Unverified Commit 2b4c1fa5 authored by Kelvin Rodriguez's avatar Kelvin Rodriguez Committed by GitHub
Browse files

Bandnorm tests (#4189) 

* init things

* updated tests

* removed old tests

* address comments
parent 1fc23d07

isis/src/base/apps/bandnorm/bandnorm.cpp

0 → 100644
+173 −0
Original line number Diff line number Diff line 
// system include files go first

#include <string>

#include <iostream>

#include <iomanip>

#include <vector>

#include <algorithm>



// Isis specific include files go next

#include "ProcessByLine.h"

#include "SpecialPixel.h"

#include "IException.h"

#include "Pvl.h"

#include "TextFile.h"

#include "Statistics.h"



#include "bandnorm.h"



using namespace std;



namespace Isis {



  static vector<int> band;

  static vector<double> average;

  static vector<double> normalizer;

  

  // function prototypes

  void getStats(Buffer &in);

  void normalize(Buffer &in, Buffer &out);

  void Tokenize(const QString &str,

                vector<QString> & tokens,

                const QString &delimiters = " ");

  

  void bandnorm(UserInterface &ui) {

    Cube icube(ui.GetFileName("FROM"), "r");

    bandnorm(&icube, ui);

  }

  

  

  void bandnorm(Cube *icube, UserInterface &ui) {

    // We will be processing by line

    ProcessByLine p;

  

    // Now get the statistics for each band or the entire cube

    QString avg = ui.GetString("AVERAGE");

    p.SetInputCube(icube);

    p.StartProcess(getStats);

    if(avg == "BAND") {

      int b = 0;

      Statistics stats;

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

        if(b == band[i]) {

          stats.AddData(&average[i], (unsigned int)1);

        }

        else {

          normalizer.push_back(stats.Average());

          b++;

          stats.Reset();

        }

      }

      normalizer.push_back(stats.Average());

    }

    else if(avg == "PENCIL") {

      TextFile pencil;

      pencil.Open(ui.GetFileName("SPECTRUM"));

      std::cout << pencil.LineCount() << " " << icube->bandCount() << std::endl;

      if(pencil.LineCount() - 1 < icube->bandCount()) {

        QString msg = "The spectral pencil file [" + ui.GetAsString("SPECTRUM") +

                      "] does not contain enough data for all bands.";

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

      }

      QString st;

      int column = -1;

      vector<QString> tokens;

      pencil.GetLine(st);     //Takes care of title line

      Tokenize(st, tokens, ", \"-+");

      if(ui.GetAsString("METHOD") == "number") {

        column = ui.GetInteger("NUMBER");

      }

      else {

        for(unsigned i = 0; i < tokens.size(); i++) {

          if(tokens[i] == ui.GetString("NAME")) {

            column = i;

        break;

          }

        }

      }

      if(column < 0  || (unsigned)column > tokens.size()) {

        QString msg = "The column specified in file [" + ui.GetFileName("SPECTRUM")

                      + "] was not found.";

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

      }

      // Add the correct column of data to normalizer

      for(int i = 0; i < icube->bandCount(); i++) {

        tokens.clear();

        pencil.GetLine(st);

        Tokenize(st, tokens, ", \"");

        std::cout << "col: " << column << std::endl;

        std::cout << Isis::IString(tokens[column]).ToDouble() << std::endl;

        normalizer.push_back(Isis::IString(tokens[column]).ToDouble());

      }

    }

    else {  // avg == "CUBE"

      Statistics stats;

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

        stats.AddData(&average[i], (unsigned int)1);

      }

      for(int b = 0; b < icube->bandCount(); b++) {

        normalizer.push_back(stats.Average());

      }

    }

  

    // Setup the output file and apply the correction

    p.SetOutputCube(ui.GetFileName("TO"), ui.GetOutputAttribute("TO"), icube->sampleCount(), icube->lineCount(), icube->bandCount());

    p.StartProcess(normalize);

  

    // Cleanup

    p.EndProcess();

    normalizer.clear();

    band.clear();

    average.clear();

  }

  

  //**********************************************************

  // Get statistics on a band or entire cube

  //**********************************************************

  void getStats(Buffer &in) {

    Statistics stats;

    stats.AddData(in.DoubleBuffer(), in.size());

    average.push_back(stats.Average());

    band.push_back(in.Band() - 1);

  }

  

  // Apply coefficients

  void normalize(Buffer &in, Buffer &out) {

    int index = in.Band() - 1;

    double coeff = normalizer[index];

  

    // Now loop and apply the coefficents

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

      if(IsSpecial(in[i])) {

        out[i] = in[i];

      }

      else {

        out[i] = Null;

        if(coeff != 0.0 && IsValidPixel(coeff)) {

          out[i] = in[i] / coeff;

        }

      }

    }

  }

  

  // Tokenizer

  void Tokenize(const QString &strQStr,

                vector<QString> & tokens,

                const QString &delimitersQStr) {

    IString str = strQStr;

    IString delimiters = delimitersQStr;

  

    //Skip delimiters at the beginning

    string::size_type lastPos = str.find_first_not_of(delimiters, 0);

    // Find first "non-delimiter".

    string::size_type pos     = str.find_first_of(delimiters, lastPos);

  

    while(string::npos != pos  ||  string::npos != lastPos) {

      // Found a token, add it to the vector

      tokens.push_back(str.substr(lastPos, pos - lastPos).c_str());

      // Skip delimiters

      lastPos = str.find_first_not_of(delimiters, pos);

      // Find next "non-delimiter"

      pos = str.find_first_of(delimiters, lastPos);

    }

  }

}
 
 No newline at end of file

isis/src/base/apps/bandnorm/bandnorm.h

0 → 100644
+12 −0
Original line number Diff line number Diff line 
#ifndef std2isis_h 

#define std2isis_h



#include "UserInterface.h"

#include "Cube.h"



namespace Isis {

  extern void bandnorm(Cube *icube, UserInterface &ui);

  extern void bandnorm(UserInterface &ui);

}



#endif
 
 No newline at end of file

isis/src/base/apps/bandnorm/main.cpp

+4 −158
Original line number Diff line number Diff line 
#include "Isis.h"



// system include files go first

#include <string>

#include <iostream>

#include <iomanip>

#include <vector>

#include <algorithm>

#include "Application.h"

#include "bandnorm.h"



// Isis specific include files go next

#include "ProcessByLine.h"

#include "SpecialPixel.h"

#include "IException.h"

#include "Pvl.h"

#include "TextFile.h"

#include "Statistics.h"



using namespace std;

using namespace Isis;



static vector<int> band;

static vector<double> average;

static vector<double> normalizer;



// function prototypes

void getStats(Buffer &in);

void normalize(Buffer &in, Buffer &out);

void Tokenize(const QString &str,

              vector<QString> & tokens,

              const QString &delimiters = " ");



void IsisMain() {

  // We will be processing by line

  ProcessByLine p;



  // Setup the input cube

  UserInterface &ui = Application::GetUserInterface();

  Cube *icube = p.SetInputCube("FROM");



  // Now get the statistics for each band or the entire cube

  QString avg = ui.GetString("AVERAGE");

  p.StartProcess(getStats);

  if(avg == "BAND") {

    int b = 0;

    Statistics stats;

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

      if(b == band[i]) {

        stats.AddData(&average[i], (unsigned int)1);

      }

      else {

        normalizer.push_back(stats.Average());

        b++;

        stats.Reset();

      }

    }

    normalizer.push_back(stats.Average());

  }

  else if(avg == "PENCIL") {

    TextFile pencil;

    pencil.Open(ui.GetFileName("SPECTRUM"));

    if(pencil.LineCount() - 1 < icube->bandCount()) {

      QString msg = "The spectral pencil file [" + ui.GetAsString("SPECTRUM") +

                    "] does not contain enough data for all bands.";

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

    }

    QString st;

    int column = -1;

    vector<QString> tokens;

    pencil.GetLine(st);     //Takes care of title line

    Tokenize(st, tokens, ", \"-+");

    if(ui.GetAsString("METHOD") == "number") {

      column = ui.GetInteger("NUMBER");

    }

    else {

      for(unsigned i = 0; i < tokens.size(); i++) {

        if(tokens[i] == ui.GetString("NAME")) {

          column = i;

          break;

        }

      }

    }

    if(column < 0  || (unsigned)column > tokens.size()) {

      QString msg = "The column specified in file [" + ui.GetFileName("SPECTRUM")

                    + "] was not found.";

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

    }

    // Add the correct column of data to normalizer

    for(int i = 0; i < icube->bandCount(); i++) {

      tokens.clear();

      pencil.GetLine(st);

      Tokenize(st, tokens, ", \"");

      normalizer.push_back(Isis::IString(tokens[column]).ToDouble());

    }

  }

  else {  // avg == "CUBE"

    Statistics stats;

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

      stats.AddData(&average[i], (unsigned int)1);

    }

    for(int b = 0; b < icube->bandCount(); b++) {

      normalizer.push_back(stats.Average());

    }

  }



  // Setup the output file and apply the correction

  p.SetOutputCube("TO");

  p.StartProcess(normalize);



  // Cleanup

  p.EndProcess();

  normalizer.clear();

  band.clear();

  average.clear();

}



//**********************************************************

// Get statistics on a band or entire cube

//**********************************************************

void getStats(Buffer &in) {

  Statistics stats;

  stats.AddData(in.DoubleBuffer(), in.size());

  average.push_back(stats.Average());

  band.push_back(in.Band() - 1);

}



// Apply coefficients

void normalize(Buffer &in, Buffer &out) {

  int index = in.Band() - 1;

  double coeff = normalizer[index];



  // Now loop and apply the coefficents

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

    if(IsSpecial(in[i])) {

      out[i] = in[i];

    }

    else {

      out[i] = Null;

      if(coeff != 0.0 && IsValidPixel(coeff)) {

        out[i] = in[i] / coeff;

      }

    }

  }

}



// Tokenizer

void Tokenize(const QString &strQStr,

              vector<QString> & tokens,

              const QString &delimitersQStr) {

  IString str = strQStr;

  IString delimiters = delimitersQStr;



  //Skip delimiters at the beginning

  string::size_type lastPos = str.find_first_not_of(delimiters, 0);

  // Find first "non-delimiter".

  string::size_type pos     = str.find_first_of(delimiters, lastPos);



  while(string::npos != pos  ||  string::npos != lastPos) {

    // Found a token, add it to the vector

    tokens.push_back(str.substr(lastPos, pos - lastPos).c_str());

    // Skip delimiters

    lastPos = str.find_first_not_of(delimiters, pos);

    // Find next "non-delimiter"

    pos = str.find_first_of(delimiters, lastPos);

  }

  bandnorm(ui);

}
 
 No newline at end of file

isis/src/base/apps/bandnorm/tsts/Makefile

deleted100644 → 0
+0 −4
Original line number Diff line number Diff line 
BLANKS = "%-6s"    

LENGTH = "%-40s"



include $(ISISROOT)/make/isismake.tststree

isis/src/base/apps/bandnorm/tsts/batchlist/Makefile

deleted100644 → 0
+0 −7
Original line number Diff line number Diff line 
APPNAME = bandnorm



include $(ISISROOT)/make/isismake.tsts



commands:

	$(APPNAME) from=$(INPUT)/\$$\1.cub \

	  to=$(OUTPUT)/\$$\1.norm.cub average=band -batchlist=$(INPUT)/testInput.lis > /dev/null;