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ISIS 3 Application Documentation


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Calibrates Hayabusa 1 AMICA images

Overview Parameters


This program calibrates images from the Messenger mission's MDIS instrument. The input image is corrected for the following, in order, during calibration:

Step 1: Bias removal.

The signal level of AMICA is determined by a combination of an electronic offset which defines the "zero" level of the analog-to-digital converter (the bias) as well as any additional signal due to thermal electrons (the dark current). In general, the bias offset depends upon the electronics and CCD temperature. The bias for AMICA was empirically modeled as a function of time:
BIAS(t) = B0 + B1*t + B2*t2, where t is in units of days.
The constants B0, B1 and B2 were chosen to fit the curve to the data as closely as possible with the following values:
Variable Value
B0 3.18x10E02
B1 -4.12x10E-03
B2 2.00x10E-05

Step 2: Linearity correction:

The DN level stored in raw images is approximately proportional to the number of photons detected in each CCD pixel over the exposure time. Linearity is a measure of the degree to which the CCD response is proportional to the incident flux. Linearity was tested during the pre-flight and mission phase of the mission. During the pre-flight phase, DN values taken at different exposure times showed a linear intensity with an incidence flux between 1000 DN and 3500 DN. By curve-fitting the pre-flight data, the following equation was obtained:

Ioutput = (Iinput)c + L0*(Iinput)*exp(L1*Iinput)

Variable Value Description
Ioutput The observed intensity of the input.
Iinput 1000 DN - 3500 DN The actual intensity of the input.
c 1-5.0x10E-08 The power index of the output signal.
L0 -4.87x10E-11 Linearity correction term determined empirically.
L1 5.09x10E-03 Correction for the nonlinearity around the saturation limit (Iinput > 3800 DN)

Step 3: Hot pixel removal:

During the mission the CCD was exposed to intense radiation from cosmic rays. This resulted in some pixels with an aberrant dark current value that was higher than their neighbors (the hot pixels). The number of hot pixels increased during the mission. This made accurate measurement of faint objects such as stars difficult. The following hot pixels were identified and removed from the output images during calibration by setting their values to ISIS::Null:

Line Sample Dark Rate (DN/s)
407 300
599 408
820 14
930 624
897 716

Step 4: Read-out smear:

The AMICA instrument is shuttered electronically. Images are exposed for a certain exposure time in addition to the vertical charge-transfer period of 12.288 milliseconds. It is during the charge-transfer period that a read-out smear in the vertical direction is produced. The read-out smear is predominant in images with exposure times on the order of 100 microseconds. Originally the mission plan was to correct for this smear on-board the spacecraft. However, an anomaly in one of the reaction wheels on October 2, 2005 made this impossible. As a result of this, some of the images returned by the AMICA instrument are smear-corrected, while others are not. This necessitated creating a smear model to remove smears from images taken during the descending and ascending period. The read-out smear brightness Ismear for unbinned images is modeled from the observed images as follows:

Ismear(H) = SUM(H=0...Nv -1) { [K*[(Iraw(H,V) - Isky(H,V)]/Nv] }

Where: K = tVCT/(tVCT+texp)

For binned images a different formula is applied:
Ismear(H) = SUM(H=0...Nv - 1) { [ K1*Iraw(H,V) ] }

Where: K1 = (1/Nv)*[tVCT/ (tVCT+texp)]

A correction factor is then applied after the smear component is subtracted from the input image (Iraw):
Iout = C*(Iraw> - Ismear)

Where: C = 1/( 1 + K1 * ( (B - 1)/2*B ) )

IsmearThe read-out smear.
IrawThe intensity of the raw data taken with exposure time texp.
IskyThe sum of the bias and the dark current (~300 DN).
tVCTThe vertical charge-transfer period (0.012288 microseconds).
texpThe exposure time (in microseconds).
NvThe number of pixels along the V-direction (1024).
HThe line number of the pixel.
LThe sample number of the pixel.
BThe binning number.

Step 5: Flat-field correction:

Performs a correction for pixel-to-pixel variation in CCD response and vignetting (reduction of image brightness near the periphery compared with the center). Flat-field images for all bands were acquired using an integrating sphere at NEC Space Technologies, Ltd. at room temperature (around 30 degrees Celsius). A flat-field image is one which has constant uniform brightness everywhere. AMICA was pointed into the integrating sphere to acquire images of a field that is known be be spatially uniform to an accuracy of approximately 2%. The correction is accomplished by dividing each pixel of the output image by the corresponding pixel in the flat-field image.

Step 6 (Optional): Convert output units to Radiance or I over F:

This step is optional, and the formula used depends on the value of the UNITS user parameter. If UNITS=RADIANCE, the following formula will be used to convert the raw DN values to radiance (W/m2/sr/µm):

R = Raw*RadianceStandard*RadianceScaleFactor

RThe calibrated radiance (w/m2/sr/µm).
RawThe raw DN value.
RadianceStandardThe standard conversion factor from DNs to radiance.
RadianceScaleFactorAn adjustment factor for each filter.
If UNITS = IOF, first the above formula will be used to convert from raw DNs to calibrated Radiance, and then the following formula will be used to convert the raw DN values to I/F (radiance) units:

IoF = R*[pi*(Rs)2]/F

IoFThe calibrated radiance in units of I over F.
RThe calibrated radiance (w/m2/sr/µm).
RsThe distance in Astronomical Units (AU) between the Sun and the target body.
FThe solar flux (w/m2/µm) at 1 AU.
If UNITS=DN, no output conversion will be performed and the output units will be in raw DNs.


  1. Any in-flight dark current noise for this mission was buried in the read-out noise (~ 4 DN). When observing Itokawa, the image intensity had a range of 1000-3000 DN. Therefore, the dark current was considered negligible, and is not accounted for in this calibration application (see Ishiguro (2010) ).
  2. The derivation for the formula for smear-removal in the case of unbinned images does not appear in any of the references given below. Questions concerning the derivation steps for this formula should be directed towards the USGS.


  1. Ishiguro, Masateru, et al. "The Hayabusa Spacecraft Asteroid Multi-band Imaging Camera (AMICA)". Icarus 207(2010) 714-731.
  2. Ishiguro, Masateru. "Scattered light correction of Hayabusa/AMICA data and quantitative spectral comparisons of Itokawa". Publ. Astron. Soc. Japan (2014) 66(3), 55 (1-9).


Related Objects and Documents



Kris Becker2016-01-24 Original version
Tyler Wilson2016-07-08 Added calibration correction routines for linearity, PSF, smear removal for binned and unbinned images, and converting to I/F units. Also added hot pixel removal. Updated the application documentation. Added routines for converting a single-band ISIS cube to an OpenCV::OpenMat matrix and vice versa for the purpose of translating and scaling flat-field images so their dimensions match some AMICA images which have been cropped. Fixes #3880.
Kris Becker2016-08-25 Determined the LOSSY compression images must be scaled by a factor of 16 to match the LOSSLESS mode for proper calibration. Added the UNIT option to specify output calibration units as DN, RADIANCE or I/F. This parameter replaces the IOF parameter. Added option to allow user to determine to apply PSF correction. Added CONFIG parameter that user can provide a version of the calibration parameters to apply in amicacal.
Tyler Wilson2016-11-02 Added the "APPLYSMEAR" option which will force the smear correction calibration to be applied, and a new test for smear correction. The default is for this option to not be applied except in the case where an image is being processed for which on-board smear correction was not applied. Also made the applyPSF boolean parameter into a global variable for consistency with the applySmear global variable.
Kristin Berry2017-02-07 Removed the "APPLYSMEAR" option as a user-specifiable parameter. The smear correction will still be applied automatically when an image is being processed for which on-board smear correction was not applied (NSUB <= 1). Also updated application code for conformity with ISIS3 Coding Standards. Backward Compatibility Issue: The APPLYSMEAR parameter was removed. The smear correction will automatically be applied to images with 1 sub-image.
Kristin Berry2017-02-08 Removed the "PSF" correction option, since the PSF correction is not yet working. Related code has been commented out rather than removed entirely so that this work can potentially be resumed at a later date. Backward Compatibility Issue: The PSF parameter was removed since it is not yet working. The amicacal program cannot apply a PSF correction anymore.
Jeannie Backer2017-11-28 Updated radiance calibration to divide by exposure duration, as done with reflectance. Updated amicaCalibration????.trn file with latest radiance scale factor for sz (value provided by L. LeCorre, PSI). Updated to use filter V solar flux on all calculations. Brought code closer to ISIS3 coding standards. Fixes #5243

Parameter Groups


Name Description
FROM Input cube
TO Corrected Output cube
CONFIG Input AMICA calibration config file


Name Description
NULLPOLARPIX Set polarized pixels to ISIS::Null.
UNITS Convert to specified output calibrated units.

Files: FROM


This is the ISIS cube to be calibrated.

Type cube
File Mode input
Filter *.cub
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Files: TO


This is the output file. The output cube will be a calibrated version of the input cube.

Type cube
File Mode output
Pixel Type real
Filter *.cub
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This is the PVL file containing the input configuration parameters for the amicacal program. Users can modify the parameters as needed.

Type filename
File Mode input
Default $hayabusa/calibration/amica/amicaCalibration????.trn
Filter *.trn
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Four position angle glass polarizers (of dimension 200 x 200 pixels each) are attached to the upper left of the CCD chip. This option sets those pixels to Null in the calibrated image by default.

Type boolean
Default True
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Options: UNITS


Type string
Default IOF
Option List:
Option Brief Description
DN Convert to DN units
RADIANCE Convert to radiance unit
IOFIrradiance over flux Commonly referred to as "I over F", this option selects the output calibration units as irradiance over flux.
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