Unverified Commit 38755662 authored by AustinSanders's avatar AustinSanders Committed by GitHub
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Jitterfit app conversion, test, and test data (#4552) 



* Jitterfit app conversion, test, and test data

* Added more criteria for default test

* Added test for residuals

* Adjusted comments for readability

* Updated test to include registration results file

* Removed old comments, adjusted search/pattern size for cropped data

* Adjusted test for 1500x750 image

* New cropped data for jitterfit test

Co-authored-by: default avatarAustin Sanders <arsanders@ugs.gov>
parent ea414cc2

isis/src/clipper/apps/jitterfit/jitterfit.cpp

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#include <iostream>



#include <QList>

#include <QString>



#include "AutoReg.h"

#include "AutoRegFactory.h"

#include "BasisFunction.h"

#include "Chip.h"

#include "Cube.h"

#include "CSVReader.h"

#include "FileName.h"

#include "jitterfit.h"

#include "LeastSquares.h"

#include "NthOrderPolynomial.h"

#include "Pvl.h"

#include "Table.h"

#include "UserInterface.h"



using namespace std;



namespace Isis{

  struct RegistrationData {

    int checkLine; //0

    int checkSample; //1

    double checkTime; //2

    double matchedLine; //3

    double matchedSample; //4

    double matchedTime; //5

    double deltaLine; //6

    double deltaSample; //7

    double goodness; //8 Goodness of fit

    int success; //9

  };



  void jitterfit(UserInterface &ui) {



    bool registrationFileSpecified = false;



    Cube jitterCube;

    jitterCube.open(ui.GetFileName("FROM"), "rw");



    Cube checkCube;

    checkCube.open(ui.GetFileName("FROM2"), "r");



    Pvl defFile;

    defFile.read(ui.GetFileName("DEFFILE"));

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



    double scale = ui.GetDouble("SCALE");



    int pointSpacing = jitterCube.sampleCount();



    // Setup the registration results file

    ofstream outputFile;

    if (ui.WasEntered("TO")) {

      registrationFileSpecified = true;

      QString to(FileName(ui.GetFileName("TO")).expanded());

      outputFile.open(to.toLatin1().data());

      outputFile << "# checkline line, checkline sample, checkline time taken, "

                    "matched jittered image line, matched jittered image "

                    "sample, matched jittered image time taken, delta line, "

                    "delta sample, goodness of fit, registration success " << endl;

    }



    // ???? Question: Why use a file name here? Can't Table/blob read from an open Cube?

    Table mainReadouts(QString("Normalized Main Readout Line Times"), jitterCube.fileName());

    Table checklineReadouts(QString("Normalized Checkline Readout Line Times"), checkCube.fileName());



    // Register each check line to the area near the corresponding main image line using the

    // registration definition file

    QList<RegistrationData> registrationData;

    for (int k = 0; k < checkCube.lineCount(); k++) {



      int checklineLine = checklineReadouts[k][0];

      int mainLine = mainReadouts[checklineLine][0];



      int sample = (int)(pointSpacing / 2.0 + 0.5);



      ar->PatternChip()->TackCube(sample, k + 1);

      ar->PatternChip()->Load(checkCube);



      // The checkline will correspond to the line number that the checkCube was taken at

      ar->SearchChip()->TackCube(sample, checklineLine * scale);

      ar->SearchChip()->Load(jitterCube);



      ar->Register();



      if (registrationFileSpecified) {

        outputFile << checklineLine << "," << sample/scale << "," <<

                      std::setprecision(14) << double(checklineReadouts[k][1]) << "," <<

                      ar->CubeLine()/scale << "," << ar->CubeSample()/scale << ","  <<

                      double(mainReadouts[mainLine][1]) << "," <<

                      checklineLine - ar->CubeLine()/scale << "," <<

                      sample/scale - ar->CubeSample()/scale << "," <<

                      ar->GoodnessOfFit() << "," << ar->Success() << endl;

      }



      RegistrationData checkLineRegistration;

      checkLineRegistration.checkLine = checklineLine;

      checkLineRegistration.checkSample = sample/scale;

      checkLineRegistration.checkTime = double(checklineReadouts[k][1]);

      checkLineRegistration.matchedLine = ar->CubeLine()/scale;

      checkLineRegistration.matchedSample = ar->CubeSample()/scale;

      checkLineRegistration.matchedTime = double(mainReadouts[mainLine][1]);

      checkLineRegistration.deltaLine = checklineLine - ar->CubeLine()/scale;

      checkLineRegistration.deltaSample = sample/scale - ar->CubeSample()/scale;

      checkLineRegistration.goodness = ar->GoodnessOfFit();

      checkLineRegistration.success = ar->Success();

      registrationData.append(checkLineRegistration);

    }



    //!!!!!!!!FOR INTERNAL STORAGE BETWEEN THE REGISTRATION STEP AND THE FITTING STEP !!!!!!!

    //!!!!!!!! We are going to use a QList of registrationData structs !!!!!!!



    if (ui.WasEntered("TO2")) {

      ofstream regStatsFile;

      QString to(FileName(ui.GetFileName("TO2")).expanded());

      regStatsFile.open(to.toLatin1().data());

      Pvl regStats = ar->RegistrationStatistics();

      regStatsFile << regStats << endl;

      regStatsFile << endl;

      regStatsFile.close();

    }



    if (registrationFileSpecified) {

      outputFile.close();

    }



    // Solve for the coefficients of the Nth order polynomial

    double tolerance = ui.GetDouble("TOLERANCE");

    int degree = ui.GetInteger("DEGREE");

    double maxTime = ui.GetDouble("MAXTIME");



    BasisFunction *lineFunction = new NthOrderPolynomial(degree);

    BasisFunction *sampleFunction = new NthOrderPolynomial(degree);



    LeastSquares lsqLine(*lineFunction, false, false, false, false);

    LeastSquares lsqSample(*sampleFunction, false, false, false, false);



    std::vector<double> known(2);



    for (int i = 0; i < registrationData.size(); i++) {

      RegistrationData checkLineRow = registrationData[i];



      if (checkLineRow.goodness >= tolerance) {



        /* Normalization Equation

         *

         * a = min of scale

         * b = max of scale

         *

         * ((b - a)(x - min(x)) / (max(x) - min(x))) + a

         *

         * We're normalizing from -1 to 1 so the equation below is simplified

         */



        known[0] = ((2 * checkLineRow.matchedTime) / maxTime) - 1;

        known[1] = ((2 * checkLineRow.checkTime) / maxTime) - 1;



        lsqLine.AddKnown(known, checkLineRow.deltaLine);

        lsqSample.AddKnown(known, checkLineRow.deltaSample);

      }

    }



    lsqLine.Solve();

    lsqSample.Solve();





    // Write the coefficients to COEFFICIENTTO file and the main cube label

    ofstream outputCoefficientFile;

    QString coefficientTo(FileName(ui.GetFileName("COEFFICIENTTO")).expanded());

    outputCoefficientFile.open(coefficientTo.toLatin1().data());

    outputCoefficientFile << "# Line, Sample" << endl;



    PvlKeyword &jitterLineCoefficients =

        jitterCube.label()->findKeyword("JitterLineCoefficients", PvlObject::Traverse);

    PvlKeyword &jitterSampleCoefficients =

        jitterCube.label()->findKeyword("JitterSampleCoefficients", PvlObject::Traverse);



    for (int i = 0; i < degree; i++) {

      outputCoefficientFile << std::setprecision(14) << lineFunction->Coefficient(i) << "," <<

                               std::setprecision(14) << sampleFunction->Coefficient(i) << endl;

      if (i == 0) {

        jitterLineCoefficients.setValue(toString(lineFunction->Coefficient(i)));

        jitterSampleCoefficients.setValue(toString(sampleFunction->Coefficient(i)));

      }

      else {

        jitterLineCoefficients += toString(lineFunction->Coefficient(i));

        jitterSampleCoefficients += toString(sampleFunction->Coefficient(i));

      }

    }



    outputCoefficientFile.close();





    // Write the registered line/samp, solved line/samp, residual line/samp, time

    if (ui.WasEntered("RESIDUALTO")) {

      ofstream outputResidualFile;

      QString residualTo(FileName(ui.GetFileName("RESIDUALTO")).expanded());

      outputResidualFile.open(residualTo.toLatin1().data());



      outputResidualFile << "# Registered Line, Solved Line, Registered Line Residual, "

                            "Registered Sample, Solved Sample, Sample Residual, Time Taken" << endl;



      for (unsigned int i = 0; i < lsqLine.Residuals().size(); i++) {

        RegistrationData checkLineRow = registrationData[i];



        double solvedLine = 0;

        double solvedSample = 0;



        for (int k = 0; k < degree; k++) {

          solvedLine = solvedLine + lineFunction->Coefficient(k) * pow(checkLineRow.matchedTime, k+1);

          solvedSample = solvedSample + sampleFunction->Coefficient(k) * pow(checkLineRow.matchedTime, k+1);

        }



        outputResidualFile << std::setprecision(14) << checkLineRow.matchedLine << "," <<

                              std::setprecision(14) << checkLineRow.checkLine - solvedLine << "," <<

                              std::setprecision(14) << lsqLine.Residual(i) << "," <<

                              std::setprecision(14) << checkLineRow.matchedSample << "," <<

                              std::setprecision(14) << checkLineRow.checkSample - solvedSample << "," <<

                              std::setprecision(14) << lsqSample.Residual(i) << "," <<

                              std::setprecision(14) << checkLineRow.matchedTime << endl;

      }



      outputResidualFile.close();

    }



    delete lineFunction;

    delete sampleFunction;



  }

}

isis/src/clipper/apps/jitterfit/jitterfit.h

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#ifndef jitterfit_h

#define jitterfit_h



/** This is free and unencumbered software released into the public domain.



The authors of ISIS do not claim copyright on the contents of this file.

For more details about the LICENSE terms and the AUTHORS, you will

find files of those names at the top level of this repository. **/



/* SPDX-License-Identifier: CC0-1.0 */



#include "Cube.h"

#include "UserInterface.h"



namespace Isis{

  extern void jitterfit(UserInterface &ui);

}



#endif

isis/src/clipper/apps/jitterfit/main.cpp

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@@ -8,235 +8,12 @@ find files of those names at the top level of this repository. **/ 


#include "Isis.h"



#include <iostream>

#include "Application.h"

#include "jitterfit.h"



#include <QList>

#include <QString>



#include "AutoReg.h"

#include "AutoRegFactory.h"

#include "BasisFunction.h"

#include "Chip.h"

#include "Cube.h"

#include "CSVReader.h"

#include "FileName.h"

#include "LeastSquares.h"

#include "NthOrderPolynomial.h"

#include "Pvl.h"

#include "Table.h"

#include "UserInterface.h"



using namespace std;

using namespace Isis;



struct RegistrationData {

  int checkLine; //0

  int checkSample; //1

  double checkTime; //2

  double matchedLine; //3

  double matchedSample; //4

  double matchedTime; //5

  double deltaLine; //6

  double deltaSample; //7

  double goodness; //8 Goodness of fit

  int success; //9

};



void IsisMain() {



  bool registrationFileSpecified = false;



  UserInterface &ui = Application::GetUserInterface();



  Cube jitterCube;

  jitterCube.open(ui.GetFileName("FROM"), "rw");



  Cube checkCube;

  checkCube.open(ui.GetFileName("FROM2"), "r");



  Pvl defFile;

  defFile.read(ui.GetFileName("DEFFILE"));

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



  double scale = ui.GetDouble("SCALE");



  int pointSpacing = jitterCube.sampleCount();



  // Setup the registration results file

  ofstream outputFile;

  if (ui.WasEntered("TO")) {

    registrationFileSpecified = true;

    QString to(FileName(ui.GetFileName("TO")).expanded());

    outputFile.open(to.toLatin1().data());

    outputFile << "# checkline line, checkline sample, checkline time taken, "

                  "matched jittered image line, matched jittered image "

                  "sample, matched jittered image time taken, delta line, "

                  "delta sample, goodness of fit, registration success " << endl;

  }



  // ???? Question: Why use a file name here? Can't Table/blob read from an open Cube?

  Table mainReadouts(QString("Normalized Main Readout Line Times"), jitterCube.fileName());

  Table checklineReadouts(QString("Normalized Checkline Readout Line Times"), checkCube.fileName());



  // Register each check line to the area near the corrisponding main image line using the

  // registration definition file

  QList<RegistrationData> registrationData;

  for (int k = 0; k < checkCube.lineCount(); k++) {



    int checklineLine = checklineReadouts[k][0];

    int mainLine = mainReadouts[checklineLine][0];



    int sample = (int)(pointSpacing / 2.0 + 0.5);



    ar->PatternChip()->TackCube(sample, k + 1);

    ar->PatternChip()->Load(checkCube);



    ar->SearchChip()->TackCube(sample, checklineLine * scale); // The checkline will correspond to the line number that the checkCube was taken at

    ar->SearchChip()->Load(jitterCube);



    ar->Register();



    if (registrationFileSpecified) {

      outputFile << checklineLine << "," << sample/scale << "," <<

                    std::setprecision(14) << double(checklineReadouts[k][1]) << "," <<

                    ar->CubeLine()/scale << "," << ar->CubeSample()/scale << ","  <<

                    double(mainReadouts[mainLine][1]) << "," <<

                    checklineLine - ar->CubeLine()/scale << "," <<

                    sample/scale - ar->CubeSample()/scale << "," <<

                    ar->GoodnessOfFit() << "," << ar->Success() << endl;

    }



    RegistrationData checkLineRegistration;

    checkLineRegistration.checkLine = checklineLine;

    checkLineRegistration.checkSample = sample/scale;

    checkLineRegistration.checkTime = double(checklineReadouts[k][1]);

    checkLineRegistration.matchedLine = ar->CubeLine()/scale;

    checkLineRegistration.matchedSample = ar->CubeSample()/scale;

    checkLineRegistration.matchedTime = double(mainReadouts[mainLine][1]);

    checkLineRegistration.deltaLine = checklineLine - ar->CubeLine()/scale;

    checkLineRegistration.deltaSample = sample/scale - ar->CubeSample()/scale;

    checkLineRegistration.goodness = ar->GoodnessOfFit();

    checkLineRegistration.success = ar->Success();

    registrationData.append(checkLineRegistration);

  }



  //!!!!!!!!FOR INTERNAL STORAGE BETWEEN THE REGISTRATION STEP AND THE FITTING STEP !!!!!!!

  //!!!!!!!! We are going to use a QList of registrationData structs !!!!!!!



  if (ui.WasEntered("TO2")) {

    ofstream regStatsFile;

    QString to(FileName(ui.GetFileName("TO2")).expanded());

    regStatsFile.open(to.toLatin1().data());

    Pvl regStats = ar->RegistrationStatistics();

    regStatsFile << regStats << endl;

    regStatsFile << endl;

    regStatsFile.close();

  }



  if (registrationFileSpecified) {

    outputFile.close();

  }



  // Solve for the coefficients of the Nth order polynomial

  double tolerance = ui.GetDouble("TOLERANCE");

  int degree = ui.GetInteger("DEGREE");

  double maxTime = ui.GetDouble("MAXTIME");



  BasisFunction *lineFunction = new NthOrderPolynomial(degree);

  BasisFunction *sampleFunction = new NthOrderPolynomial(degree);



  LeastSquares lsqLine(*lineFunction, false, false, false, false);

  LeastSquares lsqSample(*sampleFunction, false, false, false, false);



  std::vector<double> known(2);



  for (int i = 0; i < registrationData.size(); i++) {

    RegistrationData checkLineRow = registrationData[i];



    if (checkLineRow.goodness >= tolerance) {



      /* Normalization Equation

       *

       * a = min of scale

       * b = max of scale

       *

       * ((b - a)(x - min(x)) / (max(x) - min(x))) + a

       *

       * We're normalizing from -1 to 1 so the equation below is simplified

       */



      known[0] = ((2 * checkLineRow.matchedTime) / maxTime) - 1;

      known[1] = ((2 * checkLineRow.checkTime) / maxTime) - 1;



      lsqLine.AddKnown(known, checkLineRow.deltaLine);

      lsqSample.AddKnown(known, checkLineRow.deltaSample);

    }

  }



  lsqLine.Solve();

  lsqSample.Solve();





  // Write the coefficients to COEFFICIENTTO file and the main cube label

  ofstream outputCoefficientFile;

  QString coefficientTo(FileName(ui.GetFileName("COEFFICIENTTO")).expanded());

  outputCoefficientFile.open(coefficientTo.toLatin1().data());

  outputCoefficientFile << "# Line, Sample" << endl;



  PvlKeyword &jitterLineCoefficients =

      jitterCube.label()->findKeyword("JitterLineCoefficients", PvlObject::Traverse);

  PvlKeyword &jitterSampleCoefficients =

      jitterCube.label()->findKeyword("JitterSampleCoefficients", PvlObject::Traverse);



  for (int i = 0; i < degree; i++) {

    outputCoefficientFile << std::setprecision(14) << lineFunction->Coefficient(i) << "," <<

                             std::setprecision(14) << sampleFunction->Coefficient(i) << endl;

    if (i == 0) {

      jitterLineCoefficients.setValue(toString(lineFunction->Coefficient(i)));

      jitterSampleCoefficients.setValue(toString(sampleFunction->Coefficient(i)));

    }

    else {

      jitterLineCoefficients += toString(lineFunction->Coefficient(i));

      jitterSampleCoefficients += toString(sampleFunction->Coefficient(i));

    }

  }



  outputCoefficientFile.close();





  // Write the registered line/samp, solved line/samp, residual line/samp, time

  if (ui.WasEntered("RESIDUALTO")) {

    ofstream outputResidualFile;

    QString residualTo(FileName(ui.GetFileName("RESIDUALTO")).expanded());

    outputResidualFile.open(residualTo.toLatin1().data());



    outputResidualFile << "# Registered Line, Solved Line, Registered Line Residual, "

                          "Registered Sample, Solved Sample, Sample Residual, Time Taken" << endl;



    for (unsigned int i = 0; i < lsqLine.Residuals().size(); i++) {

      RegistrationData checkLineRow = registrationData[i];



      double solvedLine = 0;

      double solvedSample = 0;



      for (int k = 0; k < degree; k++) {

        solvedLine = solvedLine + lineFunction->Coefficient(k) * pow(checkLineRow.matchedTime, k+1);

        solvedSample = solvedSample + sampleFunction->Coefficient(k) * pow(checkLineRow.matchedTime, k+1);

      }



      outputResidualFile << std::setprecision(14) << checkLineRow.matchedLine << "," <<

                            std::setprecision(14) << checkLineRow.checkLine - solvedLine << "," <<

                            std::setprecision(14) << lsqLine.Residual(i) << "," <<

                            std::setprecision(14) << checkLineRow.matchedSample << "," <<

                            std::setprecision(14) << checkLineRow.checkSample - solvedSample << "," <<

                            std::setprecision(14) << lsqSample.Residual(i) << "," <<

                            std::setprecision(14) << checkLineRow.matchedTime << endl;

    }



    outputResidualFile.close();

  }



  delete lineFunction;

  delete sampleFunction;



  jitterfit(ui);

}

isis/tests/FunctionalTestsJitterfit.cpp

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File added.

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isis/tests/data/jitterfit/S046mos1400x2250.def

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 Object = AutoRegistration

   Group = Algorithm

     Name         = MaximumCorrelation

     Tolerance    = 0.7

     SubPixelAccuracy = True

   EndGroup



   Group = PatternChip

     Samples = 261

     Lines   = 1

   EndGroup



   Group = SearchChip

     Samples = 266

     Lines   = 7

   EndGroup



	 Group = SurfaceModel

		WindowSize 	= 7

	 EndGroup

 EndObject