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Updated lronaccal to use time-dependent darkfiles for dark calibration #4520

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Jul 14, 2022
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Updated lronaccal to use time-dependent darkfiles for dark calibration #4520

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1950b10
updated to use time dependent darks including darks for exp zero and …
victoronline Jun 7, 2021
c21fbf0
Merge branch 'USGS-Astrogeology:dev' into dev-lronaccal-1
victoronline Oct 4, 2021
c4b17c4
Updated lronaccal.xml documentation
victoronline Oct 4, 2021
85a1fa8
Updated formatting of text
victoronline Oct 4, 2021
dc92106
Added better documentation
victoronline Oct 4, 2021
40c8caa
fixed formatting
victoronline Oct 4, 2021
d24c091
removed extra tabs
victoronline Oct 4, 2021
80aa14b
Add radiance units label in lrowaccal output cube
cordellmichaud Mar 23, 2022
35151be
Merge pull request #18 from lrocdev/dev-lrowaccal-unitsfix
victoronline Apr 12, 2022
fc1ea29
Merge branch 'dev-lronaccal-1' of github.com:lrocdev/ISIS3 into dev-l…
victoronline Apr 29, 2022
8eb71a0
refactored code to allow callable for compatibility with gtest
victoronline Apr 29, 2022
4bb81fb
added gtests for 3 file types and made app callable
victoronline Jun 7, 2022
1bc3204
Merge branch 'dev' into dev-lronaccal-1
victoronline Jun 7, 2022
4af3b9d
Added changes for lronaccal to CHANGELOG.md
victoronline Jun 7, 2022
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180 changes: 94 additions & 86 deletions isis/src/lro/apps/lronaccal/lronaccal.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,97 +8,67 @@

<description>
<p>
lronaccal performs radiometric corrections to images acquired by the Narrow Angle
Camera aboard the Lunar Reconnaissance Orbiter spacecraft.
lronaccal performs radiometric corrections to images acquired by the Narrow Angle
Camera aboard the Lunar Reconnaissance Orbiter spacecraft. The LRO NAC camera
will make observations simulteously with the HiRise camera.
</p>

<p>
The LRO NAC detector has a total of 5064 pixels, divided among an A
channel and a B channel. The pixels alternate between the two channels:
ABABABAB, etc. Images from LROC NAC may or may not include all pixels in the
acquired image. There are special summing modes that are utilized
on-board the spacecraft to average detector pixels to combine them into a
single output pixel value. The value of the ISIS label keyord,
SpatialSumming, indicates the number of samples that were summed and
averaged to result in the pixel values stored in the file. Note that this
will reduce the number of samples in the output image by a factor of at
most the SpatialSumming mode value.
The LRO NAC detector has a total of 5064 pixels, divided among an A
channel and a B channel. The pixels alternate between the two channels:
ABABABAB, etc. Images from LROC NAC may or may not include all pixels in the
acquired image. There are special summing modes that are utilized
on-board the spacecraft to average detector pixels to combine them into a
single output pixel value. The value of the ISIS label keyord,
SpatialSumming, indicates the number of samples that were summed and
averaged to result in the pixel values stored in the file. Note that this
will reduce the number of samples in the output image by a factor of at
most the SpatialSumming mode value.
</p>
<p>
The LROC NAC camera has the ability to acquire images of differing sizes in
both line and sample. The starting hardware detector pixel for the
acquired image is specified by the ISIS label keyword, SampleFirstPixel.
The first pixel in the detector is indicated by a value of 0.
The LROC NAC camera has the ability to acquire images of differing sizes in
both line and sample. The starting hardware detector pixel for the
acquired image is specified by the ISIS label keyword, SampleFirstPixel.
The first pixel in the detector is indicated by a value of 0.
</p>

<p>
Dark current pixels are taken for each line from the masked pixels
that lie along each edge of the image.
</p>

<p>
If SpatialSumming is 1 the dark current pixels are averaged together then
this average is subtracted from all image pixels. If SpatialSumming is 2,
the dark current pixels for the A and B channel are averaged separately,
then the A channel dark average is subtracted from the A channel image
pixels and the B channel dark average is subtracted from the B channel
image pixels.
Dark current pixels are taken for each line from the masked pixels
that lie along each edge of the image.
</p>

<p>
The DN level in an uncalibrated image is the sum of the true signal from the scene,
the bias, the dark current, and random noise in all 3 components. The random noise in
the true signal and dark current is called shot noise and the random noise in the bias
is called read noise. The true signal, bias, and dark current are defined as mean
values so that if the random noise were averaged down to insignificance by taking a
very large number of images and averaging them, the resulting image would be the true
scene, bias, and dark current with no systematic error. That implies the statistical
distribution of the random noise has an average of zero, and therefore the random noise
has both positive and negative values, except for the trivial case of zero random noise.
If SpatialSumming is 1 the dark current pixels are averaged together then
this average is subtracted from all image pixels. If SpatialSumming is 2,
the dark current pixels for the A and B channel are averaged separately,
then the A channel dark average is subtracted from the A channel image
pixels and the B channel dark average is subtracted from the B channel
image pixels.
</p>

<p>
The calibration equation is:
<pre> reportedDN = ObservedDN - MeanBias - DarkCurrent </pre>
The dark average produced is dependant on which options are selected.
If the custom dark file option is selected, the provided dark file will be used.

Where:
<pre>
ObservedDN = TrueDN + E
E is a randomly sampled value from (mu, sigma^2) and mu=0
TrueDN is the signal that would be reported in an idealized case of an instrument with zero noise.</pre>
</p>
If the image has exposure code of zero, the nearest dark files with exposure
code of zero will be used.

<p>
Let's look at the case of a calibrated image for which the true signal
is zero, a dark image. In calibration the mean bias and dark current are
subtracted. The random noise term is then randomly sampled from a known
distribution with a mean of zero. Since the distribution has a mean of
zero, values for the random noise can be positive or negative.
Therefore, the addition of random noise to a pixel with true signal near
zero can result in negative DN values.
</p>
If UseNearestTimeDarkFile option is selected, the dark file with the nearest
time to the image will be used for dark correction.

<p>
Negative reported DNs are possible when E &lt; -1 * TrueDN. These are
pixels in a very dark image that happen to have a strongly negative
random noise value.
</p>
If UseNearestTimeDarkFilePair option is selected, the pair of dark files that
the image time lies between, will be used, as long as the difference between
dark files doesn't exceed 45 days. If a suitable pair is not found, the
latest dark file taken before the image will be used.


pixel_dark_average =
avgDarkLine1_pixel * |darkfile1_time - time| + avgDarkLine2_pixel * |darkfile2_time - time|
/ (1.0 * ( |darkFile1_time - time| + |darkFile2_time - time| ) )

<p>
Note: ObservedDN and TrueDN both must be greater than or equal to zero.
For ObservedDN, it's because the hardware is not able to report negative
DN values . For TrueDN, it's because radiance and reflectivity cannot be
negative. The dimmest target is one that is completely dark, and for
that target TrueDN = 0.
</p>

<p>
If run on a non-spiceinited cube, this program requires access to local mission-specific
SPICE kernels, in order to find the distance between the sun and the target body.
When run on a spiceinited cube, this can be determined using the camera model.
Using a spiceinited cube as input has the advantage of not requiring that local
mission-specific kernels be available. (See spiceinit web=true.)
</p>

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</description>

<history>
Expand All @@ -108,6 +78,13 @@
<change name="Adam Licht" date="2013-02-28">
No longer treat negative DNs differently in the Non-linearity correction.
</change>
<change name="Victor Silva" date="2020-01-06">
Added option for base calibration directory
</change>
<change name="Victor Silva" date="2020-06-19">
Updated dark calibration to use nearest pair of dark images to calibrate
</change>

</history>

<category>
Expand Down Expand Up @@ -169,30 +146,61 @@
</description>
</parameter>
</group>
<group name="Dark Options">

<group name="Dark File Options">
<parameter name="Dark">
<type>boolean</type>
<default><item>True</item></default>
<brief>
Calibrate using the average dark pixels.
Calibrate using average dark pixels.
</brief>
<description>
</description>
<inclusions><item>DarkFileType</item></inclusions>
</parameter>

<parameter name="DarkFileType">
<type>string</type>
<brief>
Custom Dark, Nearest Dark, Nearest Dark Pair?
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This description doesn't mean anything to me. Is there a short, one sentence, way to describe this?

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Updated with better documentation.

</brief>
<description>
</description>
<inclusions><item>DarkFile</item></inclusions>
<default><item>Pair</item></default>
<list>
<option value="PAIR">
<brief>Pair</brief>
<description>
</description>
<exclusions><item>DarkFile</item></exclusions>
</option>
<option value="NEAREST">
<brief>Nearest</brief>
<description>
</description>
<exclusions><item>DarkFile</item></exclusions>
</option>
<option value="CUSTOM">
<brief>Custom Dark File</brief>
<description>
</description>
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<inclusions>
<item>DarkFile</item>
</inclusions>
</option>
</list>
</parameter>

<parameter name="DarkFile">
<type>filename</type>
<default><item>Default</item></default>
<default><item></item></default>
<brief>
Calibrate using the average dark pixels.
</brief>
<description>
</description>
</parameter>
</group>

<group name="Nonlinearity Options">
<parameter name="Nonlinearity">
<type>boolean</type>
Expand All @@ -207,7 +215,7 @@
<item>NonlinearityFile</item>
</inclusions>
</parameter>

<parameter name="OffsetFile">
<type>filename</type>
<default><item>Default</item></default>
Expand All @@ -217,7 +225,7 @@
<description>
</description>
</parameter>

<parameter name="NonlinearityFile">
<type>filename</type>
<default><item>Default</item></default>
Expand All @@ -228,7 +236,7 @@
</description>
</parameter>
</group>

<group name="Flatfield Options">
<parameter name="Flatfield">
<type>boolean</type>
Expand All @@ -240,7 +248,7 @@
</description>
<inclusions><item>FlatfieldFile</item></inclusions>
</parameter>

<parameter name="FlatfieldFile">
<type>filename</type>
<default><item>Default</item></default>
Expand All @@ -251,7 +259,7 @@
</description>
</parameter>
</group>

<group name="Radiometric Options">
<parameter name="Radiometric">
<type>boolean</type>
Expand All @@ -266,7 +274,7 @@
<item>RadiometricFile</item>
</inclusions>
</parameter>

<parameter name="RadiometricType">
<type>string</type>
<brief>
Expand All @@ -288,7 +296,7 @@
</option>
</list>
</parameter>

<parameter name="RadiometricFile">
<type>filename</type>
<default><item>Default</item></default>
Expand Down
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