ProcessMosaic.cpp

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#include "Preference.h"

#include "Application.h"
#include "IException.h"
#include "IString.h"
#include "Portal.h"
#include "ProcessMosaic.h"
#include "Pvl.h"
#include "SerialNumber.h"
#include "SpecialPixel.h"
#include "Table.h"
#include "TrackingTable.h"

using namespace std;

namespace Isis {
  const char *ProcessMosaic::TRACKING_TABLE_NAME = "InputImages";

  ProcessMosaic::ProcessMosaic() {
    // Set the BandBin Match
    SetBandBinMatch(true);

    // Initialize the structure Track Info
    m_trackingEnabled    = false;
    m_trackingCube = NULL;
    m_createOutputMosaic   = false;
    m_bandPriorityBandNumber  = 0;
    m_bandPriorityKeyName  = "";
    m_bandPriorityKeyValue = "";
    m_bandPriorityUseMaxValue = false;

    // Initialize the Special Pixel Flags
    m_placeHighSatPixels = false;
    m_placeLowSatPixels = false;
    m_placeNullPixels = false;

    // Default Priority OnTop
    m_imageOverlay = PlaceImagesOnTop;

    m_enforceMatchDEM = false;

    // Initialize the data members
    m_iss = -1;
    m_isl = -1;
    m_isb = -1;
    m_ins = -1;
    m_inl = -1;
    m_inb = -1;
    m_oss = -1;
    m_osl = -1;
    m_osb = -1;
    m_onb = -1;
  }


  ProcessMosaic::~ProcessMosaic() {
    if (m_trackingCube) {
      m_trackingCube->close();
      delete m_trackingCube;
      m_trackingCube = NULL;
    }
  }


  void ProcessMosaic::StartProcess(const int &os, const int &ol, const int &ob) {
    // Error checks ... there must be one input and one output
    if ((OutputCubes.size() != 1) || (InputCubes.size() != 1)) {
      QString m = "You must specify exactly one input and one output cube";
      throw IException(IException::Programmer, m, _FILEINFO_);
    }

    bool bTrackExists = false;
    if (!m_createOutputMosaic) {
      bTrackExists = GetTrackStatus();
      if (m_trackingEnabled && 
            !(OutputCubes[0]->hasGroup("Tracking") || OutputCubes[0]->hasTable("InputImages"))) {
        QString m = "Cannot enable tracking while adding to a mosaic without tracking ";
        m += "information. Confirm that your mosaic was originally created with tracking enabled.";
        throw IException(IException::User, m, _FILEINFO_);
      }
    }

    int ins = m_ins;
    int inl = m_inl;
    int inb = m_inb;
    int iss = m_iss;
    int isl = m_isl;
    int isb = m_isb;

    if (ins == -1)
      ins = (int)InputCubes[0]->sampleCount();

    if (inl == -1)
      inl = (int)InputCubes[0]->lineCount();

    if (inb == -1)
      inb = (int)InputCubes[0]->bandCount();

    // Adjust the input sub-area if it overlaps any edge of the output cube
    m_oss = os;
    m_osl = ol;
    m_osb = ob;

    // Left edge
    if (m_oss < 1) {
      iss = iss - m_oss + 1;
      ins = ins + m_oss - 1;
      m_oss = 1;
    }
    // Top edge
    if (m_osl < 1) {
      isl = isl - m_osl + 1;
      inl = inl + m_osl - 1;
      m_osl = 1;
    }
    // Right edge
    if ((m_oss + ins - 1) > OutputCubes[0]->sampleCount()) {
      ins = OutputCubes[0]->sampleCount() - m_oss + 1;
    }
    // Bottom edge
    if ((m_osl + inl - 1) > OutputCubes[0]->lineCount()) {
      inl = OutputCubes[0]->lineCount() - m_osl + 1;
    }

    PvlGroup imgPosition("ImageLocation");
    imgPosition += PvlKeyword("File", InputCubes[0]->fileName());
    imgPosition += PvlKeyword("StartSample", toString(m_oss));
    imgPosition += PvlKeyword("StartLine", toString(m_osl));
    m_imagePositions += imgPosition;

    // Tests for completly off the mosaic
    if ((ins < 1) || (inl < 1)) {
      QString m = "The input cube does not overlap the mosaic";
      throw IException(IException::User, m, _FILEINFO_);
    }

    // Band Adjustments
    if (m_osb < 1) {
      isb = isb - m_osb + 1;
      inb = inb + m_osb - 1;
      m_osb = 1;
    }

    p_progress->SetMaximumSteps(
        (int)InputCubes[0]->lineCount() * (int)InputCubes[0]->bandCount());
    p_progress->CheckStatus();

    // Tracking is done for:
    // (1) Band priority,
    // (2) Ontop and Beneath priority with number of bands equal to 1,
    // (3) Ontop priority with all the special pixel flags set to true. (All special pixel flags
    //      must be set to true in order to handle multiple bands since we need to force pixels
    //      from all bands in a single image to be copied to the mosaic with ontop priority so we
    //      don't have multiple input bands to track for any single pixel in our tracking band.)
    if (m_trackingEnabled) {
      if (!(m_imageOverlay == UseBandPlacementCriteria ||
          ((m_imageOverlay == PlaceImagesOnTop || m_imageOverlay == PlaceImagesBeneath) &&
           // tracking band was already created for Tracking=true
           (OutputCubes[0]->bandCount()) == 1) ||
          (m_imageOverlay == PlaceImagesOnTop && m_placeHighSatPixels && m_placeLowSatPixels &&
           m_placeNullPixels)) ){
        QString m = "Tracking cannot be True for multi-band Mosaic with ontop or beneath priority";
        throw IException(IException::Programmer, m, _FILEINFO_);
      }
    }

    // *******************************************************************************

    Pvl *inLab  = InputCubes[0]->label();
    // Create / Match DEM Shape Model if bMatchDEM Flag is enabled
    if (m_enforceMatchDEM){
      MatchDEMShapeModel();
    }

    // Check to make sure the bandbins match if necessary
    if (m_enforceBandBinMatch) {
      Pvl *outLab = OutputCubes[0]->label();

      if (inLab->findObject("IsisCube").hasGroup("BandBin")) {
        // Check to make sure the output cube has a bandbin group & make sure it
        // matches the input cube bandbin group
        if (!m_createOutputMosaic && outLab->findObject("IsisCube").hasGroup("BandBin")) {
          MatchBandBinGroup(isb, inb);
        }
        // Otherwise copy the input cube bandbin to the output file
        else {
          AddBandBinGroup(isb);
        }
      }
      // BandBin group is not found
      else {
        QString m = "Match BandBin cannot be True when the Image does not have the BandBin group";
        throw IException(IException::Programmer, m, _FILEINFO_);
      }
    }
    // Match BandBin set to false and CREATE and TRACKING is true
    else {
      if (m_createOutputMosaic) {
        if (inLab->findObject("IsisCube").hasGroup("BandBin")) {
          AddBandBinGroup(isb);
        }
        else {
          AddDefaultBandBinGroup();
        }
      }
    }

    // Even if the track flag is off, if the track table exists and "TRACKING" exists in bandbin
    // group continue tracking
    if (bTrackExists) {
      m_trackingEnabled = true;
    }

    // We don't want to set the filename in the table unless the band info is valid
    int bandPriorityInputBandNumber = -1;
    int bandPriorityOutputBandNumber = -1;
    if (m_imageOverlay == UseBandPlacementCriteria ) {
      bandPriorityInputBandNumber = GetBandIndex(true);
      bandPriorityOutputBandNumber = GetBandIndex(false);
    }
    
    // Set index of tracking image to the default offset of the Isis::UnsignedByte
    int iIndex = VALID_MINUI4;
    // Propogate tracking if adding to mosaic that was previouly tracked.
    if (OutputCubes[0]->hasGroup("Tracking") && !m_createOutputMosaic) {
      m_trackingEnabled = true;
    }

    // Create tracking cube if need-be, add bandbin group, and update tracking table. Add tracking
    // group to mosaic cube. 
    if (m_trackingEnabled) {
      TrackingTable *trackingTable;

      if (!m_trackingCube) {
        m_trackingCube = new Cube;

        // A new mosaic cube is being created
        if (m_createOutputMosaic) {

          // Tracking cubes are always unsigned 4 byte integer
          m_trackingCube->setPixelType(PixelType::UnsignedInteger);

          // Tracking cube has the same number of lines and samples as the mosaic and 1 band
          m_trackingCube->setDimensions(OutputCubes[0]->sampleCount(),
                                        OutputCubes[0]->lineCount(),
                                        1);

          // The tracking cube file name convention is "output_cube_file_name" + "_tracking.cub"
          QString trackingBase = FileName(OutputCubes[0]->fileName()).removeExtension().expanded().split("/").last();//toString();
          m_trackingCube->create(FileName(OutputCubes[0]->fileName()).path() 
                                  + "/" + trackingBase + "_tracking.cub");

          // Add the tracking group to the mosaic cube label
          Pvl *mosaicLabel = OutputCubes[0]->label();
          PvlGroup trackingFileGroup("Tracking");
          PvlKeyword trackingFileName("FileName");
          trackingFileName.setValue(trackingBase + "_tracking.cub");
          trackingFileGroup.addKeyword(trackingFileName);
          mosaicLabel->findObject("IsisCube").addGroup(trackingFileGroup);
          
          // Write the bandbin group to the tracking cube label
          Pvl *trackingLabel = m_trackingCube->label();
          PvlGroup bandBin("BandBin");
          PvlKeyword trackBand("FilterName");
          trackBand += "TRACKING";
          bandBin.addKeyword(trackBand);
          trackingLabel->findObject("IsisCube").addGroup(bandBin);

          // Initialize an empty TrackingTable object to manage tracking table in tracking cube
          trackingTable = new TrackingTable();
        }
        
        // An existing mosaic cube is being added to
        else {
          // Confirm tracking group exists in mosaic cube to address backwards compatibility
          if ( OutputCubes[0]->hasGroup("Tracking") ) {
            QString trackingPath = FileName(OutputCubes[0]->fileName()).path();
            QString trackingFile = OutputCubes[0]->group("Tracking").findKeyword("FileName")[0];
            m_trackingCube->open(trackingPath + "/" + trackingFile, "rw");

            // Initialize a TrackingTable object from current mosaic
            Table *table;
            try {
              table = new Table(TRACKING_TABLE_NAME, m_trackingCube->fileName());
              trackingTable = new TrackingTable(*table);
            }
            catch (IException &e) {
              QString msg = "Unable to find Tracking Table in " + m_trackingCube->fileName() + ".";
              throw IException(IException::User, msg, _FILEINFO_);
            }
          }
          // If no tracking group exists in mosaic cube, warn user to run utility application to
          // add it and create a separate tracking cube
          else {
            QString msg = "Tracking cannot be enabled when adding to an existing mosaic "
            "that does not already have a tracking cube. Mosaics with a tracking band must "
            "have the tracking band extracted into an external tracking cube.";
            throw IException(IException::User, msg, _FILEINFO_);
          }
        }
        
        // Add current file to the TrackingTable object
        iIndex = trackingTable->fileNameToPixel(InputCubes[0]->fileName(), 
                                       SerialNumber::Compose(*(InputCubes[0])));
        
        //  Write the tracking table to the tracking cube, overwriting if need-be
        if (m_trackingCube->hasTable(Isis::trackingTableName)) {
         m_trackingCube->deleteBlob("Table", Isis::trackingTableName);
        }
        Table table = trackingTable->toTable();
        m_trackingCube->write(table);
      }

    }
    else if (m_imageOverlay == AverageImageWithMosaic && m_createOutputMosaic) {
      ResetCountBands();
    }

    m_onb = OutputCubes[0]->bandCount();

    if (m_trackingEnabled) {

      // For mosaic creation, the input is copied onto mosaic by default
      if (m_imageOverlay == UseBandPlacementCriteria && !m_createOutputMosaic) {
        BandComparison(iss, isl, ins, inl,
                       bandPriorityInputBandNumber, bandPriorityOutputBandNumber, iIndex);
      }
    }
    else if (m_imageOverlay == AverageImageWithMosaic) {
      m_onb /= 2;
      if (m_onb < 1) {
        QString msg = "The mosaic cube needs a count band.";
        throw IException(IException::Unknown, msg, _FILEINFO_);
      }
    }

    // Process Band Priority with no tracking
    if (m_imageOverlay == UseBandPlacementCriteria && !m_trackingEnabled ) {
      BandPriorityWithNoTracking(iss, isl, isb, ins, inl, inb, bandPriorityInputBandNumber,
                                 bandPriorityOutputBandNumber);
    }
    else {
      // Create portal buffers for the input and output files
      Portal iPortal(ins, 1, InputCubes[0]->pixelType());
      Portal oPortal(ins, 1, OutputCubes[0]->pixelType());
      Portal countPortal(ins, 1, OutputCubes[0]->pixelType());
      Portal trackingPortal(ins, 1, PixelType::UnsignedInteger);

      for (int ib = isb, ob = m_osb; ib < (isb + inb) && ob <= m_onb; ib++, ob++) {
        for (int il = isl, ol = m_osl; il < isl + inl; il++, ol++) {
          // Set the position of the portals in the input and output cubes
          iPortal.SetPosition(iss, il, ib);
          InputCubes[0]->read(iPortal);

          oPortal.SetPosition(m_oss, ol, ob);
          OutputCubes[0]->read(oPortal);

          if (m_trackingEnabled) {
            trackingPortal.SetPosition(m_oss, ol, 1);
            m_trackingCube->read(trackingPortal);
          }
          else if (m_imageOverlay == AverageImageWithMosaic) {
            countPortal.SetPosition(m_oss, ol, (ob+m_onb));
            OutputCubes[0]->read(countPortal);
          }

          bool bChanged = false;
          // Move the input data to the output
          for (int pixel = 0; pixel < oPortal.size(); pixel++) {
            // Creating Mosaic, copy the input onto mosaic
            // regardless of the priority
            if (m_createOutputMosaic) {
              oPortal[pixel] = iPortal[pixel];
              if (m_trackingEnabled) {
                trackingPortal[pixel] = iIndex;
                bChanged = true;
              }
              else if (m_imageOverlay == AverageImageWithMosaic) {
                if (IsValidPixel(iPortal[pixel])) {
                  countPortal[pixel]=1;
                  bChanged = true;
                }
              }
            }
            // Band Priority
            else if (m_trackingEnabled && m_imageOverlay == UseBandPlacementCriteria) {
              int iPixelOrigin = qRound(trackingPortal[pixel]);

              Portal iComparePortal( ins, 1, InputCubes[0]->pixelType() );
              Portal oComparePortal( ins, 1, OutputCubes[0]->pixelType() );
              iComparePortal.SetPosition(iss, il, bandPriorityInputBandNumber);
              InputCubes[0]->read(iComparePortal);
              oComparePortal.SetPosition(m_oss, ol, bandPriorityOutputBandNumber);
              OutputCubes[0]->read(oComparePortal);

              if (iPixelOrigin == iIndex) {
                if ( ( IsValidPixel(iComparePortal[pixel]) &&
                       IsValidPixel(oComparePortal[pixel]) ) &&
                     ( (!m_bandPriorityUseMaxValue &&
                        iComparePortal[pixel] < oComparePortal[pixel]) ||
                       (m_bandPriorityUseMaxValue &&
                        iComparePortal[pixel] > oComparePortal[pixel]) ) ) {

                  if ( IsValidPixel(iPortal[pixel]) ||
                       ( m_placeHighSatPixels && IsHighPixel(iPortal[pixel]) ) ||
                       ( m_placeLowSatPixels  && IsLowPixel (iPortal[pixel]) ) ||
                       ( m_placeNullPixels    && IsNullPixel(iPortal[pixel]) ) ){
                    oPortal[pixel] = iPortal[pixel];
                    bChanged = true;
                  }
                }
                else { //bad comparison
                  if ( ( IsValidPixel(iPortal[pixel]) && !IsValidPixel(oPortal[pixel]) ) ||
                       ( m_placeHighSatPixels && IsHighPixel(iPortal[pixel]) ) ||
                       ( m_placeLowSatPixels  && IsLowPixel (iPortal[pixel]) ) ||
                       ( m_placeNullPixels    && IsNullPixel(iPortal[pixel]) ) ) {
                    oPortal[pixel] = iPortal[pixel];
                    bChanged = true;
                  }
                }
              }
            }
            // OnTop/Input Priority
            else if (m_imageOverlay == PlaceImagesOnTop) {
              if (IsNullPixel(oPortal[pixel])  ||
                 IsValidPixel(iPortal[pixel]) ||
                 (m_placeHighSatPixels && IsHighPixel(iPortal[pixel])) ||
                 (m_placeLowSatPixels  && IsLowPixel(iPortal[pixel]))  ||
                 (m_placeNullPixels    && IsNullPixel(iPortal[pixel]))) {
                oPortal[pixel] = iPortal[pixel];
                if (m_trackingEnabled) {
                  trackingPortal[pixel] = iIndex;
                  bChanged = true;
                }
              }
            }
            // AverageImageWithMosaic priority
            else if (m_imageOverlay == AverageImageWithMosaic) {
              bChanged |= ProcessAveragePriority(pixel, iPortal, oPortal, countPortal);
            }
            // Beneath/Mosaic Priority
            else if (m_imageOverlay == PlaceImagesBeneath) {
              if (IsNullPixel(oPortal[pixel])) {
                oPortal[pixel] = iPortal[pixel];
                // Set the origin if number of input bands equal to 1
                // and if the track flag was set
                if (m_trackingEnabled) {
                  trackingPortal[pixel] = iIndex;
                  bChanged = true;
                }
              }
            }
          } // End sample loop
          if (bChanged) {
            if (m_trackingEnabled) {
              m_trackingCube->write(trackingPortal);
            }
            if (m_imageOverlay == AverageImageWithMosaic) {
              OutputCubes[0]->write(countPortal);
            }
          }
          OutputCubes[0]->write(oPortal);
          p_progress->CheckStatus();
        } // End line loop
      }   // End band loop
    }
    if (m_trackingCube) {
      m_trackingCube->close();
      delete m_trackingCube;
      m_trackingCube = NULL;
    }
  } // End StartProcess


  void ProcessMosaic::EndProcess() {
    if (m_trackingCube) {
      m_trackingCube->close();
      delete m_trackingCube;
      m_trackingCube = NULL;
    }
    Process::EndProcess();
  }


  PvlObject ProcessMosaic::imagePositions() {
    return m_imagePositions;
  }


  Cube *ProcessMosaic::SetInputCube(const QString &parameter,
                                    const int ss, const int sl, const int sb,
                                    const int ns, const int nl, const int nb) {

    // Make sure only one input is active at a time
    if (InputCubes.size() > 0) {
      QString m = "You must specify exactly one input cube";
      throw IException(IException::Programmer, m, _FILEINFO_);
    }

    m_iss = ss;
    m_isl = sl;
    m_isb = sb;
    m_ins = ns;
    m_inl = nl;
    m_inb = nb;

    Cube *cInCube = Process::SetInputCube(parameter);

    //get the output label
    Pvl *cInPvl = InputCubes[0]->label();
    if (cInPvl->findGroup("Dimensions", Pvl::Traverse).hasKeyword("Bands")) {
      PvlKeyword &cBandKey = cInPvl->findGroup("Dimensions", Pvl::Traverse).findKeyword("Bands");
      QString sStr(cBandKey[0]);
      if (toInt(sStr) < nb) {
        QString m = "The parameter number of input bands exceeds the actual number of bands in the "
                   "input cube";
        throw IException(IException::Programmer, m, _FILEINFO_);
      }
    }
    return cInCube;
  }


  Cube *ProcessMosaic::SetInputCube(const QString &fname,
                                          CubeAttributeInput &att,
                                          const int ss, const int sl, const int sb,
                                          const int ns, const int nl, const int nb) {

    // Make sure only one input is active at a time
    if (InputCubes.size() > 0) {
      QString m = "You must specify exactly one input cube";
      throw IException(IException::Programmer, m, _FILEINFO_);
    }

    m_iss = ss;
    m_isl = sl;
    m_isb = sb;
    m_ins = ns;
    m_inl = nl;
    m_inb = nb;

    Cube *cInCube = Process::SetInputCube(fname, att);

    //check if the number of bands specified is not greater than the actual number of bands in the input
    Pvl *cInPvl = InputCubes[0]->label();
    if (cInPvl->findGroup("Dimensions", Pvl::Traverse).hasKeyword("Bands")) {
      PvlKeyword &cBandKey = cInPvl->findGroup("Dimensions", Pvl::Traverse).findKeyword("Bands");
      QString sStr(cBandKey[0]);
      if (toInt(sStr) < nb) {
        QString m = "The parameter number of input bands exceeds the actual number of bands in the input cube";
        throw IException(IException::Programmer, m, _FILEINFO_);
      }
    }
    return cInCube;
  }


  Cube *ProcessMosaic::SetOutputCube(const QString &psParameter) {

    // Make sure there is only one output cube
    if (OutputCubes.size() > 0) {
      QString m = "You must specify exactly one output cube";
      throw IException(IException::Programmer, m, _FILEINFO_);
    }

    // Attempt to open a cube ... get the filename from the user parameter
    // (e.g., "TO") and the cube size from an input cube
    Cube *cube = new Cube;
    try {
      QString fname = Application::GetUserInterface().GetFileName(psParameter);
      cube->open(fname, "rw");
    }
    catch (IException &) {
      delete cube;
      throw;
    }

    if (m_createOutputMosaic) {
      Pvl *outLab = cube->label();
      if (outLab->findObject("IsisCube").hasGroup("BandBin")) {
        outLab->findObject("IsisCube").deleteGroup("BandBin");
      }
    }

    // Everything is fine so save the cube on the stack
    AddOutputCube(cube);
    return cube;
  }


  void ProcessMosaic::SetBandBinMatch(bool enforceBandBinMatch) {
    m_enforceBandBinMatch = enforceBandBinMatch;
  }


  void ProcessMosaic::SetBandKeyword(QString bandPriorityKeyName, QString bandPriorityKeyValue) {
    m_bandPriorityKeyName = bandPriorityKeyName;
    m_bandPriorityKeyValue = bandPriorityKeyValue;
  }


  void ProcessMosaic::SetBandNumber(int bandPriorityBandNumber) {
    m_bandPriorityBandNumber = bandPriorityBandNumber;
  }


  void ProcessMosaic::SetBandUseMaxValue(bool useMax) {
    m_bandPriorityUseMaxValue = useMax;
  }


  void ProcessMosaic::SetCreateFlag(bool createOutputMosaic) {
    m_createOutputMosaic = createOutputMosaic;
  }


  void ProcessMosaic::SetHighSaturationFlag(bool placeHighSatPixels) {
    m_placeHighSatPixels = placeHighSatPixels;
  }


  void ProcessMosaic::SetImageOverlay(ImageOverlay placement) {
    m_imageOverlay = placement;
  }


  void ProcessMosaic::SetLowSaturationFlag(bool placeLowSatPixels) {
    m_placeLowSatPixels = placeLowSatPixels;
  }

  void ProcessMosaic::SetMatchDEM(bool matchDEM) {
    m_enforceMatchDEM = matchDEM;
  }


  void ProcessMosaic::SetNullFlag(bool placeNullPixels) {
    m_placeNullPixels = placeNullPixels;
  }


  void ProcessMosaic::SetTrackFlag(bool trackingEnabled) {
    m_trackingEnabled = trackingEnabled;
  }


  bool ProcessMosaic::GetHighSaturationFlag() const {
    return m_placeHighSatPixels;
  }


  ProcessMosaic::ImageOverlay ProcessMosaic::GetImageOverlay() const {
    return m_imageOverlay;
  }


  bool ProcessMosaic::GetLowSaturationFlag() const {
    return m_placeLowSatPixels;
  }


  bool ProcessMosaic::GetNullFlag() const {
    return m_placeNullPixels;
  }


  bool ProcessMosaic::GetTrackFlag() const {
    return m_trackingEnabled;
  }


  int ProcessMosaic::GetInputStartLineInMosaic() const {
    return m_osl;
  }


  int ProcessMosaic::GetInputStartSampleInMosaic() const {
    return m_oss;
  }


  int ProcessMosaic::GetInputStartBandInMosaic() const {
    return m_osb;
  }


  QString ProcessMosaic::OverlayToString(ImageOverlay imageOverlay) {
    QString result;

    switch (imageOverlay) {
      case PlaceImagesOnTop:
        result = "OnTop";
        break;

      case PlaceImagesBeneath:
        result = "Beneath";
        break;

      case UseBandPlacementCriteria:
        result = "Band";
        break;

      case AverageImageWithMosaic:
        result = "Average";
        break;

      case NumImageOverlayOptions:
        break;
    }

    if (result == "") {
      throw IException(IException::Unknown,
                       "Cannot convert overlay [" + toString((int)imageOverlay) + "] to a string",
                       _FILEINFO_);
    }

    return result;
  }


  ProcessMosaic::ImageOverlay ProcessMosaic::StringToOverlay(QString imageOverlayString) {
    QString imageOverlayStringUpper = imageOverlayString.toUpper();
    for (int i = 0; i < NumImageOverlayOptions; i++) {
      if (OverlayToString((ImageOverlay)i).toUpper() == imageOverlayStringUpper)
        return (ImageOverlay)i;
    }

    throw IException(IException::Unknown,
                     "The text [" + imageOverlayString + "] does not correspond to any known "
                     "image overlay modes (mosaic priorities)",
                     _FILEINFO_);
  }


  void ProcessMosaic::MatchDEMShapeModel() {
    Pvl* inLabel  = InputCubes[0]->label();
    Pvl* outLabel = OutputCubes[0]->label();

    if (outLabel->findObject("IsisCube").hasGroup("Mosaic")) {
      PvlGroup outMosaicGrp = outLabel->findObject("IsisCube").findGroup("Mosaic");
      if (outMosaicGrp.hasKeyword("ShapeModel")) {
        if (inLabel->findObject("IsisCube").hasGroup("Kernels")) {
          PvlGroup inMosaicGrp = inLabel->findObject("IsisCube").findGroup("Kernels");
          if (outMosaicGrp.hasKeyword("ShapeModel") && inMosaicGrp.hasKeyword("ShapeModel")) {
            PvlKeyword outShapeModelKey = outMosaicGrp.findKeyword("ShapeModel");
            QString sShapeModel = inMosaicGrp.findKeyword("ShapeModel")[0];
            int found = sShapeModel.lastIndexOf("/");
            if (found != -1) {
              sShapeModel.remove(0, found + 1);
            }
            if (sShapeModel == outShapeModelKey[0]) {
              return;
            }
          }
        }
        QString sErrMsg = "Input and Mosaic DEM Shape Model do not match";
        throw IException(IException::User, sErrMsg, _FILEINFO_);
      }
    }
    else {
      if (m_createOutputMosaic) {
        if (inLabel->findObject("IsisCube").hasGroup("Kernels")) {
          QString sShapeModel =
              inLabel->findObject("IsisCube").findGroup("Kernels").findKeyword("ShapeModel")[0];
          int found = sShapeModel.lastIndexOf("/");
          if (found != -1){
            sShapeModel.remove(0, found+1);
          }
          PvlObject & outIsisCubeObj = outLabel->findObject("IsisCube");
          PvlGroup mosaicGrp("Mosaic");
          PvlKeyword shapeModelKey("ShapeModel");
          shapeModelKey += sShapeModel;
          mosaicGrp += shapeModelKey;
          outIsisCubeObj += mosaicGrp;
        }
      }
    }
  }


  void ProcessMosaic::ResetCountBands()
  {
    int iBand   = OutputCubes[0]->bandCount();
    int iLines  = OutputCubes[0]->lineCount();
    int iSample = OutputCubes[0]->sampleCount();

    Portal countPortal(iSample, 1, OutputCubes[0]->pixelType());
    int iStartCountBand = iBand/2 + 1;

    for (int band=iStartCountBand; band<=iBand; band++) {
      for (int i = 1; i <= iLines; i++) {
        countPortal.SetPosition(1, i, band);  //sample, line, band position
        OutputCubes[0]->read(countPortal);
        for (int iPixel = 0; iPixel < countPortal.size(); iPixel++) {
          countPortal[iPixel] = 0;
        }
        OutputCubes[0]->write(countPortal);
      }
    }
  }


  bool ProcessMosaic::ProcessAveragePriority(int piPixel, Portal& piPortal, Portal& poPortal,
                                             Portal& countPortal)
  {
    bool bChanged=false;
    if (IsValidPixel(piPortal[piPixel]) && IsValidPixel(poPortal[piPixel])) {
      int iCount = (int)countPortal[piPixel];
      double dNewDN = (poPortal[piPixel] * iCount + piPortal[piPixel]) / (iCount + 1);
      poPortal[piPixel] = dNewDN;
      countPortal[piPixel] =iCount +1;
      bChanged = true;
    }
    // Input-Valid, Mosaic-Special
    else if (IsValidPixel(piPortal[piPixel])) {
      poPortal[piPixel] = piPortal[piPixel];
      countPortal[piPixel] = 1;
      bChanged = true;
    }
    // Input-Special, Flags-True
    else if (IsSpecial(piPortal[piPixel])) {
      if ((m_placeHighSatPixels && IsHighPixel(piPortal[piPixel])) ||
         (m_placeLowSatPixels  && IsLowPixel (piPortal[piPixel]))  ||
         (m_placeNullPixels    && IsNullPixel(piPortal[piPixel]))) {
        poPortal[piPixel]    = piPortal[piPixel];
        countPortal[piPixel] = 0;
        bChanged = true;
      }
    }
    return bChanged;
  }


  void ProcessMosaic::MatchBandBinGroup(int origIsb, int &inb) {
    Pvl *inLab  = InputCubes[0]->label();
    Pvl *outLab = OutputCubes[0]->label();

    PvlGroup &inBin  = inLab->findGroup("BandBin", Pvl::Traverse);
    PvlGroup &outBin = outLab->findGroup("BandBin", Pvl::Traverse);
    if (inBin.keywords() != outBin.keywords()) {
      QString msg = "Pvl Group [BandBin] does not match between the input and output cubes";
      throw IException(IException::User, msg, _FILEINFO_);
    }

    //pvl - zero based
    int isb = (origIsb - 1);
    int osb = (m_osb - 1);
    int iOutBandsHalf = OutputCubes[0]->bandCount()/2;

    for (int i = 0; i < outBin.keywords(); i++) {
      PvlKeyword &outKey = outBin[i];
      QString sOutName = outKey.name();
      if (inBin.hasKeyword(sOutName)) {
        PvlKeyword &inKey = inBin[sOutName];
        for (int j = osb, k = isb; j < outKey.size() && k < inKey.size(); j++, k++) {
          if (outKey[j] == "NA") {
            outKey[j] = inKey[k];
            if (m_imageOverlay == AverageImageWithMosaic) {
              if (sOutName.contains("Filter") ||
                  sOutName.contains("Name")) {
                outKey[j+iOutBandsHalf] = inKey[k] + "_Count";
              }
              else {
                outKey[j+iOutBandsHalf] = "Avg_Count";
              }
            }
          }
          else if (outKey[j] != inKey[k]) {
            QString msg = "The input cube [" + inLab->fileName() + "] and the base mosaic values "
                           "of the Pvl Group [BandBin] for Keyword [" + outKey.name() + "] do not "
                           "match. Base mosaic value at index [" + QString::number(j) + "] = " +
                           outKey[j] + ". Input cube value at index [" + QString::number(k) + "] = "
                           + inKey[k] + ". **Note: use mapmos/automos MatchBandBin = false to "
                           "override this check**";
            //QString msg = "Pvl Group [BandBin] in Key[" + outKey.name() + "] In value" + inKey[k] +
                         //"and Out value=" + outKey[j] + " do not match";
            throw IException(IException::User, msg, _FILEINFO_);
          }
        }
      }
      else {
        QString msg = "Pvl Group [BandBin] In Keyword[" + inBin[i].name() + "] and Out Keyword[" +
                     outBin[i].name() + "] does not match";
        throw IException(IException::User, msg, _FILEINFO_);
      }
    }

    int inputRange = InputCubes[0]->bandCount() - isb;
    int outputRange = OutputCubes[0]->bandCount() - osb;
    inb = min(inputRange, outputRange);
  }


  void ProcessMosaic::AddBandBinGroup(int origIsb) {
    Pvl *inLab  = InputCubes[0]->label();
    Pvl *outLab = OutputCubes[0]->label();

    int iOutBands = OutputCubes[0]->bandCount();

    // else if (m_imageOverlay == AverageImageWithMosaic) {
    if (m_imageOverlay == AverageImageWithMosaic) {
      iOutBands /= 2;
    }

    int isb = origIsb - 1; // array zero based
    int osb = m_osb - 1;

    PvlGroup &cInBin  = inLab->findGroup("BandBin", Pvl::Traverse);
    PvlGroup cOutBin("BandBin");

    for (int i = 0; i < cInBin.keywords(); i++) {
      PvlKeyword &cInKey = cInBin[i];
      int iInKeySize = cInKey.size();
      PvlKeyword cOutKey(cInKey.name());

      for (int b = 0; b < osb; b++) {
        cOutKey += "NA";
      }
      for (int b = osb; b < iOutBands; b++) {
        if (isb < iInKeySize) {
          cOutKey += cInKey[isb++];
        }
        else {
          cOutKey += "NA";
        }
      }

      // Tag the Count Bands if priority is AverageImageWithMosaic.
      if (m_imageOverlay == AverageImageWithMosaic) {

        int iTotalOutBands = OutputCubes[0]->bandCount();
        isb = origIsb - 1; // reset the input starting band
        int iOutStartBand = iOutBands + osb;
        QString sKeyName = cInKey.name();
        bool bFilterKey = false;
        if (sKeyName.contains("Filter")   ||
            sKeyName.contains("Original") ||
            sKeyName.contains("Name")) {
          bFilterKey = true;
        }
        for (int ob=iOutBands; ob<iTotalOutBands; ob++) {
          if (isb < iInKeySize && ob >= iOutStartBand) {
            if (bFilterKey) {
              cOutKey += cInKey[isb++] + "_Count";
            }
            else {
              cOutKey += 0;
              isb++;
            }
          }
          else {
            cOutKey += 0;
          }
        }
      }

      // Check for units and make sure output keyword units value is set to input
      // keyword units value
      if (cOutKey.unit() != cInKey.unit()) {
        cOutKey.setUnits((QString)(cInKey.unit()));
      }

      cOutBin += cOutKey;
      isb = origIsb - 1;        // reinitialize the input starting band
    }
    outLab->findObject("IsisCube").addGroup(cOutBin);
  }


  void ProcessMosaic::AddDefaultBandBinGroup() {
    Pvl *outLab = OutputCubes[0]->label();

    PvlGroup cOutBin("BandBin");

    int iOutBands = OutputCubes[0]->bandCount();
    int iOutBandsTotal = iOutBands;

    if (m_trackingEnabled) {
      iOutBands--; // Leave tracking band
    }
    else if (m_imageOverlay == AverageImageWithMosaic) {
      iOutBands /= 2;
    }

    PvlKeyword cOutKey("FilterName");

    for (int i=0; i<iOutBands; i++) {
      cOutKey += "NA";
    }

    if (m_imageOverlay == AverageImageWithMosaic) {
      for (int i=iOutBands; i<iOutBandsTotal; i++) {
        cOutKey += "NA_Count";
      }
    }

    if (m_trackingEnabled) {
      cOutKey += "TRACKING";
    }

    cOutBin += cOutKey;

    outLab->findObject("IsisCube").addGroup(cOutBin);
  }


  int ProcessMosaic::GetBandIndex(bool inputFile) {
    bool bFound = false;
    int iBandIndex = 0;

    Pvl cPvlLabel;

    if (inputFile) {
      cPvlLabel = *(InputCubes[0]->label());
      if (m_bandPriorityBandNumber <= InputCubes[0]->bandCount() &&
          m_bandPriorityBandNumber > 0) {
          iBandIndex = m_bandPriorityBandNumber;
          bFound = true;
      }
    }
    else {
      cPvlLabel = *(OutputCubes[0]->label());
      if (m_bandPriorityBandNumber <= OutputCubes[0]->bandCount() &&
          m_bandPriorityBandNumber > 0) {
          iBandIndex = m_bandPriorityBandNumber;
          bFound = true;
      }
    }
    
    //key name
    if (!m_bandPriorityBandNumber) {
      PvlKeyword cKeyName;
      if (cPvlLabel.findGroup("BandBin", Pvl::Traverse).hasKeyword(m_bandPriorityKeyName)) {
        cKeyName = cPvlLabel.findGroup("BandBin", Pvl::Traverse).findKeyword(m_bandPriorityKeyName);
      }
      int iSize = cKeyName.size();
      for (int i = 0; i < iSize; i++) {
        if (m_bandPriorityKeyValue.toUpper() == cKeyName[i].toUpper()) {
          iBandIndex = i + 1; //1 based get key value index
          bFound = true;
          break;
        }
      }
    }
    if (!bFound) {
      QString msg = "Invalid Band / Key Name, Value ";
      throw IException(IException::User, msg, _FILEINFO_);
    }
    return iBandIndex;
  }


  void ProcessMosaic::BandComparison(int iss, int isl, int ins, int inl,
      int bandPriorityInputBandNumber, int bandPriorityOutputBandNumber, int index) {
    //
    // Create portal buffers for the input and output files
    Portal cIportal(ins, 1, InputCubes[0]->pixelType());
    Portal cOportal(ins, 1, OutputCubes[0]->pixelType());
    Portal trackingPortal(ins, 1, PixelType::UnsignedInteger);

    for (int iIL = isl, iOL = m_osl; iIL < isl + inl; iIL++, iOL++) {
      // Set the position of the portals in the input and output cubes
      cIportal.SetPosition(iss, iIL, bandPriorityInputBandNumber);
      InputCubes[0]->read(cIportal);

      cOportal.SetPosition(m_oss, iOL, bandPriorityOutputBandNumber);
      OutputCubes[0]->read(cOportal);

      trackingPortal.SetPosition(m_oss, iOL, 1);
      m_trackingCube->read(trackingPortal);

      // Move the input data to the output
      for (int iPixel = 0; iPixel < cOportal.size(); iPixel++) {
        if ((m_placeHighSatPixels && IsHighPixel(cIportal[iPixel])) ||
            (m_placeLowSatPixels  && IsLowPixel(cIportal[iPixel])) ||
            (m_placeNullPixels    && IsNullPixel(cIportal[iPixel]))) {
          trackingPortal[iPixel] = index;
        }
        else {
          if (IsValidPixel(cIportal[iPixel])) {
            if (IsSpecial(cOportal[iPixel]) ||
                (m_bandPriorityUseMaxValue == false  && cIportal[iPixel] < cOportal[iPixel]) ||
                (m_bandPriorityUseMaxValue == true && cIportal[iPixel] > cOportal[iPixel])) {
              trackingPortal[iPixel] = index;
            }
          }
        }
      }
      m_trackingCube->write(trackingPortal);
    }
  }


void ProcessMosaic::BandPriorityWithNoTracking(int iss, int isl, int isb, int ins, int inl,
                                                 int inb, int bandPriorityInputBandNumber,
                                                 int bandPriorityOutputBandNumber) {
    /*
     * specified band for comparison
     * Create portal buffers for the input and output files pointing to the
     */
    Portal iComparePortal( ins, 1, InputCubes[0]->pixelType() );
    Portal oComparePortal( ins, 1, OutputCubes[0]->pixelType() );
    Portal resultsPortal ( ins, 1, OutputCubes[0]->pixelType() );

    // Create portal buffers for the input and output files
    Portal iPortal( ins, 1, InputCubes[0]->pixelType() );
    Portal oPortal( ins, 1, OutputCubes[0]->pixelType() );

    for (int inLine = isl, outLine = m_osl; inLine < isl + inl; inLine++, outLine++) {
//       Set the position of the portals in the input and output cubes
      iComparePortal.SetPosition(iss, inLine, bandPriorityInputBandNumber);
      InputCubes[0]->read(iComparePortal);

      oComparePortal.SetPosition(m_oss, outLine, bandPriorityOutputBandNumber);
      OutputCubes[0]->read(oComparePortal);

      Portal iPortal( ins, 1, InputCubes[0]->pixelType() );
      Portal oPortal( ins, 1, OutputCubes[0]->pixelType() );

      bool inCopy = false;
//       Move the input data to the output
      for (int iPixel = 0; iPixel < ins; iPixel++) {
        resultsPortal[iPixel] = false;
        if (m_createOutputMosaic) {
          resultsPortal[iPixel] = true;
          inCopy = true;
        }
        else if ( IsValidPixel(iComparePortal[iPixel]) && IsValidPixel(oComparePortal[iPixel]) ) {
          if ( (m_bandPriorityUseMaxValue == false  &&
                iComparePortal[iPixel] < oComparePortal[iPixel]) ||
                (m_bandPriorityUseMaxValue == true &&
                iComparePortal[iPixel] > oComparePortal[iPixel]) ) {
            resultsPortal[iPixel] = true;
            inCopy = true;
          }
        }
        else if (IsValidPixel(iComparePortal[iPixel]) && !IsValidPixel(oComparePortal[iPixel]) ) {
          resultsPortal[iPixel] = true;
          inCopy = true;
        }
      }
      if (inCopy) {
        for (int ib = isb, ob = m_osb; ib < (isb + inb) && ob <= m_onb; ib++, ob++) {
//           Set the position of the portals in the input and output cubes
          iPortal.SetPosition(iss, inLine, ib);
          InputCubes[0]->read(iPortal);

          oPortal.SetPosition(m_oss, outLine, ob);
          OutputCubes[0]->read(oPortal);

          for (int iPixel = 0; iPixel < ins; iPixel++) {
            if (resultsPortal[iPixel]) {
              if (m_createOutputMosaic) {
                oPortal[iPixel] = iPortal[iPixel];
              }
              else if ( IsValidPixel(iPortal[iPixel]) ||
                        (m_placeHighSatPixels && IsHighPixel(iPortal[iPixel]) ) ||
                        (m_placeLowSatPixels  && IsLowPixel (iPortal[iPixel]) ) ||
                        (m_placeNullPixels    && IsNullPixel(iPortal[iPixel]) ) ) {
                oPortal[iPixel] = iPortal[iPixel];
              }
            }
            else if ( IsValidPixel(iPortal[iPixel])  && !IsValidPixel(oPortal[iPixel]) ) {
              oPortal[iPixel] = iPortal[iPixel];
            }
          }
          OutputCubes[0]->write(oPortal);
        }
      }
    }
  }


  int ProcessMosaic::GetOriginDefaultByPixelType() {
    int iDefault;

    switch (SizeOf(OutputCubes[0]->pixelType())) {
      case 1:
        iDefault = NULL1;
        break;

      case 2:
        iDefault = NULL2;
        break;

      case 4:
        iDefault = INULL4;
        break;

      default:
        QString msg = "ProcessMosaic::GetOriginDefaultByPixelType - Invalid Pixel Type";
        throw IException(IException::Programmer, msg, _FILEINFO_);
    }

    return iDefault;
  }


  bool ProcessMosaic::GetTrackStatus() {
    //get the output label
    Pvl *cPvlOut = OutputCubes[0]->label();

    bool bGroupExists = false;
    PvlObject cPvlObj;

    //Check if table already exists
    if (cPvlOut->hasGroup("Tracking")) {
      bGroupExists = true;
    }

    return bGroupExists;
  }

}