Unverified Commit 2b86e8b3 authored by Kristin's avatar Kristin Committed by GitHub
Browse files

leisa2isis app test conversion and one gtest replacement (#3704) 



* Update meta.yaml to rename conda package to isis from isis3

* Initial leisa2isis app test conversion and gtest

* Remove debug code

* Update main.cpp

Added a CR at EOF

Co-authored-by: default avatarStuart Sides <ssides@usgs.gov>
parent 809981ad

isis/src/base/objs/ProcessImport/ProcessImport.cpp

+23 −9
Original line number Diff line number Diff line
@@ -1201,19 +1201,15 @@ namespace Isis { 




  /**

   * Create the output file. Note that all the appropiate calls to at least

   * SetDimensions and SetPixelType should be made prior to calling this method.

   * Given a CubeAttributeOutput object, set min/max to propagate if 

   * propagating min/max attributes was requested and set the pixel 

   * type to propagate if pixel type propagation was requested.  

   * 

   * @param parameter The parameter name that holds the output file name.

   *

   * @return @b Isis::Cube Output cube.

   *

   * @throws Isis::iException::Message "Unsupported pixel type."

   */

  Isis::Cube *ProcessImport::SetOutputCube(const QString &parameter) {

    CubeAttributeOutput &att =

      Application::GetUserInterface().GetOutputAttribute(parameter);



  void ProcessImport::SetAttributes(CubeAttributeOutput &att) {

    if (att.propagateMinimumMaximum()) {

      double min, max;

      if ((p_pixelType == Isis::Double) ||
@@ -1263,6 +1259,24 @@ namespace Isis { 
        att.setPixelType(p_pixelType);

      }

    }

  }





  /**

   * Create the output file. Note that all the appropiate calls to at least

   * SetDimensions and SetPixelType should be made prior to calling this method.

   *

   * @param parameter The parameter name that holds the output file name.

   *

   * @return @b Isis::Cube Output cube.

   *

   * @throws Isis::iException::Message "Unsupported pixel type."

   */

  Isis::Cube *ProcessImport::SetOutputCube(const QString &parameter) {

    CubeAttributeOutput &att =

      Application::GetUserInterface().GetOutputAttribute(parameter);



    SetAttributes(att);



    return Process::SetOutputCube(Application::GetUserInterface().GetFileName(parameter), att, p_ns, p_nl, p_nb);

  }

isis/src/base/objs/ProcessImport/ProcessImport.h

+1 −0
Original line number Diff line number Diff line
@@ -202,6 +202,7 @@ namespace Isis { 
      virtual Isis::Cube *SetOutputCube(const QString &fname,

                                Isis::CubeAttributeOutput &att);



      void SetAttributes(CubeAttributeOutput &att);

      void SetPixelType(const Isis::PixelType type);

      /**

       * Returns the pixel type

isis/src/newhorizons/apps/leisa2isis/leisa2isis.cpp

0 → 100644
+299 −0
Original line number Diff line number Diff line 
#include "leisa2isis.h"



#include "Cube.h"

#include "IException.h"

#include "IString.h"

#include "OriginalLabel.h"

#include "ProcessBySample.h"

#include "ProcessImportFits.h"

#include "Pvl.h"

#include "PvlGroup.h"

#include "PvlKeyword.h"

#include "UserInterface.h"

#include "iTime.h"

#include "ProgramLauncher.h"



#include <fstream>

#include <iostream>

#include <QString>



using namespace std;



namespace Isis {

  void processFunc(Buffer &in);

  Cube *outputCubeForLeisa2Isis; 



  void leisa2isis(UserInterface &ui, Pvl *log) {

    ProcessImportFits importFits;



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

    PvlGroup mainLabel;

    mainLabel = importFits.fitsImageLabel(0);



    // Get the first label and make sure this is a New Horizons LEISA file

    if (!mainLabel.hasKeyword("MISSION") || !mainLabel.hasKeyword("INSTRU")) {

      QString msg = QObject::tr("Input file [%1] does not appear to be a New Horizons LEISA FITS "

                                "file. Input file label key MISSION or INSTRU is missing").

                    arg(ui.GetFileName("FROM"));

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

    }

    else if (mainLabel["MISSION"][0] != "New Horizons" || mainLabel["INSTRU"][0] != "lei") {

      QString msg = QObject::tr("Input file [%1] does not appear to be a New Horizons LEISA FITS "

                                "file. Input file label value for MISSION is [%2], INSTRU is [%3]").

                    arg(ui.GetFileName("FROM")).arg(mainLabel["MISSION"][0]).

                    arg(mainLabel["INSTRU"][0]);

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

    }



     bool replace = ui.GetBoolean("REPLACE"); 



    // Check to see if the calibration error image was requested from the FITS file and 

    // that it has the corresponding extension

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

      PvlGroup extensionLabel; 

      try {

        extensionLabel = importFits.fitsImageLabel(5);

  /**      if (!extensionLabel.hasKeyword("XTENSION")) {

          QString msg = QObject::tr("Input file [%1] does not appear to be a calibrated New Horizons "

                        "LEISA FITS file. XTENSION keyword is missing in the fifth extension.")

                        .arg(ui.GetFileName("FROM"));

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

        }

        if (!extensionLabel.hasKeyword("EXTNAME")) {

          QString msg = QObject::tr("Input file [%1] does not appear to contain a New Horizons LEISA "

                        "calibrated image. FITS label keyword EXTNAME is missing in the fifth extension").

                        arg(ui.GetFileName("FROM"));

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

        }

        else if (extensionLabel["EXTNAME"][0] != "ERRORMAP") {

          QString msg = QObject::tr("Input file [%1] does not appear to contain a New Horizons LEISA "

                                    "calibrated image. FITS label value for EXTNAME is [%2]").

                                 arg(ui.GetFileName("FROM")).arg(extensionLabel["EXTNAME"][0]);

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

        } **/

      }

      catch (IException &e) {

        QString msg = QObject::tr("Unable to find errormap extension in [%1]").arg(ui.GetFileName("FROM"));

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

      }



    }



    // Check to see if the quality image was requested from the FITS file and 

    // that it has the corresponding extension

    if (ui.WasEntered("QUALITY") || replace) {

      PvlGroup  extensionLabel; 

      try {

        extensionLabel = importFits.fitsImageLabel(6); 

  /**      if (!extensionLabel.hasKeyword("XTENSION")) {

          QString msg = QObject::tr("Input file [%1] does not appear to be a calibrated New Horizons "

                        "LEISA FITS file. XTENSION keyword is missing in the sixth extension.")

                        .arg(ui.GetFileName("FROM"));

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

        }

        if (!extensionLabel.hasKeyword("EXTNAME")) {

          QString msg = QObject::tr("Input file [%1] does not appear to contain a New Horizons LEISA "

                        "calibrated image. FITS label keyword EXTNAME is missing in the sixth extension").

                        arg(ui.GetFileName("FROM"));

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

        }

        else if (extensionLabel["EXTNAME"][0] != "QUALITY") {

          QString msg = QObject::tr("Input file [%1] does not appear to contain a New Horizons LEISA "

                                    "calibrated image. FITS label value for EXTNAME is [%2]").

                                 arg(ui.GetFileName("FROM")).arg(extensionLabel["EXTNAME"][0]);

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

        } **/

      }

      catch (IException &e) {

        QString msg = QObject::tr("Unable to find quality extension in [%1]").arg(ui.GetFileName("FROM"));

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

      }

    }



    // Import the primary image (LEISA raw/calibrated)

    importFits.SetOrganization(ProcessImport::BIL);

    importFits.setProcessFileStructure(0);



    Cube *output = NULL; 

    FileName outputFile; 



    CubeAttributeOutput &att = ui.GetOutputAttribute("TO");



    if (replace){

      outputFile = FileName::createTempFile(FileName("$TEMPORARY/dn.cub"));

      importFits.SetPixelType(Isis::Real);

      output = importFits.SetOutputCube(outputFile.toString(), att); 

    } 

    else {

      if (importFits.PixelType() == Isis::None) {

        importFits.SetPixelType(Isis::Real);

      }

      importFits.SetAttributes(att); 

      output = importFits.SetOutputCube(ui.GetFileName("TO"), att); 

    }



    // Get the directory where the New Horizons translation tables are.

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

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



    // Temp storage of translated labels

    Pvl outLabel;



    // Get the FITS label

    Pvl fitsLabel;

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

    // Create an Instrument group

    FileName insTransFile(transDir + "leisaInstrument_fit.trn");

    PvlToPvlTranslationManager insXlater(fitsLabel, insTransFile.expanded());

    insXlater.Auto(outLabel);



  // Modify/add Instument group keywords not handled by the translater

  //  PvlGroup &inst = outLabel.findGroup("Instrument", Pvl::Traverse);

  //  QString target = (QString)inst["TargetName"];

  //  if (target.startsWith("RADEC=")) {

  //    inst.addKeyword(PvlKeyword("TargetName", "Sky"), PvlGroup::Replace);

  //  }



    output->putGroup(outLabel.findGroup("Instrument", Pvl::Traverse));



    // Create an Archive group

    FileName archiveTransFile(transDir + "leisaArchive_fit.trn");

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

    archiveXlater.Auto(outLabel);

    output->putGroup(outLabel.findGroup("Archive", Pvl::Traverse));



    //Create a Band Bin Group

    FileName bandTransFile(transDir + "leisaBandBin_fit.trn");

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

    bandBinXlater.Auto(outLabel);

    output->putGroup(outLabel.findGroup("BandBin", Pvl::Traverse));



    // Create a Kernels group

    FileName kernelsTransFile(transDir + "leisaKernels_fit.trn");

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

    kernelsXlater.Auto(outLabel);

    output->putGroup(outLabel.findGroup("Kernels", Pvl::Traverse));





    // Modify/add Instument group keywords not handled by the translater

    Pvl *isisLabel = output->label();

    PvlGroup &inst = isisLabel->findGroup("Instrument", Pvl::Traverse);

    PvlGroup &archive = isisLabel->findGroup("Archive", Pvl::Traverse);



    //Add StartTime & EndTime

    QString midTimeStr = archive["MidObservationTime"];

    iTime midTime(midTimeStr.toDouble());



    QString obsDuration = archive["ObservationDuration"];

    double obsSeconds = obsDuration.toDouble();

    iTime startTime = midTime - obsSeconds/2.0;

    iTime endTime = midTime + obsSeconds/2.0;

  //  inst.addKeyword(PvlKeyword("StartTime", startTime.EtString()), PvlGroup::Replace);

  //  inst.addKeyword(PvlKeyword("StopTime", endTime.EtString()), PvlGroup::Replace);



    //Need to make sure these times are correct. UTC != ET

    inst.addKeyword(PvlKeyword("StartTime", startTime.UTC()), PvlGroup::Replace);

    inst.addKeyword(PvlKeyword("StopTime", endTime.UTC()), PvlGroup::Replace);



    QString exposureTime = inst["ExposureDuration"];

    double frameRate = 1.0/exposureTime.toDouble();

    inst.addKeyword(PvlKeyword("FrameRate", QString::number(frameRate)), PvlGroup::Replace); 

    inst.findKeyword("FrameRate").setUnits("Hz");



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

    Pvl pvl;

    pvl += importFits.fitsImageLabel(0);

    OriginalLabel originals(pvl);

    output->write(originals);



    // Convert the main image data

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

    importFits.StartProcess();

    importFits.ClearCubes();

    importFits.Finalize();



    // If replace was selected, add this with the bad pixel mask to get the final output file

    if (replace) {

      importFits.SetOrganization(ProcessImport::BIL);

      importFits.setProcessFileStructure(6);



      FileName qualityFile = FileName::createTempFile("$TEMPORARY/quality.cub"); 

      CubeAttributeOutput &cao = ui.GetOutputAttribute("TO");



      // Set to Isis::Real

      if (cao.propagatePixelType()) {

        cao.setPixelType(Isis::Real); 

      }



      outputCubeForLeisa2Isis = importFits.SetOutputCube(qualityFile.toString(), cao); 



      importFits.Progress()->SetText("Preparing quality image for comparing against LEISA pixels");

      importFits.StartProcess(processFunc);

      importFits.ClearCubes();

      importFits.Finalize();



      // Now we have the temp cube and want to use fx to add it to the DN cube

      // fx f1=temp_quality.cub f2=temp_dn.cub to=output_name.cub equation="f1 + f2"

      QString parameters;

      parameters += " F1= " + outputFile.toString();

      parameters += " F2= " + qualityFile.toString();

      parameters += " TO= " + ui.GetFileName("TO");

      parameters += " EQUATION=" + QString("\"f1+f2\"");

      ProgramLauncher::RunIsisProgram("fx", parameters);



      // Cleanup by removing temporary cubes

      remove(qualityFile.toString().toStdString().c_str());

      remove(outputFile.toString().toStdString().c_str()); 

    }



    // Import the ERRORMAP image. It is the 6th image in the FITS file (i.e., 5th extension)

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

      PvlGroup extensionLabel = importFits.fitsImageLabel(5);

      importFits.SetOrganization(ProcessImport::BIL);

      importFits.setProcessFileStructure(5);

      Cube *output = importFits.SetOutputCube("ERRORMAP");



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

      Pvl origLabel;

      origLabel += extensionLabel;

      OriginalLabel originals(origLabel);

      output->write(originals);



      // Convert the main image data

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

      importFits.StartProcess();

      importFits.ClearCubes();

    }



    // Import the quality image. It is the 7th image in the FITS file (i.e., 6th extension)

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

      PvlGroup extensionLabel = importFits.fitsImageLabel(6);

      importFits.SetOrganization(ProcessImport::BIL);

      importFits.setProcessFileStructure(6);

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



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

      Pvl origLabel;

      origLabel += extensionLabel;

      OriginalLabel originals(origLabel);

      output->write(originals);



      // Convert the main image data

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

      importFits.StartProcess();

      importFits.ClearCubes();

    }

  }



  void processFunc(Buffer &in){

    for (int i = 0; i < in.size(); i++) {

      if (((in[i] == 1) || (in[i] == 2)) || (in[i] == 8)) {

        in[i] = Isis::NULL8;

      } 

      else {

          in[i] = 0;

      }

    }

    outputCubeForLeisa2Isis->write(in); 

  }

}

isis/src/newhorizons/apps/leisa2isis/leisa2isis.h

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+11 −0
Original line number Diff line number Diff line 
#ifndef leisa2isis_h

#define leisa2isis_h



#include "Pvl.h"

#include "UserInterface.h"



namespace Isis{

  extern void leisa2isis(UserInterface &ui, Pvl *log);

}



#endif

isis/src/newhorizons/apps/leisa2isis/main.cpp

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