source: tags/release-1.0.7/src/Cubes/cubes.hh

#ifndef CUBES_H
#define CUBES_H

#include <iostream>
#include <string>
#include <vector>

#ifndef PARAM_H
#include <param.hh>
#endif
#ifndef DETECTION_H
#include <Detection/detection.hh>
#endif
#ifndef COLUMNS_H
#include <Detection/columns.hh>
#endif
#ifndef PLOTS_H
#include <Cubes/plots.hh>
#endif
#ifndef STATS_H
#include <Utils/Statistics.hh>
#endif

using std::string;
using std::vector;
using namespace Column;
using namespace Statistics;

/****************************************************************/
/////////////////////////////////////////////////////////////
//// Definition of an n-dimensional data array:
////     array of pixel values, size & dimensions
////     array of Detection objects
/////////////////////////////////////////////////////////////


class DataArray
{
public:
  DataArray(){numDim=0; numPixels=0;};
  DataArray(short int nDim){numDim=nDim; numPixels=0;};
  DataArray(short int nDim, long size);
  DataArray(short int nDim, long *dimensions);
  virtual ~DataArray();
  // Size and Dimension related
  long                getDimX(){if(numDim>0) return axisDim[0];else return 0;};
  long                getDimY(){if(numDim>1) return axisDim[1];else return 1;};
  long                getDimZ(){if(numDim>2) return axisDim[2];else return 1;};
  void                getDim(long &x, long &y, long &z);
  long                getSize(){return numPixels;};
  short int           getNumDim(){return numDim;};
  // Related to the various arrays
  void                getDimArray(long *output);
  void                getArray(float *output);
  virtual void        saveArray(float *input, long size);
  float               getPixValue(long pos){return array[pos];};
  void                setPixValue(long pos, float f){array[pos] = f;};
  // Related to the object lists
  Detection           getObject(long number){return objectList[number];};
  void                addObject(Detection object);   
                      // adds a single detection to the object list
  vector <Detection>  getObjectList(){return objectList;};
  void                addObjectList(vector <Detection> newlist);  
                     // adds all objects in a detection list to the object list
  void                addObjectOffsets();
  long                getNumObj(){return objectList.size();};
  void                clearDetectionList(){this->objectList.clear();};
  // Parameter list related.
  int                 readParam(string paramfile){
    return par.readParams(paramfile);};
  void                showParam(std::ostream &stream){stream << par;};
  Param               getParam(){return par;};
  void                saveParam(Param newpar){par = newpar;};
  Param&              pars(){Param &rpar = par; return rpar;};
  bool                isBlank(int vox){return par.isBlank(array[vox]);};
  // Statistics
  StatsContainer<float> getStats(){return Stats;};
  StatsContainer<float>& stats(){
    StatsContainer<float> &rstats = Stats; 
    return rstats;
  };
  void saveStats(StatsContainer<float> newStats){
    Stats = newStats;
  };

  bool isDetection(float value){
    if(par.isBlank(value)) return false;
    else return Stats.isDetection(value);
  };  

  friend std::ostream& operator<< ( std::ostream& theStream, DataArray &array);

protected:
  short int               numDim;     // number of dimensions.
  long                   *axisDim;    // array of dimensions of cube 
                                      //     (ie. how large in each direction).
  long                    numPixels;  // total number of pixels in cube
  float                  *array;      // array of data
  vector <Detection>      objectList; // the list of detected objects
  Param                   par;        // a parameter list.
  StatsContainer<float>   Stats;      // The statistics for the dataArray
};


/****************************************************************/
/////////////////////////////////////////////////////////////
//// Definition of an image object (2D):
////     a DataArray object
////     arrays for: probability values (for FDR)
////                 mask image to indicate location of objects
////                 detected objects
////     statistics information
/////////////////////////////////////////////////////////////

class Cube;
class Image : public DataArray
{
public:
  Image(){numPixels=0; numDim=2;};
  Image(long nPix);
  Image(long *dimensions);
  virtual ~Image(){};

  // Defining the array
  void      saveArray(float *input, long size);
  void      extractSpectrum(float *Array, long *dim, long pixel);
  void      extractImage(float *Array, long *dim, long channel);
  void      extractSpectrum(Cube &cube, long pixel);
  void      extractImage(Cube &cube, long channel);
  // Accessing the data.
  float     getPixValue(long x, long y){return array[y*axisDim[0] + x];};
  float     getPixValue(long pos){return array[pos];};
  // the next few should have checks against array overflow...
  void      setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;};
  void      setPixValue(long pos, float f){array[pos] = f;};
  bool      isBlank(int vox){return par.isBlank(array[vox]);};
  bool      isBlank(long x,long y){return par.isBlank(array[y*axisDim[0]+x]);};

  // Detection-related
  void      lutz_detect();            // in Detection/lutz_detect.cc
  void      spectrumDetect();         // in Detection/spectrumDetect.cc
  int       getMinSize(){return minSize;};
  void      setMinSize(int i){minSize=i;};
  // the rest are in Detection/thresholding_functions.cc
  bool      isDetection(long x, long y){
    long voxel = y*axisDim[0] + x;
    if(isBlank(x,y)) return false;
    else return Stats.isDetection(array[voxel]);
  };  

  void      removeMW();
  
private: 
  int        minSize;    // the minimum number of pixels for a detection 
                         //  to be accepted.
};

/****************************************************************/
/////////////////////////////////////////////////////////////
//// Definition of an data-cube object (3D):
////     a DataArray object limited to dim=3
/////////////////////////////////////////////////////////////

class Cube : public DataArray
{
public:
  Cube(){
    numPixels=0; numDim=3; 
    reconExists = false; reconAllocated = false; baselineAllocated = false;
  };
  Cube(long nPix);
  Cube(long *dimensions);
  virtual ~Cube();

  // additional accessor functions
  //       -- in Cubes/cubes.cc unless otherwise specified.

  int     getCube(string fname);
  int     getCube(){  
    // a front-end to the getCube function, that does subsection checks
    // assumes the Param is setup properly
    string fname = par.getImageFile();
    if(par.getFlagSubsection()) fname+=par.getSubsection();
    return getCube(fname);
  };
  int     getFITSdata(string fname);         // in FitsIO/dataIO.cc
  void    initialiseCube(long *dimensions);  // in cubes.cc
  int     getopts(int argc, char ** argv);   // in cubes.cc
  void    readSavedArrays();                 // in cubes.cc
  void    saveSmoothedCube();                // in saveImage.cc
  void    saveReconstructedCube();           // in saveImage.cc
  int     readReconCube();                   // in readRecon.cc
  int     readSmoothCube();                  // in readSmooth.cc

  bool    isBlank(int vox){return par.isBlank(array[vox]);};
  bool    isBlank(long x, long y, long z){
    return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]);};
  float   getPixValue(long pos){return array[pos];};
  float   getPixValue(long x, long y, long z){
    return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];};
  short   getDetectMapValue(long pos){return detectMap[pos];};
  short   getDetectMapValue(long x, long y){return detectMap[y*axisDim[0]+x];};
  bool    isRecon(){return reconExists;};
  float   getReconValue(long pos){return recon[pos];};
  float   getReconValue(long x, long y, long z){
    return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];};
  float   getBaselineValue(long pos){return baseline[pos];};
  float   getBaselineValue(long x, long y, long z){
    return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];};
  // these should have checks against array overflow...
  void    setPixValue(long pos, float f){array[pos] = f;};
  void    setPixValue(long x, long y, long z, float f){
    array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;};
  void    setDetectMapValue(long pos, short f){detectMap[pos] = f;};
  void    setDetectMapValue(long x, long y, short f){
    detectMap[y*axisDim[0] + x] = f;};
  void    setReconValue(long pos, float f){recon[pos] = f;};
  void    setReconValue(long x, long y, long z, float f){
    recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;};
  void    setReconFlag(bool f){reconExists = f;};
  void    saveArray(float *input, long size);
  void    saveRecon(float *input, long size);
  void    getRecon(float *output);

  vector<Col>  getLogCols(){return logCols;};
  void         setLogCols(vector<Col> C){logCols=C;};
  vector<Col>  getFullCols(){return fullCols;};
  void         setFullCols(vector<Col> C){fullCols=C;};

  // Statistics for cube
  void    setCubeStatsOld(); // in Cubes/cubes.cc
  void    setCubeStats();    // in Cubes/cubes.cc
  int     setupFDR();
  bool    isDetection(long x, long y, long z){
    long voxel = z*axisDim[0]*axisDim[1] + y*axisDim[0] + x;
    return DataArray::isDetection(array[voxel]);
  };

  // Functions that act on the cube
  void    removeMW();        // in Cubes/cubes.cc
  void    trimCube();        // in Cubes/trimImage.cc
  void    unTrimCube();      // in Cubes/trimImage.cc
  void    removeBaseline();  // in ATrous/baselineSubtract.cc
  void    replaceBaseline(); // in ATrous/baselineSubtract.cc
  void    invert();          // in Cubes/invertCube.cc
  void    reInvert();        // in Cubes/invertCube.cc

  // Reconstruction and Searching functions
  void    ReconSearch();     // in ATrous/ReconSearch.cc
  void    ReconCube();       // in ATrous/ReconSearch.cc
  void    ReconCube1D();     // in ATrous/ReconSearch.cc
  void    ReconCube2D();     // in ATrous/ReconSearch.cc
  void    ReconCube3D();     // in ATrous/ReconSearch.cc
  void    CubicSearch();     // in Cubes/CubicSearch.cc
  void    SmoothSearch();    // in Cubes/smoothCube.cc
  void    SmoothCube();      // in Cubes/smoothCube.cc

  // Dealing with the WCS
  FitsHeader getHead(){return head;};
  void       setHead(FitsHeader F){head=F;};
  FitsHeader& header(){FitsHeader &h = head; return h;};
  int        wcsToPix(const double *world, double *pix){
    return this->head.wcsToPix(world,pix);}
  int        wcsToPix(const double *world, double *pix, const int npts){
    return this->head.wcsToPix(world,pix,npts);}
  int        pixToWCS(const double *pix, double *world){
    return this->head.pixToWCS(pix,world);}
  int        pixToWCS(const double *pix, double *world, const int npts){
    return this->head.pixToWCS(pix,world,npts);}
  
  // Dealing with the detections 
  void    ObjectMerger();          // in Cubes/Merger.cc
  void    calcObjectWCSparams();
  void    sortDetections();
  void    updateDetectMap();
  void    updateDetectMap(Detection obj);
  void    setObjectFlags();
  float   enclosedFlux(Detection obj);
  bool    objAtSpatialEdge(Detection obj);
  bool    objAtSpectralEdge(Detection obj);
  
  // Text outputting of detected objects.
  //    the next five in Cubes/detectionIO.cc
  void    outputDetectionsKarma(std::ostream &stream);     
  void    outputDetectionsVOTable(std::ostream &stream);   
  void    outputDetectionList();                           
  void    logDetectionList();                              
  void    logDetection(Detection obj, int counter);        
  void    setupColumns(); // in Cubes/cubes.cc

  // Graphical plotting of the cube and the detections.
  void    plotBlankEdges();  // in Cubes/cubes.cc
  //    the next three in Cubes/plotting.cc
  void    plotDetectionMap(string pgDestination);          
  void    plotMomentMap(string pgDestination);             
  void    plotMomentMap(vector<string> pgDestination);
  void    plotWCSaxes();                                   
  //    the next two in Cubes/outputSpectra.cc
  void    outputSpectra();
  void    plotSpectrum(Detection obj,Plot::SpectralPlot &plot);
  //    the next three in Cubes/drawMomentCutout.cc
  void    drawMomentCutout(Detection &object);
  void    drawScale(float xstart,float ystart,float channel);
  void    drawFieldEdge();

private: 
  float  *recon;           // reconstructed array -- used when doing a trous 
                           //   reconstruction.
  bool    reconExists;     // flag saying whether there is a reconstruction
  short  *detectMap;       // "moment map" -- x,y locations of detected pixels
  float  *baseline;        // array of spectral baseline values.

  bool    reconAllocated;   // have we allocated memory for the recon array?
  bool    baselineAllocated;// have we allocated memory for the baseline array?
        
  FitsHeader head;         // the WCS and other header information.
  vector<Col> fullCols;    // the list of all columns as printed in the 
                           //  results file
  vector<Col> logCols;     // the list of columns as printed in the log file

};

/****************************************************************/
//////////////////////////////////////////////////////
// Prototypes for functions that use above classes
//////////////////////////////////////////////////////

void findSources(Image &image);
void findSources(Image &image, float mean, float sigma); 

vector <Detection> searchReconArray(long *dim, float *originalArray,
                                    float *reconArray, Param &par,
                                    StatsContainer<float> &stats);
vector <Detection> search3DArray(long *dim, float *Array, Param &par,
                                 StatsContainer<float> &stats);

void growObject(Detection &object, Cube &cube);

#endif