm uses a ray tracing program and the solar
zenith and azimuth angles to calculate the cast shadows. The
shadow file is used as a mask so that shadows are excluded
from the atmospheric correction process.
1. Open the Atmospheric Correction Configuration
dialog box, see Opening the Atmospheric Correction
Configuration dialog box on page 251.

2. Under Elevation Information Setup, click the Setup
button.
Calculating slope, aspect, sky view, and shadow
1. In the File list under Elevation, click the file that
contains the DEM or click Browse to select a file. In the
Layer list select the layer containing the elevation values.
2. In a DEM each change in gray level represents a change
in elevation value. In the Elevation step box, type the
value that represents the change of one level of gray.
3. Under Slope, either:
• Click Calculate to calculate the slope values
automatically.
• Click From file to import the slope values from a
file. In the From file list, click the file that contains
the slope values or click Browse to select the file. In
the Layer list, click the layer of slope values.
Opening the band setup dialog box
4. Under Aspect, either:
• Click Calculate to calculate the aspect values
automatically.
• Click From file to import the aspect values from a
file. In the From file list, click the file that contains
the aspect values or click Browse to select the file.
In the Layer list, click the layer of aspect values.
5. Under Sky View, either:
• Click None if you do not want to include sky view
factor in the atmospheric correction.
• Click Calculate to calculate the sky view factor
automatically.
Chapter 7: Atmospheric correction
• Click From file to import the sky view factor from
a file. In the From file list, click the file that contains
the sky view factor or click Browse to select the file.
In the Layer list, click the layer with the sky view
factor.
6. Under Shadow, either:
• Click None if you do not want to include shadow
data in the atmospheric correction.
• Click Calculate to calculate the shadow data
automatically.
• Click From file to import the shadow data from a
file. In the From file list, click the file that contains
the shadow data or click Browse to select the file. In
the Layer list, click the layer of shadow data.
7. Click OK.
When you prepared the PCIDSK (.pix) file for atmospheric
correction, the band numbers may not match the channel
numbers. For example, band 1 from the sensor may not
necessarily be in channel 1 in your file. You may need to
match the sensor band numbers to the correct image channel
numbers.
1. Open the Atmospheric Correction Configuration
dialog box, see Opening the Atmospheric Correction
Configuration dialog box on page 251.
2. Under Sensor Information, click the Band Setup
button.
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2. Under Correction Parameter, click the Calculate

Matching band numbers to channel numbers button.
1. For each row under the Input Channel column, type
the channel number that contains the sensor band About Solar Zenith and Azimuth
corresponding to the band number under the Sensor
The Solar Azimuth and Solar Zenith express the position of
Band# column.
the sun. The Solar Azimuth is the angle of the direction of
2. In the Output Corrected column, click to select the the sun measured clockwise from the North along the
rows corresponding to the channels that you want to horizon. If the solar azimuth is measured from the South,
correct. Rows identified by a check mark will be usually referred to as the bearing, it will have to be adjusted
corrected. since Focus assumes that North is the origin. The Solar
3. If the NoData value is included in the metadata, it will Zenith is the angle measured between the local zenith and
be entered automatically. If it is not, in the NoData the line of sight of the sun.
Value column type the NoData value for each channel
Illustrating Solar Zenith and Solar Azimuth
in its corresponding row.
4. In the Gain Setting column, type the gain setting value
from the header file.
The gain setting is only needed for the MOMS and Aster
sensors. It represents the offset between the image and
the calibration.
5. Click OK.

Opening the Solar Calculations dialog box

The solar zenith and azimuth are important values used in
the atmospheric correction. If you imported you images
using a CD read algorithm, the values can be extracted from
the metadata. Calculating the solar zenith and azimuth

1. Open the Atmospheric Correction Configuration 1. In the Date boxes click the month, day, and year when
dialog box, see Opening the Atmospheric Correction the image was taken.
Configuration dialog box on page 251. 2. In the Time boxes, type hours, minutes, and seconds
when the image was taken.

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3. In the Latitude box, type the y-coordinate of the center
of the image.
4. In the Longitude box, type the x-coordinate of the center
of the image.
5. Click Calculate.
6. Click OK.
About visibility
Visibility, or optical depth, is a meteorological statistic that
calculates the opacity of the atmosphere at a certain time
and place. It measures the furthest distance that a person can
see a prominent object. In Focus the range is between 5 and
180 kilometers.
Focus uses the value set in the Visibility box. For more
information, see Opening the Atmospheric Correction
Configuration dialog box on page 251 for the Spatially
Varying Conditions, and for Constant Conditions options,
see Opening the Run Atmospheric Correction dialog box on
page 260. When you use the Spatially Varying Conditions
option, Focus calculates the visibility for each pixel in the
image using the Visibility value as a starting point for the
calculation. When you use the Constant Conditions option,
Focus uses the Visibility value as a constant for each pixel
in the image. The calculation results in a Visibility layer that
is a temporary PCIDSK (.pix) file with its default file name
being the the original file name prefixed with 'hot_level_'.
Visibility is used to more accurately specify the atmospheric
conditions at the time the image was taken. If the metadata
that came with the image does not include the visibility
values, you can obtain it from the following sources:
Chapter 7: Atmospheric correction
USA: http://www.noaa.gov/wx.html and Canada:
http://www.weatheroffice.ec.gc.ca/canada_e.html
About adjacency
Adjacency is the effect of backscattering on neighboring
pixels. It is used to more accurately specify the atmospheric
conditions at the time the image was taken.
The adjacency effect is calculated for an area around each
pixel up to a maximum of 200 pixels. For example, an image
with 30-meter resolution like Landsat will have a maximum
Adjacency value of 6, because 200 multiplied by 30 meters
is 6000 meters, which is 6 kilometers. Therefore, an
Adjacency value of 0 would not take the adjacency effect
into consideration while 6 would calculate the maximum
effect. The default is 1 and is suitable for most cases.
Determining the offset to surface temperature
value
Occasionally there may be a consistent difference in
temperature between actual temperatures measured on the
ground and those reported in the Spectral Plot. To verify if
you need to compensate for this difference, you need to
collect the temperature of identifiable points in the region
at the time the image was captured. These temperature
samples are sometimes referred to as 'ground truths'.
If you compare the ground truths to the results from the same
points collected on a temperature layer using the Spectral
Plot, the temperature for each point in both should be the
same. If you observe a consistent difference in temperature,
you can enter the value in the Offset to surface temperature
box.
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For example, you compare the actual water temperatures of
three lakes to their temperatures reported in the Spectral Plot
and discover that there is a difference of 2 degrees between
the ground truths and the Spectral Plot. Therefore, you type
2 in the Offset to surface temperature box.
you are not obtaining expected results, compare the
calibration coefficients (gain and bias values) in your data s
metadata file to those in the calibration file. If the values are
significantly different, you can create you own calibration
file specific to your data.

1. Configure and run the atmospheric correction. For more
information, see Opening the Atmospheric Correction
Configuration dialog box on page 251.
2. Position the cursor precisely on the feature that you can
clearly identify in the image for which you have a known
ground temperature.
3. In the Maps tree, right-click the ATCOR MetaLayer.
4. Click Spectra Plot.
5. On the Atcor Spectra Plotting dialog box, click From
Image.
6. Compare the actual temperature of the feature to the
temperature displayed under Report.
7. Repeat step 2 to step 6 for each ground truth.
The calibration file contains a table of the bands, the gain
value for each band, and the bias for each band. ATCOR
uses mW/cm-2 sr-1 micron-1 as the radiance unit for each
band, except the thermal band which uses mW m-2 sr-1
micron-1. Since the sensors may use a different radiance
unit, you may need to convert the values. For more
information, visit
http://www.op.dlr.de/atcor/atcor2+3_faq.html.
For example, some calibration coefficients are measured in
W m-2 sr-1 micron-1. To convert it to the ATCOR radiance
value, you multiply the values in the metadata file by 0.1.
Example of a calibration file

Editing an existing calibration file to

create a new file
The standard calibration files are in the cal folder under the
atcor folder where you installed Geomatica (for example,
C:\Program Files\Geomatica_V100\atcor\cal). Each sensor
has a set of calibration files created by Dr. Richter.
When you complete the Atmospheric Correction
Configuration dialog box, you can use one of the standard .
calibration files since they are sufficient in most cases. If

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1. Open a standard calibration file for the sensor appropriate
for your data.
2. Open the metadata file that came with your data.
3. If required, convert the values from the metadata file to
ATCOR radiance units: mW/cm-2 sr-1 micron-1 (or mW
m-2 sr-1 micron-1 for thermal bands).
4. Replace the bias and gain values for each band with the
converted values from the metadata file.
5. Save as a new file with the .cal extension in the cal folder
in the folder for the appropriate sensor.
Opening the Define Haze and Cloud
dialog box
After configuring the parameters for atmospheric correction,
you must create a mask over the hazy and cloudy areas in
the image while excluding areas covered by water or snow.
Water and snow are identified by comparing the water
reflectance values in the NIR band to the reflectance values
in the snow band (1.6 um band).
In most cases the default values for reflectance thresholds
will identify water and snow in image. However, you may
have to iteratively adjust the threshold values and recreate
the mask to achieve the desired results.
1. In the Maps tree, right-click the ATCOR MetaLayer.
2. Click Define Haze and Cloud.
Chapter 7: Atmospheric correction
Automatically creating a mask
1. Click Automatically Calculate Haze and Cloud.
2. Under Mask Size, click either:
• Large area haze mask to create a mask over all the
areas that may contain haze. This option also includes
areas where haze is suspected, but may not be
obvious upon visual inspection.
• Smaller area haze mask to create a mask only over
the areas where the haze is obvious.
3. Under Haze Thickness, click either:
• Correct thin haze to thick haze if you want to
include the thick haze (cloud cover) when you
perform the correction.
• Correct thin to medium haze if you want to ignore
the thick haze (cloud cover) when you perform the
correction.
4. In the Water Refl. Threshold in NIR (%) box, type
the value in percent representing the limit below which
is considered water reflectance values in the NIR sensor
band.
5. In the Water Refl. Threshold in Snow (1.6um) (%)
box, type the value in percent representing the limit
below which is considered water reflectance values in
the 1.6 um sensor band.
6. In the Cloud Refl. Threshold in Blue (<0.8um) (%)
box, type the value in percent representing the limit
below which is considered cloud reflectance values.
7. Under Output, click either:
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• Display to show the mask in the Focus view pane.
• Save to save the mask layer in a file. In the File list,
click the file where you want to save the mask or
click Browse to select the file. In the Haze Layer
list, click the layer where you want to save the haze
mask. In the Cloud Layer list, click the layer where
you want to save the cloud mask.
8. Click Create Mask.
Importing the masks from a file
1. Click Load Haze and/or Cloud from File.
2. Under Haze, in the File list click the file that contains
the haze mask or click Browse to select the file. In the
Layer list, click the layer containing the haze mask.
3. Under Cloud, in the File list click the file that contains
the cloud mask or click Browse to select the file. In the
Layer list, click the layer containing the cloud mask.
4. Click Create Mask.
Editing the Cloud mask
1. Right-click the ATCOR MetaLayer.
2. Click Edit Cloud Mask.
3. Use the New Shapes tools to modify the bitmap. For
more information, see Adding points to an active layer
on page 269.
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Editing the Haze mask
1. Right-click the ATCOR MetaLayer.
2. Click Edit Haze Mask.
3. Use the New Shapes tools to modify the bitmap. For
more information, see Adding points to an active layer
on page 269.
Editing the Visibility layer
1. Right-click the ATCOR MetaLayer.
2. Click Edit Visibility.
3. Use the New Shapes tools to modify the bitmap. For
more information, see Adding points to an active layer
on page 269.
Opening the Run Atmospheric
Correction dialog box
When you perform the atmospheric correction, Focus adds
a thematic raster metalayer to the Maps tree. The metalayer
contains the image being corrected, the Haze bitmap mask
layer, the Cloud bitmap mask layer, the visibility layer, and
a layer with the Value-Added Data.
To use the Spatially Varying Conditions option, you must
have the Red, near-infrared (NIR), and Short Wavelength
Infrared (SWIR) bands, and you must have reference areas
of known reflectance such as a section of dense vegetation
or a body of water present outside the haze to use as a

reference target. When you use the Spatially Varying
Conditions option, Focus calculates the visibility for each
pixel in the image using the value set in the Visibility box
on the Atmospheric Correction Configuration dialog box as
a starting point for the calculation.
Use the Constant Conditions option when you are missing
one of the bands, the image does not contain a reference
target, or you are sure that the image represents an area with
constant atmospheric conditions such as an area without
rugged terrain, large bodies of water, or mountains. When
you use the Constant Conditions option, Focus uses the value
set in the Visibility box on the Atmospheric Correction
Configuration dialog box as the visibility for each pixel in
the image.
The result of the atmospheric correction is a scaled surface
reflectance image with a range of 0 to 255 for 8-bit data and
0 to 65535 for 16-bit data. If you want unscaled values or
percent reflectance values, divide the scaled values by 4 for
8-bit data and by 10 for 16-bit data. For example, 150
divided by 10 equals 15% reflectance for a 16-bit image.
1. In the Maps tree, right-click the ATCOR MetaLayer.
2. Click Run Atmospheric Correction.
Running the correction
1. Click Constant Conditions if you want to perform the
correction assuming relatively uniform atmospheric
conditions over the image.
2. Click Spatially Varying Conditions if you want to
perform the correction assuming differing atmospheric
conditions throughout the image.
Chapter 7: Atmospheric correction
3. Under Corrected Output, in the File box click the file
where you want to save the corrected data or click
Browse to select a file.
Deriving additional data from the corrected
imagery
1. Under Value-added Data Output, in the File box click
the file where you want to save the additional data or
click Browse to select a file.
2. To perform a transformation that minimizes the influence
of soil brightness, select the Soil Adjusted Vegetation
Index check box.
3. To calculate the green leaf density, select the Leaf Area
Index check box.
If you want to change the equation used for the LAI
calculation, click LAI Options.
4. To calculate the calculate the amount of
photosynthetically active radiation absorbed by a plant
canopy, select the Fraction of Absorbed Radiation
check box.
If you want to change the values used in the FPAR
calculation, click FPAR Options.
5. To calculate ground reflectance, select the Surface
Albedo check box.
6. To calculate the difference between the emitted
atmospheric radiation and the emitted surface radiation,
select the Thermal Flux Difference check box.
7. To calculate the exchange rate of energy between the
earth s surface and the underground, select the Ground
Heat Flux check box.
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Chapter 7: Atmospheric correction
8. To calculate the shortwave solar radiation absorbed by
the surface, select the Absorbed Solar Radiation check
box.
9. To calculate the exchange rate of stored heat energy
between the air and the earth s surface, select the Latent
Heat check box. Latent heat flux is measures the amount
of energy needed to change matter from one state to
another (from solid to liquid to gas).
10. To calculate the exchange rate of excess heat energy
between the air and the earth s surface, select the
Sensible Heat check box. Sensible heat flux measures
the amount of energy needed to change air temperature.
11. To calculate the difference between absorbed and emitted
shortwave and longwave radiations, select the Net
Radiation check box.
12. Click Run Correction.
Opening the Leaf Area Index Model dialog box
The leaf area index (LAI) is the density of the green leaves
in an area. It is a measure of the green leaf area (one-side)
per unit of surface area.
You can choose one of two equations to calculate the
density: the Soil Adjusted Vegetation Index or the
Normalized Difference Vegetation Index. Both equations
contain three parameters whose values depend on the type
of vegetation being measured and on the season in which
they are being measured.
The LAI can only approximate typical trends in the
vegetation. It should not be used to replace or confirm field
measurements of other types of vegetation in different
seasons. The defaults provided for the equations are typical
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for soybean crops (Choudury et al. 1994). By using a
constant set of values, either custom or default, to calculate
the LAI for images of the same area over time, you can
uncover trends in the vegetation.
SAVI uses the red and near-infrared bands to measure the
density and vigor of green vegetation by attempting to
eliminate the reflectivity of the ground beneath the canopy.
NDVI uses the visible and near-infrared bands to measure
the density and vigor of green vegetation by comparing the
amount of visible light reflected to the amount of
near-infrared light reflected.
1. Open the Run Atmospheric Correction dialog box, see
Opening the Run Atmospheric Correction dialog box on
page 260.
2. Under Value-Added Data Output, select the Leaf Area
Index check box.
3. Click the LAI Options button.
Selecting the equation for calculating the Leaf Area
Index
1. Select one of the following:
• SAVI for the Soil Adjusted Vegetation Index
equation.
• NDVI for the Normalized Difference Vegetation
Index equation.

Changing the values for the fraction of
photosynthetically active radiation (FPAR)
equation
The Fraction of Photosynthetically Active Radiation (FPAR)
equation uses the red and near-infrared bands to calculate
the fraction of radiation between 400 and 700 nm absorbed
by green vegetation.
The FPAR equation contains three parameters whose values
depend on the type of vegetation being measured and on the
season in which they are being measured. The equation also
includes the result from the leaf area index (LAI) equation
that you selected.
The FPAR equation can only approximate typical trends in
the vegetation. It should not be used to replace or confirm
field measurements of other types of vegetation in different
seasons. The defaults provided for the equations are typical
values based on several studies (Asrar et al. 1984, Asrar
1989, Wiegand et al, 1990, 1991). By using a constant set
of values, either custom or default, to calculate the FPAR
for images of the same area over time, you can uncover
trends in the vegetation.
1. Open the Run Atmospheric Correction dialog box, see
Opening the Run Atmospheric Correction dialog box on
page 260.
2. Under Value-Added Data Output, select the Fraction
of Absorbed Radiation check box.
3. Click the FPAR Options button.
Chapter 7: Atmospheric correction
Opening the Advanced Option dialog
box
The Advanced Options are parameters used in producing
the data in the Value-Added Data Output section on the Run
Atmospheric Correction dialog box. The availability of the
parameters depends on the presence or absence of data:
• The Visibility data, BRDF Correction, and Terrain
Reflectance sections are only available in ATCOR3.
• The Emissivity and Radiation and heat flux sections are
only available if your data includes a thermal band.
• The Reference pixels section is only available if your
data does not include a Short Wavelength Infrared
(SWIR) band. If your data does include one, Focus
automatically calculates the reference pixels.
1. In the Maps tree, right-click the ATCOR MetaLayer.
2. Click Advanced Options.
Setting the parameters
1. Under Visibility data, click Calculate to calculate the
visibility values when you perform the atmospheric
correction or click Use Existing to select a visibility
layer calculated previously.
If you selected Use Existing, in the File list click the
file that contains the visibility layer or click Browse to
select a file. In the Layer list, click the layer containing
visibility values.
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