Unverified Commit 4459b142 authored by Kelvin Rodriguez's avatar Kelvin Rodriguez Committed by GitHub
Browse files

thm2isis now uses out attrs and converted to func (#4504) 

* thm2isis now uses out attrs and converted to func

* removed commented code that manually set pixel type

* added gtests

* better params

* IR test added

* reordered things

* cropped images

* cropped image for outattr tests too
parent 29b517e6

isis/src/base/apps/spkwriter/SpkSpiceSegment.cpp

+1 −0
Original line number Diff line number Diff line
@@ -220,6 +220,7 @@ bool SpkSpiceSegment::getImageTimes(Pvl &lab, double &start, double &end) const 
  return (true);

}





/**

 * @brief Add elements to top and bottom of a matrix

 *

isis/src/odyssey/apps/thm2isis/main.cpp

+4 −258
Original line number Diff line number Diff line
@@ -8,266 +8,12 @@ find files of those names at the top level of this repository. **/ 


#include "Isis.h"



#include <cstdio>

#include <string>

#include "Application.h"

#include "thm2isis.h"



#include "ProcessImportPds.h"

#include "LineManager.h"

#include "UserInterface.h"

#include "CubeAttribute.h"

#include "FileName.h"

#include "IException.h"

#include "iTime.h"

#include "ProcessByBrick.h"

#include "Brick.h"

#include "OriginalLabel.h"



using namespace std;

using namespace Isis;



vector<Cube *> outputCubes;

int frameletLines;

void TranslateLabels(Pvl &labelFile, Pvl &isis3, int numBands);

void separateFrames(Buffer &in);



void IsisMain() {

  // Grab the file to import

  ProcessImportPds p;

  outputCubes.clear();

  frameletLines = 192;

  UserInterface &ui = Application::GetUserInterface();

  FileName in = ui.GetFileName("FROM");



  // Make sure it is a Themis EDR/RDR

  bool projected;

  try {

    Pvl lab(in.expanded());

    projected = lab.hasObject("IMAGE_MAP_PROJECTION");

    QString id;

    id = (QString)lab["DATA_SET_ID"];

    id = id.simplified().trimmed();

    if(!id.startsWith("ODY-M-THM")) {

      QString msg = "Invalid DATA_SET_ID [" + id + "]";

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

    }

  }

  catch(IException &e) {

    QString msg = "Input file [" + in.expanded() +

                  "] does not appear to be " +

                  "in Themis EDR/RDR format";

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

  }



  //Checks if in file is rdr

  if(projected) {

    QString msg = "[" + in.name() + "] appears to be an rdr file.";

    msg += " Use pds2isis.";

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

  }



  // Ok looks good ... set it as the PDS file

  Pvl pdsLab;

  p.SetPdsFile(in.expanded(), "", pdsLab);



  OriginalLabel origLabels(pdsLab);



  Pvl isis3Lab;

  TranslateLabels(pdsLab, isis3Lab, p.Bands());



  // Set up the output cube

  FileName outFile(ui.GetFileName("TO"));

  PvlGroup &inst = isis3Lab.findGroup("Instrument", Pvl::Traverse);



  if((QString)inst["InstrumentId"] == "THEMIS_VIS") {

    Cube *even = new Cube();

    Cube *odd = new Cube();



    even->setDimensions(p.Samples(), p.Lines(), p.Bands());

    even->setPixelType(Isis::Real);

    odd->setDimensions(p.Samples(), p.Lines(), p.Bands());

    odd->setPixelType(Isis::Real);



    QString evenFile = outFile.path() + "/" + outFile.baseName() + ".even.cub";

    QString oddFile = outFile.path() + "/" + outFile.baseName() + ".odd.cub";



    even->create(evenFile);

    odd->create(oddFile);



    frameletLines = 192 / ((int)inst["SpatialSumming"]);



    outputCubes.push_back(odd);

    outputCubes.push_back(even);

  }

  else {

    Cube *outCube = new Cube();

    outCube->setDimensions(p.Samples(), p.Lines(), p.Bands());

    outCube->setPixelType(Isis::Real);



    outCube->create(outFile.expanded());

    outputCubes.push_back(outCube);

  }



  // Import the file and then translate labels

  p.StartProcess(separateFrames);

  p.EndProcess();



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

    for(int grp = 0; grp < isis3Lab.groups(); grp++) {



      // vis image?

      if(outputCubes.size() != 1) {

        int numFramelets = p.Lines() / frameletLines;

        isis3Lab.findGroup("Instrument").addKeyword(

          PvlKeyword("NumFramelets", toString(numFramelets)), Pvl::Replace

        );



        QString frameletType = ((i == 0) ? "Odd" : "Even");

        isis3Lab.findGroup("Instrument").addKeyword(

          PvlKeyword("Framelets", frameletType), Pvl::Replace

        );

      }



      outputCubes[i]->putGroup(isis3Lab.group(grp));

    }

    p.WriteHistory(*outputCubes[i]);

    outputCubes[i]->write(origLabels);

    outputCubes[i]->close();

    delete outputCubes[i];

  }



  outputCubes.clear();

}



//! Separates each of the individual VIS frames into their own file

void separateFrames(Buffer &in) {

  // (line-1)/frameletHeight % numOutImages

  int outputCube = (in.Line() - 1) / frameletLines % outputCubes.size();

  LineManager mgr(*outputCubes[outputCube]);

  mgr.SetLine(in.Line(), in.Band());



  // mgr.Copy(in); doesn't work because the raw buffers dont match

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

    mgr[i] = in[i];



  outputCubes[outputCube]->write(mgr);



  // Null out every other cube

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

    if(i == outputCube) continue;



    LineManager mgr(*outputCubes[i]);

    mgr.SetLine(in.Line(), in.Band());



    for(int j = 0; j < mgr.size(); j++) {

      mgr[j] = Isis::Null;

    }



    outputCubes[i]->write(mgr);

  }

}



void TranslateLabels(Pvl &pdsLab, Pvl &isis3, int numBands) {

  // Create the Instrument Group

  PvlGroup inst("Instrument");

  inst += PvlKeyword("SpacecraftName", "MARS_ODYSSEY");

  QString instId = (QString) pdsLab["InstrumentId"] + "_" +

                  (QString) pdsLab["DetectorId"];

  inst += PvlKeyword("InstrumentId", instId);

  inst += PvlKeyword("TargetName", (QString) pdsLab["TargetName"]);

  inst += PvlKeyword("MissionPhaseName", (QString) pdsLab["MissionPhaseName"]);

  inst += PvlKeyword("StartTime", (QString)pdsLab["StartTime"]);

  inst += PvlKeyword("StopTime", (QString)pdsLab["StopTime"]);

  inst += PvlKeyword("SpacecraftClockCount",

                     (QString) pdsLab["SpacecraftClockStartCount"]);



  PvlObject &sqube = pdsLab.findObject("SPECTRAL_QUBE");

  if(instId == "THEMIS_IR") {

    inst += PvlKeyword("GainNumber", (QString)sqube["GainNumber"]);

    inst += PvlKeyword("OffsetNumber", (QString)sqube["OffsetNumber"]);

    inst += PvlKeyword("MissingScanLines", (QString)sqube["MissingScanLines"]);

    inst += PvlKeyword("TimeDelayIntegration",

                       (QString)sqube["TimeDelayIntegrationFlag"]);

    if(sqube.hasKeyword("SpatialSumming")) {

      inst += PvlKeyword("SpatialSumming", (QString)sqube["SpatialSumming"]);

    }

  }

  else {

    inst += PvlKeyword("ExposureDuration", (QString)sqube["ExposureDuration"]);

    inst += PvlKeyword("InterframeDelay", (QString)sqube["InterframeDelay"]);

    inst += PvlKeyword("SpatialSumming", (QString)sqube["SpatialSumming"]);

  }



  // Add at time offset to the Instrument group

  UserInterface &ui = Application::GetUserInterface();

  double spacecraftClockOffset = ui.GetDouble("TIMEOFFSET");

  inst += PvlKeyword("SpacecraftClockOffset", toString(spacecraftClockOffset), "seconds");



  isis3.addGroup(inst);



  // Create the Band bin Group

  PvlGroup bandBin("BandBin");



  // The original band is the original ISIS cube band number upon ingestion

  PvlKeyword originalBand("OriginalBand");

  for(int i = 1; i <= numBands; i++) {

    originalBand.addValue(toString(i));

  }

  bandBin += originalBand;



  bandBin += sqube.findGroup("BandBin")["BandBinCenter"];

  bandBin["BandBinCenter"].setName("Center");



  bandBin += sqube.findGroup("BandBin")["BandBinWidth"];

  bandBin["BandBinWidth"].setName("Width");



  // The FilterNumber keyword is a list indicating the time-ordered filter number of the

  // corresponding ISIS band. These values also indicate the physical order of the bands in the

  // detector array. They are numbered by ascending times (or starting detector lines).

  bandBin += sqube.findGroup("BandBin")["BandBinFilterNumber"];

  bandBin["BandBinFilterNumber"].setName("FilterNumber");



  // The BandNumber keyword is a list of wavelength-ordered band

  // numbers corresponding to filter numbers for each ISIS band.

  //

  // For IR, BandNumber always matches filter number since the filters are found

  // on the ccd in ascending wavelength order.

  //

  // For VIS, we have the following one to one correspondence of these keywords:

  // BandNumber   {1, 2, 3, 4, 5}

  // FilterNumber {2, 5, 3, 4, 1}

  //

  // Note that the BandNumber will match the OriginalBand only if the image

  // to be imported contains band number 1 and is not missing consecutive band numbers.

  bandBin += sqube.findGroup("BandBin")["BandBinBandNumber"];

  bandBin["BandBinBandNumber"].setName("BandNumber");



  isis3.addGroup(bandBin);



  // Create the archive Group

  PvlGroup arch("Archive");

  arch += PvlKeyword("DataSetId", (QString)pdsLab["DataSetId"]);

  arch += PvlKeyword("ProducerId", (QString)pdsLab["ProducerId"]);

  arch += PvlKeyword("ProductId", (QString)pdsLab["ProductId"]);

  arch += PvlKeyword("ProductCreationTime",

                     (QString)pdsLab["ProductCreationTime"]);

  arch += PvlKeyword("ProductVersionId", (QString)pdsLab["ProductVersionId"]);

//  arch += PvlKeyword("ReleaseId",(string)pdsLab["ReleaseId"]);

  arch += PvlKeyword("OrbitNumber", (QString)pdsLab["OrbitNumber"]);



  arch += PvlKeyword("FlightSoftwareVersionId",

                     (QString)sqube["FlightSoftwareVersionId"]);

  arch += PvlKeyword("CommandSequenceNumber",

                     (QString)sqube["CommandSequenceNumber"]);

  arch += PvlKeyword("Description", (QString)sqube["Description"]);

  isis3.addGroup(arch);



  // Create the Kernel Group

  PvlGroup kerns("Kernels");

  if(instId == "THEMIS_IR") {

    kerns += PvlKeyword("NaifFrameCode", toString(-53031));

  }

  else {

    kerns += PvlKeyword("NaifFrameCode", toString(-53032));

  }

  isis3.addGroup(kerns);

  thm2isis(ui);

}
 
 No newline at end of file

isis/src/odyssey/apps/thm2isis/thm2isis.cpp

0 → 100644
+265 −0
Original line number Diff line number Diff line 
#include <cstdio>

#include <string>



#include "ProcessImportPds.h"

#include "LineManager.h"

#include "UserInterface.h"

#include "CubeAttribute.h"

#include "FileName.h"

#include "IException.h"

#include "iTime.h"

#include "ProcessByBrick.h"

#include "Brick.h"

#include "OriginalLabel.h"



#include "thm2isis.h"



using namespace std;



namespace Isis { 

  static vector<Cube *> outputCubes;

  static int frameletLines;

  static void TranslateLabels(Pvl &labelFile, Pvl &isis3, int numBands, UserInterface &ui);

  static void separateFrames(Buffer &in);





  void thm2isis(UserInterface &ui) {

    // Grab the file to import

    ProcessImportPds p;

    outputCubes.clear();

    frameletLines = 192;



    FileName in = ui.GetFileName("FROM");



    // Make sure it is a Themis EDR/RDR

    bool projected;

    try {

      Pvl lab(in.expanded());

      projected = lab.hasObject("IMAGE_MAP_PROJECTION");

      QString id;

      id = (QString)lab["DATA_SET_ID"];

      id = id.simplified().trimmed();

      if(!id.startsWith("ODY-M-THM")) {

        QString msg = "Invalid DATA_SET_ID [" + id + "]";

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

      }

    }

    catch(IException &e) {

      QString msg = "Input file [" + in.expanded() +

                    "] does not appear to be " +

                    "in Themis EDR/RDR format";

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

    }



    //Checks if in file is rdr

    if(projected) {

      QString msg = "[" + in.name() + "] appears to be an rdr file.";

      msg += " Use pds2isis.";

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

    }



    // Ok looks good ... set it as the PDS file

    Pvl pdsLab;

    p.SetPdsFile(in.expanded(), "", pdsLab);



    OriginalLabel origLabels(pdsLab);



    Pvl isis3Lab;

    TranslateLabels(pdsLab, isis3Lab, p.Bands(), ui);



    // Set up the output cube

    FileName outFile(ui.GetFileName("TO"));

    PvlGroup &inst = isis3Lab.findGroup("Instrument", Pvl::Traverse);

    CubeAttributeOutput outAttr = ui.GetOutputAttribute("to");

    

    if((QString)inst["InstrumentId"] == "THEMIS_VIS") {

      Cube *even = new Cube();

      Cube *odd = new Cube();



      even->setDimensions(p.Samples(), p.Lines(), p.Bands());

      odd->setDimensions(p.Samples(), p.Lines(), p.Bands());



      QString evenFile = outFile.path() + "/" + outFile.baseName() + ".even.cub";

      QString oddFile = outFile.path() + "/" + outFile.baseName() + ".odd.cub";



      even->create(evenFile, outAttr);

      odd->create(oddFile, outAttr);



      frameletLines = 192 / ((int)inst["SpatialSumming"]);



      outputCubes.push_back(odd);

      outputCubes.push_back(even);

    }

    else {

      Cube *outCube = new Cube();

      outCube->setDimensions(p.Samples(), p.Lines(), p.Bands());



      outCube->create(outFile.expanded(), outAttr);

      outputCubes.push_back(outCube);

    }



    // Import the file and then translate labels

    p.StartProcess(separateFrames);

    p.EndProcess();



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

      for(int grp = 0; grp < isis3Lab.groups(); grp++) {



        // vis image?

        if(outputCubes.size() != 1) {

          int numFramelets = p.Lines() / frameletLines;

          isis3Lab.findGroup("Instrument").addKeyword(

            PvlKeyword("NumFramelets", toString(numFramelets)), Pvl::Replace

          );



          QString frameletType = ((i == 0) ? "Odd" : "Even");

          isis3Lab.findGroup("Instrument").addKeyword(

            PvlKeyword("Framelets", frameletType), Pvl::Replace

          );

        }



        outputCubes[i]->putGroup(isis3Lab.group(grp));

      }

      p.WriteHistory(*outputCubes[i]);

      outputCubes[i]->write(origLabels);

      outputCubes[i]->close();

      delete outputCubes[i];

    }



    outputCubes.clear();

  }



  //! Separates each of the individual VIS frames into their own file

  void separateFrames(Buffer &in) {

    // (line-1)/frameletHeight % numOutImages

    int outputCube = (in.Line() - 1) / frameletLines % outputCubes.size();

    LineManager mgr(*outputCubes[outputCube]);

    mgr.SetLine(in.Line(), in.Band());



    // mgr.Copy(in); doesn't work because the raw buffers dont match

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

      mgr[i] = in[i];



    outputCubes[outputCube]->write(mgr);



    // Null out every other cube

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

      if(i == outputCube) continue;



      LineManager mgr(*outputCubes[i]);

      mgr.SetLine(in.Line(), in.Band());



      for(int j = 0; j < mgr.size(); j++) {

        mgr[j] = Isis::Null;

      }



      outputCubes[i]->write(mgr);

    }

  }



  void TranslateLabels(Pvl &pdsLab, Pvl &isis3, int numBands, UserInterface &ui) {

    // Create the Instrument Group

    PvlGroup inst("Instrument");

    inst += PvlKeyword("SpacecraftName", "MARS_ODYSSEY");

    QString instId = (QString) pdsLab["InstrumentId"] + "_" +

                    (QString) pdsLab["DetectorId"];

    inst += PvlKeyword("InstrumentId", instId);

    inst += PvlKeyword("TargetName", (QString) pdsLab["TargetName"]);

    inst += PvlKeyword("MissionPhaseName", (QString) pdsLab["MissionPhaseName"]);

    inst += PvlKeyword("StartTime", (QString)pdsLab["StartTime"]);

    inst += PvlKeyword("StopTime", (QString)pdsLab["StopTime"]);

    inst += PvlKeyword("SpacecraftClockCount",

                      (QString) pdsLab["SpacecraftClockStartCount"]);



    PvlObject &sqube = pdsLab.findObject("SPECTRAL_QUBE");

    if(instId == "THEMIS_IR") {

      inst += PvlKeyword("GainNumber", (QString)sqube["GainNumber"]);

      inst += PvlKeyword("OffsetNumber", (QString)sqube["OffsetNumber"]);

      inst += PvlKeyword("MissingScanLines", (QString)sqube["MissingScanLines"]);

      inst += PvlKeyword("TimeDelayIntegration",

                        (QString)sqube["TimeDelayIntegrationFlag"]);

      if(sqube.hasKeyword("SpatialSumming")) {

        inst += PvlKeyword("SpatialSumming", (QString)sqube["SpatialSumming"]);

      }

    }

    else {

      inst += PvlKeyword("ExposureDuration", (QString)sqube["ExposureDuration"]);

      inst += PvlKeyword("InterframeDelay", (QString)sqube["InterframeDelay"]);

      inst += PvlKeyword("SpatialSumming", (QString)sqube["SpatialSumming"]);

    }



    // Add at time offset to the Instrument group

    

    double spacecraftClockOffset = ui.GetDouble("TIMEOFFSET");

    inst += PvlKeyword("SpacecraftClockOffset", toString(spacecraftClockOffset), "seconds");



    isis3.addGroup(inst);



    // Create the Band bin Group

    PvlGroup bandBin("BandBin");



    // The original band is the original ISIS cube band number upon ingestion

    PvlKeyword originalBand("OriginalBand");

    for(int i = 1; i <= numBands; i++) {

      originalBand.addValue(toString(i));

    }

    bandBin += originalBand;



    bandBin += sqube.findGroup("BandBin")["BandBinCenter"];

    bandBin["BandBinCenter"].setName("Center");



    bandBin += sqube.findGroup("BandBin")["BandBinWidth"];

    bandBin["BandBinWidth"].setName("Width");



    // The FilterNumber keyword is a list indicating the time-ordered filter number of the

    // corresponding ISIS band. These values also indicate the physical order of the bands in the

    // detector array. They are numbered by ascending times (or starting detector lines).

    bandBin += sqube.findGroup("BandBin")["BandBinFilterNumber"];

    bandBin["BandBinFilterNumber"].setName("FilterNumber");



    // The BandNumber keyword is a list of wavelength-ordered band

    // numbers corresponding to filter numbers for each ISIS band.

    //

    // For IR, BandNumber always matches filter number since the filters are found

    // on the ccd in ascending wavelength order.

    //

    // For VIS, we have the following one to one correspondence of these keywords:

    // BandNumber   {1, 2, 3, 4, 5}

    // FilterNumber {2, 5, 3, 4, 1}

    //

    // Note that the BandNumber will match the OriginalBand only if the image

    // to be imported contains band number 1 and is not missing consecutive band numbers.

    bandBin += sqube.findGroup("BandBin")["BandBinBandNumber"];

    bandBin["BandBinBandNumber"].setName("BandNumber");



    isis3.addGroup(bandBin);



    // Create the archive Group

    PvlGroup arch("Archive");

    arch += PvlKeyword("DataSetId", (QString)pdsLab["DataSetId"]);

    arch += PvlKeyword("ProducerId", (QString)pdsLab["ProducerId"]);

    arch += PvlKeyword("ProductId", (QString)pdsLab["ProductId"]);

    arch += PvlKeyword("ProductCreationTime",

                      (QString)pdsLab["ProductCreationTime"]);

    arch += PvlKeyword("ProductVersionId", (QString)pdsLab["ProductVersionId"]);

  //  arch += PvlKeyword("ReleaseId",(string)pdsLab["ReleaseId"]);

    arch += PvlKeyword("OrbitNumber", (QString)pdsLab["OrbitNumber"]);



    arch += PvlKeyword("FlightSoftwareVersionId",

                      (QString)sqube["FlightSoftwareVersionId"]);

    arch += PvlKeyword("CommandSequenceNumber",

                      (QString)sqube["CommandSequenceNumber"]);

    arch += PvlKeyword("Description", (QString)sqube["Description"]);

    isis3.addGroup(arch);



    // Create the Kernel Group

    PvlGroup kerns("Kernels");

    if(instId == "THEMIS_IR") {

      kerns += PvlKeyword("NaifFrameCode", toString(-53031));

    }

    else {

      kerns += PvlKeyword("NaifFrameCode", toString(-53032));

    }

    isis3.addGroup(kerns);

  }

}
 
 No newline at end of file

isis/src/odyssey/apps/thm2isis/thm2isis.h

0 → 100644
+12 −0
Original line number Diff line number Diff line 
#ifndef thm2isis_h // Change this to your app name in all lower case suffixed with _h (e.g. campt_h, cam2map_h etc.)

#define thm2isis_h



#include "Cube.h"

#include "UserInterface.h"



namespace Isis {



  extern void thm2isis(UserInterface &ui);

}



#endif
 
 No newline at end of file

isis/src/odyssey/apps/thm2isis/tsts/Makefile

deleted100644 → 0
+0 −4
Original line number Diff line number Diff line 
BLANKS = "%-6s"    

LENGTH = "%-40s"



include $(ISISROOT)/make/isismake.tststree