[3] | 1 | #ifndef CUBES_H |
---|
| 2 | #define CUBES_H |
---|
| 3 | |
---|
| 4 | #include <iostream> |
---|
| 5 | #include <string> |
---|
| 6 | #include <vector> |
---|
| 7 | |
---|
| 8 | #ifndef PARAM_H |
---|
| 9 | #include <param.hh> |
---|
| 10 | #endif |
---|
| 11 | #ifndef DETECTION_H |
---|
| 12 | #include <Detection/detection.hh> |
---|
| 13 | #endif |
---|
[93] | 14 | #ifndef COLUMNS_H |
---|
| 15 | #include <Detection/columns.hh> |
---|
| 16 | #endif |
---|
[95] | 17 | #ifndef PLOTS_H |
---|
| 18 | #include <Cubes/plots.hh> |
---|
| 19 | #endif |
---|
[3] | 20 | |
---|
| 21 | using std::string; |
---|
| 22 | using std::vector; |
---|
[93] | 23 | using namespace Column; |
---|
[3] | 24 | |
---|
| 25 | /****************************************************************/ |
---|
| 26 | ///////////////////////////////////////////////////////////// |
---|
| 27 | //// Definition of an n-dimensional data array: |
---|
| 28 | //// array of pixel values, size & dimensions |
---|
| 29 | //// array of Detection objects |
---|
| 30 | ///////////////////////////////////////////////////////////// |
---|
| 31 | |
---|
| 32 | |
---|
| 33 | class DataArray |
---|
| 34 | { |
---|
| 35 | public: |
---|
| 36 | DataArray(){numDim=0; numPixels=0;}; |
---|
| 37 | DataArray(short int nDim){numDim=nDim; numPixels=0;}; |
---|
| 38 | DataArray(short int nDim, long size); |
---|
| 39 | DataArray(short int nDim, long *dimensions); |
---|
| 40 | virtual ~DataArray(){}; |
---|
| 41 | // Size and Dimension related |
---|
| 42 | long getDimX(){if(numDim>0) return axisDim[0]; else return 0;}; |
---|
| 43 | long getDimY(){if(numDim>1) return axisDim[1]; else return 1;}; |
---|
| 44 | long getDimZ(){if(numDim>2) return axisDim[2]; else return 1;}; |
---|
| 45 | void getDim(long &x, long &y, long &z); |
---|
| 46 | long getSize(){return numPixels;}; |
---|
| 47 | short int getNumDim(){return numDim;}; |
---|
| 48 | // Related to the various arrays |
---|
| 49 | void getDimArray(long *output); |
---|
| 50 | void getArray(float *output); |
---|
| 51 | virtual void saveArray(float *input, long size); |
---|
| 52 | float getPixValue(long pos){return array[pos];}; |
---|
| 53 | void setPixValue(long pos, float f){array[pos] = f;}; |
---|
| 54 | // Related to the object lists |
---|
| 55 | Detection getObject(long number){return objectList[number];}; |
---|
| 56 | void addObject(Detection object); |
---|
| 57 | // adds a single detection to the object list |
---|
| 58 | vector <Detection> getObjectList(){return objectList;}; |
---|
| 59 | void addObjectList(vector <Detection> newlist); |
---|
| 60 | // adds all objects in a detection list to the object list |
---|
| 61 | long getNumObj(){return objectList.size();}; |
---|
| 62 | void clearDetectionList(){this->objectList.clear();}; |
---|
| 63 | // Parameter list related. |
---|
| 64 | void readParam(string ¶mfile){par.readParams(paramfile);}; |
---|
| 65 | void showParam(std::ostream &stream){stream << par;}; |
---|
| 66 | Param getParam(){return par;}; |
---|
| 67 | void saveParam(Param newpar){par = newpar;}; |
---|
| 68 | Param& pars(){Param &rpar = par; return rpar;}; |
---|
[44] | 69 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
---|
[3] | 70 | |
---|
| 71 | friend std::ostream& operator<< ( std::ostream& theStream, DataArray &array); |
---|
| 72 | |
---|
| 73 | |
---|
| 74 | protected: |
---|
| 75 | short int numDim; // number of dimensions. |
---|
| 76 | long *axisDim; // array of dimensions of cube |
---|
| 77 | // (ie. how large in each direction). |
---|
| 78 | long numPixels; // total number of pixels in cube |
---|
| 79 | float *array; // array of data |
---|
| 80 | vector <Detection> objectList; // the list of detected objects in the image |
---|
| 81 | Param par; // a parameter list. |
---|
| 82 | }; |
---|
| 83 | |
---|
| 84 | |
---|
| 85 | /****************************************************************/ |
---|
| 86 | ///////////////////////////////////////////////////////////// |
---|
| 87 | //// Definition of an image object (2D): |
---|
| 88 | //// a DataArray object |
---|
| 89 | //// arrays for: probability values (for FDR) |
---|
| 90 | //// mask image to indicate location of objects |
---|
| 91 | //// detected objects |
---|
| 92 | //// statistics information |
---|
| 93 | ///////////////////////////////////////////////////////////// |
---|
| 94 | |
---|
| 95 | class Image : public DataArray |
---|
| 96 | { |
---|
| 97 | public: |
---|
| 98 | Image(){ |
---|
[86] | 99 | numPixels=0; |
---|
[3] | 100 | numDim=2;}; |
---|
| 101 | Image(long nPix); |
---|
| 102 | Image(long *dimensions); |
---|
| 103 | virtual ~Image(){}; |
---|
| 104 | |
---|
[53] | 105 | // Defining the array |
---|
[3] | 106 | void saveArray(float *input, long size); |
---|
[53] | 107 | void extractSpectrum(float *Array, long *dim, long pixel); |
---|
| 108 | void extractImage(float *Array, long *dim, long channel); |
---|
| 109 | // Accessing the data. |
---|
[3] | 110 | float getPixValue(long x, long y){return array[y*axisDim[0] + x];}; |
---|
| 111 | float getPixValue(long pos){return array[pos];}; |
---|
| 112 | float getPValue(long pos){return pValue[pos];}; |
---|
| 113 | float getPValue(long x, long y){return pValue[y*axisDim[0] + x];}; |
---|
| 114 | short int getMaskValue(long pos){return mask[pos];}; |
---|
| 115 | short int getMaskValue(long x, long y){return mask[y*axisDim[0] + x];}; |
---|
| 116 | // the next few should have checks against array overflow... |
---|
| 117 | void setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;}; |
---|
| 118 | void setPixValue(long pos, float f){array[pos] = f;}; |
---|
| 119 | void setPValue(long pos, float p){pValue[pos] = p;}; |
---|
| 120 | void setPValue(long x, long y, float p){pValue[y*axisDim[0] + x] = p;}; |
---|
| 121 | void setMaskValue(long pos, short int m){mask[pos] = m;}; |
---|
| 122 | void setMaskValue(long x, long y, short int m){mask[y*axisDim[0] + x] = m;}; |
---|
[96] | 123 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
---|
| 124 | bool isBlank(long x, long y){return par.isBlank(array[y*axisDim[0] + x]);}; |
---|
[3] | 125 | // Stats-related |
---|
| 126 | void setStats(float m, float s, float c){mean=m; sigma=s; cutLevel=c;}; |
---|
[53] | 127 | void findStats(int code); |
---|
[3] | 128 | float getMean(){return mean;}; |
---|
[53] | 129 | void setMean(float m){mean=m;}; |
---|
[3] | 130 | float getSigma(){return sigma;}; |
---|
[53] | 131 | void setSigma(float s){sigma=s;}; |
---|
[3] | 132 | float getCut(){return cutLevel;}; |
---|
[53] | 133 | void setCut(float c){cutLevel=c;}; |
---|
| 134 | float getPCut(){return pCutLevel;}; |
---|
[3] | 135 | void setPCut(float p){pCutLevel = p;}; |
---|
[53] | 136 | float getAlpha(){return alpha;}; |
---|
[3] | 137 | void setAlpha(float a){alpha = a;}; |
---|
[53] | 138 | int getMinSize(){return minSize;}; |
---|
[14] | 139 | void setMinSize(int s){minSize = s;}; |
---|
[3] | 140 | |
---|
| 141 | void maskObject(Detection &object); |
---|
| 142 | |
---|
| 143 | // Detection-related |
---|
| 144 | void lutz_detect(); // in Detection/lutz_detect.cc |
---|
[50] | 145 | void spectrumDetect(); // in Detection/spectrumDetect.cc |
---|
[3] | 146 | int setupFDR(); // in Detection/thresholding_functions.cc |
---|
| 147 | bool isDetection(float value); // in Detection/thresholding_functions.cc |
---|
| 148 | bool isDetection(long x, long y); // in Detection/thresholding_functions.cc |
---|
| 149 | bool isDetectionFDR(float pvalue); // in Detection/thresholding_functions.cc |
---|
| 150 | |
---|
[96] | 151 | void removeMW(); |
---|
[3] | 152 | |
---|
| 153 | private: |
---|
| 154 | float *pValue; // the array of p-values for each pixel |
---|
| 155 | // --> used by FDR method |
---|
| 156 | short int *mask; // a mask image indicating where objects are |
---|
| 157 | |
---|
| 158 | float mean; // the mean background level of the image |
---|
| 159 | float sigma; // the standard deviation of the background in the image |
---|
| 160 | float cutLevel; // the limiting value (in sigmas above the mean) for |
---|
| 161 | // a pixel to be called a detection. |
---|
| 162 | float alpha; // used by FDR routine -- significance level |
---|
| 163 | float pCutLevel; // the limiting P-value for the FDR analysis |
---|
[13] | 164 | int minSize; // the minimum number of pixels for a detection to be accepted. |
---|
[3] | 165 | }; |
---|
| 166 | |
---|
| 167 | /****************************************************************/ |
---|
| 168 | ///////////////////////////////////////////////////////////// |
---|
| 169 | //// Definition of an data-cube object (3D): |
---|
| 170 | //// a DataArray object limited to dim=3 |
---|
| 171 | ///////////////////////////////////////////////////////////// |
---|
| 172 | |
---|
| 173 | class Cube : public DataArray |
---|
| 174 | { |
---|
| 175 | public: |
---|
[90] | 176 | Cube(){numPixels=0; numDim=3; // flagWCS=false; |
---|
| 177 | }; |
---|
[3] | 178 | Cube(long nPix); |
---|
| 179 | Cube(long *dimensions); |
---|
| 180 | virtual ~Cube(){}; // destructor |
---|
| 181 | |
---|
| 182 | // additional accessor functions -- in Cubes/cubes.cc unless otherwise specified. |
---|
| 183 | |
---|
| 184 | int getCube(string fname); |
---|
[95] | 185 | int getCube(){this->getCube(this->par.getImageFile());}; |
---|
[3] | 186 | void initialiseCube(long *dimensions); |
---|
| 187 | void saveReconstructedCube(); |
---|
[71] | 188 | int readReconCube(); |
---|
[3] | 189 | |
---|
[87] | 190 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
---|
| 191 | bool isBlank(long x, long y, long z){ |
---|
| 192 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]);}; |
---|
[3] | 193 | float getPixValue(long pos){return array[pos];}; |
---|
| 194 | float getPixValue(long x, long y, long z){ |
---|
| 195 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
---|
| 196 | short getDetectMapValue(long pos){return detectMap[pos];}; |
---|
| 197 | short getDetectMapValue(long x, long y){return detectMap[y*axisDim[0] + x];}; |
---|
| 198 | bool isRecon(){return reconExists;}; |
---|
| 199 | float getReconValue(long pos){return recon[pos];}; |
---|
| 200 | float getReconValue(long x, long y, long z){ |
---|
| 201 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
---|
| 202 | float getBaselineValue(long pos){return baseline[pos];}; |
---|
| 203 | float getBaselineValue(long x, long y, long z){ |
---|
| 204 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
---|
| 205 | // these should have checks against array overflow... |
---|
| 206 | void setPixValue(long pos, float f){array[pos] = f;}; |
---|
| 207 | void setPixValue(long x, long y, long z, float f){ |
---|
| 208 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
---|
| 209 | void setDetectMapValue(long pos, short f){detectMap[pos] = f;}; |
---|
| 210 | void setDetectMapValue(long x, long y, short f){ |
---|
| 211 | detectMap[y*axisDim[0] + x] = f;}; |
---|
| 212 | void setReconValue(long pos, float f){recon[pos] = f;}; |
---|
| 213 | void setReconValue(long x, long y, long z, float f){ |
---|
| 214 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
---|
| 215 | void setReconFlag(bool f){reconExists = f;}; |
---|
| 216 | void saveArray(float *input, long size); |
---|
| 217 | void saveRecon(float *input, long size); |
---|
| 218 | void getRecon(float *output); |
---|
| 219 | |
---|
| 220 | // Statistics for cube |
---|
| 221 | float getSpecMean(int pixel){return specMean[pixel];}; |
---|
| 222 | float getSpecSigma(int pixel){return specSigma[pixel];}; |
---|
| 223 | float getChanMean(int channel){return chanMean[channel];}; |
---|
| 224 | float getChanSigma(int channel){return chanSigma[channel];}; |
---|
[86] | 225 | void setCubeStats(); // in Cubes/cubes.cc |
---|
[3] | 226 | |
---|
| 227 | // Functions that act on the cube |
---|
[86] | 228 | void removeMW(); // in Cubes/cubes.cc |
---|
| 229 | void trimCube(); // in Cubes/trimImage.cc |
---|
| 230 | void unTrimCube(); // in Cubes/trimImage.cc |
---|
[3] | 231 | void removeBaseline(); // in ATrous/baselineSubtract.cc |
---|
| 232 | void replaceBaseline(); // in ATrous/baselineSubtract.cc |
---|
[60] | 233 | void invert(); // in Cubes/invertCube.cc |
---|
| 234 | void reInvert(); // in Cubes/invertCube.cc |
---|
[3] | 235 | |
---|
| 236 | // Reconstruction and Searching functions |
---|
[96] | 237 | void ReconSearch(); // in ATrous/ReconSearch.cc |
---|
[3] | 238 | void ReconSearch1D(); // in ATrous/ReconSearch.cc |
---|
| 239 | void ReconSearch2D(); // in ATrous/ReconSearch.cc |
---|
| 240 | void ReconSearch3D(); // in ATrous/ReconSearch.cc |
---|
[97] | 241 | void CubicSearch(); // in Cubes/CubicSearch.cc |
---|
[3] | 242 | |
---|
| 243 | // Dealing with the WCS |
---|
[90] | 244 | FitsHeader getHead(){return head;}; |
---|
| 245 | void setHead(FitsHeader F){head=F;}; |
---|
[95] | 246 | FitsHeader& header(){FitsHeader &h = head; return h;}; |
---|
| 247 | int wcsToPix(const double *world, double *pix){ |
---|
| 248 | return this->head.wcsToPix(world,pix);} |
---|
| 249 | int wcsToPix(const double *world, double *pix, const int npts){ |
---|
| 250 | return this->head.wcsToPix(world,pix,npts);} |
---|
| 251 | int pixToWCS(const double *pix, double *world){ |
---|
| 252 | return this->head.pixToWCS(pix,world);} |
---|
| 253 | int pixToWCS(const double *pix, double *world, const int npts){ |
---|
| 254 | return this->head.pixToWCS(pix,world,npts);} |
---|
| 255 | |
---|
[90] | 256 | // bool isWCS(){return flagWCS;}; |
---|
| 257 | // void setWCS(wcsprm *w); |
---|
| 258 | // wcsprm *getWCS(); |
---|
| 259 | // void setNWCS(int n){nwcs = n;}; |
---|
| 260 | // int getNWCS(){return nwcs;}; |
---|
| 261 | // void setBUnit(char *s){bunit = s;}; |
---|
| 262 | // string getBUnit(){return bunit;}; |
---|
| 263 | // void setVelUnit(char *s){velunit = s;}; |
---|
| 264 | // string getVelUnit(){return velunit;}; |
---|
[3] | 265 | |
---|
| 266 | // Dealing with the detections |
---|
| 267 | void ObjectMerger(); // in Cubes/Merger.cc |
---|
| 268 | void calcObjectWCSparams(); |
---|
| 269 | void sortDetections(); |
---|
| 270 | void updateDetectMap(); |
---|
| 271 | void updateDetectMap(Detection obj); |
---|
[87] | 272 | void setObjectFlags(); |
---|
| 273 | float enclosedFlux(Detection obj); |
---|
| 274 | bool objAtEdge(Detection obj); |
---|
| 275 | |
---|
[3] | 276 | // Text outputting of detected objects. |
---|
[20] | 277 | void outputDetectionsKarma(std::ostream &stream); // in Cubes/detectionIO.cc |
---|
[3] | 278 | void outputDetectionsVOTable(std::ostream &stream); // in Cubes/detectionIO.cc |
---|
| 279 | void outputDetectionList(); // in Cubes/detectionIO.cc |
---|
| 280 | void logDetectionList(); // in Cubes/detectionIO.cc |
---|
| 281 | void logDetection(Detection obj, int counter); // in Cubes/detectionIO.cc |
---|
[93] | 282 | void setupColumns(); // in Detection/columns.cc |
---|
[3] | 283 | |
---|
| 284 | // Graphical plotting of detections. |
---|
[95] | 285 | void plotDetectionMap(string pgDestination); // in Cubes/plotting.cc |
---|
| 286 | void plotMomentMap(string pgDestination); // in Cubes/plotting.cc |
---|
| 287 | void plotWCSaxes(); // in Cubes/plotting.cc |
---|
| 288 | void outputSpectra(); // in Cubes/outputSpectra.cc |
---|
| 289 | void plotSpectrum(Detection obj,Plot::SpectralPlot &plot); // in Cubes/outputSpectra.cc |
---|
| 290 | void drawMomentCutout(Detection &object); // in Cubes/drawMomentCutout.cc |
---|
[86] | 291 | void drawScale(float xstart, float ystart, float channel, float scaleLength); |
---|
[95] | 292 | // in Cubes/drawMomentCutout.cc |
---|
[3] | 293 | |
---|
| 294 | private: |
---|
| 295 | float *recon; // reconstructed array -- used when doing a trous reconstruction. |
---|
| 296 | bool reconExists; // flag saying whether there is a reconstruction |
---|
| 297 | short *detectMap; // "moment map" -- x,y locations of detected pixels |
---|
| 298 | float *baseline; // array of spectral baseline values. |
---|
| 299 | |
---|
| 300 | float *specMean; // array of means for each spectrum in cube |
---|
| 301 | float *specSigma; // array of sigmas for each spectrum in cube |
---|
| 302 | float *chanMean; // array of means for each channel map in cube |
---|
| 303 | float *chanSigma; // array of sigmas for each channel map in cube |
---|
[90] | 304 | |
---|
| 305 | FitsHeader head; // the WCS and other header information. |
---|
[93] | 306 | ColSet fullColSet; // the list of all columns as printed in the results file |
---|
| 307 | ColSet logColSet; // the list of columns as printed in the log file |
---|
| 308 | |
---|
[90] | 309 | // bool flagWCS; // a flag indicating whether there is a valid WCS present. |
---|
| 310 | // wcsprm *wcs; // the WCS parameters for the cube -- a struct from wcslib |
---|
| 311 | // int nwcs; // number of WCS parameters |
---|
| 312 | // string bunit; // The header keyword BUNIT -- the units of brightness in the FITS file. |
---|
| 313 | // string velunit; // The header keyword CUNIT3 -- the units of the spectral dimension. |
---|
[3] | 314 | }; |
---|
| 315 | |
---|
| 316 | /****************************************************************/ |
---|
| 317 | ////////////////////////////////////////////////////// |
---|
| 318 | // Prototypes for functions that use above classes |
---|
| 319 | ////////////////////////////////////////////////////// |
---|
| 320 | |
---|
| 321 | DataArray getImage(string fname, short int maxdim); |
---|
| 322 | Image getImage(string fname); |
---|
| 323 | |
---|
| 324 | void findSources(Image &image); |
---|
| 325 | void findSources(Image &image, float mean, float sigma); |
---|
| 326 | |
---|
[96] | 327 | vector <Detection> searchReconArray(long *dim,float *originalArray,float *reconArray, Param &par); |
---|
| 328 | vector <Detection> search3DArray(long *dim, float *Array, Param &par); |
---|
[3] | 329 | |
---|
| 330 | void growObject(Detection &object, Image &image); |
---|
| 331 | void growObject(Detection &object, Cube &cube); |
---|
| 332 | |
---|
| 333 | #endif |
---|