Commit bac68d02 authored by Adam Goins's avatar Adam Goins
Browse files

Merge branch 'dev' of github.com:AgoinsUSGS/ISIS3 into Goins_Adam_M05361

parents fb5f0daa dbffb2d9

isis/src/base/objs/Application/Application.cpp

+0 −8
Original line number Diff line number Diff line
@@ -102,14 +102,6 @@ namespace Isis { 
    strncpy(env, "LANG=en_US", 1023);

    putenv(env);



    // Verify ISISROOT was set

    if (getenv("ISISROOT") == NULL || QString(getenv("ISISROOT")) == "") {

      QString message = "Please set ISISROOT before running any Isis "

          "applications";

      cerr << message << endl;

      abort();

    }



    // Get the starting cpu time, direct I/Os, page faults, and swaps

    //p_startClock = clock();

    p_startDirectIO = DirectIO();

isis/src/base/objs/EmbreeShapeModel/EmbreeShapeModel.cpp

+0 −44
Original line number Diff line number Diff line
@@ -593,50 +593,6 @@ namespace Isis { 
  }





  /**

   * Computes and returns emission angle, in degrees, given the observer

   * position. The surface normal vector is calculated using an ellipsoid, not

   * the local normal of the actual target shape.

   *

   * Emission Angle: The angle between the surface normal vector at the

   * intersection point and the vector from the intersection point to the

   * observer (usually the spacecraft). The emission angle varies from 0 degrees

   * when the observer is viewing the sub-spacecraft point (nadir viewing) to 90

   * degrees when the intercept is tangent to the surface of the target body.

   * Thus, higher values of emission angle indicate more oblique viewing of the

   * target.

   *

   * @param observerBodyFixedPosition  Three dimensional position of the observer,

   *                                   in the coordinate system of the target body.

   *

   * @return The emission angle, in decimal degrees.

   *

   */

  double EmbreeShapeModel::emissionAngle(const std::vector<double> &observerBodyFixedPosition) {



    // If there is already a normal save it, because it's probably the local normal

    std::vector<double> localNormal;

    bool hadNormal = hasNormal();

    if ( hadNormal ) {

      localNormal = normal();

    }



    // Calculate the ellipsoid surface normal

    calculateDefaultNormal();

    

    // Use ShapeModel to calculate the ellipsoid emission angle

    double ellipsoidEmission = ShapeModel::emissionAngle(observerBodyFixedPosition);



    // If there's a saved normal, reset it

    if ( hadNormal ) {

      setNormal(localNormal);

    }



    // Return the ellipsoid emission angle

    return ellipsoidEmission;

  }





  /**

   * Computes and returns incidence angle, in degrees, given the illuminator position.

   * The surface normal vector is calculated using an ellipsoid, not the local

isis/src/base/objs/EmbreeShapeModel/EmbreeShapeModel.h

+2 −2
Original line number Diff line number Diff line
@@ -47,6 +47,8 @@ namespace Isis { 
   *

   * @internal

   *   @history 2017-04-22 Jesse Mapel and Jeannie Backer - Original Version

   *   @history 2018-05-01 Christopher Combs - Removed emissionAngle function to

   *                fix issues with using ellipsoids to find normals. Fixes #5387.

   */

  class EmbreeShapeModel : public ShapeModel {

    public:
@@ -84,10 +86,8 @@ namespace Isis { 
      virtual void calculateSurfaceNormal();

      QVector<double> ellipsoidNormal();



      virtual double emissionAngle(const std::vector<double> &sB);

      virtual double incidenceAngle(const std::vector<double> &uB);





      virtual Distance localRadius(const Latitude &lat, const Longitude &lon);



      // Determine if the internal intercept is occluded from the observer/lookdir

isis/src/base/objs/Isis/Isis.h

+9 −1
Original line number Diff line number Diff line
@@ -107,6 +107,14 @@ void InterruptSignal(int); 
 * @return int

 */

int main(int argc, char *argv[]) {

  // Verify ISISROOT was set

  // Note: as printing and logging IExceptions requires ISISROOT to be set (for preferences),

  //       The case below cannot be handled with IExceptions

  if (getenv("ISISROOT") == NULL || QString(getenv("ISISROOT")) == "") {

    std::cerr << "Please set ISISROOT before running any Isis applications" << std::endl;

    exit(1);

  }



#ifdef CWDEBUG

  startMonitoringMemory();

  signal(SIGSEGV, SegmentationFault);

isis/src/base/objs/ProcessImport/ProcessImport.cpp

+42 −60
Original line number Diff line number Diff line
@@ -1847,11 +1847,6 @@ namespace Isis { 
   */

  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();
@@ -1902,6 +1897,11 @@ namespace Isis { 
    p_progress->SetMaximumSteps(p_nl);

    p_progress->CheckStatus();



    // Figure out the number of bytes to read for a single line

    int sampleBytes = Isis::SizeOf(p_pixelType) * p_nb + p_dataPreBytes + p_dataPostBytes;

    int readBytes = p_ns * sampleBytes;

    char *in = new char [readBytes];



    // Loop for each line

    for(int line = 0; line < p_nl; line++) {

      // Check the last io
@@ -1915,16 +1915,6 @@ namespace Isis { 
      // 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 [" +
@@ -1960,31 +1950,32 @@ namespace Isis { 
        // to special pixels

        int osamp = 0;



        for(int samp = band; samp < p_ns * p_nb; samp += p_nb) {

        for(int samp = 0; samp < p_ns; samp++) {

          int bufferIndex = p_dataPreBytes + Isis::SizeOf(p_pixelType)*band + samp*sampleBytes;

          switch(p_pixelType) {

            case Isis::UnsignedByte:

              (*out)[osamp] = (double)((unsigned char *)in)[samp];

              (*out)[osamp] = (double)((unsigned char *)in)[bufferIndex];

              break;

            case Isis::UnsignedWord:

              (*out)[osamp] =

                (double)swapper.UnsignedShortInt((unsigned short int *)in+samp);

                (double)swapper.UnsignedShortInt(&in[bufferIndex]);

              break;

            case Isis::SignedWord:

              (*out)[osamp] = (double)swapper.ShortInt((short int *)in+samp);

              (*out)[osamp] = (double)swapper.ShortInt(&in[bufferIndex]);

              break;

            case Isis::SignedInteger:

              (*out)[samp] = (double)swapper.Int((int *)in+samp);

              (*out)[samp] = (double)swapper.Int(&in[bufferIndex]);

              break;

            case Isis::Real:

              if(p_vax_convert) {

                (*out)[osamp]= VAXConversion( (float *)in+samp );

                (*out)[osamp]= VAXConversion(&in[bufferIndex]);

              }

              else {

                (*out)[osamp] = (double)swapper.Float((float *)in+samp);

                (*out)[osamp] = (double)swapper.Float(&in[bufferIndex]);

              }

              break;

            case Isis::Double:

              (*out)[osamp] = (double)swapper.Double((double *)in+samp);

              (*out)[osamp] = (double)swapper.Double(&in[bufferIndex]);

              break;

            default:

              break;
@@ -2008,33 +1999,25 @@ namespace Isis { 
          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_);

        }



      } // End band loop



        // Save off the prefix bytes vector

      // Handle record prefix and suffix

      if (p_saveDataPre) {

        for(int samp = 0; samp < p_ns; samp++) {

          char *samplePrefix = new char[p_dataPreBytes];

          memcpy(samplePrefix, &in[samp*sampleBytes], p_dataPreBytes);

          tempPre.push_back(samplePrefix);

        }

        p_dataPre.push_back(tempPre);

        tempPre.clear();

      }



        // Save off the suffix bytes vector

      if (p_saveDataPost) {

        for(int samp = 0; samp < p_ns; samp++) {

          char *sampleSuffix = new char[p_dataPostBytes];

          int suffixIndex = p_dataPreBytes + Isis::SizeOf(p_pixelType)*p_nb + samp*sampleBytes;

          memcpy(sampleSuffix, &in[suffixIndex], p_dataPostBytes);

          tempPost.push_back(sampleSuffix);

        }

        p_dataPost.push_back(tempPost);

        tempPost.clear();

      }
@@ -2043,12 +2026,11 @@ namespace Isis { 
      if (!fin.good()) {

        QString msg = "Cannot read file [" + p_inFile + "]. Position [" +

                     toString((int)pos) + "]. Byte count [" +

                       toString(p_fileHeaderBytes) + "]" ;

                     toString(p_dataPreBytes) + "]" ;

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

      }



      } // End band loop



      // Handle the data trailer

      pos = fin.tellg();

      if (p_saveDataTrailer) {

        p_dataTrailer.push_back(new char[p_dataTrailerBytes]);