Updated cisscal to match IDL version 3.9.1 (#3406) (56bb32fc) · Commits · aflab / astrogeology / ISIS3

isis/src/cassini/apps/cisscal/cisscal.xml

+12 −5

Original line number	Diff line number	Diff line
		@@ -113,11 +113,12 @@
		Step 7: Divide by Correction Factor
		</strong>
		This step is implemented in order to force theory and observation to match.
		It consists of 2 processes. First, the image is divided by its correction
		factor. Next, if the target of the image is Jupiter it is divided by another
		correction factor specific to Jupiter images. This step requires no user defined
		parameters. It uses a correction factor file and Jupiter correction factor found
		It consists of 2 processes. First, the image is divided by its correction factor.
		This step requires no user defined parameters. It uses a correction factor file found
		in the Cassini calibration correction directory.
		Second, a sensitivity vs time correction is completed.
		A sensitivity value is calculated based off of the instrument Id and
		the image is multiplied by this value.
		</p>
		<p>
		<strong>
		@@ -136,7 +137,7 @@
		method requires large regions of dark sky pixels present for all lines and
		uses an image mean to construct a 2-Hz signal.

		The second omited step is <strong>A-B pixel pairs correction</strong>
		The second omitted step is <strong>A-B pixel pairs correction</strong>
		(also referred to as anti-blooming correction or bright/dark pixel pair
		removal). In the IDL program, this correction is only performed if the
		labels of the image indicate that the AntiBloomingStateFlag is "On" and
		@@ -213,6 +214,12 @@
		<change name="Adam Paqeutte" date="2019-08-07">
		Added a version number to the cisscal label output. Currently at version 3.8.
		</change>
		<change name="Kaitlyn Lee" date="2019-08-14">
		Updated to match IDL version 3.9.1. Removed jupiter correction, added
		checks for ShutterStateId, added check for bias mean strip,
		updated values in divideByAreaPixel, and added sensitivity vs
		time correction. Fixes #3351.
		</change>
		</history>

		<category>

isis/src/cassini/apps/cisscal/main.cpp

+174 −77

Original line number	Diff line number	Diff line
		@@ -47,6 +47,7 @@ namespace gbl {
		void FindDustRingParameters();
		FileName FindFlatFile();
		void FindCorrectionFactors();
		void FindSensitivityCorrection();
		void DNtoElectrons();
		void FindShutterOffset();
		void DivideByAreaPixel();
		@@ -78,8 +79,9 @@ namespace gbl {
		double sumFactor;
		double efficiencyFactor;
		//correction factor variables
		double jupiterCorrectionFactor;
		double correctionFactor;
		bool sensCorrection;
		double sensVsTimeCorr;
		}

		void IsisMain() {
		@@ -103,8 +105,9 @@ void IsisMain() {
		gbl::opticsArea = 1.0;
		gbl::sumFactor = 1.0;
		gbl::efficiencyFactor = 1.0;
		gbl::jupiterCorrectionFactor = 1.0;
		gbl::correctionFactor = 1.0;
		gbl::sensCorrection = false;
		gbl::sensVsTimeCorr = 1.0;

		// Set up our ProcessByLine objects
		// we will take 2 passes through the input cube
		@@ -132,7 +135,7 @@ void IsisMain() {

		// Add the radiometry group
		gbl::calgrp.setName("Radiometry");
		gbl::calgrp += PvlKeyword("CisscalVersion", "3.8");
		gbl::calgrp += PvlKeyword("CisscalVersion", "3.9.1");

		// The first ProcessByLine pass will either compute bitweight values or copy input values

		@@ -223,6 +226,7 @@ void IsisMain() {
		// Set the remaining necessary input cube files for second pass
		CubeAttributeInput att;
		gbl::FindCorrectionFactors();
		gbl::FindSensitivityCorrection();
		if(gbl::flatCorrection) { // Calibrate() parameter in[1]
		secondpass.SetInputCube(flatFile.expanded(), att);
		}
		@@ -264,6 +268,12 @@ void IsisMain() {
		* new idl cisscal version, 3.6.
		* @history 2017-06-08 Cole Neubauer - Added dustfile2 correction.
		* Updated ConstOffset value to match new idl cisscal version, 3.8.
		* @history 2019-08-14 Kaitlyn Lee - Removed jupiter correction. Added
		* check for ShutterStateId, and if it is Disabled,
		* do not subtract an offset from the exposure time.
		* Added Sensitivity vs Time Correction after
		* correction factors.
		* Matches cisscal version 3.9.1.
		*/
		void gbl::Calibrate(vector<Buffer > &in, vector<Buffer > &out) {
		Buffer *flat = 0;
		@@ -361,8 +371,12 @@ void gbl::Calibrate(vector<Buffer > &in, vector<Buffer > &out) {
		// UPDATE #3: Rhea SATCAL obs from rev 163 give NAC offset of 2.74 and
		// WAC offset of 2.67 ms, much less noisy results than using stars.
		// (1/31/2013 - BDK)
		// UPDATE #4: From S100 Vega (WAC) and 77/78 Tau (NAC): NAC offset of
		// 2.51, WAC offset of 2.63, but analysis far more noisy than for Rhea
		// so keep previous values. (8/4/2017 - BDK)

		double ConstOffset;
		if(gbl::cissLab->ShutterStateId() != "Disabled") {
		if(gbl::cissLab->InstrumentId() == "ISSNA") {
		ConstOffset = 2.75;
		}
		@@ -370,6 +384,7 @@ void gbl::Calibrate(vector<Buffer > &in, vector<Buffer > &out) {
		ConstOffset = 2.67;
		}
		exposureTime = exposureTime - ConstOffset;
		}
		outLine[sampIndex] = outLine[sampIndex] * 1000 / exposureTime; // 1000 to scale ms to seconds
		}
		// 6c Divide By Area Pixel
		@@ -378,10 +393,15 @@ void gbl::Calibrate(vector<Buffer > &in, vector<Buffer > &out) {
		outLine[sampIndex] = outLine[sampIndex] / gbl::efficiencyFactor;
		///////////////////////////////////////////////////////////////////////////////////////////////////////////
		// STEP 7) correction factors
		outLine[sampIndex] = outLine[sampIndex] * ((gbl::jupiterCorrectionFactor / gbl::correctionFactor));
		// 7a Correction Factors
		outLine[sampIndex] = outLine[sampIndex] / gbl::correctionFactor;
		if (outLine[sampIndex] < 0) {
		outLine[sampIndex] = 0;
		}
		// 7b Sensitivity vs Time Correction
		if(gbl::sensCorrection) {
		outLine[sampIndex] = outLine[sampIndex] * gbl::sensVsTimeCorr;
		}
		///////////////////////////////////////////////////////////////////////////////////////////////////////////
		}
		else if (IsSpecial(bitweightCorrected[sampIndex][lineIndex])) {
		@@ -543,6 +563,8 @@ FileName gbl::FindBitweightFile() {
		* @history 2008-11-05 Jeannie Walldren - Original version
		* @history 2009-05-27 Jeannie Walldren - Commented out table
		* if-statement as done idl cisscal version 3.6.
		* @history 2019-08-14 Kaitlyn Lee - Added check for a corrupt
		* bias strip mean to match cisscal version 3.9.1.
		*/
		void gbl::ComputeBias() {
		gbl::calgrp += PvlKeyword("BiasSubtractionPerformed", "Yes");
		@@ -599,6 +621,17 @@ void gbl::ComputeBias() {
		gbl::bias = gbl::OverclockFit();
		}
		else { // use BiasStripMean in image label if can't use overclock

		// Corrupt bias strip mean
		if(gbl::cissLab->BiasStripMean() < 0.0) {
		gbl::calgrp.findKeyword("BiasSubtractionPerformed").setValue("No: Bias strip mean value corrupt.");
		gbl::calgrp += PvlKeyword("BiasSubtractionMethod", "Not applicable: No bias subtraction");
		gbl::calgrp += PvlKeyword("NumberOfOverclocks", "Not applicable: No bias subtraction");
		gbl::bias.resize(1);
		gbl::bias[0] = 0.0;
		return;
		}

		gbl::bias.resize(1);
		gbl::bias[0] = gbl::cissLab->BiasStripMean();
		}
		@@ -798,6 +831,9 @@ void gbl::Linearize() {
		* updated with new idl cisscal version, 3.6. Added
		* effective wavelength to calibration group in
		* labels.
		* @history 2019-08-14 Kaitlyn Lee - Added check for
		* ShutterStateId to disable dust ring correction.
		* Matches cisscal version 3.9.1.
		*/
		void gbl::FindDustRingParameters() {
		// No dustring or mottle correction for WAC
		@@ -814,6 +850,20 @@ void gbl::FindDustRingParameters() {
		return;
		}

		// Disable dust ring and mottle correction if ShutterStateId is Disabled
		if(gbl::cissLab->ShutterStateId() == "Disabled") {
		gbl::dustCorrection = false;
		gbl::mottleCorrection = false;
		gbl::calgrp += PvlKeyword("DustRingCorrectionPerformed", "No: ShutterStateId is Disabled.");
		gbl::calgrp.findKeyword("DustRingCorrectionPerformed").addComment("DustRing Correction Parameters");
		gbl::calgrp += PvlKeyword("DustRingFile", "Not applicable: No dustring correction");
		gbl::calgrp += PvlKeyword("MottleCorrectionPerformed", "No: dustring correction");
		gbl::calgrp += PvlKeyword("MottleFile", "Not applicable: No dustring correction");
		gbl::calgrp += PvlKeyword("EffectiveWavelengthFile", "Not applicable: No dustring correction");
		gbl::calgrp += PvlKeyword("StrengthFactor", "Not applicable: No dustring correction");
		return;
		}

		// dustring correct for NAC
		gbl::dustCorrection = true;
		gbl::calgrp += PvlKeyword("DustRingCorrectionPerformed", "Yes");
		@@ -1019,8 +1069,20 @@ void gbl::FindDustRingParameters() {
		* @return <B>FileName</B> Name of the flat file for this image.
		* @internal
		* @history 2008-11-05 Jeannie Walldren - Original version
		* @history 2019-08-14 Kaitlyn Lee - Added check for
		* ShutterStateId to disable flat field correction.
		* Matches cisscal version 3.9.1.
		*/
		FileName gbl::FindFlatFile() {
		// Disable flat field correction if ShutterStateId is Disabled
		if(gbl::cissLab->ShutterStateId() == "Disabled") {
		gbl::calgrp += PvlKeyword("FlatfieldCorrectionPerformed", "No: ShutterStateId is Disabled.");
		gbl::calgrp.findKeyword("FlatfieldCorrectionPerformed").addComment("Flatfield Correction Parameters");
		gbl::calgrp += PvlKeyword("SlopeDataBase", "Not applicable: No flat field correction");
		gbl::flatCorrection = false;
		return "";
		}

		// There is a text database file in the slope files directory
		// that maps filter combinations (and camera temperature)
		// to the corresponding slope field files.
		@@ -1252,22 +1314,38 @@ void gbl::FindShutterOffset() {
		*
		* @internal
		* @history 2008-11-05 Jeannie Walldren - Original version
		* @history 2019-08-14 Kaitlyn Lee - Added check for
		* ShutterStateId. Updated solid angle and optics
		* area values. Matches cisscal version 3.9.1.
		*/
		void gbl::DivideByAreaPixel() {
		// Disable flat field correction if ShutterStateId is Disabled
		if(gbl::cissLab->ShutterStateId() == "Disabled") {
		gbl::calgrp += PvlKeyword("DividedByAreaPixel", "No: ShutterStateId is Disabled.");
		gbl::calgrp += PvlKeyword("SolidAngle", "Not applicable: No division by area pixel");
		gbl::calgrp += PvlKeyword("OpticsArea", "Not applicable: No division by area pixel");
		gbl::calgrp += PvlKeyword("SumFactor", "Not applicable: No division by area pixel");
		return;
		return;
		}
		// These values as per ISSCAL
		// SolidAngle is (FOV of Optics) / (Number of Pixels)
		// OpticsArea is (Diameter of Primary Mirror)^2 * Pi/4
		// Optics areas below come from radii in "Final Report, Design
		// and Analysis of Filters for the Cassini Narrow and Wide
		// Optics" by David Hasenauer, May 19, 1994.

		// We will adjust here for the effects of SUM modes
		// (which effectively give pixels of 4 or 16 times normal size)

		gbl::calgrp += PvlKeyword("DividedByAreaPixel", "Yes");
		if(gbl::cissLab->NarrowAngle()) {
		gbl::solidAngle = 3.6 * pow(10.0, -11.0);
		gbl::opticsArea = 264.84;
		gbl::solidAngle = 3.58885 * pow(10.0, -11.0);
		gbl::opticsArea = 284.86;
		}
		else {
		gbl::solidAngle = 3.6 * pow(10.0, -9);
		gbl::opticsArea = 29.32;
		gbl::solidAngle = 3.56994 * pow(10.0, -9);
		gbl::opticsArea = 29.43;
		}
		// Normalize summed images to real pixels

		@@ -1313,9 +1391,24 @@ void gbl::DivideByAreaPixel() {
		* the effic_db (now called omega0) to calculate the
		* efficiency factor for intensity units. Now, the
		* method is not far off from the I/F method.
		* @history 2019-08-14 Kaitlyn Lee - Added check for
		* ShutterStateId. Matches cisscal version 3.9.1.
		*/

		void gbl::FindEfficiencyFactor(QString fluxunits) {
		// Disable flat field correction if ShutterStateId is Disabled
		if(gbl::cissLab->ShutterStateId() == "Disabled") {
		gbl::calgrp += PvlKeyword("DividedByEfficiency", "No: ShutterStateId is Disabled.");
		gbl::calgrp += PvlKeyword("EfficiencyFactorMethod", "Not applicable: No division by efficiency");
		gbl::calgrp += PvlKeyword("TransmissionFile", "Not applicable: No division by efficiency");
		gbl::calgrp += PvlKeyword("QuantumEfficiencyFile", "Not applicable: No division by efficiency");
		gbl::calgrp += PvlKeyword("SpectralFile", "Not applicable: No division by efficiency");
		gbl::calgrp += PvlKeyword("SolarDistance", "Not applicable: No division by efficiency");
		gbl::calgrp += PvlKeyword("EfficiencyFactor", "Not applicable: No division by efficiency");
		gbl::calgrp += PvlKeyword("TotalEfficiency", "Not applicable: No division by efficiency");
		return;
		}

		// for polarized filter combinations, use corresponding clear transmission:
		QString filter1 = gbl::cissLab->FilterName()[0];
		QString filter2 = gbl::cissLab->FilterName()[1];
		@@ -1585,7 +1678,7 @@ void gbl::FindEfficiencyFactor(QString fluxunits) {
		//=====End DN to Flux Methods====================================================================//


		//=====1 Correction Factors Methods================================================================//
		//=====2 Correction Factors Methods================================================================//

		/**
		* This method is modelled after IDL CISSCAL's
		@@ -1601,8 +1694,18 @@ void gbl::FindEfficiencyFactor(QString fluxunits) {
		* available.
		* @history 2017-06-08 Cole Neubauer - removed polarization correcton
		* factor and added Jupiter correction factor to match 3.8 update
		* @history 2019-08--14 Kaitlyn Lee - Removed Jupiter correction factor
		* since it was removed in the 3.9.1 update.
		*/
		void gbl::FindCorrectionFactors() {
		// Disable correction factor if ShutterStateId is Disabled
		if(gbl::cissLab->ShutterStateId() == "Disabled") {
		gbl::calgrp += PvlKeyword("CorrectionFactorPerformed", "No: ShutterStateId is Disabled.");
		gbl::calgrp.findKeyword("CorrectionFactorPerformed").addComment("Correction Factor Parameters");
		gbl::calgrp += PvlKeyword("CorrectionFactorFile", "Not applicable: No correction factions.");
		return;
		}

		QString filter1 = gbl::cissLab->FilterName()[0];
		QString filter2 = gbl::cissLab->FilterName()[1];
		if(filter1 == "IRP0" \|\| filter1 == "P120" \|\| filter1 == "P60" \|\| filter1 == "P0"
		@@ -1674,68 +1777,62 @@ void gbl::FindCorrectionFactors() {

		}
		gbl::calgrp += PvlKeyword("CorrectionFactor", toString(gbl::correctionFactor));
		// Now find Jupiter correction if neccesary
		if (gbl::cissLab->TargetName() == QString("jupiter")){
		FileName jupiterCorrectionFactorFile(gbl::GetCalibrationDirectory("correction") + "jupiter_correction.tab");
		if(!jupiterCorrectionFactorFile.fileExists()) { // correction factor file not found, stop calibration
		throw IException(IException::Io,
		"Unable to calibrate image. JupiterCorrectionFactorFile ***"
		+ jupiterCorrectionFactorFile.expanded() + "*** not found.", _FILEINFO_);
		}
		gbl::calgrp += PvlKeyword("JupiterCorrectionFactorPerformed", "Yes");
		gbl::calgrp += PvlKeyword("JupiterCorrectionFactorFile", jupiterCorrectionFactorFile.expanded());
		CisscalFile *jCorrFact = new CisscalFile(jupiterCorrectionFactorFile.expanded());
		gbl::jupiterCorrectionFactor = 0.0;
		for(int i = 0; i < jCorrFact->LineCount(); i++) {
		QString line;
		jCorrFact->GetLine(line); //assigns value to line
		line = line.simplified().trimmed();
		QStringList cols = line.split(" ");
		col1 = cols.takeFirst();
		if(col1 == gbl::cissLab->InstrumentId()) {
		col2 = cols.takeFirst();
		if(col2 == filter1) {
		col3 = cols.takeFirst();
		if(col3 == filter2) {
		col4 = cols.takeFirst();
		if(col4 == "") {
		gbl::jupiterCorrectionFactor = 1.0;
		// dividing 1.0 by correction factor implies this correction is not performed
		gbl::calgrp.findKeyword("JupiterCorrectionFactorPerformed").setValue("No: JupiterCorrectionFactorFile contained no factor for filter combination");
		}
		else {
		gbl::jupiterCorrectionFactor = toDouble(col4);
		}
		break;
		}
		else {
		continue;
		}
		}
		else {
		continue;
		return;
		}


		/**
		* This method is modelled after IDL CISSCAL's
		* cassimg_sensvstime.pro. IDL documentation:
		* Sensitivity vs. time correction derived from stellar photometry:
		*
		* NAC, all data (~8% total decline from S03 to S100):
		* slope = -1.89457e-10
		*
		* WAC, all data (~3% total decline from S17 to S100):
		* slope = -9.28360e-11
		*
		* @internal
		* @history 2019-08-14 Kaitlyn Lee - Original version
		*/
		void gbl::FindSensitivityCorrection() {
		if(gbl::cissLab->ShutterStateId() == "Disabled") {
		gbl::calgrp += PvlKeyword("SensitivityCorrectionPerformed", "No: ShutterStateId is Disabled.");
		gbl::sensCorrection = false;
		gbl::calgrp += PvlKeyword("SensVsTimeCorr", "Not applicable: No Sensitivity correction.");
		return;
		}
		else {
		continue;
		double imgNumber = gbl::cissLab->ImageNumber();
		// Values taken from IDL
		double imgNumberS03 = 1.47036e9;
		double imgNumberS17 = 1.51463e9;

		if(gbl::cissLab->InstrumentId() == "ISSNA" && imgNumber < imgNumberS03) {
		gbl::calgrp += PvlKeyword("SensitivityCorrectionPerformed", "No: No NAC correction before S03");
		gbl::sensCorrection = false;
		gbl::calgrp += PvlKeyword("SensVsTimeCorr", "Not applicable: No NAC correction before S03");
		return;
		}
		if(gbl::cissLab->InstrumentId() == "ISSWA" && imgNumber < imgNumberS17) {
		gbl::calgrp += PvlKeyword("SensitivityCorrectionPerformed", "No: No WAC correction before S17");
		gbl::sensCorrection = false;
		gbl::calgrp += PvlKeyword("SensVsTimeCorr", "Not applicable: No WAC correction before S17");
		return;
		}
		jCorrFact->Close();

		// if no factor was found for instrument ID and filter combination
		if(gbl::jupiterCorrectionFactor == 0.0) {
		gbl::jupiterCorrectionFactor = 1.0;
		// dividing 1.0 by correction factor implies this correction is not performed
		gbl::calgrp.findKeyword("JupiterCorrectionFactorPerformed").setValue("No: JupiterCorrectionFactorFile contained no factor for filter combination");
		}
		//}
		else {
		gbl::jupiterCorrectionFactor = 1.0;
		if(gbl::cissLab->InstrumentId() == "ISSNA") {
		gbl::sensVsTimeCorr = 1.0 + (1.89457e-10 * (imgNumber - imgNumberS03));
		}
		else if(gbl::cissLab->InstrumentId() == "ISSWA") {
		gbl::sensVsTimeCorr = 1.0 + (9.28360e-11 * (imgNumber - imgNumberS17));
		}
		gbl::calgrp += PvlKeyword("JupiterCorrectionFactor", toString(gbl::jupiterCorrectionFactor));
		return;
		gbl::calgrp += PvlKeyword("SensitivityCorrectionPerformed", "Yes");
		gbl::calgrp.findKeyword("SensitivityCorrectionPerformed").addComment("Sensitivity vs Time Correction Parameters");
		gbl::sensCorrection = true;
		gbl::calgrp += PvlKeyword("SensVsTimeCorr", toString(gbl::sensVsTimeCorr));
		}


		//=====End Correction Factor Methods=============================================================//

		/**

isis/src/cassini/objs/CissLabels/CissLabels.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -73,6 +73,7 @@ namespace Isis {
		p_readoutCycleIndex = (QString) inst["ReadoutCycleIndex"]; //valid values: Unknown or integers 0-15
		p_readoutOrder = (int) inst["ReadoutOrder"]; //valid values: 0 or 1
		p_shutterModeId = (QString) inst["ShutterModeId"]; //valid values: BothSim, NacOnly, WacOnly
		p_shutterStateId = (QString) inst["ShutterStateId"]; //valid values: Enabled or Disabled
		p_summingMode = (int) inst["SummingMode"]; //valid values: 1, 2, 4
		p_frontOpticsTemp = toDouble(inst["OpticsTemperature"][0]); //valid values: real numbers
		p_imageTime = (QString) inst["ImageTime"];

isis/src/cassini/objs/CissLabels/CissLabels.h

+16 −0

Original line number	Diff line number	Diff line
		@@ -44,6 +44,7 @@ namespace Isis {
		* @history 2008-11-07 Jeannie Walldren - Fixed documentation.
		* @history 2011-05-03 Jeannie Walldren - Fixed documentation.
		* @history 2017-08-22 Cole Neubauer - Added labels for latest Cisscal upgrade
		* @history 2019-08-14 Kaitlyn Lee - Added ShutterStateId.
		*/

		class CissLabels {
		@@ -388,6 +389,19 @@ namespace Isis {
		};


		/**
		* @brief Returns ShutterStateId from the Instrument group.
		*
		* Indicates whether the shutter was enabled during image
		* exposure. Valid values include "Disabled" and "Enabled".
		*
		* @returns @b QString ShutterStateId
		*/
		inline QString ShutterStateId() const {
		return p_shutterStateId;
		};


		/**
		* @brief Returns SummingMode from the Instrument group.
		*
		@@ -493,6 +507,8 @@ namespace Isis {
		int p_readoutOrder;
		//! Value of the PDS keyword ShutterModeId in the cube's labels
		QString p_shutterModeId;
		//! Value of the PDS keyword ShutterState in the cube's labels
		QString p_shutterStateId;
		//! Value of the PDS keyword SummingMode in the cube's labels
		int p_summingMode;
		//! Value of the PDS keyword TargetName in the cube's labels