HiCalUtil.h

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#if !defined(HiCalUtil_h)
#define HiCalUtil_h
/**                                                                       
 * @file                                                                  
 * $Revision: 3878 $
 * $Date: 2012-01-18 10:23:13 -0700 (Wed, 18 Jan 2012) $
 *                                                                        
 *   Unless noted otherwise, the portions of Isis written by the USGS are 
 *   public domain. See individual third-party library and package descriptions 
 *   for intellectual property information, user agreements, and related  
 *   information.                                                         
 *                                                                        
 *   Although Isis has been used by the USGS, no warranty, expressed or   
 *   implied, is made by the USGS as to the accuracy and functioning of such 
 *   software and related material nor shall the fact of distribution     
 *   constitute any such warranty, and no responsibility is assumed by the
 *   USGS in connection therewith.                                        
 *                                                                        
 *   For additional information, launch                                   
 *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html                
 *   in a browser or see the Privacy & Disclaimers page on the Isis website,
 *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
 *   http://www.usgs.gov/privacy.html.                                    
 */                                                                       

#include <cmath>
#include <string>
#include <vector>
#include <iostream>
#include <sstream>

#include "HiCalTypes.h"
#include "DbProfile.h"
#include "iString.h"
#include "Statistics.h"
#include "PvlKeyword.h"
#include "NumericalApproximation.h"
#include "Filename.h"
#include "Pvl.h"
#include "iException.h"

namespace Isis {

 template <typename T> inline T MIN(const T &A, const T &B) {
   if ( A < B ) { return (A); }
   else         { return (B); }
 }

 template <typename T> inline T MAX(const T &A, const T &B) {
   if ( A > B ) { return (A); }
   else         { return (B); }
 }

/**
 * @brief Counts number of valid pixels in vector
 * @param v Vector to inspect
 * @return int Number valid pixels in vector
 */
inline int ValidCount(const HiVector &v) {
  int n = 0;
  for (int i = 0 ; i < v.dim() ; i++) {
    if (!IsSpecial(v[i])) n++;
  }
  return (n);
}

/**
 * @brief Counts number of invalid pixels in vector
 * @param v Vector to inspect
 * @return int Number invalid (special) pixels in vector
 */
inline int InValidCount(const HiVector &v) {
  int n = 0;
  for (int i = 0 ; i < v.dim() ; i++) {
    if (IsSpecial(v[i])) n++;
  }
  return (n);
}

/** 
 * @brief Convert HiRISE Cpmm number to Ccd number
 * 
 * @param cpmm Cpmm number
 */
inline int CpmmToCcd(int cpmm) {
  const int cpmm2ccd[] = {0,1,2,3,12,4,10,11,5,13,6,7,8,9};
  if ( (cpmm < 0) || (cpmm >= (int)(sizeof(cpmm2ccd)/sizeof(int))) ) { 
    std::string mess = "CpmmToCdd: Bad CpmmNumber (" + iString(cpmm) + ")";
    throw iException::Message(iException::User, mess.c_str(), _FILEINFO_);
  }
  return (cpmm2ccd[cpmm]);
}


/** 
 * @brief Convert HiRISE Ccd number to string filter name
 * 
 * @param ccd Ccd number of device
 */
inline std::string CcdToFilter(int ccd) {
  if ( (ccd < 0) || (ccd > 13) ) {
    std::string mess = "CcdToFilter: Bad Ccd Number (" + iString(ccd) + ")";
    throw iException::Message(iException::User, mess.c_str(), _FILEINFO_);
  }

  std::string filter;
  if ( ccd <= 9 )     { filter = "RED"; }
  else if (ccd <= 11) { filter = "IR";  }
  else                { filter = "BG";  }
  return (filter);
}

/**
 * @brief Crop specified lines from a buffer
 * 
 * This function extracts lines from a buffer and returns a new buffer with the
 * extracted lines.
 * 
 * @param m      Buffer to extract lines from
 * @param sline  Starting line number (first line is 0)
 * @param eline  Last line to extract
 * 
 * @return HiMatrix Buffer containing cropped lines
 */
inline HiMatrix cropLines(const HiMatrix &m, int sline, int eline) {
  int nlines(eline-sline+1);
  HiMatrix mcrop(nlines, m.dim2());
  for (int l =  0 ; l < nlines ; l++) {
    for (int s = 0 ; s < m.dim2() ; s++) {
      mcrop[l][s] = m[l+sline][s];
    }
  }
  return (mcrop);
}

/**
 * @brief Crop specified samples from a buffer
 * 
 * This function extracts samples from a buffer and returns a new buffer with
 * the extracted samples.
 * 
 * @param m      Buffer to extract samples from
 * @param ssamp  Startling sample (first sample 0)
 * @param esamp  Ending sample to extract
 * 
 * @return HiMatrix  Buffer with cropped samples
 */
inline HiMatrix cropSamples(const HiMatrix &m, int ssamp, int esamp) {
  int nsamps(esamp-ssamp+1);
  HiMatrix mcrop(m.dim1(), nsamps);
  for (int l =  0 ; l < m.dim1() ; l++) {
    for (int s = 0 ; s < nsamps ; s++) {
      mcrop[l][s] = m[l][s+ssamp]; 
    }
  }
  return (mcrop);
}

/**
 * @brief Reduces by averaging specified lines from a buffer
 * 
 * This function produces a vector from a 2-D buffer of averaged lines at each
 * vertical sample location
 * 
 * @param m      Buffer to reduce
 * @param sline  Starting line number (first line is 0)
 * @param eline  Last line to average (-1 means use all lines)
 * 
 * @return HiVector Buffer containing averaged lines
 */
inline HiVector averageLines(const HiMatrix &m, int sline = 0, int eline = -1) {
  eline = (eline == -1) ? m.dim1() - 1 : eline;
  HiVector v(m.dim2());
  for (int s =  0 ; s < m.dim2() ; s++) {
    Statistics stats;
    for (int l = sline ; l <= eline ; l++) {
      stats.AddData(&m[l][s], 1);
    }
    v[s] = stats.Average();
  }
  return (v);
}

/**
 * @brief Reduces by averaging specified samples from a buffer
 * 
 * This function produces a vector from a 2-D buffer of averaged samples at each
 * horizontal line location
 * 
 * @param m      Buffer to reduce
 * @param ssamp  Starting sample number (first sample is 0)
 * @param esamp  Last sample to average (-1 means use all samples)
 * 
 * @return HiVector Buffer containing averaged samples
 */
inline HiVector averageSamples(const HiMatrix &m, int ssamp = 0, 
                               int esamp = -1) {
  esamp = (esamp == -1) ? m.dim2() - 1 : esamp;
  HiVector v(m.dim1());
  for (int l =  0 ; l < m.dim1() ; l++) {
    Statistics stats;
    for (int s = ssamp ; s <= esamp ; s++) {
      stats.AddData(&m[l][s], 1);
    }
    v[l] = stats.Average();
  }
  return (v);
}

/**
 * @brief Find a keyword in a profile using default for non-existant keywords
 * 
 * This template function will extract keyword values from a profile and provide
 * the values at the indicated index.  If the keyword does not exist or the
 * indicated value at index, the provided default will be used instead.
 * 
 */
template <typename T> 
  T ConfKey(const DbProfile &conf, const std::string &keyname, const T &defval,
            int index = 0) {
  if (!conf.exists(keyname)) { return (defval); }
  if (conf.count(keyname) < index) { return (defval); }
  iString iValue(conf.value(keyname, index));
  T value = iValue;  // This makes it work with a string?
  return (value);
}

/** 
 * @brief Helper function to convert values to Integers
 * 
 * @param T Type of value to convert
 * @param value Value to convert
 * 
 * @return int Converted value
 */
template <typename T> int ToInteger(const T &value) {
    return (iString(value).Trim(" \r\t\n").ToInteger());
}

/** 
 * @brief Helper function to convert values to doubles
 * 
 * @param T Type of value to convert
 * @param value Value to convert
 * 
 * @return double Converted value
 */
template <typename T> double ToDouble(const T &value) {
    return (iString(value).Trim(" \r\t\n").ToDouble());
}

/** 
 * @brief Helper function to convert values to strings
 * 
 * @param T Type of value to convert
 * @param value Value to convert
 * 
 * @return string Converted value
 */
template <typename T> std::string ToString(const T &value) {
    return (iString(value).Trim(" \r\t\n"));
}

/** 
 * @brief Shortened string equality test
 * 
 * @param v1 First value
 * @param v2 Second value
 * 
 * @return bool True if they are equal w/o regard to case
 */
inline bool IsEqual(const std::string &v1, const std::string &v2 = "TRUE") {
    return (iString::UpCase(v1) == iString::UpCase(v2));
}

/** 
 * @brief Determines if the keyword value is the expected value
 *  
 * This function checks the existance of a keyword in a profile, extracts the 
 * first value and tests it for equivelance to the expected value.  Note this 
 * test is case insensitive. 
 *  
 * @param prof Profile to find the expected keyword in
 * @param key  Name of keyword in profile to test
 * @param value Value to test for in keyword
 * 
 * @return bool Returns true only if the keyword exists in the profile and it is 
 *              the value expected.
 */
inline bool IsTrueValue(const DbProfile &prof, const std::string &key, 
                   const std::string &value = "TRUE") {
  if ( prof.exists(key) ) {
    return (IsEqual(prof(key), value));
  }
  return (false);
}

/** 
 * @brief Checks profile flag to skip the current Module
 *  
 * This function looks for the keyword \b Debug::SkipModule and checks its 
 * value. True is returned if the value is TRUE (case insensentive). 
 *  
 * @param prof Module profile from config file
 * 
 * @return bool  True if the value of the Debug::SkipModule keyword is TRUE, 
 *         otherwise it returns false for all other values.
 */
inline bool SkipModule(const DbProfile &prof) {
  return (IsTrueValue(prof, "Debug::SkipModule", "TRUE"));
}


inline HiMatrix appendLines(const HiMatrix &top, const HiMatrix &bottom) {
  //  Ensure same number samples
  if (top.dim2() != bottom.dim2()) {
       std::ostringstream mess;
        mess << "Top buffer samples (" << top.dim2() 
             << ") do not match bottom buffer samples (" << bottom.dim2()
             << ")";
        throw iException::Message(iException::User, mess.str(), _FILEINFO_);
  }

  int nlines(top.dim1()+bottom.dim1());
  HiMatrix mat(nlines, top.dim2());
  for (int lt = 0 ; lt < top.dim1() ; lt++) {
    for (int s = 0 ; s < top.dim2() ; s++) {
      mat[lt][s] = top[lt][s];
    }
  }

  int topl = top.dim1();
  for (int lb = 0 ; lb < bottom.dim1() ; lb++) {
    for (int s = 0 ; s < top.dim2() ; s++) {
      mat[topl+lb][s] = bottom[lb][s];
    }
  }
  return (mat);
}

inline HiMatrix appendSamples(const HiMatrix &left, const HiMatrix &right) {
  //  Ensure same number samples
  if (right.dim1() != right.dim1()) {
       std::ostringstream mess;
        mess << "Left buffer lines (" << left.dim1() 
             << ") do not match right buffer lines (" << right.dim1()
             << ")";
        throw iException::Message(iException::User, mess.str(), _FILEINFO_);
  }

  int nsamps(left.dim2()+right.dim2());
  HiMatrix mat(left.dim1(), nsamps);
  for (int ll = 0 ; ll < left.dim1() ; ll++) {
    for (int s = 0 ; s < left.dim2() ; s++) {
      mat[ll][s] = left[ll][s];
    }
  }

  int lefts = left.dim2();
  for (int lr = 0 ; lr < right.dim1() ; lr++) {
    for (int s = 0 ; s < right.dim2() ; s++) {
      mat[lr][lefts+s] = right[lr][s];
    }
  }
  return (mat);
}

/** 
 * @brief Compute HiRISE line times
 * 
 * This class will compute the time (in seconds) for a HiRISE observation line
 * based upon the binning mode and line number.  It is assumed that the first
 * line will be time 0, but that is up to the caller to keep that straight.
 *
 * @author ????-??-?? Unknown
 *
 * @internal
 */
class HiLineTimeEqn {
  public:
    HiLineTimeEqn() : _bin(1), _ltime(1.0) { }
    HiLineTimeEqn(int bin, double ltime) : _bin(bin), _ltime(ltime) { }
    virtual ~HiLineTimeEqn() { }

    void setLineTime(double ltime) { _ltime = ltime; }
    void setBin(int bin) { _bin = bin; }
    double Time(const double line) const {
      return (line * (_bin * _ltime * 1.0E-6)); 
    } 
    double operator()(const double line) const { return (Time(line)); }

  private:
    double _bin;
    double _ltime;
};

/** 
 * @brief Implements (classic) HiRISE temperature equation 
 *  
 * This function computes the dark current temperature and returns the results 
 * in electrons/sec/pixel. 
 * 
 * @param temperature Temperature (typically of the FPGA)
 * @param napcm2      Dark current for silicone diodes (nano-ampres/cm^2)
 * @param px          Pixel size in microns
 * 
 * @return double     Dark current temperature (electrons/sec/pixel)
 */
inline double HiTempEqn(const double temperature, const double napcm2 = 2.0, 
                        const double px = 12.0) {
  double temp = temperature + 273.0;
  double eg   = 1.1557 - (7.021E-4 * temp * temp) / (1108.0 + temp);
  const double K = 1.38E-23;
  const double Q = 1.6E-19;
  return (napcm2*(px*px)*2.55E7*std::pow(temp,1.5)*std::exp(-eg*Q/2.0/K/temp));
}

/** 
 * @brief Rebins a vector to a different size 
 *  
 * This function can rebin to both larger and smaller sizes.  It fits the data 
 * to a cubic spline and then computes the value at the rebin pixel index.  One 
 * advantage to this approach is that on input, special pixels are ignored - on 
 * output there will never be special pixels unless there are not enough points 
 * to conpute the cubic spline on which case this function throws an exception. 
 * 
 * @param v  Input vector to rebin
 * @param n  Size of the new output vector
 * 
 * @return HiVector 
 * @history 2008-11-05 Jeannie Walldren Replaced references to 
 *          DataInterp class with NumericalApproximation.
 */
inline HiVector rebin(const HiVector &v, int n) {
  if ( n == v.dim() ) { return (v); }
  NumericalApproximation nterp(NumericalApproximation::CubicNatural);
  double mag((double) v.dim()/ (double) n);

  for ( int i = 0 ; i < v.dim() ; i++ ) {
    double x((double) i);
    if ( !IsSpecial(v[i]) ) {
      nterp.AddData(x,v[i]);
    }
  }

  // Compute the spline and fill the output vector
  HiVector vout(n);
  for ( int j = 0 ; j < n ; j++ ) {
    double x = (double) j * mag;
    vout[j] = nterp.Evaluate(x, NumericalApproximation::NearestEndpoint);
  }
  return (vout);
}

/** 
 * @brief Deletes HiRISE specific BLOBS from cube file
 *  
 * Ths function removes only the HiRISE specific  
 * 
 * @param label Input label associated with file from which to remove the HiRISE 
 *              blobs
 */
inline void RemoveHiBlobs(Pvl &label) {
  for ( int blob = 0 ; blob < label.Objects() ; blob++ ) {
    if ( label.Object(blob).IsNamed("Table") ) {
      std::string name = label.Object(blob)["Name"][0];
      if ( iString::Equal(name,"HiRISE Calibration Ancillary") ||
           iString::Equal(name,"HiRISE Calibration Image")  ||
           iString::Equal(name,"HiRISE Ancillary") ) {
        label.DeleteObject(blob);
        blob--;
      }
    }
  }
  return;
}

/**
 * @brief Return the statistics for a vector of data 
 *  
 * The default statistic returned is the median of the dataset but can be 
 * changed with a compile time change.  The vector passed in will be sorted so 
 * that the median can be determined.  If the vector has an even number of 
 * elements in it, the average of the two center values will be returned.  The 
 * array is assumed to be clean data, no ISIS special pixels. 
 * 
 * @param data    Vector containing data compute the statistic.  It will be 
 *                altered (sorted) upon return to the caller.
 * 
 * @return double The median (default) of the data
 */
inline double GainLineStat(std::vector<double> &data) {

  //  Check for special conditions
  if (data.size() == 0)  return (Null);
  if (data.size() == 1) return (data[0]);

#if defined(USE_AVERAGE)
  Statistics stats;
  stats.AddData(&data[0], data.size());
  return (stat.Average());
#else
  std::sort(data.begin(), data.end());
  int meanIndex = data.size()/2;
  if ((data.size() % 2) == 1)  return data[meanIndex];
  return ((data[meanIndex-1]+data[meanIndex])/2.0);
#endif
}

};     // namespace Isis
#endif