ProcessImportFits.cpp

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#include "ProcessImportFits.h"

#include <QDebug>
#include <QString>

#include <iostream>
#include <math.h>
#include <sstream>

#include "IException.h"
#include "IString.h"
#include "LineManager.h"
#include "Preference.h"
#include "Pvl.h"
#include "PvlGroup.h"
#include "PixelType.h"
#include "SpecialPixel.h"
#include "UserInterface.h"

namespace Isis {

  ProcessImportFits::ProcessImportFits() {
    m_fitsImageLabels = NULL;
    m_extraFitsLabels = NULL;
    m_headerSizes = NULL;
    m_dataStarts = NULL;
  }


  ProcessImportFits::~ProcessImportFits() {
    delete m_fitsImageLabels;
    delete m_extraFitsLabels;
    delete m_headerSizes;
    delete m_dataStarts;
    m_file.close();
  }


  void ProcessImportFits::extractFitsLabels() {

    m_fitsImageLabels = new QList< PvlGroup * >;
    m_extraFitsLabels = new QList< PvlGroup * >;
    m_headerSizes = new QList < int >;
    m_dataStarts = new QList < int >;

    // Process each FITS label area, storing each in its own PvlGroup.
    char readBuf[81];
    IString line = "";
    unsigned int place;

    // The main FITS label starts at the beginning of the file.
    // FITS extension labels start after the previous data and on a 2880 byte boundry
    // Each FITS keyword in all lables is stored in 80 bytes (space padded to 80 if
    // necessary).

    // Start at the beginning of the file for the main FITS label
    m_file.seekg(0, std::ios_base::beg);

    // Read the first label line (80 chars)
    // We are assuming the file pointer is set to the beginning of the first/next label
    while (m_file.read(readBuf, 80) && m_file.gcount() == 80) {

      PvlGroup *fitsLabel = new PvlGroup("FitsLabels");

      readBuf[80] = '\0';
      line = readBuf;
      place = 80;

      // Process each fits label record (80 bytes) and place keyword, value pairs into PvlKeywords
      // with any associated comments.
      while (line.substr(0, 3) != "END") {

        // Check for blank lines
        if (line.substr(0, 1) != " " && line.substr(0, 1) != "/") {
          // Name of keyword
          PvlKeyword label(line.Token(" =").ToQt()); // Stop on spaces OR equal sign
          if (QString::compare(label.name(), "OBJECT", Qt::CaseInsensitive) == 0) {
            label.setName("TARGET");
            label.addComment("NOTE: This keyword name was changed from 'OBJECT' in the original "
                             "fit header file.");
          }
          // Remove up to beginning of data
          line.TrimHead(" =");
          line.TrimTail(" ");
          if (label.name() == "COMMENT" || label.name() == "HISTORY") {
            label += line.ToQt();
          }
          else {
            // Check for a quoted value
            if (line.substr(0,1) == "'") {
              line.TrimHead("'");
              label += line.Token("'").TrimHead(" ").TrimTail(" ").ToQt();
              line.TrimHead(" '");
            }
            else {
              // Access any remaining data without the trailing comment if there is one
              IString value = line.Token("/");
              // Clear to end of data
              value.TrimTail(" ");
              label += value.ToQt();
              line.TrimHead(" ");
            }
            // If the line still has anything in it, treat it is as a comment.
            if (line.size() > 0) {
              line.TrimHead(" /");
              label.addComment(line.ToQt());
              // A possible format for units, other possiblites exist.
              if (line != line.Token("[")) {
                label.setUnits(line.Token("[").Token("]").ToQt());
              }
            }
          }
          fitsLabel->addKeyword(label);
        }

        // Read the next label line
        m_file.read(readBuf, 80);
        readBuf[80] = '\0';
        line = readBuf;
        place += 80;
      }

      // Save off the PvlGroup and the number of records read from this label
      m_fitsImageLabels->append(fitsLabel);
      m_headerSizes->append((int)ceil(place / 2880.0));

      // The file pointer should be pointing at the end of the record that contained "END"
      // Move the file pointer past the padding after the "END" (i.e., points to start of data)
      std::streamoff jump;
      jump = m_headerSizes->last() * 2880 - place;
      m_file.seekg(jump, std::ios_base::cur);

      m_dataStarts->append(m_file.tellg());

      // Does this look like a label for a FITS image? Stop after the first label that does not
      // because we don't know how to move the file pointer past a non-image data extension.
      if (fitsLabel->hasKeyword("BITPIX") && fitsLabel->hasKeyword("NAXIS")) {
        
        // This section can only handle image data 
        // (i.e., keywords BITPIX & NAXIS & NAXISx must exist).
        if((int)fitsLabel->findKeyword("NAXIS") > 0) {
          int bytesPerPixel = 0;
          bytesPerPixel = (int)((*fitsLabel)["BITPIX"]);
          bytesPerPixel = std::abs(bytesPerPixel);
          bytesPerPixel /= 8;
          
          unsigned int axis1 = 1;
          axis1 = toInt((*fitsLabel)["NAXIS1"]);
          
          unsigned int axis2 = 1;
          if (fitsLabel->hasKeyword("NAXIS2")) {
            axis2 = toInt((*fitsLabel)["NAXIS2"]);
          }
          
          unsigned int axis3 = 1;
          if (fitsLabel->hasKeyword("NAXIS3")) {
            axis3 = toInt((*fitsLabel)["NAXIS3"]);
          }
          
          jump = (int)(ceil(bytesPerPixel * axis1 * axis2 * axis3 / 2880.0) * 2880.0);
          m_file.seekg(jump, std::ios_base::cur);
        }
        else {
          // Note: this will allow us to read extra label sections that have 0 axes,
          // but has image-related info (so BITPIX and NAXIS keywords exist). This
          // includes informational labels, as seen at the beginning of hayabusa2
          // images in this case, there is NO DATA, so no jump should be needed to
          // get to the next section.
          PvlGroup *extraLabelGroup = m_fitsImageLabels->last();
          extraLabelGroup->setName("FitsExtras");
          m_extraFitsLabels->append(extraLabelGroup);

          m_fitsImageLabels->removeLast();
          m_headerSizes->removeLast();
          m_dataStarts->removeLast();
        }
      }
      // Do we have at least on header that looks like it has image data? If so, we can continue,
      // but ignore the rest of the file because we don't know how to skip over a non-image data.
      else if (m_fitsImageLabels->size() > 1) {
        m_fitsImageLabels->removeLast();
        m_headerSizes->removeLast();
        m_dataStarts->removeLast();
        break;
      }

      else {
        QString msg = QObject::tr("The FITS file does not contain a section header that appears "
                                  "to describe an image [%1].").arg(m_name.toString());
        throw IException(IException::User, msg, _FILEINFO_);
      }
    }
  }


  PvlGroup ProcessImportFits::extraFitsLabel(int labelNumber) const {
    if (labelNumber >= m_extraFitsLabels->size()) {
      QString msg = QObject::tr("The requested label number [%1], from file [%2] is "
                                "past the last extra group found in this FITS file. "
                                "Extra label count is [%3]").arg(labelNumber).
                                arg(m_name.expanded()).arg(m_extraFitsLabels->size()-1);
      throw IException(IException::User, msg, _FILEINFO_);
    }

    if (!m_extraFitsLabels) {
      QString msg = QObject::tr("The FITS label has not been initialized, "
                                "call setFitsFile() first.");
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
    else if (m_extraFitsLabels->size() < labelNumber) {
      QString msg = QObject::tr("The requested FITS label number "
                                "was not found in file [%1].").arg(m_name.toString());
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }

    return *(*m_extraFitsLabels)[labelNumber];
  }


  PvlGroup ProcessImportFits::fitsImageLabel(int labelNumber) const {

    if (labelNumber >= m_fitsImageLabels->size()) {
      QString msg = QObject::tr("The requested label number [%1], from file [%2] is "
                                "past the last image group found in this FITS file. "
                                "Image label count is [%3]").arg(labelNumber).
                                arg(m_name.expanded()).arg(m_fitsImageLabels->size()-1);
      throw IException(IException::User, msg, _FILEINFO_);
    }

    if (!m_fitsImageLabels) {
      QString msg = QObject::tr("The FITS label has not been initialized, "
                                "call setFitsFile first.");
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }
    else if (m_fitsImageLabels->size() < labelNumber) {
      QString msg = QObject::tr("The requested FITS label number "
                                "was not found in file [%1].").arg(m_name.toString());
      throw IException(IException::Programmer, msg, _FILEINFO_);
    }

    return *(*m_fitsImageLabels)[labelNumber];
  }


  PvlGroup ProcessImportFits::standardInstrumentGroup(PvlGroup fitsLabel) const {

    // NOTE: This needs to be changed over to use translation files

    // Attempt to extract the standard instrument group keywords
    PvlGroup inst("Instrument");
    if (fitsLabel.hasKeyword("DATE-OBS")) {
      inst += PvlKeyword("StartTime", fitsLabel["DATE-OBS"][0]);
    }
    if (fitsLabel.hasKeyword("TARGET")) {
      inst += PvlKeyword("Target", fitsLabel["TARGET"][0]);
    }
    if (fitsLabel.hasKeyword("INSTRUME")) {
      inst += PvlKeyword("InstrumentId", fitsLabel["INSTRUME"][0]);
    }
    if (fitsLabel.hasKeyword("OBSERVER")) {
      inst += PvlKeyword("SpacecraftName", fitsLabel["OBSERVER"][0]);
    }

    return inst;
  }


  void ProcessImportFits::setFitsFile(FileName fitsFile) {
    m_name = fitsFile;

    SetInputFile(fitsFile.toString()); // Make sure the file exists

    m_file.open(fitsFile.expanded().toLocal8Bit().constData(), std::ios::in  | std::ios::binary);

    if (!m_file.is_open()) {
      QString msg = QObject::tr("Unable to open FITS formatted file [%1].")
                               .arg(fitsFile.toString());
      throw IException(IException::User, msg, _FILEINFO_);
    }

    // Get the FITS labels internalized
    extractFitsLabels();

    // Check to make sure it is a FITS file we can handle
    PvlGroup label = fitsImageLabel(0);
    if (label.hasKeyword("SIMPLE") && label["SIMPLE"][0] == "F") {
      QString msg = QObject::tr("The file [%1] cannot be processed. "
                                "It is an unsupported format.").
          arg(fitsFile.toString());
      throw IException(IException::User, msg, _FILEINFO_);
    }

    m_file.close();
  }


  void ProcessImportFits::setProcessFileStructure(int labelNumber) {

    if (labelNumber >= m_fitsImageLabels->size()) {
      QString msg = QObject::tr("The requested label number [%1], from file [%2] is "
                                "past the last image in this FITS file [%3].").arg(labelNumber).
                                arg(InputFile()).arg(m_fitsImageLabels->size()-1);
      throw IException(IException::User, msg, _FILEINFO_);
    }

    PvlGroup label = *(*m_fitsImageLabels)[labelNumber];

    // Set the ProcessImport to skip over all the previous images and their labels and the label for
    // this image. Don't save this info (think memory)
    SetFileHeaderBytes((*m_dataStarts)[labelNumber]);

    // Find pixel type. NOTE: There are several unsupported possiblites
    Isis::PixelType type;
    QString msg = "";
    switch (toInt(label["BITPIX"][0])) {
      case 8:
        type = Isis::UnsignedByte;
        break;
      case 16:
        type = Isis::SignedWord;
        break;
      case 32:
        type = Isis::SignedInteger;
        break;
      case -32:
        type = Isis::Real;
        break;
      case 64:
        msg = "Signed 64-bit integer (long) pixel type is not supported for FITS imports.";
        throw IException(IException::User, msg, _FILEINFO_);
        break;
      case -64:
        type = Isis::Double;
        break;
      default:
        msg = "Unknown pixel type [" + label["BITPIX"][0] + "] is not supported for FITS imports.";
        throw IException(IException::User, msg, _FILEINFO_);
        break;
    }

    SetPixelType(type);

    // It is possible to have a NAXIS value of 0 meaning no data, the file could include
    // xtensions with data, however, those aren't supported because we need the code to know
    // how to skip over them.
    // NOTE: FITS files, at least the ones seen till now, do not specify a line prefix or suffix
    // data byte count. Some FITS files do have them and ISIS needs to remove them so it is not
    // considered part of the DNs. So, use the parent class' prefix/suffix byte count to reduce
    // the number of samples.
    if (Organization() == BSQ) {
      if (toInt(label["NAXIS"][0]) == 2) {
        SetDimensions(toInt(label["NAXIS1"][0])
                      - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
                      toInt(label["NAXIS2"][0]), 1);
      }
      else if (toInt(label["NAXIS"][0]) == 3) {
        SetDimensions(toInt(label["NAXIS1"][0]) 
                      - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
                      toInt(label["NAXIS2"][0]), toInt(label["NAXIS3"][0]));
      }
      else {
        QString msg = "NAXIS count of [" 
                      + label["NAXIS"][0]
                      + "] is not supported for FITS imports.";
        throw IException(IException::User, msg, _FILEINFO_);
      }
    }
    else if (Organization() == BIL) {
      if (toInt(label["NAXIS"][0]) == 2) {
        SetDimensions(toInt(label["NAXIS1"][0]) 
                      - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
                      1, toInt(label["NAXIS2"][0]));
      }
      else if (toInt(label["NAXIS"][0]) == 3) {
        SetDimensions(toInt(label["NAXIS1"][0]) 
                      - (DataPrefixBytes()+DataSuffixBytes())/SizeOf(type),
                      toInt(label["NAXIS3"][0]), toInt(label["NAXIS2"][0]));
      }
      else {
        QString msg = "NAXIS count of [" 
                      + label["NAXIS"][0] 
                      + "] is not supported for FITS imports.";
        throw IException(IException::User, msg, _FILEINFO_);
      }
    }
    else if (Organization() == BIP) {
      QString msg = "BIP (Band Interleaved by Pixel) "
                    "organization is not supported for FITS imports.";
      throw IException(IException::User, msg, _FILEINFO_);
    }
    else {
      QString msg = "Unknown organization is not supported for FITS imports.";
      throw IException(IException::User, msg, _FILEINFO_);
    }

    // Base and multiplier
    if (label.hasKeyword("BZERO")) {
      SetBase(toDouble(label["BZERO"][0]));
    }
    else {
      SetBase(0.0);
    }
    if (label.hasKeyword("BSCALE")) {
      SetMultiplier(toDouble(label["BSCALE"][0]));
    }
    else {
      SetMultiplier(1.0);
    }

    // Byte order
    SetByteOrder(Isis::Msb);

  }

} // end namespace Isis