Commit 32c72646 authored by Tyler Wilson's avatar Tyler Wilson Committed by Adam Paquette
Browse files

Added AlphaCube group to outputlabel in the event the image is cropped. (#645) 

* Added AlphaCube group to outputlabel in the event the image is cropped.

* Fix libtiff dependency (#636) (#644)

* Upgrade libtiff to 4.0.10 (#636)

* Switch libtiff to 4.0.9 or higher to remove geotiff conflict

* Moved ISIS3 conda-build recipe from ISIS3_deps repository (#650)

* Fixed warning in Pixel unit tests

* Made a tweak to the dimensions of the alpha cube for cropped images to give it the correct dimensions.

* Changed the transform function so it could process an array of doubles instead of an array of ints.

* Smear correction was being incorrectly applied to onboard smear corrected images and screwing things up.  Fixed it.

* Added gtest capability to hyb2onc2isis

* Removing build numbers from external libraries (#660)

* Moved ISIS3 conda-build recipe from ISIS3_deps repository

* Un-pinned non-astro build numbers

* Removing build numbers from external libraries in the environment and meta.yeml files

* Final merging

* Added pixel type attribute to the output image of program shadow. Fixes #5187 (#659)

* Removed bolding of some text to decrease distraction.

* Fixed some typos.

* Reworded documentation.

* Added section for Environment and PreferemcesSetup in the Getting Started Section. (#663)

* Updated .gitmodules to use https rather than ssh (#673)

* Added build type release to conda recipe (#676)

* Modified isis/tests/CMakeLists.txt as well as hyb2onc2isis to fix unresolved symbol errors (CMakeLists.txt) and to fix some bugs in hyb2onc2isis involved with turning it into a callable function.

* Added w1 test to hyb2onc2isisTests.cpp

* Modified hyb2onccal to be a callable function.
parent fe79ae4f

isis/src/hayabusa2/apps/hyb2onc2isis/hyb2onc2isis.cpp

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#include "hyb2onc2isis.h"



#include "AlphaCube.h"

#include "Application.h"

#include "CubeAttribute.h"

#include "FileName.h"

#include "iTime.h"

#include "OriginalLabel.h"

#include "ProcessImportFits.h"

#include "Pvl.h"

#include "PvlGroup.h"

#include "PvlKeyword.h"

#include "PvlObject.h"

#include "PvlToPvlTranslationManager.h"



#include "UserInterface.h"



#include <QDebug>

#include <QString>





using namespace std;

using namespace Isis;

namespace Isis {





void hyb2onc2isis(UserInterface &ui) {







  QString fitsFileName = FileName(ui.GetFileName("FROM")).expanded();  



  QString outputCubeFileName = FileName(ui.GetFileName("TO")).expanded();





  QString target("");

  if (ui.WasEntered("TARGET")) {

    target = ui.GetString("TARGET");

  }



  CubeAttributeOutput &att =

    ui.GetOutputAttribute("TO");







  // Create a PVL to store the translated labels in

  hyb2onc2isis(fitsFileName,outputCubeFileName,att,target);



  return;



  }





Pvl hyb2onc2isis(QString fitsFileName, QString outputCubeFileName, CubeAttributeOutput att, QString target) {



  ProcessImportFits importFits;

  importFits.setFitsFile(FileName(fitsFileName));

  importFits.setProcessFileStructure(0);

  bool updatedKeywords = true;

  bool distortionCorrection = true;



  Cube *outputCube = importFits.SetOutputCube(outputCubeFileName,att);



  // Get the directory where the Hayabusa translation tables are.

  PvlGroup dataDir (Preference::Preferences().findGroup("DataDirectory"));

  QString transDir = (QString) dataDir["Hayabusa2"] + "/translations/";



  // Create a PVL to store the translated labels in

  Pvl outputLabel;



  //Uncropped # of samples/lines

  int N = 1024;



  // Get the FITS label

  Pvl fitsLabel;

  fitsLabel.addGroup(importFits.fitsImageLabel(0));

  try {

    fitsLabel.addGroup(importFits.extraFitsLabel(0));

  }

  catch (IException &e) {

    QString msg = "Input file [" + fitsFileName +

                  "] does not appear to be a Hayabusa2/ONC label file.";

    throw IException(e, IException::Unknown, msg, _FILEINFO_);

  }



  QString instid;

  QString missid;

  QString naifid;

  QString formatType;



  try {

    instid = fitsLabel.findGroup("FitsLabels").findKeyword("INSTRUME")[0];

    missid = fitsLabel.findGroup("FitsLabels").findKeyword ("SPCECRFT")[0];

  }

  catch (IException &e) {

    QString msg = "Unable to read instrument ID, [INSTRUME], or spacecraft ID, [SPCECRFT], "

                  "from input file [" + fitsFileName + "]";

    throw IException(e, IException::Io,msg, _FILEINFO_);

  }

  try {

    naifid = fitsLabel.findGroup("FitsLabels").findKeyword("NAIFID")[0];

  }

  catch(IException &e) {

    updatedKeywords=false;

  }



  try {

    formatType = fitsLabel.findGroup("FitsLabels").findKeyword("EXTNAME")[0];

  }

  catch(IException &e) {

    QString msg = "Unable to read EXTNAME from input file ["

        +fitsFileName + "]";

    throw IException(e, IException::Io,msg, _FILEINFO_);

  }



  try {

    naifid = fitsLabel.findGroup("FitsLabels").findKeyword("NAIFID")[0];

  }

  catch(IException &e) {

    updatedKeywords=false;

  }



  if (formatType.contains("2a") || formatType.contains("2b"))

    distortionCorrection = false;



  missid = missid.simplified().trimmed();

  if (QString::compare(missid, "HAYABUSA-2", Qt::CaseInsensitive) != 0) {

    QString msg = "Input file [" + fitsFileName +

                  "] does not appear to be a Hayabusa2 label file.";

    throw IException(IException::Unknown, msg, _FILEINFO_);

  }

  instid = instid.simplified().trimmed();

  if (QString::compare(instid, "Optical Navigation Camera", Qt::CaseInsensitive) != 0) {

    QString msg = "Input file [" + fitsFileName +

                  "] does not appear to be a Hayabusa2/ONC label file.";

    throw IException(IException::Unknown, msg, _FILEINFO_);

  }



  // Translate the Instrument group



  FileName transFile(transDir + "hyb2oncInstrument1.trn");



  if (updatedKeywords) {

    transFile = transDir+"hyb2oncInstrumentUpdated.trn";

  }

  PvlToPvlTranslationManager instrumentXlater (fitsLabel, transFile.expanded());

  instrumentXlater.Auto(outputLabel);





  //  Update target if user specifies it

  PvlGroup &instGrp = outputLabel.findGroup("Instrument",Pvl::Traverse);



  //Check for cropped image

  int ss = instGrp["SelectedImageAreaX1"];

  int sl = instGrp["SelectedImageAreaY1"];

  int es = instGrp["SelectedImageAreaX2"];

  int el = instGrp["SelectedImageAreaY2"];



  if (ss > 1 || sl >1 || es < N || el < N) {



    AlphaCube aCube(N, N, outputCube->sampleCount(), outputCube->lineCount(),

                    ss-0.5, sl - 0.5, es + 0.5, el + 0.5);

    aCube.UpdateGroup(*outputCube);



    instGrp["SelectedImageAreaX1"] = "1";

    instGrp["SelectedImageAreaY1"] = "1";

    instGrp["SelectedImageAreaX2"] = QString("%1").arg(N);

    instGrp["SelectedImageAreaY2"] = QString("%1").arg(N);





  }



  QString labelTarget;

  instGrp.addKeyword(PvlKeyword("DistortionCorrection"));

  try {

    labelTarget = fitsLabel.findGroup("FitsLabels").findKeyword("TARGET")[0];

  }

  catch(IException &e) {

    QString msg = "Unable to read TARGET from input file ["

        +fitsFileName + "]";

    throw IException(e, IException::Io,msg, _FILEINFO_);

  }

  if (labelTarget=="SKY") {

    instGrp["TargetName"] = "RYUGU";

  }



  if (distortionCorrection) {

    instGrp["DistortionCorrection"] = "yes";

  }

  else {

     instGrp["DistortionCorrection"] = "no";

  }





  //If the user wants to specify a different target, overwrite this value

  if (target !="") {

    instGrp["TargetName"] = target;

  }

  instGrp["ExposureDuration"].setUnits("seconds");

  outputCube->putGroup(instGrp);



  // Translate the BandBin group



  transFile = transDir + "hyb2oncBandBin.trn";

  if (updatedKeywords) {

    transFile = transDir + "hyb2oncBandBinUpdated.trn";

  }





  PvlToPvlTranslationManager bandBinXlater (fitsLabel, transFile.expanded());

  bandBinXlater.Auto(outputLabel);

  PvlGroup &bandGrp = outputLabel.findGroup("BandBin",Pvl::Traverse);

  if (bandGrp.hasKeyword("Width")) { // if width exists, then so must center

    bandGrp["Width"].setUnits("nanometers");

    bandGrp["Center"].setUnits("nanometers");

  }

  outputCube->putGroup(outputLabel.findGroup("BandBin",Pvl::Traverse));



  // Translate the Archive group



  transFile = transDir + "hyb2oncArchive.trn";

  if (updatedKeywords) {

    transFile = transDir + "hyb2oncArchiveUpdated.trn";

  }



  PvlToPvlTranslationManager archiveXlater (fitsLabel, transFile.expanded());

  archiveXlater.Auto(outputLabel);

  PvlGroup &archGrp = outputLabel.findGroup("Archive", Pvl::Traverse);

  QString source = archGrp.findKeyword("SourceProductId")[0];

  archGrp["SourceProductId"].setValue(FileName(source).baseName());



  //  Create YearDoy keyword in Archive group

  iTime stime(outputLabel.findGroup("Instrument", Pvl::Traverse)["StartTime"][0]);

  PvlKeyword yeardoy("YearDoy", toString(stime.Year()*1000 + stime.DayOfYear()));

  archGrp.addKeyword(yeardoy);

  outputCube->putGroup(archGrp);





  // Create a Kernels group

  if (updatedKeywords) {

    transFile = transDir + "hyb2oncKernelsUpdated.trn";

  }

  else {

    transFile = transDir + "hyb2oncKernels.trn";

  }



  PvlToPvlTranslationManager kernelsXlater(fitsLabel, transFile.expanded());

  kernelsXlater.Auto(outputLabel);

  outputCube->putGroup(outputLabel.findGroup("Kernels", Pvl::Traverse));



  // Now write the FITS augmented label as the original label

  // Save the input FITS label in the Cube original labels

  OriginalLabel originalLabel(fitsLabel);

  outputCube->write(originalLabel);



  // Convert the image data

  importFits.Progress()->SetText("Importing Hayabusa2 image");

   Pvl finalLabel = *(outputCube->label() );

  importFits.StartProcess();

  importFits.Finalize();





  return outputLabel;





  }











}

isis/src/hayabusa2/apps/hyb2onc2isis/hyb2onc2isis.h

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#ifndef hyb2onc2isis_h

#define hyb2onc2isis_h



#include <QDebug>

#include <QString>



#include "CubeAttribute.h"

#include "Pvl.h"

#include "UserInterface.h"



namespace Isis {



extern void hyb2onc2isis(UserInterface &ui);

extern Pvl hyb2onc2isis(QString fitsFileName, QString outputCubeFileName,CubeAttributeOutput att,

                        QString target="");



}



#endif

isis/src/hayabusa2/apps/hyb2onc2isis/main.cpp

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#include "Isis.h"

#include "UserInterface.h"



#include <QDebug>

#include <QString>

#include "hyb2onc2isis.h"



#include "FileName.h"

#include "iTime.h"

#include "OriginalLabel.h"

#include "ProcessImportFits.h"

#include "Pvl.h"

#include "PvlGroup.h"

#include "PvlKeyword.h"

#include "PvlObject.h"

#include "PvlToPvlTranslationManager.h"

#include "UserInterface.h"



using namespace std;

using namespace Isis;



void IsisMain () {



  ProcessImportFits importFits;

  UserInterface &ui = Application::GetUserInterface();

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

  importFits.setProcessFileStructure(0);

  bool updatedKeywords = true;

  bool distortionCorrection = true;

  Cube *outputCube = importFits.SetOutputCube("TO");



  // Get the directory where the Hayabusa translation tables are.

  PvlGroup dataDir (Preference::Preferences().findGroup("DataDirectory"));

  QString transDir = (QString) dataDir["Hayabusa2"] + "/translations/";



  // Create a PVL to store the translated labels in

  Pvl outputLabel;



  // Get the FITS label

  Pvl fitsLabel;

  fitsLabel.addGroup(importFits.fitsImageLabel(0));

  try {

    fitsLabel.addGroup(importFits.extraFitsLabel(0));

  }

  catch (IException &e) {

    QString msg = "Input file [" + FileName(ui.GetFileName("FROM")).expanded() + 

                  "] does not appear to be a Hayabusa2/ONC label file.";

    throw IException(e, IException::Unknown, msg, _FILEINFO_);

  }







  QString instid;

  QString missid;

  QString naifid;

  QString formatType;



  try {

    instid = fitsLabel.findGroup("FitsLabels").findKeyword("INSTRUME")[0];

    missid = fitsLabel.findGroup("FitsLabels").findKeyword ("SPCECRFT")[0]; 

  }

  catch (IException &e) {

    QString msg = "Unable to read instrument ID, [INSTRUME], or spacecraft ID, [SPCECRFT], " 

                  "from input file [" + FileName(ui.GetFileName("FROM")).expanded() + "]";

    throw IException(e, IException::Io,msg, _FILEINFO_);

  }



  try {

    naifid = fitsLabel.findGroup("FitsLabels").findKeyword("NAIFID")[0];

  }

  catch(IException &e) {

    updatedKeywords=false;

  }



  try {

    formatType = fitsLabel.findGroup("FitsLabels").findKeyword("EXTNAME")[0];

  }

  catch(IException &e) {

    QString msg = "Unable to read EXTNAME from input file ["

        +FileName(ui.GetFileName("FROM")).expanded() + "]";

    throw IException(e, IException::Io,msg, _FILEINFO_);

  }



  try {

    naifid = fitsLabel.findGroup("FitsLabels").findKeyword("NAIFID")[0];

  }

  catch(IException &e) {

    updatedKeywords=false;

  }



  if (formatType.contains("2a") || formatType.contains("2b"))

    distortionCorrection = false;





  missid = missid.simplified().trimmed();

  if (QString::compare(missid, "HAYABUSA-2", Qt::CaseInsensitive) != 0) {

    QString msg = "Input file [" + FileName(ui.GetFileName("FROM")).expanded() + 

                  "] does not appear to be a Hayabusa2 label file.";

    throw IException(IException::Unknown, msg, _FILEINFO_);

  }

  instid = instid.simplified().trimmed();

  if (QString::compare(instid, "Optical Navigation Camera", Qt::CaseInsensitive) != 0) {

    QString msg = "Input file [" + FileName(ui.GetFileName("FROM")).expanded() + 

                  "] does not appear to be a Hayabusa2/ONC label file.";

    throw IException(IException::Unknown, msg, _FILEINFO_);

  }



  // Translate the Instrument group



  FileName transFile(transDir + "hyb2oncInstrument.trn");



  if (updatedKeywords) {

    transFile = transDir+"hyb2oncInstrumentUpdated.trn";

  }

  PvlToPvlTranslationManager instrumentXlater (fitsLabel, transFile.expanded());

  instrumentXlater.Auto(outputLabel);





  //  Update target if user specifies it

  PvlGroup &instGrp = outputLabel.findGroup("Instrument",Pvl::Traverse);

  QString target;



  instGrp.addKeyword(PvlKeyword("DistortionCorrection"));

  try {

    target = fitsLabel.findGroup("FitsLabels").findKeyword("TARGET")[0];

  }

  catch(IException &e) {

    QString msg = "Unable to read TARGET from input file ["

        +FileName(ui.GetFileName("FROM")).expanded() + "]";

    throw IException(e, IException::Io,msg, _FILEINFO_);

  }

  if (target=="SKY") {

    instGrp["TargetName"] = "RYUGU";

  }



  if (distortionCorrection) {

    instGrp["DistortionCorrection"] = "yes";

  }

  else {

     instGrp["DistortionCorrection"] = "no";

  }





  //If the user wants to specify a different target, overwrite this value

  if (ui.WasEntered("TARGET")) {

    instGrp["TargetName"] = ui.GetString("TARGET");

  }

  instGrp["ExposureDuration"].setUnits("seconds");

  outputCube->putGroup(instGrp);



  // Translate the BandBin group



  transFile = transDir + "hyb2oncBandBin.trn";

  if (updatedKeywords) {

    transFile = transDir + "hyb2oncBandBinUpdated.trn";

  }





  PvlToPvlTranslationManager bandBinXlater (fitsLabel, transFile.expanded());

  bandBinXlater.Auto(outputLabel);

  PvlGroup &bandGrp = outputLabel.findGroup("BandBin",Pvl::Traverse);

  if (bandGrp.hasKeyword("Width")) { // if width exists, then so must center

    bandGrp["Width"].setUnits("nanometers");

    bandGrp["Center"].setUnits("nanometers");

  }

  outputCube->putGroup(outputLabel.findGroup("BandBin",Pvl::Traverse));



  // Translate the Archive group



  transFile = transDir + "hyb2oncArchive.trn";

  if (updatedKeywords) {

    transFile = transDir + "hyb2oncArchiveUpdated.trn";

  }



  PvlToPvlTranslationManager archiveXlater (fitsLabel, transFile.expanded());

  archiveXlater.Auto(outputLabel);

  PvlGroup &archGrp = outputLabel.findGroup("Archive", Pvl::Traverse);

  QString source = archGrp.findKeyword("SourceProductId")[0];

  archGrp["SourceProductId"].setValue(FileName(source).baseName());



  //  Create YearDoy keyword in Archive group

  iTime stime(outputLabel.findGroup("Instrument", Pvl::Traverse)["StartTime"][0]);

  PvlKeyword yeardoy("YearDoy", toString(stime.Year()*1000 + stime.DayOfYear()));

  archGrp.addKeyword(yeardoy);

  outputCube->putGroup(archGrp);





  // Create a Kernels group

  if (updatedKeywords) {

    transFile = transDir + "hyb2oncKernelsUpdated.trn";

  }

  else {

    transFile = transDir + "hyb2oncKernels.trn";

  }



  PvlToPvlTranslationManager kernelsXlater(fitsLabel, transFile.expanded());

  kernelsXlater.Auto(outputLabel);

  outputCube->putGroup(outputLabel.findGroup("Kernels", Pvl::Traverse));



  // Now write the FITS augmented label as the original label

  // Save the input FITS label in the Cube original labels

  OriginalLabel originalLabel(fitsLabel);

  outputCube->write(originalLabel);



  // Convert the image data

  importFits.Progress()->SetText("Importing Hayabusa2 image");

  importFits.StartProcess();

  importFits.Finalize();

  hyb2onc2isis(ui);



}

isis/src/hayabusa2/apps/hyb2onccal/Hyb2OncCalUtils.h

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isis/src/hayabusa2/apps/hyb2onccal/hyb2onccal.cpp

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