Added AlphaCube group to outputlabel in the event the image is croppe…

…d. (DOI-USGS#645)

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

* Fix libtiff dependency (DOI-USGS#636) (DOI-USGS#644)

* Upgrade libtiff to 4.0.10 (DOI-USGS#636)

* Switch libtiff to 4.0.9 or higher to remove geotiff conflict

* Moved ISIS3 conda-build recipe from ISIS3_deps repository (DOI-USGS#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 (DOI-USGS#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 DOI-USGS#5187 (DOI-USGS#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. (DOI-USGS#663)

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

* Added build type release to conda recipe (DOI-USGS#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.

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

@@ -0,0 +1,273 @@
+#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

@@ -0,0 +1,19 @@
+#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