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The information in this document is subject to change without
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ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
PCI Geomatica’s Atmospheric Correction wizard provides users
with the easiest and fastest way to perform a variety of
atmospheric corrections. The wizard automatically populates most of
the required parameters using the image metadata and guides the
user through each major step. This tutorial outlines the
atmospheric correction workflow which now includes two new
features, added in Geomatica 2015. These new features are:
Interactive cloud masking and interactive spectral plot. More
information about the ATCOR workflow is available from the
Geomatica Help (Contents Tab > +Geomatica Help +Focus
+Atmospheric Correction).
In this tutorial atmospheric correction is being performed on
Landsat-8 Imagery (LC80180302014247LGN00) which is available online
from the Earth Explorer website:
http://earthexplorer.usgs.gov/.
Initial Project Setup
1. Open the Geomatica 2015 Focus application
2. Turn Auto Re-enhance on: a. In the menu bar, click on the
Tools dropdown menu and select Options… b. In the Options panel,
click on the Layers branch in the left pane c. Click the checkbox
next to Auto re-enhance grayscale and RGB layers
3. Open the ATCOR-Ground Reflectance window: select Analysis
Atmospheric Correction ATCOR – Ground Reflectance…
http://earthexplorer.usgs.gov/
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
4. The Atmospheric Correction panel opens and contains 4
standalone workflows.
5. Select the Sensor and image settings step in the ATCOR –
Ground Reflectance workflow
Sensor and Image Settings
1. Click browse beside the multispectral box and select the MTL
file from the Landsat-8 dataset. A box will appear with the options
PAN, MS and Thermal. Choose MS (Multispectral).
2. You can also choose to add a panchromatic band to the
Panchromatic box using the same method as above but choosing
PAN.
ATCOR Wizard General Design The ATCOR wizard includes 4
completely standalone workflows that can be run completely
independently of one another. The four (4) workflows are:
TOA (Top of Atmosphere) Reflectance Calculates top of atmosphere
reflectance for any supported sensor
Haze Removal Performs Cloud masking and haze removal and outputs
the result in DN values (Scaled at-sensor radiance)
ATCOR – Ground Reflectance Calculates ground reflectance values
for supported optical imagery and optionally performs haze removal
and cloud masking. The output is in reflectance values (0-100%)
ATCOR – Surface Temperature Calculates surface temperature for
TIR bands from supported satellite sensors.
The ATCOR wizard is equipped with indicator symbols that
indicate to a user that a given major step in the workflow is
correctly setup and the user can proceed to the next step. Red -
Step is not correctly setup Green - Step is correctly setup
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
3. Once the MS and PAN bands have been chosen the sensor
information will automatically be filled in.
Automatic Parameter Setup: The ATCOR wizard will automatically
read the metadata that is ingested when the image is imported into
a PIX file. Where necessary, these values will be converted so that
they can be used inside ATCOR. The following is a list of Sensor
parameters that are automatically set:
Sensor Type
Solar Zenith & Azimuth
Acquisition Date
Calibration Coefficients
Band-Channel Combination
Note: This is only a partial listing of the parameters that are
automatically set using the image metadata. Channel-Band setup
& Calculation of Calibration Coefficients
1. In the Radiometric Information section, choose the
calibration coefficients source: Channel Metadata (used in this
example), Import from Text File or Manual Entry. Click on Band
Setup… button
2. The Band Setup panel opens with the following table
Calibration coefficients (Gain/Offset) are automatically
calculated and converted to ATCOR units. Each input band has been
associated to their correct channel
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
4. In the Output Files section, click on the Browse button and
select your output file directory 5. Click OK 6. Click Next
Haze and Cloud Masking
The new cloud masking window has been added to this step of the
ATCOR workflow. 1. At the top of the next page is the Cloud Masking
section. Click on the Settings… button.
2. The Cloud Masking Settings widow will open.
3. In this window you can adjust the Seed TOA, Lowest TOA and
Maximum Dilation values. As you change these values you can see the
changes that are made to the cloud masks in the Preview window.
Experiment with different values to achieve the amount of cloud
masking that you prefer. As you change the values make sure to pan
around the image using the Overview window. The following
definitions from the help briefly outline each of the Threshold
values.
a. Seed TOA value: The Seed TOA value represents the brightest
pixels on clouds. If a cloud has at least one pixel above this
value, it is included in the mask. If all pixels in a cloud are
below this value, the cloud is excluded from the cloud mask. If
urban or other bright features are being misclassified as clouds,
try increasing this value. If the mask is missing most of the
clouds, try decreasing this value.
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
b. Lowest TOA value: The Lowest TOA value represents the lowest
value of all pixels in a cloud. If some portion of the cloud is
being excluded from the mask, try decreasing this value. If clouds
extend to urban features or other bright features, try increasing
this value.
c. Maximum Dilation value: The Maximum dilation value represents
the growing distance (in pixels) of each cloud. This distance does
not consider the pixel values.
4. Once you have the correct Threshold values click OK. The
values will have populated in the ATCOR GUI.
5. For the data in this tutorial the following values worked
well: Seed: 10, Lowest: 17 and Dilation: 2. You will notice in the
preview image that clouds are masked but haze and water are
not.
6. In the next section of this ATCOR step you can specify the
water masking options. You can choose to create a new water mask,
import a mask from file or omit the mask. The following values were
set for the water mask.
7. The final section in this step is to set the haze removal
parameters. You can choose whether to perform haze removal or not.
If you choose to perform haze removal you will need to enter the
percentage of the image that is covered in haze and the maximum
wavelength of the band on which to apply haze removal. The defaults
of 50% and 0.85 micrometers we kept for this tutorial.
8. Click Next
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
Illumination Conditions
1. In the next window you can define the Elevation Information
Setup by specifying a Constant Height value or by selecting a
digital elevation model (DEM).
a. If you do not have a DEM file, you can accept the default
Constant Height which is a value that represents a constant
elevation for the area covered by the image. This value is
automatically populated using the gmted2010.pix file and the image
center.
b. Otherwise, select the DEM File option and click the down
arrow beside the field to select a DEM file available in the
current session, or click Browse to select a file. When you select
a DEM file, the DEM File window automatically appears listing the
information for the selected DEM. This is automatically populated
using the file’s metadata. The selected file must be reprojectable.
You may also click the DEM Settings button to access this
window.
2. Click Next
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
Visibility Information
The new spectral plot tool has been added to this step of the
workflow. This tool allows users to experiment with different
atmospheric settings to determine how they affect the reflectance
values in the data. Users add library signatures to the graph and
compare the reflectance values of their image to the library
spectra. The graph will adjust the image reflectance values based
on the placement of the crosshair pointer on your image. With this
tool you can compare analogous ground cover types in the image to
their corresponding library spectra. For example, the user can
compare a pixel of a pine tree in an image to the library signature
for pine trees and test different atmospheric settings to get the
closest match. This provides confidence to the user that the
atmospheric settings accurately model the atmosphere at the time of
the image capture. In addition to imagery, a spectral library is
also required for use with the spectral plot tool. Spectral
libraries are available from the Geomatica 2014 atcor folder
(C:\PCI Geomatics\Geomatica 2014\atcor\spec_lib).
1. On the final window of the ATCOR GUI there are five sections.
You can leave the first two sections as their defaults for now.
2. Visibility Map is the third section. By default, the ATCOR
workflows use a constant visibility of 30 km. You can set the
constant visibility to a different value up to 180km.
Alternatively, you may also calculate a visibility map for varying
atmospheric conditions (if the red and NIR bands are provided).
Select Calculate (spatially varying conditions) and click Settings
to calculate a visibility map for varying conditions. The program
will compute a visibility map for the scene, using Dark Vegetation
pixels. These are defined based on NDVI and top-of-the-atmosphere
reflectance in the red band. The final option is to choose an
existing file that contains the visibility values. This specified
file must be reprojectable to the image, and the image must be
fully contained within the visibility map.
3. Once visibility has been determined you can click on the
Spectral Plot button.
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
4. The new spectral plotting window will open. Make sure that
the Window size around cursor is
set to 1, the Spectra quantity to sample is set to ground
reflectance and that the Use these
parameters for entire image checkbox is checked.
5. With the Spectral Plotting window open you can move the
cursor on your image in Focus. The graph will change depending upon
the pixel that is covered by the cursor. Move the cursor around
onto different land cover types to see the changes in the
graph.
6. The main purpose of this window is to determine how similar
your atmospherically corrected values are to library spectra. In
the Spectral Plotting window choose From Spectra File.
7. Navigate to the spec_lib folder (C:\PCI Geomatics\Geomatica
2014\atcor\spec_lib) and choose Landsat8.spl.
8. You can then choose which land type spectra you want to add
to the Spectral Plotting graph. In the example below Bright Soil
has been added to the graph. The red line represents the bright
soil library spectra and the black line represents a bright soil
pixel from the image. The spectral signature from the image pixel
is similar to the library spectral signature.
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
9. In the Spectral Plotting window there are many different
options that can be modified. The variable below the spectra table
is Adjacency Correction. If adjacency is set to 1 only the one
pixel that the cursor is on is displayed on the graph. If adjacency
is set to n, a window of n x n pixels around the cursor pixel is
taken into account and the adjacency effects of these pixels are
calculated. The graph will then display the calculated value of the
window of pixels.
10. In the Actor section of the Spectral Plot panel you can
change the Atmospheric Conditions, Aerosol type, visibility and
height.
a. This specific image was collected in September so the
Atmospheric information is set to Fall/Spring. The majority of this
image is rural area so the Aerosol type is Rural. You can adjust
this information based on your specific imagery.
b. Experiment with the atmospheric information to see which
information best matches your data.
Visibility and ground reflectance step: The atmospheric
Information parameters are used to define the atmospheric model
that is used to convert the at-sensor radiance values to surface
reflectance values. Three pieces of information are required:
1) Aerosol type (molecular and particulate makeup of atmosphere)
a. This parameter must be defined by the user
2) Condition (Water vapor content of atmosphere) a. This
parameter is automatically estimated based on the scene’s
latitude
and acquisition date/time 3) Visibility (aerosol optical depth
(AOD))
a. User can manually adjust this value until an optimum is found
or select Calculate to auto-estimate the AOD from dark
vegetation
The satellite viewing geometry is automatically calculated from
sensor metadata for those sensors with tilt capabilities. The
default output is the reflectance value in floating point precision
from 0-100%. The user can optionally scale the values to fit into 8
or 16 bit channels.
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
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ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
c. The third and fourth options are Constant Height and
Visibility. Both of these options were set previously. If these
were set as constant values you can experiment with these values to
determine how changing the values will affect the spectral
plot.
d. Check the box Use these parameters for the entire image. 11.
Once you are satisfied with the variables from the Spectral
Plotting window click Close. The
values that you changed in this window will be saved in the
ATCOR GUI.
Run ATCOR
1. You can now run the atmospheric correction. At the bottom of
the ATCOR window click Run. 2. If you have chosen the same options
as specified in this tutorial, the following files will be
created: Atmospherically Corrected Image Cloud Mask
Haze Mask Water Mask
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The information in this document is subject to change without
notice and should not be construed as a commitment by PCI
Geomatics. PCI Geomatics assumes no responsibility for any errors
that may appear in this document.
ATCOR- Ground Reflectance Workflow Geomatica 2015 Tutorial
The atmospherically corrected image can now be used in further
analysis. You will notice that the cloud mask is identical to the
mask that you defined in the cloud masking tool. The masks can be
used in future workflows to exclude these areas of the image from
the analysis.
Illumination Map Resampled & Clipped DEM
The illumination map helps to normalize affects caused by solar
illumination. The map helps the algorithm determine how illuminated
a pixel is regardless of the surface feature type. This is based
off of the solar angle, relative to the slope and aspect angle of
the pixel. For example, pixels oriented towards the sun are
brighter, whereas pixels oriented away from the sun will be darker
in the map.