ProcessImport.cpp

Go to the documentation of this file.

#include "ProcessImport.h"

#include <float.h>
#include <iostream>
#include <QString>
#include <sstream>

#include "Application.h"
#include "BoxcarCachingAlgorithm.h"
#include "Brick.h"
#include "Cube.h"
#include "CubeAttribute.h"
#include "IException.h"
#include "IString.h"
#include "JP2Decoder.h"
#include "LineManager.h"
#include "PixelType.h"
#include "Process.h"
#include "Pvl.h"
#include "PvlTokenizer.h"
#include "SpecialPixel.h"

using namespace std;
namespace Isis {

  ProcessImport::ProcessImport() : Isis::Process() {

    p_progress->SetText("Importing");

    //  Initialize input file information
    p_inFile = "";
    p_pixelType = Isis::None;
    p_ns = p_nl = p_nb = 0;
    p_byteOrder = Isis::NoByteOrder;
    p_fileHeaderBytes = 0;
    p_dataHeaderBytes = 0;
    p_dataTrailerBytes = 0;
    p_dataPreBytes = 0;
    p_dataPostBytes = 0;
    p_organization = ProcessImport::BSQ;
    p_base.push_back(0.0);
    p_mult.push_back(1.0);
    // Make all special pixels invalid
    SetNull(DBL_MAX, -DBL_MAX);
    SetHRS(DBL_MAX, -DBL_MAX);
    SetLRS(DBL_MAX, -DBL_MAX);
    SetHIS(DBL_MAX, -DBL_MAX);
    SetLIS(DBL_MAX, -DBL_MAX);

    p_saveFileHeader = false;
    p_saveDataHeader = false;
    p_saveDataTrailer = false;
    p_saveDataPre = false;
    p_saveDataPost = false;
    p_saveFileTrailer = false;

    p_fileHeader = NULL;
    p_fileTrailer = NULL;
  }


  ProcessImport::~ProcessImport() {
    if (p_fileHeader) {
      delete [] p_fileHeader;
      p_fileHeader = NULL;
    }

    for(unsigned int i = 0; i < p_dataHeader.size(); i++) {
      delete [] p_dataHeader[i];
    }

    for(unsigned int i = 0; i < p_dataTrailer.size(); i++) {
      delete [] p_dataTrailer[i];
    }

    vector<char *> temp;
    for(unsigned int j = 0; j < p_dataPre.size(); j++) {
      temp = p_dataPre[j];
      for(unsigned int i = 0; i < temp.size(); i++) delete [] temp[i];
    }

    for(unsigned int j = 0; j < p_dataPost.size(); j++) {
      temp = p_dataPost[j];
      for(unsigned int i = 0; i < temp.size(); i++) delete [] temp[i];
    }

    if (p_fileTrailer) {
      delete p_fileTrailer;
    }
  }


  void ProcessImport::SetPixelType(const Isis::PixelType type) {

    if ((type == Isis::Double) || (type == Isis::Real) || (type == Isis::SignedWord) ||
        (type == Isis::UnsignedWord) || (type == Isis::UnsignedByte)) {
      p_pixelType = type;
    }
    else {
      QString msg = "Unsupported pixel type [" +
                   Isis::PixelTypeName(type) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SetDimensions(const int ns, const int nl, const int nb) {
    if (ns > 0 && nl > 0 && nb > 0) {
      p_ns = ns;
      p_nl = nl;
      p_nb = nb;
    }
    else {
      QString msg = "Illegal dimension [" + toString(ns) + ", " +
                   toString(nl) + ", " + toString(nb) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SetByteOrder(const Isis::ByteOrder order) {
    p_byteOrder = order;
  };


  void ProcessImport::SetFileHeaderBytes(const int bytes) {
    if (bytes >= 0) {
      p_fileHeaderBytes = bytes;
    }
    else {
      QString msg = "Illegal file header size [" + toString(bytes) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SetFileTrailerBytes(const int bytes) {
    if (bytes >= 0) {
      p_fileTrailerBytes = bytes;
    }
    else {
      QString msg = "Illegal file trailer size [" + toString(bytes) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SetDataHeaderBytes(const int bytes) {
    if (bytes >= 0) {
      p_dataHeaderBytes = bytes;
    }
    else {
      QString msg = "Illegal data header size [" + toString(bytes) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SetDataTrailerBytes(const int bytes) {

    if (bytes >= 0) {
      p_dataTrailerBytes = bytes;
    }
    else {
      QString msg = "Illegal data trailer size [" + toString(bytes) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SetDataPrefixBytes(const int bytes) {

    if (bytes >= 0) {
      p_dataPreBytes = bytes;
    }
    else {
      QString msg = "Illegal data prefix size [" + toString(bytes) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SetDataSuffixBytes(const int bytes) {

    if (bytes >= 0) {
      p_dataPostBytes = bytes;
    }
    else {
      QString msg = "Illegal data suffix size [" + toString(bytes) + "]";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  };


  void ProcessImport::SaveFileHeader() {
    if (p_fileHeaderBytes == 0) {
      QString msg = "File header bytes equals 0.  There is nothing to save.  "
                    "Use SetFileHeaderBytes() first.";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
    p_saveFileHeader = true;
  };


  void ProcessImport::SaveFileTrailer() {
    if (p_fileTrailerBytes == 0) {
      QString msg = "File trailer bytes equals 0.  There is nothing to save.  "
                    "Use SetFileTrailerBytes() first.";
      throw IException(IException::Programmer, msg,
                                _FILEINFO_);
    }
    p_saveFileTrailer = true;
  };


  void ProcessImport::SaveDataHeader() {
    if (p_dataHeaderBytes == 0) {
      QString msg = "Data header bytes equals 0.  There is nothing to save.  "
                    "Use SetDataHeaderBytes() first.";
      throw IException(IException::Programmer, msg,
                                _FILEINFO_);
    }
    p_saveDataHeader = true;
  };


  void ProcessImport::SaveDataTrailer() {
    if (p_dataTrailerBytes == 0) {
      QString msg = "Data trailer bytes equals 0.  There is nothing to save.  "
                    "Use SetDataTrailerBytes() first.";
      throw IException(IException::Programmer, msg,
                                _FILEINFO_);
    }
    p_saveDataTrailer = true;
  };


  void ProcessImport::SaveDataPrefix() {
    if (p_dataPreBytes == 0) {
      QString msg = "Data prefix bytes equals 0.  There is nothing to save.  "
                    "Use SetDataPrefixBytes() first.";
      throw IException(IException::Programmer, msg,
                                _FILEINFO_);
    }
    p_saveDataPre = true;
  };


  void ProcessImport::SaveDataSuffix() {
    if (p_dataPostBytes == 0) {
      QString msg = "Data suffix bytes equals 0.  There is nothing to save.  "
                    "Use SetDataSuffixBytes() first.";
      throw IException(IException::Programmer, msg,
                                _FILEINFO_);
    }
    p_saveDataPost = true;
  };


  int ProcessImport::FileHeaderBytes() const {
    return p_fileHeaderBytes;
  }


  int ProcessImport::FileTrailerBytes() const {
    return p_fileTrailerBytes;
  }


  int ProcessImport::DataHeaderBytes() const {
    return p_dataHeaderBytes;
  }


  int ProcessImport::DataTrailerBytes() const {
    return p_fileTrailerBytes;
  }


  int ProcessImport::DataPrefixBytes() const {
    return p_dataPreBytes;
  }


  int ProcessImport::DataSuffixBytes() const {
    return p_dataPostBytes;
  }


  char *ProcessImport::FileHeader() {
    if (p_saveFileHeader) {
      return p_fileHeader;
    }
    QString msg = "File header was not saved.  Use SaveFileHeader().";
    throw IException(IException::Programmer, msg, _FILEINFO_);
  };


  char *ProcessImport::FileTrailer() {
    if (p_saveFileTrailer) {
      return p_fileTrailer;
    }
    QString msg = "File trailer was not saved.  Use SaveFileTrailer()";
    throw IException(IException::Programmer, msg, _FILEINFO_);
  };


  std::vector<char *> ProcessImport::DataHeader() {
    if (p_saveDataHeader) {
      return p_dataHeader;
    }
    QString msg = "Data header was not saved.  Use SaveDataHeader()";
    throw IException(IException::Programmer, msg, _FILEINFO_);
  };


  std::vector<char *> ProcessImport::DataTrailer() {
    if (p_saveDataTrailer) {
      return p_dataTrailer;
    }
    QString msg = "Data trailer was not saved.  Use SaveDataTrailer()";
    throw IException(IException::Programmer, msg, _FILEINFO_);
  };


  std::vector<std::vector<char *> > ProcessImport::DataPrefix() {
    if (p_saveDataPre) {
      return p_dataPre;
    }
    QString msg = "Data prefix was not saved.  Use SaveDataPrefix()";
    throw IException(IException::Programmer, msg, _FILEINFO_);
  };


  std::vector<std::vector<char *> > ProcessImport::DataSuffix() {
    if (p_saveDataPost) {
      return p_dataPost;
    }
    QString msg = "Data suffix was not saved.  Use SaveDataSuffix()";
    throw IException(IException::Programmer, msg, _FILEINFO_);
  };


  void ProcessImport::SetOrganization(const ProcessImport::Interleave org) {
    p_organization = org;
  };


  ProcessImport::Interleave ProcessImport::Organization() const {
    return p_organization;
  };


  void ProcessImport::SetBase(const double base) {
    p_base.clear();
    p_base.push_back(base);
  };


  void ProcessImport::SetBase(const std::vector<double> base) {
    p_base = base;
  };


  void ProcessImport::SetMultiplier(const double mult) {
    p_mult.clear();
    p_mult.push_back(mult);
  };


  void ProcessImport::SetMultiplier(const std::vector<double> mult) {
    p_mult = mult;
  };


  void ProcessImport::SetSpecialValues(const double null, const double lrs,
                                       const double lis, const double hrs,
                                       const double his) {
    SetNull(null, null);
    SetLRS(lrs, lrs);
    SetLIS(lis, lis);
    SetHRS(hrs, hrs);
    SetHIS(his, his);
  };


  void ProcessImport::SetNull(const double null_min, const double null_max) {
    CheckPixelRange("Null", null_min, null_max);
    p_null_min = null_min;
    p_null_max = null_max;
  }


  void ProcessImport::SetLRS(const double lrs_min, const double lrs_max) {
    CheckPixelRange("LRS", lrs_min, lrs_max);
    p_lrs_min = lrs_min;
    p_lrs_max = lrs_max;
  }


  void ProcessImport::SetLIS(const double lis_min, const double lis_max) {
    CheckPixelRange("LIS", lis_min, lis_max);
    p_lis_min = lis_min;
    p_lis_max = lis_max;
  }


  void ProcessImport::SetHRS(const double hrs_min, const double hrs_max) {
    CheckPixelRange("HRS", hrs_min, hrs_max);
    p_hrs_min = hrs_min;
    p_hrs_max = hrs_max;
  }


  void ProcessImport::SetHIS(const double his_min, const double his_max) {
    CheckPixelRange("HIS", his_min, his_max);
    p_his_min = his_min;
    p_his_max = his_max;
  }


  void ProcessImport::CheckPixelRange(QString pixelName, double pixelMin,
                                      double pixelMax) {
    if (pixelMin == DBL_MAX || pixelMax == -DBL_MAX) return;

    if (p_null_min != DBL_MAX && p_null_max != -DBL_MAX && ( //-null has been set
          (pixelMin > p_null_min && pixelMin < p_null_max) ||  // --min crossing
          (pixelMax > p_null_min && pixelMax < p_null_max) ||  // --max crossing
          (pixelMin < p_null_min && pixelMax > p_null_max))) { // --straddling
                                                               //   values
      QString msg = "The " + pixelName + " range [" + toString(pixelMin) +
                   "," + toString(pixelMax) + "] overlaps the NULL range [" +
                   toString(p_null_min) + "," + toString(p_null_max) + "]";
      throw IException(IException::User, msg, _FILEINFO_);
    }

    if (p_lrs_min != DBL_MAX && p_lrs_max != -DBL_MAX && (
          (pixelMin > p_lrs_min && pixelMin < p_lrs_max) ||
          (pixelMax > p_lrs_min && pixelMax < p_lrs_max) ||
          (pixelMin < p_lrs_min && pixelMax > p_lrs_max))) {
      QString msg = "The " + pixelName + " range [" + toString(pixelMin) +
                   "," + toString(pixelMax) + "] overlaps the LRS range [" +
                   toString(p_lrs_min) + "," + toString(p_lrs_max) + "]";
      throw IException(IException::User, msg, _FILEINFO_);
    }

    if (p_lis_min != DBL_MAX && p_lis_max != -DBL_MAX && (
          (pixelMin > p_lis_min && pixelMin < p_lis_max) ||
          (pixelMax > p_lis_min && pixelMax < p_lis_max) ||
          (pixelMin < p_lis_min && pixelMax > p_lis_max))) {
      QString msg = "The " + pixelName + " range [" + toString(pixelMin) +
                   "," + toString(pixelMax) + "] overlaps the LIS range [" +
                   toString(p_lis_min) + "," + toString(p_lis_max) + "]";
      throw IException(IException::User, msg, _FILEINFO_);
    }

    if (p_hrs_min != DBL_MAX && p_hrs_max != -DBL_MAX && (
          (pixelMin > p_hrs_min && pixelMin < p_hrs_max) ||
          (pixelMax > p_hrs_min && pixelMax < p_hrs_max) ||
          (pixelMin < p_hrs_min && pixelMax > p_hrs_max))) {
      QString msg = "The " + pixelName + " range [" + toString(pixelMin) +
                   "," + toString(pixelMax) + "] overlaps the HRS range [" +
                   toString(p_hrs_min) + "," + toString(p_hrs_max) + "]";
      throw IException(IException::User, msg, _FILEINFO_);
    }

    if (p_his_min != DBL_MAX && p_his_max != -DBL_MAX && (
          (pixelMin > p_his_min && pixelMin < p_his_max) ||
          (pixelMax > p_his_min && pixelMax < p_his_max) ||
          (pixelMin < p_his_min && pixelMax > p_his_max))) {
      QString msg = "The " + pixelName + " range [" + toString(pixelMin) +
                   "," + toString(pixelMax) + "] overlaps the HIS range [" +
                   toString(p_his_min) + "," + toString(p_his_max) + "]";
      throw IException(IException::User, msg, _FILEINFO_);
    }

  }


  double ProcessImport::TestPixel(const double pixel) {
    if (pixel <= p_null_max && pixel >= p_null_min) {
      return Isis::NULL8;
    }
    else if (pixel <= p_hrs_max && pixel >= p_hrs_min) {
      return Isis::HIGH_REPR_SAT8;
    }
    else if (pixel <= p_lrs_max && pixel >= p_lrs_min) {
      return Isis::LOW_REPR_SAT8;
    }
    else if (pixel <= p_his_max && pixel >= p_his_min) {
      return Isis::HIGH_INSTR_SAT8;
    }
    else if (pixel <= p_lis_max && pixel >= p_lis_min) {
      return Isis::LOW_INSTR_SAT8;
    }
    else {
      return pixel;
    }
  }


  Isis::Cube *ProcessImport::SetOutputCube(const QString &parameter) {
    CubeAttributeOutput &att =
      Application::GetUserInterface().GetOutputAttribute(parameter);

    if (att.propagateMinimumMaximum()) {
      double min, max;
      if ((p_pixelType == Isis::Double) ||
          (p_pixelType == Isis::Real) ||
          (p_base.size() > 1) || (p_mult.size() > 1)) {
        min = Isis::VALID_MIN4;
        max = Isis::VALID_MAX4;
      }
      else if (p_pixelType == Isis::SignedWord) {
        min = Isis::VALID_MIN2 * p_mult[0] + p_base[0];
        max = Isis::VALID_MAX2 * p_mult[0] + p_base[0];
      }
      else if (p_pixelType == Isis::UnsignedWord) {
        min = Isis::VALID_MINU2 * p_mult[0] + p_base[0];
        max = Isis::VALID_MAXU2 * p_mult[0] + p_base[0];
      }
      else if (p_pixelType == Isis::UnsignedByte) {
        min = Isis::VALID_MIN1 * p_mult[0] + p_base[0];
        max = Isis::VALID_MAX1 * p_mult[0] + p_base[0];
      }
      else {
        QString msg = "Unsupported pixel type [" +
                     Isis::PixelTypeName(p_pixelType) + "]";
        throw IException(IException::Programmer, msg, _FILEINFO_);
      }
      att.setMinimum(min);
      att.setMaximum(max);
    }

    if (att.propagatePixelType()) {
      if ((p_base.size() > 1) || (p_mult.size() > 1)) {
        att.setPixelType(Isis::Real);
      }
      else if (p_pixelType == Isis::UnsignedWord || p_pixelType == Isis::Double) {
        att.setPixelType(Isis::Real);
      }
      else {
        att.setPixelType(p_pixelType);
      }
    }

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


  Isis::Cube *ProcessImport::SetOutputCube(const QString &fname,
      Isis::CubeAttributeOutput &att) {
    return Isis::Process::SetOutputCube(fname, att, p_ns, p_nl, p_nb);
  }


  void ProcessImport::StartProcess() {
    if (p_organization == ProcessImport::JP2) {
      ProcessJp2();
    }
    else if (p_organization == ProcessImport::BSQ) {
      ProcessBsq();
    }
    else if (p_organization == ProcessImport::BIL) {
      ProcessBil();
    }
    else if (p_organization == ProcessImport::BIP) {
      ProcessBip();
    }
    else {
      QString msg = "File [" + p_inFile
                   + "] is not in a supported organization.";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  }


  void ProcessImport::StartProcess(void funct(Isis::Buffer &out)) {
    if (p_organization == ProcessImport::JP2) {
      ProcessJp2(funct);
    }
    else if (p_organization == ProcessImport::BSQ) {
      ProcessBsq(funct);
    }
    else if (p_organization == ProcessImport::BIL) {
      ProcessBil(funct);
    }
    else if (p_organization == ProcessImport::BIP) {
      ProcessBip(funct);
    }
    else {
      QString msg = "File [" + p_inFile + "] is not in a supported organization.";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
  }


  void ProcessImport::ProcessBsq(void funct(Isis::Buffer &out)) {
    // Figure out the number of bytes to read for a single line
    int readBytes = Isis::SizeOf(p_pixelType);
    readBytes = readBytes * p_ns;
    char *in = new char [readBytes];

    // Set up an Isis::EndianSwapper object
    QString tok(Isis::ByteOrderName(p_byteOrder));
    tok = tok.toUpper();
    Isis::EndianSwapper swapper(tok);

    ifstream fin;
    // Open input file
    Isis::FileName inFile(p_inFile);
    QString inFileName(inFile.expanded());
    fin.open(inFileName.toAscii().data(), ios::in | ios::binary);
    if (!fin.is_open()) {
      QString msg = "Cannot open input file [" + p_inFile + "]";
      throw IException(IException::Io, msg, _FILEINFO_);
    }

    // Handle the file header
    streampos pos = fin.tellg();
    if (p_saveFileHeader) {
      p_fileHeader = new char[p_fileHeaderBytes];
      fin.read(p_fileHeader, p_fileHeaderBytes);
    }
    else {
      fin.seekg(p_fileHeaderBytes, ios_base::beg);
    }

    // Check the last io
    if (!fin.good()) {
      QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                   toString((int)pos) + "]. Byte count [" +
                   toString(p_fileHeaderBytes) + "]" ;
      throw IException(IException::Io, msg, _FILEINFO_);
    }

    // Construct a line buffer manager
    Isis::Buffer *out = NULL;

    if (funct != NULL) {
      out = new Isis::Brick(p_ns, 1, 1, p_pixelType);
    }
    else {
      out = new Isis::LineManager(*OutputCubes[0]);
    }

    // Loop once for each band in the image
    p_progress->SetMaximumSteps(p_nl * p_nb);
    p_progress->CheckStatus();

    // Loop for each band
    for(int band = 0; band < p_nb; band++) {
      // Set the base multiplier
      double base, mult;
      if (p_base.size() > 1) {
        base = p_base[band];
        mult = p_mult[band];
      }
      else {
        base = p_base[0];
        mult = p_mult[0];
      }

      // Handle any data headers (e.g., the data at the beginning of each band)
      pos = fin.tellg();
      if (p_saveDataHeader) {
        p_dataHeader.push_back(new char[p_dataHeaderBytes]);
        fin.read(p_dataHeader.back(), p_dataHeaderBytes);
      }
      else {
        fin.seekg(p_dataHeaderBytes, ios_base::cur);
      }

      // Check the last io
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(p_dataHeaderBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

      // Space for storing prefix and suffix data pointers
      vector<char *> tempPre, tempPost;

      // Loop for each line in a band
      for(int line = 0; line < p_nl; line++) {

        // Handle any line prefix bytes
        pos = fin.tellg();
        if (p_saveDataPre) {
          tempPre.push_back(new char[p_dataPreBytes]);
          fin.read(tempPre.back(), p_dataPreBytes);
        }
        else {
          fin.seekg(p_dataPreBytes, ios_base::cur);
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_dataPreBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }


        // Get a line of data from the input file
        pos = fin.tellg();
        fin.read(in, readBytes);
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(readBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }

        // Swap the bytes if necessary and convert any out of bounds pixels
        // to special pixels
        for(int samp = 0; samp < p_ns; samp++) {
          switch(p_pixelType) {
            case Isis::UnsignedByte:
              (*out)[samp] = (double)((unsigned char *)in)[samp];
              break;
            case Isis::UnsignedWord:
              (*out)[samp] =
                (double)swapper.UnsignedShortInt((unsigned short int *)in+samp);
              break;
            case Isis::SignedWord:
              (*out)[samp] = (double)swapper.ShortInt((short int *)in+samp);
              break;
            case Isis::Real:
              (*out)[samp] = (double)swapper.Float((float *)in+samp);
              break;
            case Isis::Double:
              (*out)[samp] = (double)swapper.Double((double *)in+samp);
              break;
            default:
              break;
          }

          // Sets out to isis special pixel or leaves it if valid
          (*out)[samp] = TestPixel((*out)[samp]);

          if (Isis::IsValidPixel((*out)[samp])) {
            (*out)[samp] = mult * ((*out)[samp]) + base;
          }
        } // End sample loop

        if (funct == NULL) {
          // Set the buffer position and write the line to the output file
          ((Isis::LineManager *)out)->SetLine((band * p_nl) + line + 1);
          OutputCubes[0]->write(*out);
        }
        else {
          ((Isis::Brick *)out)->SetBaseSample(1);
          ((Isis::Brick *)out)->SetBaseLine(line + 1);
          ((Isis::Brick *)out)->SetBaseBand(band + 1);
          funct(*out);
        }

        p_progress->CheckStatus();

        // Handle any line suffix bytes
        pos = fin.tellg();
        if (p_saveDataPost) {
          tempPost.push_back(new char[p_dataPostBytes]);
          fin.read(tempPost.back(), p_dataPostBytes);
        }
        else {
          fin.seekg(p_dataPostBytes, ios_base::cur);
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_dataPreBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }
      } // End line loop

      // Save off the prefix bytes vector
      if (p_saveDataPre) {
        p_dataPre.push_back(tempPre);
        tempPre.clear();
      }

      // Save off the suffix bytes vector
      if (p_saveDataPost) {
        p_dataPost.push_back(tempPost);
        tempPost.clear();
      }

      // Handle the band trailer
      pos = fin.tellg();
      if (p_saveDataTrailer) {
        p_dataTrailer.push_back(new char[p_dataTrailerBytes]);
        fin.read(p_dataTrailer.back(), p_dataTrailerBytes);
      }
      else {
        fin.seekg(p_dataTrailerBytes, ios_base::cur);
      }

      // Check the last io
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(p_fileHeaderBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

    } // End band loop

    // Handle the file trailer
    pos = fin.tellg();
    if (p_saveFileTrailer) {
      fin.seekg(0, ios_base::end);
      streampos e = fin.tellg();
      p_fileTrailerBytes = (int)(e - pos + (streampos)1);
      p_fileTrailer = new char[p_fileTrailerBytes];
      fin.seekg(pos);
      fin.read(p_fileTrailer, p_fileTrailerBytes);

      // Check the io
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(p_fileTrailerBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

    }

    // Close the file and clean up
    fin.close();
    delete [] in;
  }


  void ProcessImport::ProcessBil(void funct(Isis::Buffer &someBuf)) {

    // Figure out the number of bytes to read for a single line
    int readBytes = Isis::SizeOf(p_pixelType);
    readBytes = readBytes * p_ns;
    char *in = new char [readBytes];

    // Set up an Isis::EndianSwapper object
    QString tok(Isis::ByteOrderName(p_byteOrder));
    tok = tok.toUpper();
    Isis::EndianSwapper swapper(tok);

    ifstream fin;
    // Open input file
    Isis::FileName inFile(p_inFile);
    QString inFileName(inFile.expanded());
    fin.open(inFileName.toAscii().data(), ios::in | ios::binary);
    if (!fin.is_open()) {
      QString msg = "Cannot open input file [" + p_inFile + "]";
      throw IException(IException::Io, msg, _FILEINFO_);
    }

    // Handle the file header
    streampos pos = fin.tellg();
    if (p_saveFileHeader) {
      p_fileHeader = new char[p_fileHeaderBytes];
      fin.read(p_fileHeader, p_fileHeaderBytes);
    }
    else {
      fin.seekg(p_fileHeaderBytes, ios_base::beg);
    }

    // Check the last io
    if (!fin.good()) {
      QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                   toString((int)pos) + "]. Byte count [" +
                   toString(p_fileHeaderBytes) + "]" ;
      throw IException(IException::Io, msg, _FILEINFO_);
    }

    // Construct a line buffer manager
    Isis::Buffer *out = NULL;

    if (funct != NULL) {
      out = new Isis::Brick(p_ns, p_nl, p_nb, p_ns, 1, 1, p_pixelType, true);
      ((Isis::Brick *)out)->setpos(0);
    }
    else {
      OutputCubes[0]->addCachingAlgorithm(new BoxcarCachingAlgorithm());
      out = new Isis::LineManager(*OutputCubes[0]);
    }

    // Loop once for each line in the image
    p_progress->SetMaximumSteps(p_nb * p_nl);
    p_progress->CheckStatus();

    // Loop for each line
    for(int line = 0; line < p_nl; line++) {
      // Loop for each band
      for(int band = 0; band < p_nb; band++) {
        // Set the base multiplier
        double base, mult;
        if (p_base.size() > 1) {
          base = p_base[band];
          mult = p_mult[band];
        }
        else {
          base = p_base[0];
          mult = p_mult[0];
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_dataHeaderBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }

        // Space for storing prefix and suffix data pointers
        vector<char *> tempPre, tempPost;


        // Handle any line prefix bytes
        pos = fin.tellg();
        if (p_saveDataPre) {
          tempPre.push_back(new char[p_dataPreBytes]);
          fin.read(tempPre.back(), p_dataPreBytes);
        }
        else {
          fin.seekg(p_dataPreBytes, ios_base::cur);
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_dataPreBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }


        // Get a line of data from the input file
        pos = fin.tellg();
        fin.read(in, readBytes);
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(readBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }

        // Swap the bytes if necessary and convert any out of bounds pixels
        // to special pixels
        for(int samp = 0; samp < p_ns; samp++) {
          switch(p_pixelType) {
            case Isis::UnsignedByte:
              (*out)[samp] = (double)((unsigned char *)in)[samp];
              break;
            case Isis::UnsignedWord:
              (*out)[samp] =
                (double)swapper.UnsignedShortInt((unsigned short int *)in+samp);
              break;
            case Isis::SignedWord:
              (*out)[samp] = (double)swapper.ShortInt((short int *)in+samp);
              break;
            case Isis::Real:
              (*out)[samp] = (double)swapper.Float((float *)in+samp);
              break;
            case Isis::Double:
              (*out)[samp] = (double)swapper.Double((double *)in+samp);
              break;
            default:
              break;
          }

          // Sets out to isis special pixel or leaves it if valid
          (*out)[samp] = TestPixel((*out)[samp]); 

          if (Isis::IsValidPixel((*out)[samp])) {
            (*out)[samp] = mult * ((*out)[samp]) + base;
          }
        } // End sample loop

        if (funct == NULL) {
          ((Isis::LineManager *)out)->SetLine((band * p_nl) + line + 1);
          OutputCubes[0]->write(*out);
        }
        else {
          funct(*out);
          (*((Isis::Brick *)out))++;
        }

        p_progress->CheckStatus();

        // Handle any line suffix bytes
        pos = fin.tellg();
        if (p_saveDataPost) {
          tempPost.push_back(new char[p_dataPostBytes]);
          fin.read(tempPost.back(), p_dataPostBytes);
        }
        else {
          fin.seekg(p_dataPostBytes, ios_base::cur);
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_dataPreBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }


        // Save off the prefix bytes vector
        if (p_saveDataPre) {
          p_dataPre.push_back(tempPre);
          tempPre.clear();
        }

        // Save off the suffix bytes vector
        if (p_saveDataPost) {
          p_dataPost.push_back(tempPost);
          tempPost.clear();
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_fileHeaderBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }

      } // End band loop

    } // End line loop

    // Handle the file trailer
    pos = fin.tellg();
    if (p_saveFileTrailer) {
      fin.seekg(0, ios_base::end);
      streampos e = fin.tellg();
      p_fileTrailerBytes = (int)(e - pos + (streampos)1);
      p_fileTrailer = new char[p_fileTrailerBytes];
      fin.seekg(pos);
      fin.read(p_fileTrailer, p_fileTrailerBytes);

      // Check the io
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(p_fileTrailerBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

    }

    // Close the file and clean up
    fin.close();
    delete [] in;

  }


  void ProcessImport::ProcessBip(void funct(Isis::Buffer &out)) {

    // Figure out the number of bytes to read for a single line
    int readBytes = Isis::SizeOf(p_pixelType);
    readBytes = readBytes * p_ns * p_nb;
    char *in = new char [readBytes];

    // Set up an Isis::EndianSwapper object
    QString tok(Isis::ByteOrderName(p_byteOrder));
    tok = tok.toUpper();
    Isis::EndianSwapper swapper(tok);

    ifstream fin;
    // Open input file
    Isis::FileName inFile(p_inFile);
    QString inFileName(inFile.expanded());
    fin.open(inFileName.toAscii().data(), ios::in | ios::binary);
    if (!fin.is_open()) {
      QString msg = "Cannot open input file [" + p_inFile + "]";
      throw IException(IException::Io, msg, _FILEINFO_);
    }

    // Handle the file header
    streampos pos = fin.tellg();
    if (p_saveFileHeader) {
      p_fileHeader = new char[p_fileHeaderBytes];
      fin.read(p_fileHeader, p_fileHeaderBytes);
    }
    else {
      fin.seekg(p_fileHeaderBytes, ios_base::beg);
    }

    // Check the last io
    if (!fin.good()) {
      QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                   toString((int)pos) + "]. Byte count [" +
                   toString(p_fileHeaderBytes) + "]" ;
      throw IException(IException::Io, msg, _FILEINFO_);
    }

    OutputCubes[0]->addCachingAlgorithm(new BoxcarCachingAlgorithm());
        
    // Construct a line buffer manager
    Isis::Buffer *out = NULL;

    if (funct != NULL) {
      out = new Isis::Buffer(p_ns, p_nl, p_nb, p_pixelType);
    }
    else {
      out = new Isis::LineManager(*OutputCubes[0]);
    }

    // Loop once for each line in the image
    p_progress->SetMaximumSteps(p_nl);
    p_progress->CheckStatus();

    // Loop for each line
    for(int line = 0; line < p_nl; line++) {
      // Check the last io
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(p_dataHeaderBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

      // Space for storing prefix and suffix data pointers
      vector<char *> tempPre, tempPost;


      // Handle any line prefix bytes
      pos = fin.tellg();
      if (p_saveDataPre) {
        tempPre.push_back(new char[p_dataPreBytes]);
        fin.read(tempPre.back(), p_dataPreBytes);
      }
      else {
        fin.seekg(p_dataPreBytes, ios_base::cur);
      }

      // Check the last io
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(p_dataPreBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

      // Get a line of data from the input file
      pos = fin.tellg();
      fin.read(in, readBytes);
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(readBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

      // Loop for each band
      for(int band = 0; band < p_nb; band++) {
        // Set the base multiplier
        double base, mult;
        if (p_base.size() > 1) {
          base = p_base[band];
          mult = p_mult[band];
        }
        else {
          base = p_base[0];
          mult = p_mult[0];
        }

        // Swap the bytes if necessary and convert any out of bounds pixels
        // to special pixels
        int osamp = 0;
        for(int samp = band; samp < p_ns * p_nb; samp += p_nb) {
          switch(p_pixelType) {
            case Isis::UnsignedByte:
              (*out)[osamp] = (double)((unsigned char *)in)[samp];
              break;
            case Isis::UnsignedWord:
              (*out)[osamp] =
                (double)swapper.UnsignedShortInt((unsigned short int *)in+samp);
              break;
            case Isis::SignedWord:
              (*out)[osamp] = (double)swapper.ShortInt((short int *)in+samp);
              break;
            case Isis::Real:
              (*out)[osamp] = (double)swapper.Float((float *)in+samp);
              break;
            case Isis::Double:
              (*out)[samp] = (double)swapper.Double((double *)in+samp);
              break;
            default:
              break;
          }

          // Sets out to isis special pixel or leaves it if valid
          (*out)[osamp] = TestPixel((*out)[osamp]);

          if (Isis::IsValidPixel((*out)[osamp])) {
            (*out)[osamp] = mult * ((*out)[osamp]) + base;
          }
          osamp++;
        } // End sample loop

        if (funct == NULL) {
          //Set the buffer position and write the line to the output file
          ((Isis::LineManager *)out)->SetLine((band * p_nl) + line + 1);
          OutputCubes[0]->write(*out);
        }
        else {
          funct(*out);
        }

        // Handle any line suffix bytes
        pos = fin.tellg();
        if (p_saveDataPost) {
          tempPost.push_back(new char[p_dataPostBytes]);
          fin.read(tempPost.back(), p_dataPostBytes);
        }
        else {
          fin.seekg(p_dataPostBytes, ios_base::cur);
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_dataPreBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }


        // Save off the prefix bytes vector
        if (p_saveDataPre) {
          p_dataPre.push_back(tempPre);
          tempPre.clear();
        }

        // Save off the suffix bytes vector
        if (p_saveDataPost) {
          p_dataPost.push_back(tempPost);
          tempPost.clear();
        }

        // Check the last io
        if (!fin.good()) {
          QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                       toString((int)pos) + "]. Byte count [" +
                       toString(p_fileHeaderBytes) + "]" ;
          throw IException(IException::Io, msg, _FILEINFO_);
        }

      } // End band loop

      p_progress->CheckStatus();

    } // End line loop

    // Handle the file trailer
    pos = fin.tellg();
    if (p_saveFileTrailer) {
      fin.seekg(0, ios_base::end);
      streampos e = fin.tellg();
      p_fileTrailerBytes = (int)(e - pos + (streampos)1);
      p_fileTrailer = new char[p_fileTrailerBytes];
      fin.seekg(pos);
      fin.read(p_fileTrailer, p_fileTrailerBytes);

      // Check the io
      if (!fin.good()) {
        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +
                     toString((int)pos) + "]. Byte count [" +
                     toString(p_fileTrailerBytes) + "]" ;
        throw IException(IException::Io, msg, _FILEINFO_);
      }

    }

    // Close the file and clean up
    fin.close();
    delete [] in;

  }


  void ProcessImport::ProcessJp2(void funct(Isis::Buffer &out)) {

    // Set up an Isis::Jp2Decoder object
    JP2Decoder *JP2_decoder;
    JP2_decoder = new JP2Decoder(p_inFile);

    // Open JP2 file
    JP2_decoder->OpenFile();

    // Make sure JP2 file dimensions match PDS labels
    p_ns = JP2_decoder->GetSampleDimension();
    p_nl = JP2_decoder->GetLineDimension();
    p_nb = JP2_decoder->GetBandDimension();

    // Figure out the number of bytes to read for a single line
    // from all bands
    int sizeofpixel = Isis::SizeOf(p_pixelType);
    int startsamp = p_dataPreBytes / sizeofpixel;
    int endsamp = startsamp + p_ns;
    int readBytes = sizeofpixel * p_ns * p_nb
                    + p_dataPreBytes + p_dataPostBytes;
    char **in = new char* [p_nb];
    for(int i = 0; i < p_nb; i++) {
      in[i] = new char [readBytes];
    }

    // Construct a line buffer manager
    Isis::Buffer *out = NULL;

    if (funct != NULL) {
      out = new Isis::Buffer(p_ns, p_nl, p_nb, p_pixelType);
    }
    else {
      out = new Isis::LineManager(*OutputCubes[0]);
    }

    // Loop once for each line in the image
    p_progress->SetMaximumSteps(p_nb * p_nl);
    p_progress->CheckStatus();

    // Loop for each line
    for(int line = 0; line < p_nl; line++) {
      if (p_pixelType == Isis::UnsignedByte) {
        JP2_decoder->Read((unsigned char **)in);
      }
      else {
        JP2_decoder->Read((short int **)in);
      }
      // Loop for each band
      for(int band = 0; band < p_nb; band++) {
        // Set the base multiplier
        double base, mult;
        if (p_base.size() > 1) {
          base = p_base[band];
          mult = p_mult[band];
        }
        else {
          base = p_base[0];
          mult = p_mult[0];
        }

        // Space for storing prefix and suffix data pointers
        vector<char *> tempPre, tempPost;


        // Handle any line prefix bytes
        if (p_saveDataPre) {
          tempPre.push_back(new char[p_dataPreBytes]);
          memcpy(&tempPre[0], in[band], p_dataPreBytes);
        }

        // Swap the bytes if necessary and convert any out of bounds pixels
        // to special pixels
        for(int samp = startsamp; samp < endsamp; samp++) {
          switch(p_pixelType) {
            case Isis::UnsignedByte:
              (*out)[samp] = (double)((unsigned char *)in[band])[samp];
              break;
            case Isis::UnsignedWord:
              (*out)[samp] = (double)((unsigned short int *)in[band])[samp];
              break;
            case Isis::SignedWord:
              (*out)[samp] = (double)((short int *)in[band])[samp];
              break;
            default:
              break;
          }

          // Sets out to isis special pixel or leaves it if valid
          (*out)[samp] = TestPixel((*out)[samp]);

          if (Isis::IsValidPixel((*out)[samp])) {
            (*out)[samp] = mult * ((*out)[samp]) + base;
          }
        } // End sample loop

        if (funct == NULL) {
          //Set the buffer position and write the line to the output file
          ((Isis::LineManager *)out)->SetLine((band * p_nl) + line + 1);
          OutputCubes[0]->write(*out);
        }
        else {
          funct(*out);
        }

        p_progress->CheckStatus();

        // Handle any line suffix bytes
        if (p_saveDataPost) {
          tempPost.push_back(new char[p_dataPostBytes]);
          memcpy(&tempPost[0], &in[band][p_dataPreBytes+p_ns*sizeofpixel],
                 p_dataPostBytes);
        }

        // Save off the prefix bytes vector
        if (p_saveDataPre) {
          p_dataPre.push_back(tempPre);
          tempPre.clear();
        }

        // Save off the suffix bytes vector
        if (p_saveDataPost) {
          p_dataPost.push_back(tempPost);
          tempPost.clear();
        }

      } // End band loop

    } // End line loop

    // Close the file and clean up
    delete JP2_decoder;
    delete [] in;
  }


#if 0

  void ProcessImport::AddLabel(Isis::Pvl &label) {

    label.Root();

    Isis::Pvl *output = OutputCubes[0]->Label();
    output->Find("IsisCube");
    output->Insert(label);
  }

  void ProcessImport::AddImportLabel(Isis::Pvl &importLab) {

    importLab.Root();

    Isis::Pvl *output = OutputCubes[0]->Label();
    output->Find("IsisCube");
    output->addObject("ImportLabel");
    output->Insert(importLab);
  }
#endif


  void ProcessImport::SetInputFile(const QString &file) {
    p_inFile = file;
    if (!Isis::FileName(file).fileExists()) {
      QString msg = "File [" + file + "] does not exist";
      throw IException(IException::User, msg, _FILEINFO_);
    }
  }


  QString ProcessImport::InputFile() {
    if (p_inFile.size() <= 0) {
      QString msg = "No input file has been set";
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
    return p_inFile;
  }

  
}