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Mvic App and Test Update #4102

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Nov 4, 2020
Merged

Mvic App and Test Update #4102

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dfb9d79
Updated mvic app and added the associated tests
acpaquette Nov 2, 2020
dfaf170
Removed old mvic tests
acpaquette Nov 2, 2020
5697cb5
Updated mvic tests with smart pointers for cubes and histograms
acpaquette Nov 3, 2020
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347 changes: 11 additions & 336 deletions isis/src/newhorizons/apps/mvic2isis/main.cpp
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Original file line number Diff line number Diff line change
@@ -1,352 +1,27 @@
#include "Isis.h"

#include <fstream>
#include <iostream>
#include "mvic2isis.h"

#include <QString>

#include "Cube.h"
#include "IException.h"
#include "IString.h"
#include "iTime.h"
#include "LineManager.h"
#include "NaifStatus.h"
#include "OriginalLabel.h"
#include "ProcessBySample.h"
#include "ProcessImportFits.h"
#include "Application.h"
#include "Pvl.h"
#include "PvlGroup.h"
#include "PvlKeyword.h"
#include "UserInterface.h"

using namespace std;
using namespace Isis;

void translateLabels(Pvl &fitsLabel, Cube *ocube);
//void flip(Buffer &in);

void IsisMain() {

UserInterface &ui = Application::GetUserInterface();

ProcessImportFits importFits;
importFits.setFitsFile(FileName(ui.GetFileName("FROM")));

// Get the primary FITS label
Pvl primaryLabel;
primaryLabel.addGroup(importFits.fitsImageLabel(0));

// Make sure this is a New Horizons MVIC image FITS formatted file
bool mvic = true;
if (primaryLabel.hasKeyword("MISSION", Pvl::Traverse)) {
QString mission = primaryLabel.findKeyword("MISSION", Pvl::Traverse);
if (!mission.contains("New Horizons")) mvic = false;
if (primaryLabel.hasKeyword("INSTRU", Pvl::Traverse)) {
QString instrument = primaryLabel.findKeyword("INSTRU", Pvl::Traverse);
if (!instrument.contains("mvi")) mvic = false;
}
else {
mvic = false;
}
}
else {
mvic = false;
}

if (!mvic) {
FileName in = ui.GetFileName("FROM");
QString msg = "Input file [" + in.expanded() + "] does not appear to be " +
"in New Horizons/MVIC FITS format.";
throw IException(IException::User, msg, _FILEINFO_);
}

// Check to see if the undistorted image was requested from the FITS file and that it has the
// corresponding extension and keywords
if (ui.WasEntered("UNDISTORTED")) {
PvlGroup undistortedLabel = importFits.fitsImageLabel(1);
if (!undistortedLabel.hasKeyword("COMMENT") ||
!undistortedLabel["COMMENT"][0].startsWith("This is the bias-subtracted, "
"flattened, distortion-removed image cube.")) {

QString msg = QObject::tr("Input file [%1] does not appear to contain an MVIC undistorted "
"image in XTENSION [2]").arg(ui.GetFileName("FROM"));
throw IException(IException::User, msg, _FILEINFO_);
}
Pvl appLog;
try {
mvic2isis(ui, &appLog);
}

// Check to see if the error image was requested from the FITS file and it has the
// corresponding extension and keywords
if (ui.WasEntered("ERROR")) {
PvlGroup errorLabel = importFits.fitsImageLabel(2);
if (!errorLabel.hasKeyword("COMMENT") ||
errorLabel["COMMENT"][0] != "1-sigma error per pixel for the image in extension 1.") {

QString msg = QObject::tr("Input file [%1] does not appear to contain an MVIC Error image "
"in the XTENSION [3]").arg(ui.GetFileName("FROM"));
throw IException(IException::User, msg, _FILEINFO_);
catch (...) {
for (auto grpIt = appLog.beginGroup(); grpIt!= appLog.endGroup(); grpIt++) {
Application::Log(*grpIt);
}
throw;
}

// Check to see if the quality image was requested from the FITS file and it has the
// corresponding extension and keywords
if (ui.WasEntered("QUALITY")) {
PvlGroup qualityLabel = importFits.fitsImageLabel(3);
if (!qualityLabel.hasKeyword("COMMENT") ||
qualityLabel["COMMENT"][0] != "Data quality flag for the image in extension 1.") {

QString msg = QObject::tr("Input file [%1] does not appear to contain an MVIC Quality image "
"in extension [3]").arg(ui.GetFileName("FROM"));
throw IException(IException::User, msg, _FILEINFO_);
}
}

// Convert the primary image
QString bitpix = primaryLabel.findKeyword("BITPIX", Pvl::Traverse);
int bytesPerPix = abs(toInt(bitpix)) / 8;
importFits.SetDataPrefixBytes(bytesPerPix * 12);
importFits.SetDataSuffixBytes(bytesPerPix * 12);
importFits.setProcessFileStructure(0);

// Set up the output cube
Cube *output = importFits.SetOutputCube("TO");

translateLabels(primaryLabel, output); // Results are put directly into the cube label (output)

// Save the input FITS label in the output cube original labels
OriginalLabel originals(primaryLabel);
output->write(originals);

// Import the file
importFits.Progress()->SetText("Importing main MVIC image");
importFits.StartProcess();
importFits.EndProcess();


// Convert the bias-subtracted, flattened, distortion removed image. It is currently assumed
// to be the 2rd image in the FITS file (i.e., 1st extension)
if (ui.WasEntered("UNDISTORTED")) {
PvlGroup undistortedLabel = importFits.fitsImageLabel(1);

QString bitpix = undistortedLabel.findKeyword("BITPIX");
int bytesPerPix = abs(toInt(bitpix)) / 8;
importFits.SetDataPrefixBytes(bytesPerPix * 12);
importFits.SetDataSuffixBytes(bytesPerPix * 12);
importFits.setProcessFileStructure(1);

Cube *outputError = importFits.SetOutputCube("UNDISTORTED");

// Save the input FITS label in the Cube original labels
Pvl pvlError;
pvlError += undistortedLabel;
OriginalLabel originals(pvlError);
outputError->write(originals);

// Convert the main image data
importFits.Progress()->SetText("Importing MVIC Undistorted image");
importFits.StartProcess();
importFits.ClearCubes();
}


// Convert the Error image. It is currently assumed to be the 3rd image in the FITS file
if (ui.WasEntered("ERROR")) {
// Get the label of the Error image and make sure this is a New Horizons MVIC Error image
PvlGroup errorLabel = importFits.fitsImageLabel(2);
QString bitpix = errorLabel.findKeyword("BITPIX");
int bytesPerPix = abs(toInt(bitpix)) / 8;
importFits.SetDataPrefixBytes(bytesPerPix * 12);
importFits.SetDataSuffixBytes(bytesPerPix * 12);
importFits.setProcessFileStructure(2);

Cube *outputError = importFits.SetOutputCube("ERROR");

// Save the input FITS label in the Cube original labels
Pvl pvlError;
pvlError += errorLabel;
OriginalLabel originals(pvlError);
outputError->write(originals);

// Convert the main image data
importFits.Progress()->SetText("Importing MVIC Error image");
importFits.StartProcess();
importFits.ClearCubes();
}


// Convert the Quality image. It is currently assumed to be the 4th image in the FITS file
if (ui.WasEntered("QUALITY")) {
// Get the label of the Error image and make sure this is a New Horizons MVIC Quality image
PvlGroup qualityLabel = importFits.fitsImageLabel(3);
QString bitpix = qualityLabel.findKeyword("BITPIX");
int bytesPerPix = abs(toInt(bitpix)) / 8;
importFits.SetDataPrefixBytes(bytesPerPix * 12);
importFits.SetDataSuffixBytes(bytesPerPix * 12);
importFits.setProcessFileStructure(3);

Cube *outputError = importFits.SetOutputCube("QUALITY");

// Save the input FITS label in the Cube original labels
Pvl pvlError;
pvlError += qualityLabel;
OriginalLabel originals(pvlError);
outputError->write(originals);

// Convert the main image data
importFits.Progress()->SetText("Importing MVIC Quality image");
importFits.StartProcess();
importFits.ClearCubes();
}
}



void translateLabels(Pvl &label, Cube *ocube) {

// Get the path where the New Horizons translation tables are.
QString transDir = "$ISISROOT/appdata/translations/";

Pvl *isisLabel = ocube->label();
// Create an Instrument group
FileName insTransFile(transDir + "NewHorizonsMvicInstrument_fit.trn");
PvlToPvlTranslationManager insXlater(label, insTransFile.expanded());
insXlater.Auto(*(isisLabel));

// Modify/add Instument group keywords not handled by the translater
PvlGroup &inst = isisLabel->findGroup("Instrument", Pvl::Traverse);

QString instId = (QString)inst["InstrumentId"];
QString scanType = (QString)inst["ScanType"];
instId = instId + "_" + scanType;
inst.addKeyword(PvlKeyword("InstrumentId", instId), PvlGroup::Replace);

// Not tested because we didn't have any files that do this at the time the test were done
QString target = (QString)inst["TargetName"];
if (target.startsWith("RADEC=")) {
inst.addKeyword(PvlKeyword("TargetName", "Sky"), PvlGroup::Replace);
}

if (inst.hasKeyword("TdiRate")) {
inst.findKeyword("TdiRate").setUnits("hz");
}

// Create StartTime (UTC) from the SpacecraftClockStartCount. Need to load the leapsecond
// and spacecraft clock kernels to calculate time.
NaifStatus::CheckErrors();
// Leapsecond kernel
QString lsk = "$ISISDATA/base/kernels/lsk/naif????.tls";
FileName lskName(lsk);
lskName = lskName.highestVersion();
furnsh_c(lskName.expanded().toLatin1().data());

// Spacecraft clock kernel
QString sclk = "$ISISDATA/newhorizons/kernels/sclk/new_horizons_???.tsc";
FileName sclkName(sclk);
sclkName = sclkName.highestVersion();
furnsh_c(sclkName.expanded().toLatin1().data());

SpiceInt sclkCode;
if (label.hasKeyword("SPCSCID", Pvl::Traverse)) {
sclkCode = label.findKeyword("SPCSCID", Pvl::Traverse);
}
else {
QString msg = "Input file is missing the spacecraft Naif Id.";
throw IException(IException::User, msg, _FILEINFO_);
}

QString scTime = inst["SpacecraftClockStartCount"];
double et;
scs2e_c(sclkCode, scTime.toLatin1().data(), &et);
SpiceChar utc[30];
et2utc_c(et, "ISOC", 3, 30, utc);
inst.addKeyword(PvlKeyword("StartTime", QString(utc)));

// Create a Band Bin group
FileName bandTransFile(transDir + "NewHorizonsMvicBandBin_fit.trn");
PvlToPvlTranslationManager bandBinXlater(label, bandTransFile.expanded());
bandBinXlater.Auto(*(isisLabel));
// Add units and OriginalBand keyword
PvlGroup &bandBin = isisLabel->findGroup("BandBin", Pvl::Traverse);
bandBin.addKeyword(PvlKeyword("OriginalBand", "1"));
PvlKeyword &center = bandBin.findKeyword("Center");
center.setUnits("nanometers");
PvlKeyword &width = bandBin.findKeyword("Width");
width.setUnits("nanometers");

// If image is in the framing mode, the BandBin keywords will need to be duplicated for each
// band. Also, add BandStartTime
if (scanType.contains("FRAMING")) {
PvlGroup &bandBin = isisLabel->findGroup("BandBin", Pvl::Traverse);
QString name = bandBin.findKeyword("Name")[0];
QString center = QString(bandBin.findKeyword("Center")[0]);
QString width = QString(bandBin.findKeyword("Width")[0]);
for (int i = 1; i < ocube->bandCount(); i++) {
bandBin.findKeyword("Name").addValue(name);
bandBin.findKeyword("Center").addValue(center, "nanometers");
bandBin.findKeyword("Width").addValue(width, "nanometers");
bandBin.findKeyword("OriginalBand").addValue(QString::number(i+1));
QString fitsKey = QString("UTCMID%1").arg(i, 2, 10, QChar('0'));
QString fitsVal = label.findKeyword(fitsKey, Pvl::Traverse);
bandBin.findKeyword("UtcTime").addValue(fitsVal);
}
}

// Create an Archive group
FileName archiveTransFile(transDir + "NewHorizonsMvicArchive_fit.trn");
PvlToPvlTranslationManager archiveXlater(label, archiveTransFile.expanded());
archiveXlater.Auto(*(isisLabel));

// Create a Kernels group
FileName kernelsTransFile(transDir + "NewHorizonsMvicKernels_fit.trn");
PvlToPvlTranslationManager kernelsXlater(label, kernelsTransFile.expanded());
kernelsXlater.Auto(*(isisLabel));

// If Level 2 product, Create a RadiometricCalibration group
if (label.hasKeyword("SOCL2VER", Pvl::Traverse)) {
FileName calibrationTransFile(transDir + "NewHorizonsMvicCalibration_fit.trn");
PvlToPvlTranslationManager calibrationXlater(label, calibrationTransFile.expanded());
calibrationXlater.Auto(*(isisLabel));

// Add comments to calibration keywords. This is done by hand because the translation tables
// did not handle comments at the time this was written.
PvlGroup &calibration = isisLabel->findGroup("RadiometricCalibration", Pvl::Traverse);
if (calibration.hasKeyword("PixelSize")) {
calibration.findKeyword("PixelSize").setUnits("microns");
}
if (calibration.hasKeyword("PixelFov")) {
calibration.findKeyword("PixelFov").setUnits("microrad/pix");
}
if (calibration.hasKeyword("Gain")) {
calibration.findKeyword("Gain").setUnits("electrons/DN");
}
if (calibration.hasKeyword("ReadNoise")) {
calibration.findKeyword("ReadNoise").setUnits("electrons");
}
if (calibration.hasKeyword("TdiRate")) {
calibration.findKeyword("TdiRate").setUnits("hz");
}
// The following do not need hasKeyword tests because the translater creats them everytime
// due to them having default values if none is in the FITS file.
calibration.findKeyword("SolarSpectrumResolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("SolarSpectrumUnresolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("PholusSpectrumResolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("PholusSpectrumUnresolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("CharonSpectrumResolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("CharonSpectrumUnresolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("JupiterSpectrumResolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("JupiterSpectrumUnresolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("PlutoSpectrumResolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("PlutoSpectrumUnresolved").setUnits("(erg/cm^2/s/sr)/(DN/s/pix)");
calibration.findKeyword("SolarPivotWavelength").setUnits("cm");
calibration.findKeyword("JupiterPivotWavelength").setUnits("cm");
calibration.findKeyword("PholusPivotWavelength").setUnits("cm");
calibration.findKeyword("PlutoPivotWavelength").setUnits("cm");
calibration.findKeyword("CharonPivotWavelength").setUnits("cm");
for (auto grpIt = appLog.beginGroup(); grpIt!= appLog.endGroup(); grpIt++) {
Application::Log(*grpIt);
}
}


//void flip(Buffer &in) {
// for(int i = 0; i < in.size() / 2; i++) {
// swap(in[i], in[in.size() - i - 1]);
// }
//}
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