Unverified Commit 58ca313b authored by Amy Stamile's avatar Amy Stamile Committed by GitHub
Browse files

lorri2isis Test Conversion (#4286) 

* lorri2isis Test Conversion

* lorri2isis Test Conversion
parent a2154a08

isis/src/newhorizons/apps/lorri2isis/lorri2isis.cpp

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#include "lorri2isis.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 <fstream>

#include <iostream>

#include <QString>



using namespace std;



namespace Isis {



  void flip(Buffer &in);





  void lorri2isis(UserInterface &ui) {

    // NOTE:

    // Still to be done/considered

    //   Process the other FITS channels. One of them contains pixel quality info

    //   May want to set special pixel values using this channel



    ProcessImportFits importFits;



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



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

    PvlGroup mainLabel = importFits.fitsImageLabel(0);

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

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

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

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

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

    }



    // Get the label of extension #1 and make sure this is a New Horizons LORRI Error image

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

      PvlGroup errorLabel = importFits.fitsImageLabel(1);

      if (errorLabel["XTENSION"][0] != "IMAGE" || errorLabel["EXTNAME"][0] != "LORRI Error image") {

        QString msg = QObject::tr("Input file [%1] does not appear to contain a LORRI Error image. "

            "Input file label value for EXTNAME is [%2] and XTENSION is [%3]").

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

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

      }

    }



    // Get the label of extension #2 and make sure this is a New Horizons LORRI Quality image

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

      PvlGroup qualityLabel = importFits.fitsImageLabel(2);

      if (qualityLabel["XTENSION"][0] != "IMAGE" ||

          qualityLabel["EXTNAME"][0] != "LORRI Quality flag image") {

        QString msg = QObject::tr("Input file [%1] does not appear to contain a LORRI Quality image. "

            "Input file label value for EXTNAME is [%2] and XTENSION is [%3]").

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

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

      }

    }



    importFits.setProcessFileStructure(0);



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

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



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

    QString transDir = "$ISISROOT/appdata/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 + "NewHorizonsLorriInstrument_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 a Band Bin group

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

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

    bandBinXlater.Auto(outLabel);

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



    // Create an Archive group

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

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

    archiveXlater.Auto(outLabel);

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



    // Create a Kernels group

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

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

    kernelsXlater.Auto(outLabel);

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



    // 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 LORRI image");

    importFits.StartProcess();

    importFits.ClearCubes();





    // Convert the Error image. It is currently assumed to be the second image in the FITS file

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



      importFits.setProcessFileStructure(1);



      CubeAttributeOutput &attErr = ui.GetOutputAttribute("ERROR");

      Cube *outputError = importFits.SetOutputCube(ui.GetFileName("ERROR"), attErr);



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

      Pvl pvlError;

      pvlError += importFits.fitsImageLabel(1);

      OriginalLabel originals(pvlError);

      outputError->write(originals);



      // Convert the main image data

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

      importFits.StartProcess();

      importFits.ClearCubes();

    }





    // Convert the Quality image. It is currently assumed to be the third image in the FITS file

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



      importFits.setProcessFileStructure(2);



      CubeAttributeOutput &attQual = ui.GetOutputAttribute("QUALITY");

      Cube *outputError = importFits.SetOutputCube(ui.GetFileName("QUALITY"), attQual);



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

      Pvl pvlError;

      pvlError += importFits.fitsImageLabel(2);

      OriginalLabel originals(pvlError);

      outputError->write(originals);



      // Convert the main image data

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

      importFits.StartProcess();

      importFits.ClearCubes();

    }



    importFits.Finalize();



  // The images need to be flipped from top to bottom to put the origin in the upper left for ISIS

  // Commented out because we don't need to do this. If we find later that we do, remove comments

  //  ProcessBySample flipLines;

  //  CubeAttributeInput inAttribute;

  //  Cube *cube = flipLines.SetInputCube(ui.GetFileName("TO"), inAttribute);

  //  cube->reopen("rw");

  //  flipLines.Progress()->SetText("Flipping top to bottom");

  //  flipLines.ProcessCubeInPlace(flip, false);

  }





  //void flip(Buffer &in) {

  //  for(int i = 0; i < in.size() / 2; i++) {

  //    swap(in[i], in[in.size() - i - 1]);

  //  }

  //}

}

isis/src/newhorizons/apps/lorri2isis/lorri2isis.h

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#ifndef lorri2isis_h

#define lorri2isis_h



#include "Pvl.h"

#include "UserInterface.h"



namespace Isis{

  extern void lorri2isis(UserInterface &ui);

}



#endif

isis/src/newhorizons/apps/lorri2isis/main.cpp

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@@ -8,184 +8,12 @@ find files of those names at the top level of this repository. **/ 


#include "Isis.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 "Application.h"

#include "lorri2isis.h"



#include <fstream>

#include <iostream>

#include <QString>



using namespace std;

using namespace Isis;



void flip(Buffer &in);





void IsisMain() {



  // NOTE:

  // Still to be done/considered

  //   Process the other FITS channels. One of them contains pixel quality info

  //   May want to set special pixel values using this channel



  UserInterface &ui = Application::GetUserInterface();



  ProcessImportFits importFits;



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



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

  PvlGroup mainLabel = importFits.fitsImageLabel(0);

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

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

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

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

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

  }



  // Get the label of extension #1 and make sure this is a New Horizons LORRI Error image

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

    PvlGroup errorLabel = importFits.fitsImageLabel(1);

    if (errorLabel["XTENSION"][0] != "IMAGE" || errorLabel["EXTNAME"][0] != "LORRI Error image") {

      QString msg = QObject::tr("Input file [%1] does not appear to contain a LORRI Error image. "

          "Input file label value for EXTNAME is [%2] and XTENSION is [%3]").

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

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

    }

  }



  // Get the label of extension #2 and make sure this is a New Horizons LORRI Quality image

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

    PvlGroup qualityLabel = importFits.fitsImageLabel(2);

    if (qualityLabel["XTENSION"][0] != "IMAGE" ||

        qualityLabel["EXTNAME"][0] != "LORRI Quality flag image") {

      QString msg = QObject::tr("Input file [%1] does not appear to contain a LORRI Quality image. "

          "Input file label value for EXTNAME is [%2] and XTENSION is [%3]").

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

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

    }

  }



  importFits.setProcessFileStructure(0);



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



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

  QString transDir = "$ISISROOT/appdata/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 + "NewHorizonsLorriInstrument_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);

  lorri2isis(ui);

}
 


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



  // Create a Band Bin group

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

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

  bandBinXlater.Auto(outLabel);

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



  // Create an Archive group

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

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

  archiveXlater.Auto(outLabel);

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



  // Create a Kernels group

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

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

  kernelsXlater.Auto(outLabel);

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



  // 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 LORRI image");

  importFits.StartProcess();

  importFits.ClearCubes();





  // Convert the Error image. It is currently assumed to be the second image in the FITS file

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



    importFits.setProcessFileStructure(1);



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



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

    Pvl pvlError;

    pvlError += importFits.fitsImageLabel(1);

    OriginalLabel originals(pvlError);

    outputError->write(originals);



    // Convert the main image data

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

    importFits.StartProcess();

    importFits.ClearCubes();

  }





  // Convert the Quality image. It is currently assumed to be the third image in the FITS file

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



    importFits.setProcessFileStructure(2);



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



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

    Pvl pvlError;

    pvlError += importFits.fitsImageLabel(2);

    OriginalLabel originals(pvlError);

    outputError->write(originals);



    // Convert the main image data

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

    importFits.StartProcess();

    importFits.ClearCubes();

  }



  importFits.Finalize();



// The images need to be flipped from top to bottom to put the origin in the upper left for ISIS

// Commented out because we don't need to do this. If we find later that we do, remove comments

//  ProcessBySample flipLines;

//  CubeAttributeInput inAttribute;

//  Cube *cube = flipLines.SetInputCube(ui.GetFileName("TO"), inAttribute);

//  cube->reopen("rw");

//  flipLines.Progress()->SetText("Flipping top to bottom");

//  flipLines.ProcessCubeInPlace(flip, false);

}





//void flip(Buffer &in) {

//  for(int i = 0; i < in.size() / 2; i++) {

//    swap(in[i], in[in.size() - i - 1]);

//  }

//}

isis/src/newhorizons/apps/lorri2isis/tsts/badfile/Makefile

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APPNAME = lorri2isis



include $(ISISROOT)/make/isismake.tsts



commands:

	if [ `$(APPNAME) \

	  from=$(INPUT)/lor_0034974380_0x630_sci_1_badimage.fit \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  >& $(OUTPUT)/temp.txt` ]; then \

	  true; \

	fi;

	$(SED) 's/\[.*\/\(lor_0034974380_0x630_sci_1_badimage.fit\)\]/[\1]/' < $(OUTPUT)/temp.txt > $(OUTPUT)/error_image.txt;

	$(RM) $(OUTPUT)/temp.txt;

	if [ `$(APPNAME) \

	  from=$(INPUT)/lor_0034974380_0x630_sci_1_baderror.fit \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  error=$(OUTPUT)/lor_0034974380_0x630_sci_1_Error.cub \

	  >& $(OUTPUT)/temp.txt` ]; then \

	  true; \

	fi;

	$(SED) 's/\[.*\/\(lor_0034974380_0x630_sci_1_baderror.fit\)\]/[\1]/' < $(OUTPUT)/temp.txt > $(OUTPUT)/error_error.txt;

	$(RM) $(OUTPUT)/temp.txt;

	if [ `$(APPNAME) \

	  from=$(INPUT)/lor_0034974380_0x630_sci_1_badquality.fit \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  quality=$(OUTPUT)/lor_0034974380_0x630_sci_1_Quality.cub \

	  >& $(OUTPUT)/temp.txt` ]; then \

	  true; \

	fi;

	$(SED) 's/\[.*\/\(lor_0034974380_0x630_sci_1_badquality.fit\)\]/[\1]/' < $(OUTPUT)/temp.txt > $(OUTPUT)/error_quality.txt;

	$(RM) $(OUTPUT)/temp.txt;

	if [ `$(APPNAME) \

	  from=$(INPUT)/lor_0034974380_0x630_sci_1_badimageinstr.fit \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  >& $(OUTPUT)/temp.txt` ]; then \

	  true; \

	fi;

	$(SED) 's/\[.*\/\(lor_0034974380_0x630_sci_1_badimageinstr.fit\)\]/[\1]/' < $(OUTPUT)/temp.txt > $(OUTPUT)/error_image_instr.txt;

	$(RM) $(OUTPUT)/temp.txt;

	if [ `$(APPNAME) \

	  from=$(INPUT)/lor_0034974380_0x630_sci_1_baderrorimage.fit \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  error=$(OUTPUT)/lor_0034974380_0x630_sci_1_Error.cub \

	  >& $(OUTPUT)/temp.txt` ]; then \

	  true; \

	fi;

	$(SED) 's/\[.*\/\(lor_0034974380_0x630_sci_1_baderrorimage.fit\)\]/[\1]/' < $(OUTPUT)/temp.txt > $(OUTPUT)/error_errorimage.txt;

	$(RM) $(OUTPUT)/temp.txt;

	if [ `$(APPNAME) \

	  from=$(INPUT)/lor_0034974380_0x630_sci_1_badqualityimage.fit \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  quality=$(OUTPUT)/lor_0034974380_0x630_sci_1_Quality.cub \

	  >& $(OUTPUT)/temp.txt` ]; then \

	  true; \

	fi;

	$(SED) 's/\[.*\/\(lor_0034974380_0x630_sci_1_badqualityimage.fit\)\]/[\1]/' < $(OUTPUT)/temp.txt > $(OUTPUT)/error_qualityimage.txt;

	$(RM) $(OUTPUT)/temp.txt;

isis/src/newhorizons/apps/lorri2isis/tsts/default/Makefile

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APPNAME = lorri2isis



include $(ISISROOT)/make/isismake.tsts



commands:

	$(APPNAME) from=$(INPUT)/lor_0034974380_0x630_sci_1.fit \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  > /dev/null;

	catlab from=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.cub \

	  to=$(OUTPUT)/lor_0034974380_0x630_sci_1_Truth.pvl> /dev/null;