source: tags/release-1.0.1/src/param.hh @ 1323

#ifndef PARAM_H
#define PARAM_H

#include <iostream>
#include <string>
#include <vector>
#include <wcs.h>

using std::string;
using std::vector;

/**
 * Param class.
 *   Used for storing parameters used by all functions.
 */

class FitsHeader; // foreshadow this so that Param knows it exists

class Param
{
public:
  Param();
  virtual ~Param(){};
  void parseSubsection();               // in param.cc
  void readParams(string paramfile);    // in param.cc
  void copyHeaderInfo(FitsHeader &head);// in param.cc
  bool isBlank(float &value);           // in param.cc
  bool isInMW(int z){return ( this->flagMW && (z>=this->minMW) && (z<=this->maxMW) );};
  string outputReconFile();             // in param.cc
  string outputResidFile();             // in param.cc
  friend std::ostream& operator<< ( std::ostream& theStream, Param& par);
  friend class Image;
 
  //
  string getImageFile(){return imageFile;};
  void   setImageFile(string fname){imageFile = fname;};
  string getFullImageFile(){
    if(flagSubsection) return imageFile+subsection;
    else return imageFile;
  };
  bool   getFlagSubsection(){return flagSubsection;};
  void   setFlagSubsection(bool flag){flagSubsection=flag;};
  string getSubsection(){return subsection;};
  void   setSubsection(string range){subsection = range;};
  bool   getFlagReconExists(){return flagReconExists;};
  void   setFlagReconExists(bool flag){flagReconExists=flag;};
  string getReconFile(){return reconFile;};
  void   setReconFile(string file){reconFile = file;};
  //
  bool   getFlagLog(){return flagLog;};
  void   setFlagLog(bool flag){flagLog=flag;};
  string getLogFile(){return logFile;};
  void   setLogFile(string fname){logFile = fname;};
  string getOutFile(){return outFile;};
  void   setOutFile(string fname){outFile = fname;};
  string getSpectraFile(){return spectraFile;};
  void   setSpectraFile(string fname){spectraFile = fname;};
  bool   getFlagOutputRecon(){return flagOutputRecon;};
  void   setFlagOutputRecon(bool flag){flagOutputRecon=flag;};
  bool   getFlagOutputResid(){return flagOutputResid;};
  void   setFlagOutputResid(bool flag){flagOutputResid=flag;};
  bool   getFlagVOT(){return flagVOT;};
  void   setFlagVOT(bool flag){flagVOT=flag;};
  string getVOTFile(){return votFile;};
  void   setVOTFile(string fname){votFile = fname;};
  bool   getFlagKarma(){return flagKarma;};
  void   setFlagKarma(bool flag){flagKarma=flag;};
  string getKarmaFile(){return karmaFile;};
  void   setKarmaFile(string fname){karmaFile = fname;};
  bool   getFlagMaps(){return flagMaps;};
  void   setFlagMaps(bool flag){flagMaps=flag;};
  string getDetectionMap(){return detectionMap;};
  void   setDetectionMap(string fname){detectionMap = fname;};
  string getMomentMap(){return momentMap;};
  void   setMomentMap(string fname){momentMap = fname;};
  //
  bool   getFlagNegative(){return flagNegative;};
  void   setFlagNegative(bool flag){flagNegative=flag;};
  bool   getFlagBlankPix(){return flagBlankPix;};
  void   setFlagBlankPix(bool flag){flagBlankPix=flag;};
  bool   getNanFlag(){return nanAsBlank;};
  void   setNanFlag(bool flag){nanAsBlank = flag;};
  float  getBlankPixVal(){return blankPixValue;};
  void   setBlankPixVal(float v){blankPixValue=v;};
  int    getBlankKeyword(){return blankKeyword;};
  void   setBlankKeyword(int v){blankKeyword=v;};
  float  getBscaleKeyword(){return bscaleKeyword;};
  void   setBscaleKeyword(float v){bscaleKeyword=v;};
  float  getBzeroKeyword(){return bzeroKeyword;};
  void   setBzeroKeyword(float v){bzeroKeyword=v;};
  bool   getFlagUsingBlank(){return flagUsingBlank;};
  void   setFlagUsingBlank(bool b){flagUsingBlank=b;};
  bool   getFlagMW(){return flagMW;};
  bool   setFlagMW(bool flag){flagMW=flag;};
  int    getMaxMW(){return maxMW;};
  void   setMaxMW(int m){maxMW=m;};
  int    getMinMW(){return minMW;};
  void   setMinMW(int m){minMW=m;};
  void   setBeamSize(float s){numPixBeam = s;};
  float  getBeamSize(){return numPixBeam;};
  //
  bool   getFlagCubeTrimmed(){return flagTrimmed;};
  void   setFlagCubeTrimmed(bool flag){flagTrimmed = flag;};
  long   getBorderLeft(){return borderLeft;};
  void   setBorderLeft(long b){borderLeft = b;};
  long   getBorderRight(){return borderRight;};
  void   setBorderRight(long b){borderRight = b;};
  long   getBorderBottom(){return borderBottom;};
  void   setBorderBottom(long b){borderBottom = b;};
  long   getBorderTop(){return borderTop;};
  void   setBorderTop(long b){borderTop = b;};
  //
  long   getXOffset(){return xSubOffset;};
  void   setXOffset(long o){xSubOffset = o;};
  long   getYOffset(){return ySubOffset;};
  void   setYOffset(long o){ySubOffset = o;};
  long   getZOffset(){return zSubOffset;};
  void   setZOffset(long o){zSubOffset = o;};
  //
  int    getMinPix(){return minPix;};
  void   setMinPix(int m){minPix=m;};
  //     
  bool   getFlagGrowth(){return flagGrowth;};
  void   setFlagGrowth(bool flag){flagGrowth=flag;};
  float  getGrowthCut(){return growthCut;};
  void   setGrowthCut(float c){growthCut=c;};
  //     
  bool   getFlagFDR(){return flagFDR;};
  void   setFlagFDR(bool flag){flagFDR=flag;};
  float  getAlpha(){return alphaFDR;};
  void   setAlpha(float a){alphaFDR=a;};
  //
  bool   getFlagBaseline(){return flagBaseline;};
  void   setFlagBaseline(bool flag){flagBaseline = flag;};
  //
  float  getCut(){return snrCut;};
  void   setCut(float c){snrCut=c;};
  //     
  bool   getFlagATrous(){return flagATrous;};
  void   setFlagATrous(bool flag){flagATrous=flag;};
  int    getReconDim(){return reconDim;};
  void   setReconDim(int i){reconDim=i;};
  int    getMinScale(){return scaleMin;};
  void   setMinScale(int s){scaleMin=s;};
  float  getAtrousCut(){return snrRecon;};
  void   setAtrousCut(float c){snrRecon=c;};
  int    getFilterCode(){return filterCode;};
  void   setFilterCode(int c){filterCode=c;};
  string getFilterName(){return filterName;};
  void   setFilterName(string s){filterName=s;};
  //     
  bool   getFlagAdjacent(){return flagAdjacent;};
  void   setFlagAdjacent(bool flag){flagAdjacent=flag;};
  float  getThreshS(){return threshSpatial;};
  void   setThreshS(float t){threshSpatial=t;};
  float  getThreshV(){return threshVelocity;};
  void   setThreshV(float t){threshVelocity=t;};
  int    getMinChannels(){return minChannels;};
  void   setMinChannels(int n){minChannels=n;};
  //
  string getSpectralMethod(){return spectralMethod;};
  void   setSpectralMethod(string s){spectralMethod=s;};
  string getSpectralUnits(){return spectralUnits;};
  void   setSpectralUnits(string s){spectralUnits=s;};
  bool   drawBorders(){return borders;};
  void   setDrawBorders(bool f){borders=f;};
  bool   isVerbose(){return verbose;};
  void   setVerbosity(bool f){verbose=f;};
  
private:
  // Input files
  string imageFile;       // The image to be analysed.
  bool   flagSubsection;  // Whether we just want a subsection of the image
  string subsection;      // The subsection requested, of the form [x1:x2,y1:y2,z1:z2]
                          //   If you want the full range of one index, use *
  bool   flagReconExists; // The reconstructed array is in a FITS file on disk.
  string reconFile;       // The FITS file containing the reconstructed array.

  // Output files
  bool   flagLog;         // Should we do the intermediate logging?
  string logFile;         // Where the intermediate logging goes.
  string outFile;         // Where the final results get put.
  string spectraFile;     // Where the spectra are displayed
  bool   flagOutputRecon; // Should the reconstructed cube be written?
  bool   flagOutputResid; // Should the reconstructed cube be written?
  bool   flagVOT;         // Should we save results in VOTable format?
  string votFile;         // Where the VOTable goes.
  bool   flagKarma;       // Should we save results in Karma annotation format?
  string karmaFile;       // Where the Karma annotation file goes.
  bool   flagMaps;        // Should we produce detection and moment maps in postscript form?
  string detectionMap;    // The name of the detection map (ps file).
  string momentMap;       // The name of the 0th moment map (ps file).

  // Cube related parameters 
  bool   flagNegative;    // Are we going to search for negative features? (Need to invert the cube.)
  bool   flagBlankPix;    // A flag that indicates whether there are pixels defined as BLANK,
                          //   with the value given by the next parameter.
  float  blankPixValue;   // Pixel value that is considered BLANK.
  int    blankKeyword;    // The FITS header keyword BLANK.
  float  bscaleKeyword;   // The FITS header keyword BSCALE.
  float  bzeroKeyword;    // The FITS header keyword BZERO.
  bool   flagUsingBlank;  // If true, we are using the blankPixValue keyword, 
                          // otherwise we are using the value in the FITS header.
  bool   nanAsBlank;      // Are the BLANK pixels defined by NaNs?
  bool   flagMW;          // A flag that indicates whether to excise the Milky Way.
  int    maxMW;           // Last  Galactic velocity plane for HIPASS cubes
  int    minMW;           // First Galactic velocity plane for HIPASS cubes
  float  numPixBeam;      // Size (area) of the beam in pixels.
  // Trim-related         
  bool   flagTrimmed;     // Has the cube been trimmed of excess BLANKs around the edge?
  long   borderLeft;      // The number of BLANK pixels trimmed from the Left of the cube;
  long   borderRight;     // The number of BLANK pixels trimmed from the Right of the cube;
  long   borderBottom;    // The number of BLANK pixels trimmed from the Bottom of the cube;
  long   borderTop;       // The number of BLANK pixels trimmed from the Top of the cube;
  // Subsection offsets
  long   xSubOffset;      // The offset in the x-direction from the subsection
  long   ySubOffset;      // The offset in the y-direction from the subsection
  long   zSubOffset;      // The offset in the z-direction from the subsection
  // Baseline related;
  bool   flagBaseline;    // Whether to do baseline subtraction before reconstruction and/or searching.
  // Detection-related    
  int    minPix;          // Minimum number of pixels for a detected object to be counted
  // Object growth        
  bool   flagGrowth;      // Are we growing objects once they are found?
  float  growthCut;       // The SNR that we are growing objects down to.
  // FDR analysis         
  bool   flagFDR;         // Should the FDR method be used? 
  float  alphaFDR;        // Alpha value for FDR detection algorithm
  // Other detection      
  float  snrCut;          // How many sigma above mean is a detection when sigma-clipping
  // A trous reconstruction parameters
  bool   flagATrous;      // Are we using the a trous reconstruction?
  int    reconDim;        // How many dimensions to use for the reconstruction?
  int    scaleMin;        // Min scale used in a trous reconstruction
  float  snrRecon;        // SNR cutoff used in a trous reconstruction
                          //   (only wavelet coefficients that survive this threshold are kept)
  int    filterCode;      // The code number for the filter to be used (saves having to parse names)
  string filterName;      // The code number converted into a name, for outputting purposes.

  // Volume-merging parameters
  bool   flagAdjacent;    // Whether to use the adjacent criterion for 
                          //    judging if objects are to be merged.
  float  threshSpatial;   // Maximum spatial separation between objects
  float  threshVelocity;  // Maximum channels separation between objects
  int    minChannels;     // Minimum no. of channels to make an object 
  // Input-Output related
  string spectralMethod;  // A string indicating choice of spectral plotting method:
                          //   choices are "peak" or "sum" (peak is the default).
  string spectralUnits;   // A string indicating what units the spectral axis should be quoted in.
  bool   borders;         // Whether to draw a border around the individual
                          //   pixels of a detection in the spectral display
  bool   verbose;         // Whether to use maximum verbosity -- progress indicators in the 
                          //   reconstruction & merging functions.

};

class FitsHeader
{
  /**
   *  FitsHeader Class
   *
   *   Stores information from a FITS header, including WCS information
   *    in the form of a wcsprm struct, as well as various keywords.
   */

public:
  FitsHeader();
  ~FitsHeader(){};
  FitsHeader(const FitsHeader& h);
  FitsHeader& operator= (const FitsHeader& h);

  wcsprm *getWCS();             // in param.cc
  void    setWCS(wcsprm *w);    // in param.cc
  bool    isWCS(){return wcsIsGood;};
  int     getNWCS(){return nwcs;};
  void    setNWCS(int i){nwcs=i;};
  string  getSpectralUnits(){return spectralUnits;};
  void    setSpectralUnits(string s){spectralUnits=s;};
  string  getFluxUnits(){return fluxUnits;};
  void    setFluxUnits(string s){fluxUnits=s;};
  string  getIntFluxUnits(){return intFluxUnits;};
  void    setIntFluxUnits(string s){intFluxUnits=s;};
  float   getBeamSize(){return beamSize;};
  void    setBeamSize(float f){beamSize=f;};
  float   getBmajKeyword(){return bmajKeyword;};
  void    setBmajKeyword(float f){bmajKeyword=f;};
  float   getBminKeyword(){return bminKeyword;};
  void    setBminKeyword(float f){bminKeyword=f;};
  int     getBlankKeyword(){return blankKeyword;};
  void    setBlankKeyword(int f){blankKeyword=f;};
  float   getBzeroKeyword(){return bzeroKeyword;};
  void    setBzeroKeyword(float f){bzeroKeyword=f;};
  float   getBscaleKeyword(){return bscaleKeyword;};
  void    setBscaleKeyword(float f){bscaleKeyword=f;};

  // front ends to WCS functions
  int     wcsToPix(const double *world, double *pix);
  int     pixToWCS(const double *pix, double *world);
  int     wcsToPix(const double *world, double *pix, const int npts);
  int     pixToWCS(const double *pix, double *world, const int npts);
  double  pixToVel(double &x, double &y, double &z);
  double *pixToVel(double &x, double &y, double *zarray, int size);
  double  specToVel(const double &z);
  double  velToSpec(const float &vel);
  string  getIAUName(double ra, double dec);

  void    fixUnits(Param &par);
 
private:
  wcsprm *wcs;             // The WCS parameters for the cube -- a struct from wcslib
  int     nwcs;            // The number of WCS parameters
  bool    wcsIsGood;       // A flag indicating whether there is a valid WCS present.
  string  spectralUnits;   // The units of the spectral dimension
  string  fluxUnits;       // The units of pixel flux (from header)
  string  intFluxUnits;    // The units of pixel flux (from header)
  float   beamSize;        // The calculated beam size in pixels.
  float   bmajKeyword;     // The FITS header keyword BMAJ.
  float   bminKeyword;     // The FITS header keyword BMIN.
  int     blankKeyword;    // The FITS header keyword BLANK.
  float   bzeroKeyword;    // The FITS header keyword BZERO.
  float   bscaleKeyword;   // The FITS header keyword BSCALE.
  double  scale;           // scale parameter for converting spectral coords
  double  offset;          // offset parameter for converting spectral coords
  double  power;           // power parameter for converting spectral coords
};

string makelower( string s );

#endif