[299] | 1 | // ----------------------------------------------------------------------- |
---|
| 2 | // detectionIO.cc: Screen and File output of the detected objects. |
---|
| 3 | // ----------------------------------------------------------------------- |
---|
| 4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
---|
| 5 | // |
---|
| 6 | // This program is free software; you can redistribute it and/or modify it |
---|
| 7 | // under the terms of the GNU General Public License as published by the |
---|
| 8 | // Free Software Foundation; either version 2 of the License, or (at your |
---|
| 9 | // option) any later version. |
---|
| 10 | // |
---|
| 11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
---|
| 12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
---|
| 13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
---|
| 14 | // for more details. |
---|
| 15 | // |
---|
| 16 | // You should have received a copy of the GNU General Public License |
---|
| 17 | // along with Duchamp; if not, write to the Free Software Foundation, |
---|
| 18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
---|
| 19 | // |
---|
| 20 | // Correspondence concerning Duchamp may be directed to: |
---|
| 21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
---|
| 22 | // Postal address: Dr. Matthew Whiting |
---|
| 23 | // Australia Telescope National Facility, CSIRO |
---|
| 24 | // PO Box 76 |
---|
| 25 | // Epping NSW 1710 |
---|
| 26 | // AUSTRALIA |
---|
| 27 | // ----------------------------------------------------------------------- |
---|
[3] | 28 | #include <iostream> |
---|
| 29 | #include <sstream> |
---|
| 30 | #include <fstream> |
---|
| 31 | #include <iomanip> |
---|
| 32 | #include <string> |
---|
[258] | 33 | #include <vector> |
---|
[80] | 34 | #include <time.h> |
---|
[393] | 35 | #include <duchamp/param.hh> |
---|
| 36 | #include <duchamp/fitsHeader.hh> |
---|
| 37 | #include <duchamp/Cubes/cubes.hh> |
---|
| 38 | #include <duchamp/PixelMap/Object3D.hh> |
---|
| 39 | #include <duchamp/Detection/detection.hh> |
---|
| 40 | #include <duchamp/Detection/columns.hh> |
---|
| 41 | #include <duchamp/Utils/utils.hh> |
---|
| 42 | #include <duchamp/Utils/Statistics.hh> |
---|
[103] | 43 | |
---|
[3] | 44 | using std::endl; |
---|
| 45 | using std::setw; |
---|
| 46 | using std::setprecision; |
---|
[258] | 47 | using namespace PixelInfo; |
---|
[298] | 48 | using namespace Statistics; |
---|
[3] | 49 | |
---|
[378] | 50 | namespace duchamp |
---|
[20] | 51 | { |
---|
| 52 | |
---|
[378] | 53 | void Cube::outputDetectionsKarma(std::ostream &stream) |
---|
| 54 | { |
---|
[528] | 55 | /// @details |
---|
| 56 | /// Prints to a stream (provided) the list of detected objects in the cube |
---|
| 57 | /// in the format of an annotation file for the Karma suite of programs. |
---|
| 58 | /// Annotation file draws a box enclosing the detection, and writes the |
---|
| 59 | /// ID number of the detection to the right of the box. |
---|
[378] | 60 | |
---|
| 61 | std::string fname = this->par.getImageFile(); |
---|
| 62 | if(this->par.getFlagSubsection()) fname+=this->par.getSubsection(); |
---|
| 63 | stream << "# Duchamp Source Finder results for FITS file: " << fname << endl; |
---|
| 64 | if(this->par.getFlagFDR()) |
---|
| 65 | stream<<"# FDR Significance = " << this->par.getAlpha() << endl; |
---|
| 66 | else |
---|
| 67 | stream<<"# Threshold = " << this->par.getCut() << endl; |
---|
| 68 | if(this->par.getFlagATrous()){ |
---|
| 69 | stream<<"# The a trous reconstruction method was used, with the following parameters." << endl; |
---|
| 70 | stream<<"# ATrous Dimension = " << this->par.getReconDim() << endl; |
---|
| 71 | stream<<"# ATrous Threshold = " << this->par.getAtrousCut() << endl; |
---|
| 72 | stream<<"# ATrous Minimum Scale =" << this->par.getMinScale() << endl; |
---|
| 73 | stream<<"# ATrous Filter = " << this->par.getFilterName() << endl; |
---|
[156] | 74 | } |
---|
[431] | 75 | else if(this->par.getFlagSmooth()){ |
---|
| 76 | stream<<"# The data was smoothed prior to searching, with the following parameters." << endl; |
---|
| 77 | stream<<"# Smoothing type = " << this->par.getSmoothType() << endl; |
---|
| 78 | if(this->par.getSmoothType()=="spectral"){ |
---|
| 79 | stream << "# Hanning width = " << this->par.getHanningWidth() << endl; |
---|
| 80 | } |
---|
| 81 | else{ |
---|
| 82 | stream << "# Kernel Major axis = " << this->par.getKernMaj() << endl; |
---|
| 83 | if(this->par.getKernMin()>0) |
---|
| 84 | stream << "# Kernel Minor axis = " << this->par.getKernMin() << endl; |
---|
| 85 | else |
---|
| 86 | stream << "# Kernel Minor axis = " << this->par.getKernMaj() << endl; |
---|
| 87 | stream << "# Kernel Major axis = " << this->par.getKernPA() << endl; |
---|
| 88 | } |
---|
| 89 | } |
---|
[378] | 90 | else stream << "# No ATrous reconstruction done." << endl; |
---|
| 91 | stream << "#\n"; |
---|
| 92 | stream << "COLOR RED" << endl; |
---|
| 93 | stream << "COORD W" << endl; |
---|
[509] | 94 | stream << "FONT lucidasans-12" << endl; |
---|
[431] | 95 | stream << std::setprecision(6); |
---|
| 96 | stream.setf(std::ios::fixed); |
---|
| 97 | double *pix = new double[3]; |
---|
| 98 | double *wld = new double[3]; |
---|
| 99 | std::vector<Detection>::iterator obj; |
---|
| 100 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
[446] | 101 | |
---|
| 102 | if(this->par.getAnnotationType()=="borders"){ |
---|
| 103 | std::vector<int> vertexSet = obj->getVertexSet(); |
---|
[536] | 104 | for(uint i=0;i<vertexSet.size()/4;i++){ |
---|
[446] | 105 | pix[0] = vertexSet[i*4]-0.5; |
---|
| 106 | pix[1] = vertexSet[i*4+1]-0.5; |
---|
| 107 | pix[2] = obj->getZcentre(); |
---|
| 108 | this->head.pixToWCS(pix,wld); |
---|
| 109 | stream << "LINE " << wld[0] << " " << wld[1]; |
---|
| 110 | pix[0] = vertexSet[i*4+2]-0.5; |
---|
| 111 | pix[1] = vertexSet[i*4+3]-0.5; |
---|
| 112 | this->head.pixToWCS(pix,wld); |
---|
| 113 | stream << " " << wld[0] << " " << wld[1] << "\n"; |
---|
| 114 | } |
---|
[378] | 115 | } |
---|
[446] | 116 | else if(this->par.getAnnotationType()=="circles"){ |
---|
[450] | 117 | float radius = obj->getRAWidth()/120.; |
---|
| 118 | if(obj->getDecWidth()/120.>radius) |
---|
| 119 | radius = obj->getDecWidth()/120.; |
---|
[446] | 120 | stream << "CIRCLE " |
---|
[450] | 121 | << obj->getRA() << " " |
---|
| 122 | << obj->getDec() << " " |
---|
[446] | 123 | << radius << "\n"; |
---|
| 124 | } |
---|
| 125 | |
---|
[431] | 126 | stream << "TEXT " |
---|
| 127 | << obj->getRA() << " " |
---|
| 128 | << obj->getDec() << " " |
---|
| 129 | << obj->getID() << "\n\n"; |
---|
| 130 | } |
---|
[468] | 131 | |
---|
| 132 | delete [] pix; |
---|
| 133 | delete [] wld; |
---|
| 134 | |
---|
[378] | 135 | } |
---|
[20] | 136 | |
---|
[378] | 137 | void Cube::prepareOutputFile() |
---|
| 138 | { |
---|
[528] | 139 | /// @details |
---|
| 140 | /// A function to write the paramters, time of execution, and |
---|
| 141 | /// statistical information to the output file. |
---|
[3] | 142 | |
---|
[378] | 143 | std::string outfile; |
---|
| 144 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
---|
| 145 | else outfile = this->par.getOutFile(); |
---|
| 146 | std::ofstream output(outfile.c_str()); |
---|
| 147 | output<<"Results of the Duchamp source finder: "; |
---|
| 148 | time_t now = time(NULL); |
---|
| 149 | output << asctime( localtime(&now) ); |
---|
| 150 | this->showParam(output); |
---|
| 151 | output<<"--------------------\n"; |
---|
| 152 | output.close(); |
---|
| 153 | this->outputStats(); |
---|
[275] | 154 | |
---|
[378] | 155 | } |
---|
[275] | 156 | |
---|
[378] | 157 | void Cube::outputStats() |
---|
| 158 | { |
---|
[528] | 159 | /// @details |
---|
| 160 | /// A function to write the statistical information to the output |
---|
| 161 | /// file. This writes the threshold, its equivalent S/N ratio, and |
---|
| 162 | /// the noise level and spread. |
---|
| 163 | /// |
---|
| 164 | /// If smoothing has been done, the noise level & spread for the |
---|
| 165 | /// original array are calculated and printed as well. |
---|
[275] | 166 | |
---|
[378] | 167 | std::string outfile; |
---|
| 168 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
---|
| 169 | else outfile = this->par.getOutFile(); |
---|
| 170 | std::ofstream output(outfile.c_str(),std::ios::app); |
---|
| 171 | output<<"Summary of statistics:\n"; |
---|
[385] | 172 | output<<"Detection threshold = " << this->Stats.getThreshold() |
---|
[378] | 173 | <<" " << this->head.getFluxUnits(); |
---|
| 174 | if(this->par.getFlagFDR()) |
---|
| 175 | output<<" (or S/N=" << this->Stats.getThresholdSNR()<<")"; |
---|
| 176 | if(this->par.getFlagSmooth()){ |
---|
| 177 | output << " in smoothed cube."; |
---|
| 178 | if(!this->par.getFlagUserThreshold()) |
---|
[385] | 179 | output<<"\nNoise level = " << this->Stats.getMiddle() |
---|
[378] | 180 | <<", Noise spread = " << this->Stats.getSpread() |
---|
| 181 | <<" in smoothed cube."; |
---|
| 182 | |
---|
| 183 | // calculate the stats for the original array, so that we can |
---|
| 184 | // quote S/N values correctly. |
---|
| 185 | this->par.setFlagSmooth(false); |
---|
| 186 | bool verb=this->par.isVerbose(); |
---|
| 187 | bool fdrflag=this->par.getFlagFDR(); |
---|
| 188 | this->par.setVerbosity(false); |
---|
| 189 | this->par.setFlagFDR(false); |
---|
| 190 | this->setCubeStats(); |
---|
| 191 | this->par.setVerbosity(verb); |
---|
| 192 | this->par.setFlagFDR(fdrflag); |
---|
| 193 | this->par.setFlagSmooth(true); |
---|
| 194 | |
---|
[385] | 195 | output << "\nNoise properties for the original cube are:"; |
---|
[378] | 196 | } |
---|
| 197 | |
---|
[275] | 198 | if(!this->par.getFlagUserThreshold()) |
---|
[385] | 199 | output<<"\nNoise level = " << this->Stats.getMiddle() |
---|
[461] | 200 | <<", Noise spread = " << this->Stats.getSpread(); |
---|
[275] | 201 | |
---|
[378] | 202 | if(this->par.getFlagGrowth()){ |
---|
| 203 | StatsContainer<float> growthStats = this->Stats; |
---|
[461] | 204 | if(this->par.getFlagUserGrowthThreshold()) |
---|
| 205 | growthStats.setThreshold(this->par.getGrowthThreshold()); |
---|
| 206 | else |
---|
| 207 | growthStats.setThresholdSNR(this->par.getGrowthCut()); |
---|
[378] | 208 | growthStats.setUseFDR(false); |
---|
[461] | 209 | output<<"\nDetections grown down to threshold of " |
---|
| 210 | << growthStats.getThreshold() << " " |
---|
| 211 | << this->head.getFluxUnits(); |
---|
[378] | 212 | } |
---|
| 213 | |
---|
[422] | 214 | if(!this->par.getFlagUserThreshold()) |
---|
| 215 | output << "\nFull stats:\n" << this->Stats; |
---|
| 216 | else |
---|
[461] | 217 | output << "\n\nNot calculating full stats since threshold was provided directly.\n"; |
---|
[385] | 218 | |
---|
[378] | 219 | output<<"--------------------\n"; |
---|
| 220 | output.close(); |
---|
[298] | 221 | } |
---|
| 222 | |
---|
[378] | 223 | void Cube::outputDetectionList() |
---|
| 224 | { |
---|
[528] | 225 | /// @details |
---|
| 226 | /// A front-end to writing the full list of detected objects to a results |
---|
| 227 | /// file and to cout. |
---|
| 228 | /// Leaves the testing of whether the WCS parameters for each object |
---|
| 229 | /// have been calculated to the printing function. |
---|
[275] | 230 | |
---|
[378] | 231 | std::string outfile; |
---|
| 232 | if(this->par.getFlagSeparateHeader()) outfile = this->par.getHeaderFile(); |
---|
| 233 | else outfile = this->par.getOutFile(); |
---|
| 234 | std::ofstream output(outfile.c_str(),std::ios::app); |
---|
| 235 | output<<"Total number of detections = "<<this->objectList->size()<<endl; |
---|
| 236 | output<<"--------------------\n"; |
---|
| 237 | output.close(); |
---|
[275] | 238 | |
---|
[378] | 239 | if(this->par.getFlagSeparateHeader()) |
---|
| 240 | output.open(this->par.getOutFile().c_str()); |
---|
| 241 | else |
---|
| 242 | output.open(this->par.getOutFile().c_str(),std::ios::app); |
---|
[363] | 243 | |
---|
[378] | 244 | if(this->objectList->size()>0){ |
---|
| 245 | this->setupColumns(); |
---|
[439] | 246 | outputTableHeader(output,this->fullCols,"file",this->head.isWCS()); |
---|
| 247 | outputTableHeader(std::cout,this->fullCols,"screen",this->head.isWCS()); |
---|
[440] | 248 | std::vector<Detection>::iterator obj; |
---|
| 249 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
| 250 | obj->printTableRow(output,this->fullCols,"file"); |
---|
| 251 | obj->printTableRow(std::cout,this->fullCols,"screen"); |
---|
[378] | 252 | } |
---|
| 253 | } |
---|
[363] | 254 | |
---|
[378] | 255 | output.close(); |
---|
[3] | 256 | } |
---|
[275] | 257 | |
---|
[418] | 258 | void Cube::prepareLogFile(int argc, char *argv[]) |
---|
| 259 | { |
---|
[528] | 260 | /// @details |
---|
| 261 | /// Opens the log file so that it can be written to, and writes |
---|
| 262 | /// the parameter summary as well as the time of execution to the |
---|
| 263 | /// file. |
---|
| 264 | /// |
---|
| 265 | /// It also writes the command-line statement, hence the need for |
---|
| 266 | /// argv and argc. |
---|
| 267 | |
---|
[418] | 268 | // Open the logfile and write the time on the first line |
---|
| 269 | std::ofstream logfile(this->par.getLogFile().c_str()); |
---|
| 270 | logfile << "New run of the Duchamp sourcefinder: "; |
---|
| 271 | time_t now = time(NULL); |
---|
| 272 | logfile << asctime( localtime(&now) ); |
---|
| 273 | // Write out the command-line statement |
---|
| 274 | logfile << "Executing statement : "; |
---|
| 275 | for(int i=0;i<argc;i++) logfile << argv[i] << " "; |
---|
| 276 | logfile << std::endl; |
---|
| 277 | logfile << this->par; |
---|
| 278 | logfile.close(); |
---|
| 279 | |
---|
| 280 | } |
---|
| 281 | |
---|
| 282 | |
---|
[378] | 283 | void Cube::logDetectionList() |
---|
| 284 | { |
---|
[528] | 285 | /// @details |
---|
| 286 | /// A front-end to writing a list of detected objects to the log file. |
---|
| 287 | /// Does not assume WCS is present. |
---|
| 288 | /// Designed to be used by searching routines before returning their |
---|
| 289 | /// final list. |
---|
[3] | 290 | |
---|
[378] | 291 | if(this->objectList->size()>0){ |
---|
[3] | 292 | |
---|
[378] | 293 | long left = this->par.getBorderLeft(); |
---|
| 294 | long bottom = this->par.getBorderBottom(); |
---|
[258] | 295 | |
---|
[378] | 296 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
---|
[420] | 297 | this->calcObjectFluxes(); |
---|
[378] | 298 | this->setupColumns(); |
---|
[440] | 299 | outputTableHeader(fout,this->fullCols,"log",this->head.isWCS()); |
---|
[258] | 300 | |
---|
[378] | 301 | if(this->par.getFlagBaseline()){ |
---|
| 302 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
---|
| 303 | this->array[i] += this->baseline[i]; |
---|
| 304 | } |
---|
[258] | 305 | |
---|
[536] | 306 | for(uint objCtr=0;objCtr<this->objectList->size();objCtr++){ |
---|
[378] | 307 | Detection *obj = new Detection; |
---|
| 308 | *obj = objectList->at(objCtr); |
---|
| 309 | obj->setOffsets(par); |
---|
| 310 | if(this->par.getFlagCubeTrimmed()){ |
---|
| 311 | obj->pixels().addOffsets(left,bottom,0); |
---|
| 312 | } |
---|
| 313 | obj->calcFluxes(this->array, this->axisDim); |
---|
[440] | 314 | obj->setID(objCtr+1); |
---|
| 315 | obj->printTableRow(fout,this->fullCols,"log"); |
---|
[378] | 316 | delete obj; |
---|
| 317 | } |
---|
[348] | 318 | |
---|
[378] | 319 | if(this->par.getFlagBaseline()){ |
---|
| 320 | for(int i=0;i<this->axisDim[0]*this->axisDim[1]*this->axisDim[2];i++) |
---|
| 321 | this->array[i] -= this->baseline[i]; |
---|
[348] | 322 | } |
---|
[378] | 323 | fout.close(); |
---|
| 324 | |
---|
[348] | 325 | } |
---|
| 326 | |
---|
[3] | 327 | } |
---|
[258] | 328 | |
---|
[378] | 329 | void Cube::logDetection(Detection obj, int counter) |
---|
| 330 | { |
---|
[528] | 331 | /// @details |
---|
| 332 | /// A front-end to writing a detected object to the log file. |
---|
| 333 | /// Does not assume WCS is present. |
---|
| 334 | /// Corrects for changes to positions of pixels and removal of baselines. |
---|
| 335 | /// Designed to be used by searching routines before returning their final |
---|
| 336 | /// list. |
---|
| 337 | /// \param obj Detection object to be written : passed by value, as we want |
---|
| 338 | /// to potentially change positions etc, but not for the object in the |
---|
| 339 | /// calling function. |
---|
| 340 | /// \param counter The number to assign to the object : ideally its number |
---|
| 341 | /// in a list of some kind. |
---|
[3] | 342 | |
---|
[378] | 343 | std::ofstream fout(this->par.getLogFile().c_str(),std::ios::app); |
---|
| 344 | // Need to deal with possibility of trimmed array |
---|
| 345 | long left = this->par.getBorderLeft(); |
---|
| 346 | long right = this->par.getBorderRight(); |
---|
| 347 | long top = this->par.getBorderTop(); |
---|
| 348 | long bottom = this->par.getBorderBottom(); |
---|
| 349 | long *tempDim = new long[3]; |
---|
| 350 | tempDim[0] = (this->axisDim[0] + left + right); |
---|
| 351 | tempDim[1] = (this->axisDim[1] + bottom + top); |
---|
| 352 | tempDim[2] = this->axisDim[2]; |
---|
| 353 | long tempsize = tempDim[0] * tempDim[1] * tempDim[2]; |
---|
| 354 | float *temparray = new float[tempsize]; |
---|
| 355 | // for(int i=0;i<this->numPixels;i++){ // loop over this->array |
---|
| 356 | for(int z=0;z<tempDim[2];z++){ |
---|
| 357 | for(int y=0;y<tempDim[1];y++){ |
---|
| 358 | for(int x=0;x<tempDim[0];x++){ |
---|
[3] | 359 | |
---|
[378] | 360 | bool isDud = (x<left) || (x>=this->axisDim[0]+left) || |
---|
| 361 | (y<bottom) || (y>=this->axisDim[1]+bottom); |
---|
[258] | 362 | |
---|
[378] | 363 | int temppos = x + tempDim[0]*y + tempDim[1]*tempDim[0]*z; |
---|
[258] | 364 | |
---|
[378] | 365 | int pos = (x-left) + (y-bottom)*this->axisDim[0] + |
---|
| 366 | z*this->axisDim[0]*this->axisDim[1]; |
---|
[258] | 367 | |
---|
[378] | 368 | if(isDud) temparray[temppos] = this->par.getBlankPixVal(); |
---|
| 369 | else temparray[temppos] = this->array[pos]; |
---|
[258] | 370 | |
---|
[378] | 371 | if(this->par.getFlagBaseline() && !isDud) |
---|
| 372 | temparray[temppos] += this->baseline[pos]; |
---|
[258] | 373 | |
---|
[378] | 374 | } |
---|
[258] | 375 | } |
---|
[3] | 376 | } |
---|
[378] | 377 | |
---|
| 378 | if(this->par.getFlagCubeTrimmed()){ |
---|
| 379 | obj.pixels().addOffsets(left,bottom,0); |
---|
| 380 | } |
---|
| 381 | obj.calcFluxes(temparray, this->axisDim); |
---|
[441] | 382 | obj.printTableRow(fout,this->fullCols,"log"); |
---|
[378] | 383 | delete [] temparray; |
---|
| 384 | delete [] tempDim; |
---|
| 385 | fout.close(); |
---|
[3] | 386 | } |
---|
[258] | 387 | |
---|
[3] | 388 | } |
---|