コード例 #1
0
ファイル: unitTest.cpp プロジェクト: assutech/isis3
int main () {
  Isis::Preference::Preferences(true);

  try {
  PvlGroup alg("Algorithm");
  alg += PvlKeyword("Name","MinimumDifference");
  alg += PvlKeyword("Tolerance",5.0);
  alg += PvlKeyword("SubpixelAccuracy", "True");

  PvlGroup pchip("PatternChip");
  pchip += PvlKeyword("Samples",15);
  pchip += PvlKeyword("Lines",15);
  pchip += PvlKeyword("Sampling",25);
  pchip += PvlKeyword("ValidPercent", 10);

  PvlGroup schip("SearchChip");
  schip += PvlKeyword("Samples",35);
  schip += PvlKeyword("Lines",35);
  schip += PvlKeyword("Sampling", 50);

  PvlObject o("AutoRegistration");
  o.AddGroup(alg);
  o.AddGroup(pchip);
  o.AddGroup(schip);

  Pvl pvl;
  pvl.AddObject(o);
  std::cout << pvl << std::endl;

  AutoReg *ar = AutoRegFactory::Create(pvl);

  Cube c;
  c.Open("$mgs/testData/ab102401.cub");

  ar->SearchChip()->TackCube(125.0,50.0);
  ar->SearchChip()->Load(c);
  ar->PatternChip()->TackCube(120.0,45.0);
  ar->PatternChip()->Load(c);

  std::cout << "Register = " << ar->Register() << std::endl;
  std::cout << "Position = " << ar->CubeSample() << " " << 
                                ar->CubeLine() << std::endl;
  }
  catch (iException &e) {
    e.Report();
  }

  return 0;
}
コード例 #2
0
ファイル: pointreg.cpp プロジェクト: assutech/isis3
void IsisMain() {
  // Get user interface
  UserInterface &ui = Application::GetUserInterface();

  bool register_ignored = ui.GetBoolean("REGISTERIGNOREDONLY");

  // Open the files list in a SerialNumberList for
  // reference by SerialNumber
  SerialNumberList files(ui.GetFilename("FILES"));

  // Create a ControlNet from the input file
  ControlNet inNet(ui.GetFilename("CNET"));

  // Create an AutoReg from the template file
  Pvl pvl(ui.GetFilename("TEMPLATE"));
  AutoReg *ar = AutoRegFactory::Create(pvl);

  // Create the output ControlNet
  ControlNet outNet;
  outNet.SetType(inNet.Type());
  outNet.SetUserName(Application::UserName());
  outNet.SetDescription(inNet.Description());
  outNet.SetCreatedDate(iTime::CurrentLocalTime());
  outNet.SetTarget(inNet.Target());
  outNet.SetNetworkId(inNet.NetworkId());

  Progress progress;
  progress.SetMaximumSteps(inNet.Size());
  progress.CheckStatus();

  int ignored=0, unmeasured=0, registered=0, unregistered=0, validated=0;

  CubeManager cubeMgr;
  cubeMgr.SetNumOpenCubes(50);

  // Register the points and create a new
  // ControlNet containing the refined measurements
  for (int i=0; i<inNet.Size(); i++) {
    ControlPoint &inPoint = inNet[i];

    ControlPoint outPoint;
    outPoint.SetType(inPoint.Type());
    outPoint.SetId(inPoint.Id());
    outPoint.SetUniversalGround(inPoint.UniversalLatitude(), inPoint.UniversalLongitude(), inPoint.Radius());
    outPoint.SetHeld(inPoint.Held());
    outPoint.SetIgnore(inPoint.Ignore());

    // CHECK TO SEE IF THE CONTROL POINT SHOULD BE REGISTERED

    // "Ignore" point and we are not registering ignored
    if (inPoint.Ignore() && !register_ignored){
      ignored++;
      // add "Ignored" to network only if indicated
      if (ui.GetBoolean("OUTPUTIGNORED")) {
        // only include appropriate control measures
        for (int j = 0; j < inPoint.Size(); j++) {
          if (inPoint[j].IsMeasured()){
            outPoint.Add(inPoint[j]); 
          } 
          else{
            unmeasured++;
            if (ui.GetBoolean("OUTPUTUNMEASURED")){
              outPoint.Add(inPoint[j]); 
            } 
          }
        }
        // only add this point if OUTPUTIGNORED
        outNet.Add(outPoint);
      }
      // go to next control point
      continue;
    }
    // Not "Ignore" point (i.e. "valid") and we are only registering "Ignored"
    else if (!inPoint.Ignore() && register_ignored) {
      // add all "valid" points to network
      // only include appropriate control measures
      for (int j = 0; j < inPoint.Size(); j++) {
        if (inPoint[j].IsMeasured()){
          outPoint.Add(inPoint[j]); 
        } 
        else{
          unmeasured++;
          if (ui.GetBoolean("OUTPUTUNMEASURED")) {
            outPoint.Add(inPoint[j]);
          } 
        }
      }
      // add this point since it is not ignored
      outNet.Add(outPoint);
      // go to next control point
      continue;
    }
    // "Ignore" point or "valid" point to be registered
    else { // if ( (inPoint.Ignore() && register_ignored) || (!inPoint.Ignore() && !register_ignored ) ) {
      if (inPoint.Ignore()) { outPoint.SetIgnore(false); }
      
      ControlMeasure &patternCM = inPoint[inPoint.ReferenceIndex()];
      Cube &patternCube = *cubeMgr.OpenCube(files.Filename(patternCM.CubeSerialNumber()));
      
      ar->PatternChip()->TackCube(patternCM.Sample(), patternCM.Line());
      ar->PatternChip()->Load(patternCube);
      
      if (patternCM.IsValidated()) validated++;
      if (!patternCM.IsMeasured()) continue;
      if(!patternCM.IsReference()) {
        patternCM.SetReference(true);
        patternCM.SetChooserName("Application pointreg");
        patternCM.SetDateTime();
      }
      outPoint.Add(patternCM);
      
      // reset goodMeasureCount for this point before looping measures
      int goodMeasureCount = 0; 
      // Register all the unvalidated measurements
      for (int j = 0; j < inPoint.Size(); j++) {
        // don't register the reference, go to next measure
        if (j == inPoint.ReferenceIndex()){
          if (!inPoint[j].Ignore()) goodMeasureCount++;
          continue;
        }
        // if the measurement is valid, keep it as is and go to next measure
        if (inPoint[j].IsValidated()) {
          validated++;
          outPoint.Add(inPoint[j]);
          if (!inPoint[j].Ignore()) goodMeasureCount++;
          continue;
        }
        // if the point is unmeasured, add to output only if necessary and go to next measure
        if (!inPoint[j].IsMeasured()) {
          unmeasured++;
          if (ui.GetBoolean("OUTPUTUNMEASURED")) {
            outPoint.Add(inPoint[j]);
          }
          continue;
        }
      
        ControlMeasure searchCM = inPoint[j];
      
        // refresh pattern cube pointer to ensure it stays valid
        Cube &patternCube = *cubeMgr.OpenCube(files.Filename(patternCM.CubeSerialNumber()));
        Cube &searchCube = *cubeMgr.OpenCube(files.Filename(searchCM.CubeSerialNumber()));

        ar->SearchChip()->TackCube(searchCM.Sample(), searchCM.Line());
      
        try {
          ar->SearchChip()->Load(searchCube,*(ar->PatternChip()),patternCube);
      
          // If the measurements were correctly registered
          // Write them to the new ControlNet
          AutoReg::RegisterStatus res = ar->Register();
      
          double score1, score2;
          ar->ZScores(score1, score2);
          searchCM.SetZScores(score1, score2);
      
          if(res == AutoReg::Success) {
            registered++;
            searchCM.SetType(ControlMeasure::Automatic);
            searchCM.SetError(searchCM.Sample() - ar->CubeSample(), searchCM.Line() - ar->CubeLine());
            searchCM.SetCoordinate(ar->CubeSample(),ar->CubeLine());
            searchCM.SetGoodnessOfFit(ar->GoodnessOfFit());
            searchCM.SetChooserName("Application pointreg");
            searchCM.SetDateTime();
            searchCM.SetIgnore(false);
            outPoint.Add(searchCM);
            goodMeasureCount++;
          }
          // Else use the original marked as "Estimated"
          else {
            unregistered++;
            searchCM.SetType(ControlMeasure::Estimated);
      
            if(res == AutoReg::FitChipToleranceNotMet) {
              searchCM.SetError(inPoint[j].Sample() - ar->CubeSample(), inPoint[j].Line() - ar->CubeLine());
              searchCM.SetGoodnessOfFit(ar->GoodnessOfFit());
            }
            searchCM.SetChooserName("Application pointreg");
            searchCM.SetDateTime();
            searchCM.SetIgnore(true);
            outPoint.Add(searchCM);
          }
        } catch (iException &e) {
          e.Clear();
          unregistered++;
          searchCM.SetType(ControlMeasure::Estimated);
          searchCM.SetChooserName("Application pointreg");
          searchCM.SetDateTime();
          searchCM.SetIgnore(true);
          outPoint.Add(searchCM);
        }
      }

      // Jeff Anderson put in this test (Dec 2, 2008) to allow for control 
      // points to be good so long as at least two measure could be 
      // registered. When a measure can't be registered to the reference then
      // that measure is set to be ignored where in the past the whole point
      // was ignored
      if (goodMeasureCount < 2) {
        if (!outPoint.Held() && outPoint.Type() != ControlPoint::Ground) {
          outPoint.SetIgnore(true);
        }
      }
      // Otherwise, ignore=false. This is already set at the beginning of the registration process

      // Check to see if the control point has now been assigned
      // to "ignore".  If not, add it to the network. If so, only 
      // add it to the output if the OUTPUTIGNORED parameter is selected
      // 2008-11-14 Jeannie Walldren
      if (!outPoint.Ignore()) {                             
        outNet.Add(outPoint);
      }
      else{                                              
        ignored++;                                   
        if (ui.GetBoolean("OUTPUTIGNORED")) outNet.Add(outPoint);
      }
    }
    progress.CheckStatus();
  }

  // If flatfile was entered, create the flatfile
  // The flatfile is comma seperated and can be imported into an excel
  // spreadsheet
  if (ui.WasEntered("FLATFILE")) {
    string fFile = Filename(ui.GetFilename("FLATFILE")).Expanded();
    ofstream os;
    os.open(fFile.c_str(),ios::out);
    os << "PointId,OriginalMeasurementSample,OriginalMeasurementLine," <<
      "RegisteredMeasurementSample,RegisteredMeasurementLine,SampleDifference," <<
      "LineDifference,ZScoreMin,ZScoreMax,GoodnessOfFit" << endl;
    os << NULL8 << endl;
    for (int i=0; i<outNet.Size(); i++) {
      // get point from output control net and its
      // corresponding point from input control net
      ControlPoint outPoint = outNet[i];
      ControlPoint *inPoint = inNet.Find(outPoint.Id());
      if (outPoint.Ignore()) continue;
      for (int i = 0; i<outPoint.Size();i++) {
        // get measure and find its corresponding measure from input net
        ControlMeasure cmTrans = outPoint[i];
        ControlMeasure cmOrig = (*inPoint)[cmTrans.CubeSerialNumber()];
        double inSamp = cmOrig.Sample();
        double inLine = cmOrig.Line();
        double outSamp = cmTrans.Sample();
        double outLine = cmTrans.Line();
        double sampErr = cmTrans.SampleError();
        double lineErr = cmTrans.LineError();
        double zScoreMin = cmTrans.GetZScoreMin();
        if (fabs(zScoreMin) <= DBL_EPSILON || zScoreMin == NULL8) zScoreMin = 0;
        double zScoreMax = cmTrans.GetZScoreMax();
        if (fabs(zScoreMax) <= DBL_EPSILON || zScoreMax == NULL8) zScoreMax = 0;
        double goodnessOfFit = cmTrans.GoodnessOfFit();
        if (fabs(goodnessOfFit) <= DBL_EPSILON || goodnessOfFit == NULL8) goodnessOfFit = 0;
        string pointId = outPoint.Id();
        
        os << pointId << "," << inSamp << ","
           << inLine << "," << outSamp << ","
           << outLine << "," << sampErr << "," 
           << lineErr << "," << zScoreMin << ","
           << zScoreMax << "," << goodnessOfFit << endl;
      }
    }
  }

  PvlGroup pLog("Points");
  pLog+=PvlKeyword("Ignored", ignored);
  Application::Log(pLog);

  PvlGroup mLog("Measures");
  mLog+=PvlKeyword("Validated", validated);
  mLog+=PvlKeyword("Registered", registered);
  mLog+=PvlKeyword("Unregistered", unregistered);
  mLog+=PvlKeyword("Unmeasured", unmeasured);
  Application::Log(mLog);

  // Log Registration Statistics
  Pvl arPvl = ar->RegistrationStatistics();

  for(int i = 0; i < arPvl.Groups(); i++) {
    Application::Log(arPvl.Group(i));
  }

  // add the auto registration information to print.prt
  PvlGroup autoRegTemplate = ar->RegTemplate(); 
  Application::Log(autoRegTemplate); 

  outNet.Write(ui.GetFilename("TO"));

  delete ar;
}
コード例 #3
0
ファイル: hijitreg.cpp プロジェクト: assutech/isis3
void IsisMain() {

  // Get user interface
  UserInterface &ui = Application::GetUserInterface();

//  Open the shift definitions file
  Pvl shiftdef;
  if (ui.WasEntered("SHIFTDEF")) {
    shiftdef.Read(ui.GetFilename("SHIFTDEF"));
  }
  else {
    shiftdef.AddObject(PvlObject("Hiccdstitch"));
  }

  PvlObject &stitch = shiftdef.FindObject("Hiccdstitch", Pvl::Traverse);


  // Open the first cube.  It will be matched to the second input cube.
  HiJitCube trans;
  CubeAttributeInput &attTrans = ui.GetInputAttribute("FROM");
  vector<string> bandTrans = attTrans.Bands();
  trans.SetVirtualBands(bandTrans);
  trans.OpenCube(ui.GetFilename("FROM"), stitch);

 
  // Open the second cube, it is held in place.  We will be matching the
  // first to this one by attempting to compute a sample/line translation
  HiJitCube match;
  CubeAttributeInput &attMatch = ui.GetInputAttribute("MATCH");
  vector<string> bandMatch = attMatch.Bands();
  match.SetVirtualBands(bandMatch);
  match.OpenCube(ui.GetFilename("MATCH"), stitch);

//  Ensure only one band
  if ((trans.Bands() != 1) || (match.Bands() != 1)) {
    string msg = "Input Cubes must have only one band!";
    throw Isis::iException::Message(Isis::iException::User,msg,_FILEINFO_);
  }

//  Now test compatability (basically summing)
  trans.Compatable(match);

//  Determine intersection
  if (!trans.intersects(match)) {
    string msg = "Input Cubes do not overlap!";
    throw Isis::iException::Message(Isis::iException::User,msg,_FILEINFO_);
  }

//  Get overlapping regions of each cube
  HiJitCube::Corners fcorns, mcorns;
  trans.overlap(match, fcorns);
  match.overlap(trans, mcorns);

#if defined(ISIS_DEBUG)
  cout << "FROM Poly:  " << trans.PolyToString() << std::endl;
  cout << "MATCH Poly: " << match.PolyToString() << std::endl;
  cout << "From Overlap:  (" << fcorns.topLeft.sample << ","
                             << fcorns.topLeft.line   << "), ("
                             << fcorns.lowerRight.sample << "," 
                             << fcorns.lowerRight.line << ")\n" ;
  cout << "Match Overlap: (" << mcorns.topLeft.sample << ","
                             << mcorns.topLeft.line   << "), ("
                             << mcorns.lowerRight.sample << "," 
                             << mcorns.lowerRight.line << ")\n" ;
#endif


  // We need to get a user definition of how to auto correlate around each
  // of the grid points.
  Pvl regdef;
  Filename regFile(ui.GetFilename("REGDEF"));
  regdef.Read(regFile.Expanded());
  AutoReg *ar = AutoRegFactory::Create(regdef);


  double flines(fcorns.lowerRight.line - fcorns.topLeft.line + 1.0);
  double fsamps(fcorns.lowerRight.sample - fcorns.topLeft.sample + 1.0);

  // We want to create a grid of control points that is N rows by M columns.
  // Get row and column variables, if not entered, default to 1% of the input
  // image size
  int rows(1), cols(1);
  if (ui.WasEntered("ROWS")) {
    rows = ui.GetInteger("ROWS");
  }
  else {
    rows = (int)(((flines - 1.0) / ar->SearchChip()->Lines()) + 1);
  }

  cols = ui.GetInteger("COLUMNS");
  if (cols == 0) {
    cols = (int)(((fsamps - 1.0) / ar->SearchChip()->Samples()) + 1);
  }

  // Calculate spacing for the grid of points
  double lSpacing = floor(flines / rows);
  double sSpacing = floor(fsamps / cols);

#if defined(ISIS_DEBUG)
  cout << "# Samples in Overlap: " << fsamps << endl;
  cout << "# Lines in Overlap  : " << flines << endl;
  cout << "# Rows:    " << rows << endl;
  cout << "# Columns: " << cols << endl;
  cout << "Line Spacing:   " << lSpacing << endl;
  cout << "Sample Spacing: " << sSpacing << endl;
#endif

  // Display the progress...10% 20% etc.
  Progress prog;
  prog.SetMaximumSteps(rows * cols);
  prog.CheckStatus();

  // Initialize control point network
  ControlNet cn;
  cn.SetType(ControlNet::ImageToImage);
  cn.SetUserName(Application::UserName());
  cn.SetCreatedDate(iTime::CurrentLocalTime());

  //  Get serial numbers for input cubes
  string transSN = SerialNumber::Compose(trans, true);
  string matchSN = SerialNumber::Compose(match, true);

  cn.SetTarget(transSN);
  cn.SetDescription("Records s/c jitter between two adjacent HiRISE images");

//  Set up results parameter saves
  JitterParms jparms;
  jparms.fromCorns = fcorns;
  jparms.fromJit = trans.GetInfo();
  jparms.matchCorns = mcorns;
  jparms.matchJit = match.GetInfo();
  jparms.regFile =  regFile.Expanded();
  jparms.cols = cols;
  jparms.rows = rows;
  jparms.lSpacing = lSpacing;
  jparms.sSpacing = sSpacing;
  jparms.nSuspects = 0;

  // Loop through grid of points and get statistics to compute
  // translation values
  RegList reglist;
  double fline0(fcorns.topLeft.line-1.0), fsamp0(fcorns.topLeft.sample-1.0);
  double mline0(mcorns.topLeft.line-1.0), msamp0(mcorns.topLeft.sample-1.0);

  for (int r=0; r<rows; r++) {
    int line = (int)(lSpacing / 2.0 + lSpacing * r + 0.5);
    for (int c=0; c<cols; c++) {
      int samp = (int)(sSpacing / 2.0 + sSpacing * c + 0.5);

      ar->PatternChip()->TackCube(msamp0+samp, mline0+line);
      ar->PatternChip()->Load(match);
      ar->SearchChip()->TackCube(fsamp0+samp, fline0+line);
      ar->SearchChip()->Load(trans);

     // Set up ControlMeasure for cube to translate
      ControlMeasure cmTrans;
      cmTrans.SetCubeSerialNumber(transSN);
      cmTrans.SetCoordinate(msamp0+samp, mline0+line, 
                            ControlMeasure::Unmeasured);
      cmTrans.SetChooserName("hijitreg");
      cmTrans.SetReference(false);

      // Set up ControlMeasure for the pattern/Match cube 
      ControlMeasure cmMatch;
      cmMatch.SetCubeSerialNumber(matchSN);
      cmMatch.SetCoordinate(fsamp0+samp, fline0+line, 
                            ControlMeasure::Automatic);
      cmMatch.SetChooserName("hijitreg");
      cmMatch.SetReference(true);


      // Match found
      if (ar->Register()==AutoReg::Success) {
        RegData reg;
        reg.fLine = fline0 + line;
        reg.fSamp = fsamp0 + samp;
        reg.fLTime = trans.getLineTime(reg.fLine);
        reg.mLine = mline0 + line;
        reg.mSamp = msamp0 + samp;
        reg.mLTime = match.getLineTime(reg.mLine);
        reg.regLine = ar->CubeLine();
        reg.regSamp = ar->CubeSample();
        reg.regCorr = ar->GoodnessOfFit();


        if (fabs(reg.regCorr) > 1.0) jparms.nSuspects++;

        double sDiff = reg.fSamp - reg.regSamp;
        double lDiff = reg.fLine - reg.regLine;
        jparms.sStats.AddData(&sDiff,(unsigned int)1);
        jparms.lStats.AddData(&lDiff,(unsigned int)1);

//  Record the translation in the control point
        cmTrans.SetCoordinate(ar->CubeSample(), ar->CubeLine(), 
                              ControlMeasure::Automatic);
        cmTrans.SetError(sDiff, lDiff);
        cmTrans.SetGoodnessOfFit(ar->GoodnessOfFit());

//  Reread the chip location centering the offset and compute
//  linear regression statistics
        try {
          Chip &pchip(*ar->PatternChip());
          Chip fchip(pchip.Samples(), pchip.Lines());
          fchip.TackCube(ar->CubeSample(), ar->CubeLine());
          fchip.Load(trans);

//  Writes correlated chips to files for visual inspection
#if defined(ISIS_DEBUG)
          ostringstream tstr;
          tstr << "R" << r << "C" << c << "_chip.cub";
          string fcname("from"  + tstr.str());
          string mcname("match" + tstr.str());

          pchip.Write(mcname);
          fchip.Write(fcname);
#endif

          MultivariateStatistics mstats;
          for (int line = 1 ; line <= fchip.Lines() ; line++) {
            for(int sample = 1; sample < fchip.Samples(); sample++) {
              double fchipValue = fchip.GetValue(sample,line);
              double pchipValue = pchip.GetValue(sample,line);
              mstats.AddData(&fchipValue, &pchipValue, 1);
            }
          }

//  Get regression and correlation values
          mstats.LinearRegression(reg.B0, reg.B1);
          reg.Bcorr = mstats.Correlation();
          if (IsSpecial(reg.B0)) throw 1;
          if (IsSpecial(reg.B1)) throw 2;
          if (IsSpecial(reg.Bcorr)) throw 3;
        } 
        catch (...) {
//  If fails, flag this condition
          reg.B0 = 0.0;
          reg.B1= 0.0;
          reg.Bcorr = 0.0;
        }

        reglist.push_back(reg);
      }

      // Add the measures to a control point
      string str = "Row " + iString(r) + " Column " + iString(c);
      ControlPoint cp(str);
      cp.SetType(ControlPoint::Tie);
      cp.Add(cmTrans);
      cp.Add(cmMatch);
      if (!cmTrans.IsMeasured()) cp.SetIgnore(true);
      cn.Add(cp);
      prog.CheckStatus();
    }
  }

  // If flatfile was entered, create the flatfile
  // The flatfile is comma seperated and can be imported into an excel
  // spreadsheet
  if (ui.WasEntered("FLATFILE")) {
    string fFile = ui.GetFilename("FLATFILE");
    ofstream os;
    string fFileExpanded = Filename(fFile).Expanded();
    os.open(fFileExpanded.c_str(),ios::out);
    dumpResults(os, reglist, jparms, *ar);
  }

  // If a cnet file was entered, write the ControlNet pvl to the file
  if (ui.WasEntered("CNETFILE")) {
    cn.Write(ui.GetFilename("CNETFILE"));
  }

  // Don't need the cubes opened anymore
  trans.Close();
  match.Close();


  // Write translation to log
  PvlGroup results("AverageTranslation");
  if (jparms.sStats.ValidPixels() > 0) {
    double sTrans = (int)(jparms.sStats.Average() * 100.0) / 100.0;
    double lTrans = (int)(jparms.lStats.Average() * 100.0) / 100.0;
    results += PvlKeyword ("Sample",sTrans);
    results += PvlKeyword ("Line",lTrans);
    results += PvlKeyword ("NSuspects",jparms.nSuspects);
  }
  else {
    results += PvlKeyword ("Sample","NULL");
    results += PvlKeyword ("Line","NULL");
  }

  Application::Log(results);

  // add the auto registration information to print.prt
  PvlGroup autoRegTemplate = ar->RegTemplate(); 
  Application::Log(autoRegTemplate); 

  return;
}
コード例 #4
0
ファイル: apollopaninit.cpp プロジェクト: corburn/ISIS
void IsisMain() {
  UserInterface &ui = Application::GetUserInterface();
  double  time0,//start time
          time1,//end time
          alti,  //altitude of the spacecraftmore
          fmc,  //forward motion compensation rad/sec
          horV,  //horizontal velocity km/sec
          radV,  //radial velocity km/sec
          rollV,//roll speed in rad/sec
          led;  //line exposure duration in seconds

  Cube  panCube;
  iTime  isisTime;
  QString iStrTEMP;

  int i,j,k,scFrameCode,insCode;

  QString mission;

  SpicePosition *spPos;
  SpiceRotation *spRot;

  //int nlines,nsamples,nbands;

  double deg2rad = acos(-1.0)/180.0;

  ProcessImport jp;
  FileName transFile("$apollo15/translations/apollopantranstable.trn");
  PvlTranslationTable transTable(transFile);
  PvlGroup kernels_pvlG;

  //scFrameCode and insCode from user input
  mission = ui.GetString("MISSION");
  if (mission == "APOLLO12") scFrameCode = -912000;
  if (mission == "APOLLO14") scFrameCode = -914000;
  if (mission == "APOLLO15") scFrameCode = -915000;
  if (mission == "APOLLO16") scFrameCode = -916000;
  if (mission == "APOLLO17") scFrameCode = -917000;

  insCode = scFrameCode - 230;

  try {
    panCube.open(ui.GetFileName("FROM"),"rw");
  }
  catch (IException &e) {
    throw IException(IException::User,
                     "Unable to open the file [" + ui.GetFileName("FROM") + "] as a cube.",
                     _FILEINFO_);
  }

  ////////////////////////////////////////////build the cube header instrament group
  PvlGroup inst_pvlG("Instrument");

  PvlKeyword keyword;

  //four that are the same for every panaramic mission
  keyword.setName("SpacecraftName");
  keyword.setValue(mission);
  inst_pvlG.addKeyword(keyword);

  keyword.setName("InstrumentName");
  keyword.setValue(transTable.Translate("InstrumentName","whatever"));
  inst_pvlG.addKeyword(keyword);

  keyword.setName("InstrumentId");
  keyword.setValue(transTable.Translate("InstrumentId","whatever"));
  inst_pvlG.addKeyword(keyword);

  keyword.setName("TargetName");
  keyword.setValue(transTable.Translate("TargetName","whatever"));
  inst_pvlG.addKeyword(keyword);

  //three that need to be calculated from input values
  horV = ui.GetDouble("VEL_HORIZ");
  radV = ui.GetDouble("VEL_RADIAL");
  alti = ui.GetDouble("CRAFT_ALTITUDE");

  //caculate the LineExposureDuration (led)
  if( ui.WasEntered("V/H_OVERRIDE") )
    fmc = ui.GetDouble("V/H_OVERRIDE")/1000.0;
  else
    //forward motion compensation is directly equivalent to V/H
    fmc = sqrt(horV*horV + radV*radV)/alti;  
  rollV = fmc*ROLLC;  //roll angular velcoity is equal to  V/H * constant    (units rad/sec)
  //led = rad/mm * sec/rad = radians(2.5)/FIDL / rollV    (final units: sec/mm)
  led = (2.5*acos(-1.0)/180.0)/rollV/FIDL;  

  //use led and the number of mm to determine the start and stop times
  isisTime = ui.GetString("GMT");

  //calculate starting and stoping times
  time0 = isisTime.Et() - led*FIDL*21.5;
  time1 = time0 + led*FIDL*43;

  isisTime = time0;
  keyword.setName("StartTime");
  keyword.setValue(iStrTEMP=isisTime.UTC());
  inst_pvlG.addKeyword(keyword);

  isisTime = time1;
  keyword.setName("StopTime");
  keyword.setValue(iStrTEMP=isisTime.UTC());
  inst_pvlG.addKeyword(keyword);

  keyword.setName("LineExposureDuration");
  //converted led to msec/mm--negative sign to account for the anti-parallel time and line axes
  keyword.setValue(iStrTEMP=toString(-led),"sec/mm");  
  inst_pvlG.addKeyword(keyword);

  panCube.putGroup(inst_pvlG);

  ///////////////////////////////////The kernals group
  kernels_pvlG.setName("Kernels");
  kernels_pvlG.clear();

  keyword.setName("NaifFrameCode");
  keyword.setValue(toString(insCode));
  kernels_pvlG.addKeyword(keyword);

  keyword.setName("LeapSecond");
  keyword.setValue( transTable.Translate("LeapSecond","File1") );
  kernels_pvlG.addKeyword(keyword);

  keyword.setName("TargetAttitudeShape");
  keyword.setValue( transTable.Translate("TargetAttitudeShape", "File1") );
  keyword.addValue( transTable.Translate("TargetAttitudeShape", "File2") );
  keyword.addValue( transTable.Translate("TargetAttitudeShape", "File3") );
  kernels_pvlG.addKeyword(keyword);

  keyword.setName("TargetPosition");
  keyword.setValue("Table");
  keyword.addValue( transTable.Translate("TargetPosition", "File1") );
  keyword.addValue( transTable.Translate("TargetPosition", "File2") );
  kernels_pvlG.addKeyword(keyword);

  keyword.setName("ShapeModel");
  keyword.setValue( transTable.Translate("ShapeModel", "File1") );
  kernels_pvlG.addKeyword(keyword);

  keyword.setName("InstrumentPointing");
  keyword.setValue("Table");
  kernels_pvlG.addKeyword(keyword);

  keyword.setName("InstrumentPosition");
  keyword.setValue("Table");
  kernels_pvlG.addKeyword(keyword);

  keyword.setName("InstrumentAddendum");
  keyword.setValue( transTable.Translate("InstrumentAddendum",mission));
  kernels_pvlG.addKeyword(keyword);

  panCube.putGroup(kernels_pvlG);

  //Load all the kernals
  Load_Kernel(kernels_pvlG["TargetPosition"]);
  Load_Kernel(kernels_pvlG["TargetAttitudeShape"]);
  Load_Kernel(kernels_pvlG["LeapSecond"]);

  //////////////////////////////////////////attach a target rotation table
  char frameName[32];
  SpiceInt frameCode;
  SpiceBoolean found;
  //get the framecode from the body code (301=MOON)
  cidfrm_c(301, sizeof(frameName), &frameCode, frameName, &found);  
  if(!found) {
    QString naifTarget = QString("IAU_MOOM");
    namfrm_c(naifTarget.toAscii().data(), &frameCode);
    if(frameCode == 0) {
      QString msg = "Can not find NAIF code for [" + naifTarget + "]";
      throw IException(IException::Io, msg, _FILEINFO_);
    }
  }
  spRot = new SpiceRotation(frameCode);
  //create a table from starttime to endtime (streched by 3%) with NODES entries
  spRot->LoadCache(time0-0.015*(time1-time0), time1+0.015*(time1-time0), NODES);  
  Table tableTargetRot = spRot->Cache("BodyRotation");
  tableTargetRot.Label() += PvlKeyword("Description", "Created by apollopaninit");
  panCube.write(tableTargetRot);


  //////////////////////////////////////////////////attach a sun position table
  spPos = new SpicePosition(10,301);  //Position of the sun (10) WRT to the MOON (301)
  //create a table from starttime to endtime (stretched by 3%) with NODES entries
  spPos->LoadCache(time0-0.015*(time1-time0), time1+0.015*(time1-time0), NODES);  
  Table tableSunPos = spPos->Cache("SunPosition");
  tableSunPos.Label() += PvlKeyword("SpkTableStartTime", toString(time0-0.015*(time1-time0)));
  tableSunPos.Label() += PvlKeyword("SpkTablleEndTime", toString(time1+0.015*(time1-time0)));
  tableSunPos.Label() += PvlKeyword("Description", "Created by apollopaninit");
  panCube.write(tableSunPos);  //attach the table to the cube


  /////////////Finding the principal scan line position and orientation
  //get the radii of the MOON
  SpiceInt tempRadii = 0;
  bodvcd_c(301,"RADII",3,&tempRadii,R_MOON);  //units are km
  double  omega,phi,kappa;

  std::vector<double>  posSel;  //Seleno centric position
  std::vector<double> sunPos;  //sunPosition used to transform to J2000
  std::vector<double> posJ20;  //camera position in J2000
  posSel.resize(3);
  sunPos.resize(3);
  posJ20.resize(3);

  double  temp,
          vel[3] = { 0.0, 0.0, 0.0 },  //the total velocity vector (combined Horizonatal and normal components) 
                   //  in km/sec
          M[3][3] = { { 0.0, 0.0, 0.0 },
                      { 0.0, 0.0, 0.0 },
                      { 0.0, 0.0, 0.0 } },    //rotation matrix
          zDir[] = { 0.0, 0.0, 1.0 },  //selenographic Z axis
          northPN[3]  = { 0.0, 0.0, 0.0 }, //normal to the plane containing all the north/south directions, 
                      //  that is plane containing 
                      //  the origin, the z axis, and the primary point of intersection
          northL[3] = { 0.0, 0.0, 0.0 },    //north direction vector in local horizontal plane
          azm[3] = { 0.0, 0.0, 0.0 },   //azm direction of the veclocity vector in selenographic coordinates
          azmP[3] = { 0.0, 0.0, 0.0 },  //azm rotated (partially) and projected into the image plane
          norm[3] = { 0.0, 0.0, 0.0 },  //normal to the local horizontal plane
          look[3] = { 0.0, 0.0, 0.0 };  //unit direction vector in the pincipal cameral look direction, 
                    //  parallel to the vector from the center of the moon through the spacecraft

  double  pos0[3] = { 0.0, 0.0, 0.0 },  //coordinate of the camera position
          pInt[3] = { 0.0, 0.0, 0.0 };  //coordinate of the principle intersection point

  /////////////////calculating the camera position for the center (principal scan line)
  pos0[1] = ui.GetDouble("LON_NADIR")*deg2rad;
  pos0[0] = ui.GetDouble("LAT_NADIR")*deg2rad;
  pos0[2] = ui.GetDouble("CRAFT_ALTITUDE");  //units are km
  Geographic2GeocentricLunar(pos0,pos0);    //function is written so the input can also be the 
                                            //  output

  /////////////////////calculating the camera orientation for the center (principal) scan line
  pInt[1] = ui.GetDouble("LON_INT")*deg2rad;
  pInt[0] = ui.GetDouble("LAT_INT")*deg2rad;
  pInt[2] = 0.0;
  Geographic2GeocentricLunar(pInt,pInt); //function is written so the input can also be the output
  //calculate the unit look direction vector in object space
  look[0] = -pos0[0] + pInt[0];
  look[1] = -pos0[1] + pInt[1];
  look[2] = -pos0[2] + pInt[2];
  temp = sqrt(look[0]*look[0] + look[1]*look[1] + look[2]*look[2]);
  look[0] /= temp;
  look[1] /= temp;
  look[2] /= temp;
  //the local normal vector is equal to pInt0/|pInt0|
  temp = sqrt(pInt[0]*pInt[0] + pInt[1]*pInt[1] + pInt[2]*pInt[2]);
  norm[0] = pInt[0]/temp;
  norm[1] = pInt[1]/temp;
  norm[2] = pInt[2]/temp;
  //omega and phi are defined so that M(phi)M(omega)look = [0 0 -1]  leaving only the roation 
  //  around z axis to be found
  omega = -atan2(look[1], look[2]);  //omega rotation to zero look[1]
  phi   = atan2(-look[0], sin(omega)*look[1] - cos(omega)*look[2]);  //phi rotation to zero look[0]
  //use the horizontal velocity vector direction to solve for the last rotation; we will make the 
  //  image x axis parallel to the in-image-plane projection of the horizontal direction of flight.
  //  The local normal cross the selenogrpahic z gives northPN (normal to the plane containing all 
  //  the north/south directions), that is, the plane containing the origin, the z axis, and the 
  //  primary point of intersection.
  crossp(northPN,norm,northL);   
  //The normal to the plane containing all the north/south directions cross the local normal 
  //  direction gives the local north/south direction in the local normal plane
  crossp(norm, zDir, northPN); 
  if (northL[2] < 0) {  //if by chance we got the south direction change the signs
    northL[0] = -northL[0];
    northL[1] = -northL[1];
    northL[2] = -northL[2];
  }
  //define the rotation matrix to convert northL to the azimuth of flight.
  //  A left handed rotation of "VEL_AZM" around the positive normal direction will convert northL 
  //  to azm
  MfromVecLeftAngle(M,norm,ui.GetDouble("VEL_AZM")*deg2rad);    
  azm[0] = M[0][0]*northL[0] + M[0][1]*northL[1] + M[0][2]*northL[2];
  azm[1] = M[1][0]*northL[0] + M[1][1]*northL[1] + M[1][2]*northL[2];
  azm[2] = M[2][0]*northL[0] + M[2][1]*northL[1] + M[2][2]*northL[2];
  //apply the two rotations we already know
  MfromLeftEulers(M,omega,phi,0.0);
  azmP[0] = M[0][0]*azm[0] + M[0][1]*azm[1] + M[0][2]*azm[2];
  azmP[1] = M[1][0]*azm[1] + M[1][1]*azm[1] + M[1][2]*azm[2];
  azmP[2] = M[2][0]*azm[2] + M[2][1]*azm[1] + M[2][2]*azm[2];
  //subtract that portion of the azm that is perpindicular to the image plane (also the portion 
  //  which is parallel to look) making azm a vector parrallel to the image plane
  //  Further, since we're now rotated into some coordinate system that differs from 
  //  the image coordinate system by only a kappa rotation making the vector parrallel to the 
  //  image plan is as simple as zeroing the z component (and as pointless to further calculations 
  //  as a nat's fart in hurricane) nevertheless it completes the logical transition
  azmP[2] = 0.0;  

  //finally the kappa rotation that will make azmP parallel (including sign) to the camera x axis                  
  kappa = -atan2(-azmP[1], azmP[0]);  


  ////////////////////Add an instrument position table
  //Define the table records
  TableRecord recordPos;  // reacord to be added to table
  // add x,y,z position labels and ephemeris time et to record
  TableField x("J2000X", TableField::Double);  
  TableField y("J2000Y", TableField::Double);
  TableField z("J2000Z", TableField::Double);
  TableField t("ET", TableField::Double);
  recordPos += x;
  recordPos += y;
  recordPos += z;
  recordPos += t;
  Table tablePos("InstrumentPosition", recordPos);
  //now that the azm and norm vectors are defined 
  //  the total velocity vector can be calcualted (km/sec)
  vel[0] = horV*azm[0] + radV * norm[0];
  vel[1] = horV*azm[1] + radV * norm[1];
  vel[2] = horV*azm[2] + radV * norm[2];
  //we'll provide a two ellement table (more is redundant because the motion is modeled as linear 
  //  at this point)  we'll extend the nodes 3% beyond the edges of the images to be sure 
  //  rounding errors don't cause problems
  temp = 0.515*(time1-time0);  //3% extension
  posSel[0] = pos0[0] - temp*vel[0];    //selenocentric coordinate calculation
  posSel[1] = pos0[1] - temp*vel[1];
  posSel[2] = pos0[2] - temp*vel[2];
  //converting to J2000
  temp = time0 - 0.005*(time1-time0);  //et just before the first scan line
  spPos->SetEphemerisTime(temp);
  spRot->SetEphemerisTime(temp);
  //Despite being labeled as J2000, the coordinates for the instrument position are in fact in 
  //  target centric coordinated rotated to a system centered at the target with aces parallel 
  //  to J2000, whatever that means
  posJ20 = spRot->J2000Vector(posSel); //J2000Vector calls rotates the position vector into J2000,
                                       //  completing the transformation
  recordPos[0] = posJ20[0];
  recordPos[1] = posJ20[1];
  recordPos[2] = posJ20[2];
  recordPos[3] = temp;  //temp = et (right now anyway)
  tablePos += recordPos;
  tablePos.Label() += PvlKeyword("SpkTableStartTime",toString(temp));
  //now the other node
  temp = 0.515*(time1-time0);      //3% extension
  posSel[0] = pos0[0] + temp*vel[0];    //selenocentric coordinate calculation
  posSel[1] = pos0[1] + temp*vel[1];
  posSel[2] = pos0[2] + temp*vel[2];
  //converting to J2000
  temp = time1 + 0.015*(time1-time0);  //et just after the last scan line
  spPos->SetEphemerisTime(temp);
  spRot->SetEphemerisTime(temp);
  //Despite being labeled as J2000, the coordinates for the instrument position are in fact 
  //  in target centric coordinated rotated to a system centered at the target with aces 
  //  parallel to J2000, whatever that means
  posJ20 = spRot->J2000Vector(posSel); //J2000Vector calls rotates the position vector into J2000,
                                       //  completing the transformation
  recordPos[0] = posJ20[0];
  recordPos[1] = posJ20[1];
  recordPos[2] = posJ20[2];
  recordPos[3] = temp;  //temp = et (right now anyway)
  tablePos += recordPos;
  tablePos.Label() += PvlKeyword("SpkTableEndTime",toString(temp));
  tablePos.Label() += PvlKeyword("CacheType","Linear");
  tablePos.Label() += PvlKeyword("Description","Created by apollopaninit");
  panCube.write(tablePos);  //now attach it to the table

  /////////////////////////////attach a camera pointing table
  double  cacheSlope,  //time between epoches in the table
          rollComb,  //magnitude of roll relative to the center in the middle of the epoch
          relT,  //relative time at the center of each epoch
          Q[NODES][5],  //NODES four ellement unit quarternions and et (to be calculated).
          gimVec[3],  //the direction of the gimbal rotation vector (to the cameras persepective 
                      //  this is always changing because the camera is mounted to the roll frame 
                      //  assembly which is mounted to the gimbal)
          M0[3][3],  //rotation matrix of the previous epoch
          Mtemp1[3][3],  //intermediate step in the multiplication of rotation matricies
          Mtemp2[3][3],  //intermediate step in the multiplication of rotation matricies
          Mdg[3][3],  //incremental rotation due the the gimbal motion in the camera frame
          Mdr[3][3];  //the contribution of the roll motion in the camera frame during time 
                      //  cacheSlope
  std::vector <double> M_J2toT;  //rotation matrix from J2000 to the target frame
  M_J2toT.resize(9);
  //Table Definition
  TableField q0("J2000Q0", TableField::Double);
  TableField q1("J2000Q1", TableField::Double);
  TableField q2("J2000Q2", TableField::Double);
  TableField q3("J2000Q3", TableField::Double);
  TableField et("ET", TableField::Double);
  TableRecord recordRot;
  recordRot += q0;
  recordRot += q1;
  recordRot += q2;
  recordRot += q3;
  recordRot += et;
  Table tableRot("InstrumentPointing",recordRot);
  //From the cameras perspective the gimbal motion is around a constantly changing axis, 
  //  this is handled by combining a series of incremental rotations
  MfromLeftEulers(M0, omega, phi, kappa);  //rotation matrix in the center Q[(NOPDES-1)/2]
  spRot->SetEphemerisTime(isisTime.Et());
  M_J2toT = spRot->Matrix();   //this actually gives the rotation from J2000 to target centric
  for(j=0; j<3; j++)    //reformating M_J2toT to a 3x3
    for(k=0; k<3; k++)
      Mtemp1[j][k] = M_J2toT[3*j+k];
  mxm_c(M0, Mtemp1, Mtemp2);
  M2Q(Mtemp2, Q[(NODES-1)/2]);  //save the middle scan line quarternion

  Q[(NODES-1)/2][4] = (time1 + time0)/2.0;  //time in the center of the image
  //the total time is scaled up slightly so that nodes will extend just beyond the edge of the image
  cacheSlope = 1.03*(time1 - time0)/(NODES-1);    
  //Mdr is constant for all the forward time computations
  MfromLeftEulers(Mdr,cacheSlope*rollV,0.0,0.0);  
  for (i=(NODES-1)/2+1; i<NODES; i++) {    //moving foward in time first
    Q[i][4] = Q[i-1][4] + cacheSlope;    //new time epoch
    //epoch center time relative to the center line
    relT = double(i - (NODES-1)/2 - 0.5)*cacheSlope;  
    rollComb = relT*rollV;
    gimVec[0] = 0.0;      //gimbal rotation vector direction in the middle of the epoch
    gimVec[1] =  cos(rollComb);
    gimVec[2] = -sin(rollComb);
    //incremental rotation due to the gimbal (forward motion compensation)
    MfromVecLeftAngle(Mdg, gimVec, fmc*cacheSlope);    
    //the new rotation matrix is Transpose(Mdr)*Transpose(Mdg)*M0--NOTE the order swap and 
    //  transposes are needed because both Mdr and Mdg were caculated in image space and need to be 
    //  transposed to apply to object space
    mtxm_c(Mdg, M0, Mtemp1);  
    //M0 is now what would typically be considered the rotation matrix of an image.  It rotates a 
    //  vector from the target centric space into camera space.  However, what is standard to 
    //  include in the cube labels is a rotation from camera space to J2000.  M0 is therefore the 
    //  transpose of the first part of this rotation.  Transpose(M0) is the rotation from camera 
    //  space to target centric space
    mtxm_c(Mdr, Mtemp1, M0);  
    //now adding the rotation from the target frame to J2000
    spRot->SetEphemerisTime(Q[i][4]);
    //this actually gives the rotation from J2000 to target centric--hence the mxmt_c function being 
    //  used later
    M_J2toT = spRot->Matrix();   
    for(j=0; j<3; j++)  //reformating M_J2toT to a 3x3
      for(k=0; k<3; k++)
        Mtemp1[j][k] = M_J2toT[3*j+k];
    mxm_c(M0, Mtemp1, Mtemp2);
    M2Q(Mtemp2, Q[i]);    //convert to a quarterion
  }

  MfromLeftEulers(M0, omega, phi, kappa);  //rotation matrix in the center Q[(NOPDES-1)/2]
  //Mdr is constant for all the backward time computations
  MfromLeftEulers(Mdr, -cacheSlope*rollV, 0.0, 0.0);    
  for (i=(NODES-1)/2-1; i>=0; i--) {  //moving backward in time
    Q[i][4] = Q[i+1][4] - cacheSlope;  //new time epoch
    //epoch center time relative to the center line
    relT = double(i  - (NODES-1)/2 + 0.5)*cacheSlope;  
    rollComb = relT*rollV;
    gimVec[0] = 0.0;      //gimbal rotation vector direction in the middle of the epoch
    gimVec[1] =  cos(rollComb);
    gimVec[2] = -sin(rollComb);
    //incremental rotation due to the gimbal (forward motion compensation)
    MfromVecLeftAngle(Mdg, gimVec, -fmc*cacheSlope);    
    //the new rotation matrix is Transpose(Mdr)*Transpose(Mdg)*M0    NOTE the order swap and 
    //  transposes are needed because both Mdr and Mdg were caculated in image space and need to be
    //  transposed to apply to object space
    mtxm_c(Mdg, M0, Mtemp1);  
    //M0 is now what would typically be considered the rotation matrix of an image.  It rotates a 
    //  vector from the target centric space into camera space.  However, what is standard to 
    //  include in the cube labels is a rotation from camera space to J2000.  M0 is therefore the 
    //  transpose of the first part of this rotation.  Transpose(M0) is the rotation from camera 
    //  space to target centric space
    mtxm_c(Mdr, Mtemp1, M0);  
    //now adding the rotation from the target frame to J2000
    spRot->SetEphemerisTime(Q[i][4]);
    M_J2toT = spRot->Matrix();
    for(j=0; j<3; j++)  //reformating M_J2toT to a 3x3
      for(k=0; k<3; k++)
        Mtemp1[j][k] = M_J2toT[3*j+k];
    mxm_c(M0, Mtemp1, Mtemp2);
    M2Q(Mtemp2, Q[i]);    //convert to a quarterion
  }
  //fill in the table
  for (i=0; i<NODES; i++) {
    recordRot[0] = Q[i][0];
    recordRot[1] = Q[i][1];
    recordRot[2] = Q[i][2];
    recordRot[3] = Q[i][3];
    recordRot[4] = Q[i][4];
    tableRot += recordRot;
  }
  tableRot.Label() += PvlKeyword("CkTableStartTime", toString(Q[0][4]));
  tableRot.Label() += PvlKeyword("CkTableEndTime", toString(Q[NODES-1][4]));
  tableRot.Label() += PvlKeyword("Description", "Created by appollopan2isis");

  keyword.setName("TimeDependentFrames");
  keyword.setValue(toString(scFrameCode));
  keyword.addValue("1");
  tableRot.Label() += keyword;

  keyword.setName("ConstantFrames");
  keyword.setValue(toString(insCode));
  keyword.addValue(toString(scFrameCode));
  tableRot.Label() += keyword;

  keyword.setName("ConstantRotation");
  keyword.setValue("1");
  for (i=1;i<9;i++)
    if (i%4 == 0) keyword.addValue("1");
    else keyword.addValue("0");
  tableRot.Label() += keyword;
  panCube.write(tableRot);


  /////////////////////////Attach a table with all the measurements of the fiducial mark locations.
  Chip patternS,searchS;   //scaled pattern and search chips
  Cube  fidC;  //Fiducial image

  //line and sample coordinates for looping through the panCube
  double l=1,s=1,sample,line,sampleInitial=1,lineInitial=1,play;  

  int  regStatus,
       fidn,
       panS,
       refL,  //number of lines in the patternS
       refS;  //number of samples in the patternS
  Pvl pvl;

  bool foundFirst=false;

  QString fileName;

  panS = panCube.sampleCount();

  //Table definition
  TableRecord recordFid;
  TableField indexFid("FID_INEX",TableField::Integer);
  TableField xFid("X_COORD",TableField::Double);
  TableField yFid("Y_COORD",TableField::Double);
  recordFid += indexFid;
  recordFid += xFid;
  recordFid += yFid;
  Table tableFid("Fiducial Measurement",recordFid);

  //read the image resolutions and scale the constants acordingly
  double  resolution = ui.GetDouble("MICRONS"),    //pixel size in microns
          scale            = SCALE  *5.0/resolution,  //reduction scale for fast autoregistrations
          searchHeight     = SEARCHh*5.0/resolution,  //number of lines (in 5-micron-pixels) in 
                                                      //  search space for the first fiducial
          searchCellSize   = SEARCHc*5.0/resolution,  //height/width of search chips block
          averageSamples   = AVERs  *5.0/resolution,  //scaled smaples between fiducials
          averageLines     = AVERl  *5.0/resolution;  //scaled average distance between the top and 
                                                      //bottom fiducials

  if( 15.0/resolution < 1.5) play=1.5;
  else play = 15.0/resolution; 

  //copy the patternS chip (the entire ApolloPanFiducialMark.cub)
  FileName fiducialFileName("$apollo15/calibration/ApolloPanFiducialMark.cub");
  fidC.open(fiducialFileName.expanded(),"r");
  if( !fidC.isOpen() ) {
    QString msg = "Unable to open the fiducial patternS cube: ApolloPanFiducialMark.cub\n";
    throw IException(IException::User, msg, _FILEINFO_);
  }
  refL = fidC.lineCount();
  refS = fidC.sampleCount();
  //scaled pattern chip for fast matching
  patternS.SetSize(int((refS-2)/SCALE), int((refL-2)/SCALE));  
  patternS.TackCube((refS-1)/2, (refL-1)/2);
  patternS.Load(fidC, 0, SCALE);

  //parameters for maximum correlation autoregestration  
  // see:  file:///usgs/pkgs/isis3nightly2011-09-21/isis/doc/documents/patternSMatch/patternSMatch.html#DistanceTolerance
  FileName fiducialPvl("$apollo15/templates/apolloPanFiducialFinder.pvl");
  pvl.read(fiducialPvl.expanded());  //read in the autoreg parameters
  AutoReg *arS = AutoRegFactory::Create(pvl);

  *arS->PatternChip()   = patternS;  //patternS chip is constant

  //set up a centroid measurer
  CentroidApolloPan centroid(resolution);
  Chip inputChip,selectionChip;
  inputChip.SetSize(int(ceil(200*5.0/resolution)), int(ceil(200*5.0/resolution)));
  fileName = ui.GetFileName("FROM");
  if( panCube.pixelType() == 1)  //UnsignedByte
    centroid.setDNRange(12, 1e99);  //8 bit bright target
  else
    centroid.setDNRange(3500, 1e99);  //16 bit bright target

  Progress progress;
  progress.SetText("Locating Fiducials");
  progress.SetMaximumSteps(91);

  //Search for the first fiducial, search sizes are constanst
  searchS.SetSize(int(searchCellSize/scale),int(searchCellSize/scale));  
  //now start searching along a horizontal line for the first fiducial mark
  for(l = searchCellSize/2;
      l<searchHeight+searchCellSize/2.0 && !foundFirst;
      l+=searchCellSize-125*5.0/resolution) {
    for (s = searchCellSize/2;
         s < averageSamples + searchCellSize/2.0 && !foundFirst;
         s += searchCellSize-125*5.0/resolution) {
      searchS.TackCube(s, l);
      searchS.Load(panCube, 0, scale);
      *arS->SearchChip() = searchS;
      regStatus = arS->Register();
      if (regStatus == AutoReg::SuccessPixel) {
        inputChip.TackCube(arS->CubeSample(), arS->CubeLine());
        inputChip.Load(panCube, 0, 1);
        inputChip.SetCubePosition(arS->CubeSample(), arS->CubeLine());
        //continuous dynamic range selection
        centroid.selectAdaptive(&inputChip, &selectionChip);    
        //elliptical trimming/smoothing
        if (centroid.elipticalReduction(&selectionChip, 95, play, 2000)) {  
          //center of mass to reduce selection to a single measure
          centroid.centerOfMass(&selectionChip, &sample, &line);    
          inputChip.SetChipPosition(sample, line);
          sampleInitial = inputChip.CubeSample();
          lineInitial   = inputChip.CubeLine();
          foundFirst = true;  //once the first fiducial is found stop
        }
      }
    }
  }
  if(s>=averageLines+searchCellSize/2.0) {
     QString msg = "Unable to locate a fiducial mark in the input cube [" + fileName + 
                  "].  Check FROM and MICRONS parameters.";
     throw IException(IException::Io, msg, _FILEINFO_);
     return;
  }
  progress.CheckStatus();

  //record first fiducial measurement in the table
  recordFid[0] = 0;
  recordFid[1] = sampleInitial;
  recordFid[2] = lineInitial;
  tableFid += recordFid;
  for (s= sampleInitial, l=lineInitial, fidn=0;  s<panS;  s+=averageSamples, fidn++) {
     //corrections for half spacing of center fiducials
     if (fidn == 22) s -= averageSamples/2.0;
     if (fidn == 23) s -= averageSamples/2.0;

     //look for the bottom fiducial
     searchS.TackCube(s,l+averageLines);
     searchS.Load(panCube, 0, scale);
     *arS->SearchChip()   = searchS;
     regStatus = arS->Register();
     if (regStatus == AutoReg::SuccessPixel) {
       inputChip.TackCube(arS->CubeSample(), arS->CubeLine());
       inputChip.Load(panCube,0,1);
       inputChip.SetCubePosition(arS->CubeSample(), arS->CubeLine());
     }
     else {  //if autoreg is unsuccessful, a larger window will be used
       inputChip.TackCube(s, l+averageLines);
       inputChip.Load(panCube, 0, 1);
       inputChip.SetCubePosition(s, l+averageLines);
     }
     centroid.selectAdaptive(&inputChip, &selectionChip);  //continuous dynamic range selection
     //elliptical trimming/smoothing... if this fails move on
     if (centroid.elipticalReduction(&selectionChip, 95, play, 2000) != 0 ) {      
       //center of mass to reduce selection to a single measure
       centroid.centerOfMass(&selectionChip, &sample, &line);      
       inputChip.SetChipPosition(sample, line);
       sample = inputChip.CubeSample();
       line   = inputChip.CubeLine();
       recordFid[0] = fidn*2+1;
       recordFid[1] = sample;
       recordFid[2] = line;
       tableFid += recordFid;
     }
     progress.CheckStatus();

     //look for the top fiducial
     if (s == sampleInitial) //first time through the loop?
       continue;  //then the top fiducial was already found
     searchS.TackCube(s, l);
     searchS.Load(panCube, 0, scale);
     *arS->SearchChip()   = searchS;
     regStatus = arS->Register();
     if (regStatus == AutoReg::SuccessPixel) {
       inputChip.TackCube(arS->CubeSample(), arS->CubeLine());
       inputChip.Load(panCube, 0, 1);
       inputChip.SetCubePosition(arS->CubeSample(), arS->CubeLine());
     }
     else {  //if autoreg is unsuccessful, a larger window will be used
       inputChip.TackCube(s, l);
       inputChip.Load(panCube, 0, 1);
       inputChip.SetCubePosition(s, l);
     }
     centroid.selectAdaptive(&inputChip, &selectionChip);//continuous dynamic range selection
     //inputChip.Write("inputTemp.cub");//debug
     //selectionChip.Write("selectionTemp.cub");//debug
     //elliptical trimming/smoothing... if this fails move on
     if (centroid.elipticalReduction(&selectionChip, 95, play, 2000) !=0) {    
       //center of mass to reduce selection to a single measure
       centroid.centerOfMass(&selectionChip, &sample, &line);  
       inputChip.SetChipPosition(sample, line);
       //when finding the top fiducial both s and l are refined for a successful measurement, 
       //  this will help follow trends in the scaned image
       s = inputChip.CubeSample(); 
       l = inputChip.CubeLine();
       recordFid[0] = fidn*2;
       recordFid[1] = s;
       recordFid[2] = l;
       tableFid += recordFid;
     }
     progress.CheckStatus();
  }

  panCube.write(tableFid);
  //close the new cube
  panCube.close(false);
  panCube.open(ui.GetFileName("FROM"),"rw");
 
  delete spPos;
  delete spRot;

  //now instantiate a camera to make sure all of this is working
  ApolloPanoramicCamera* cam = (ApolloPanoramicCamera*)(panCube.camera());
  //log the residual report from interior orientation 
  PvlGroup residualStats("InteriorOrientationStats");
  residualStats += PvlKeyword("FiducialsFound",  toString(tableFid.Records()));
  residualStats += PvlKeyword("ResidualMax",  toString(cam->intOriResidualMax()),"pixels");
  residualStats += PvlKeyword("ResidualMean", toString(cam->intOriResidualMean()),"pixels");
  residualStats += PvlKeyword("ResidualStdev", toString(cam->intOriResidualStdev()),"pixels");

  Application::Log( residualStats ); 


  return;
}