[299] | 1 | // ----------------------------------------------------------------------- |
---|
| 2 | // param.hh: Definition of the parameter set. |
---|
| 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 | #ifndef PARAM_H |
---|
| 29 | #define PARAM_H |
---|
| 30 | |
---|
| 31 | #include <iostream> |
---|
| 32 | #include <string> |
---|
| 33 | #include <vector> |
---|
[170] | 34 | #include <math.h> |
---|
[394] | 35 | #include <wcslib/wcs.h> |
---|
| 36 | #include <wcslib/wcshdr.h> |
---|
[393] | 37 | #include <duchamp/Utils/Section.hh> |
---|
| 38 | #include <duchamp/ATrous/filter.hh> |
---|
[3] | 39 | |
---|
[378] | 40 | namespace duchamp |
---|
| 41 | { |
---|
[221] | 42 | |
---|
[112] | 43 | |
---|
[378] | 44 | class FitsHeader; // foreshadow this so that Param knows it exists |
---|
[272] | 45 | |
---|
[528] | 46 | /// @brief Class to store general parameters. |
---|
| 47 | /// |
---|
| 48 | /// @details This is a general repository for parameters that are used by all |
---|
| 49 | /// functions. This is how the user interacts with the program, as |
---|
| 50 | /// parameters are read in from disk files through functions in this |
---|
| 51 | /// class. |
---|
[272] | 52 | |
---|
[378] | 53 | class Param |
---|
| 54 | { |
---|
| 55 | public: |
---|
[528] | 56 | /// @brief Default constructor. |
---|
[378] | 57 | Param(); |
---|
[272] | 58 | |
---|
[528] | 59 | /// @brief Copy constructor for Param. |
---|
[378] | 60 | Param(const Param& p); |
---|
[309] | 61 | |
---|
[528] | 62 | /// @brief Assignment operator for Param. |
---|
[378] | 63 | Param& operator= (const Param& p); |
---|
[309] | 64 | |
---|
[528] | 65 | /// @brief Destructor function. |
---|
[378] | 66 | virtual ~Param(); |
---|
[266] | 67 | |
---|
[528] | 68 | /// @brief Define the default values of each parameter. |
---|
[378] | 69 | void defaultValues(); |
---|
[221] | 70 | |
---|
[378] | 71 | //----------------- |
---|
| 72 | // Functions in param.cc |
---|
| 73 | // |
---|
[528] | 74 | /// @brief Parse the command line parameters correctly. |
---|
[474] | 75 | int getopts(int argc, char ** argv, std::string progname="Duchamp"); |
---|
[221] | 76 | |
---|
[528] | 77 | /// @brief Read in parameters from a disk file. |
---|
[378] | 78 | int readParams(std::string paramfile); |
---|
[221] | 79 | |
---|
[528] | 80 | /// @brief Check the parameter list for inconsistencies |
---|
[503] | 81 | void checkPars(); |
---|
| 82 | |
---|
[528] | 83 | /// @brief Copy certain necessary FITS header parameters from a FitsHeader object |
---|
[378] | 84 | void copyHeaderInfo(FitsHeader &head); |
---|
[221] | 85 | |
---|
[528] | 86 | /// @brief Determine filename in which to save the mask array. |
---|
[379] | 87 | std::string outputMaskFile(); |
---|
| 88 | |
---|
[528] | 89 | /// @brief Determine filename in which to save the smoothed array. |
---|
[378] | 90 | std::string outputSmoothFile(); |
---|
[221] | 91 | |
---|
[528] | 92 | /// @brief Determine filename in which to save the reconstructed array. |
---|
[378] | 93 | std::string outputReconFile(); |
---|
[272] | 94 | |
---|
[528] | 95 | /// @brief Determine filename in which to save the residual array from the atrous reconstruction. |
---|
[378] | 96 | std::string outputResidFile(); |
---|
[221] | 97 | |
---|
[528] | 98 | /// @brief Print the parameter set in a readable fashion. |
---|
[378] | 99 | friend std::ostream& operator<< ( std::ostream& theStream, Param& par); |
---|
| 100 | friend class Image; |
---|
[258] | 101 | |
---|
[378] | 102 | //------------------ |
---|
| 103 | // Functions in FitsIO/subsection.cc |
---|
| 104 | // |
---|
[528] | 105 | /// @brief Make sure the subsection strings are OK. |
---|
[378] | 106 | int verifySubsection(); |
---|
[309] | 107 | |
---|
[528] | 108 | /// @brief Set the correct offset values for each axis |
---|
[378] | 109 | void setOffsets(struct wcsprm *wcs); |
---|
[221] | 110 | |
---|
[528] | 111 | /// @brief Set the correct offset values for each axis |
---|
[378] | 112 | void setOffsets(struct wcsprm &wcs); |
---|
[221] | 113 | |
---|
[378] | 114 | //------------------ |
---|
| 115 | // These are in param.cc |
---|
[528] | 116 | /// @brief Is a pixel value a BLANK? |
---|
[378] | 117 | bool isBlank(float &value); |
---|
[258] | 118 | |
---|
[528] | 119 | /// @brief Is a given channel flagged as being in the Milky Way? |
---|
[378] | 120 | bool isInMW(int z); |
---|
[275] | 121 | |
---|
[528] | 122 | /// @brief Is a given pixel position OK for use with stats calculations? |
---|
[378] | 123 | bool isStatOK(int x, int y, int z); |
---|
[275] | 124 | |
---|
[528] | 125 | /// @brief Make a mask array -- an array saying whether each pixel is BLANK or not |
---|
[378] | 126 | bool *makeBlankMask(float *array, int size); |
---|
[221] | 127 | |
---|
[528] | 128 | /// @brief Make a mask array -- an array saying whether each pixel is able to be used for statistics calculations |
---|
[506] | 129 | bool *makeStatMask(float *array, long *dim); |
---|
[378] | 130 | |
---|
| 131 | //-------------------- |
---|
| 132 | // Basic inline accessor functions |
---|
| 133 | // |
---|
| 134 | std::string getImageFile(){return imageFile;}; |
---|
| 135 | void setImageFile(std::string fname){imageFile = fname;}; |
---|
| 136 | std::string getFullImageFile(){ |
---|
| 137 | if(flagSubsection) return imageFile+pixelSec.getSection(); |
---|
| 138 | else return imageFile; |
---|
| 139 | }; |
---|
| 140 | bool getFlagSubsection(){return flagSubsection;}; |
---|
| 141 | void setFlagSubsection(bool flag){flagSubsection=flag;}; |
---|
| 142 | std::string getSubsection(){return pixelSec.getSection();}; |
---|
| 143 | void setSubsection(std::string range){pixelSec.setSection(range);}; |
---|
| 144 | Section §ion(){Section &rsection = pixelSec; return rsection;}; |
---|
| 145 | bool getFlagReconExists(){return flagReconExists;}; |
---|
| 146 | void setFlagReconExists(bool flag){flagReconExists=flag;}; |
---|
| 147 | std::string getReconFile(){return reconFile;}; |
---|
| 148 | void setReconFile(std::string file){reconFile = file;}; |
---|
| 149 | bool getFlagSmoothExists(){return flagSmoothExists;}; |
---|
| 150 | void setFlagSmoothExists(bool flag){flagSmoothExists=flag;}; |
---|
| 151 | std::string getSmoothFile(){return smoothFile;}; |
---|
| 152 | void setSmoothFile(std::string file){smoothFile = file;}; |
---|
| 153 | // |
---|
[475] | 154 | bool getFlagUsePrevious(){return usePrevious;}; |
---|
| 155 | void setFlagUsePrevious(bool flag){usePrevious=flag;}; |
---|
| 156 | std::string getObjectList(){return objectList;}; |
---|
| 157 | void setObjectList(std::string s){objectList = s;}; |
---|
| 158 | std::vector<int> getObjectRequest(); |
---|
| 159 | std::vector<bool> getObjectChoices(); |
---|
| 160 | std::vector<bool> getObjectChoices(int numObjects); |
---|
| 161 | // |
---|
[378] | 162 | bool getFlagLog(){return flagLog;}; |
---|
| 163 | void setFlagLog(bool flag){flagLog=flag;}; |
---|
| 164 | std::string getLogFile(){return logFile;}; |
---|
| 165 | void setLogFile(std::string fname){logFile = fname;}; |
---|
| 166 | std::string getOutFile(){return outFile;}; |
---|
| 167 | void setOutFile(std::string fname){outFile = fname;}; |
---|
| 168 | bool getFlagSeparateHeader(){return flagSeparateHeader;}; |
---|
| 169 | void setFlagSeparateHeader(bool b){flagSeparateHeader=b;}; |
---|
| 170 | std::string getHeaderFile(){return headerFile;}; |
---|
| 171 | void setHeaderFile(std::string s){headerFile=s;}; |
---|
| 172 | std::string getSpectraFile(){return spectraFile;}; |
---|
| 173 | void setSpectraFile(std::string fname){spectraFile = fname;}; |
---|
[424] | 174 | bool getFlagTextSpectra(){return flagTextSpectra;}; |
---|
| 175 | void setFlagTextSpectra(bool b){flagTextSpectra = b;}; |
---|
| 176 | std::string getSpectraTextFile(){return spectraTextFile;}; |
---|
| 177 | void setSpectraTextFile(std::string fname){spectraTextFile = fname;}; |
---|
[379] | 178 | bool getFlagOutputMask(){return flagOutputMask;}; |
---|
| 179 | void setFlagOutputMask(bool flag){flagOutputMask=flag;}; |
---|
[525] | 180 | std::string getFileOutputMask(){return fileOutputMask;}; |
---|
| 181 | void setFileOutputMask(std::string s){fileOutputMask=s;}; |
---|
[521] | 182 | bool getFlagMaskWithObjectNum(){return flagMaskWithObjectNum;}; |
---|
| 183 | void setFlagMaskWithObjectNum(bool flag){flagMaskWithObjectNum=flag;}; |
---|
[378] | 184 | bool getFlagOutputSmooth(){return flagOutputSmooth;}; |
---|
| 185 | void setFlagOutputSmooth(bool flag){flagOutputSmooth=flag;}; |
---|
[525] | 186 | std::string getFileOutputSmooth(){return fileOutputSmooth;}; |
---|
| 187 | void setFileOutputSmooth(std::string s){fileOutputSmooth=s;}; |
---|
[378] | 188 | bool getFlagOutputRecon(){return flagOutputRecon;}; |
---|
| 189 | void setFlagOutputRecon(bool flag){flagOutputRecon=flag;}; |
---|
[525] | 190 | std::string getFileOutputRecon(){return fileOutputRecon;}; |
---|
| 191 | void setFileOutputRecon(std::string s){fileOutputRecon=s;}; |
---|
[378] | 192 | bool getFlagOutputResid(){return flagOutputResid;}; |
---|
| 193 | void setFlagOutputResid(bool flag){flagOutputResid=flag;}; |
---|
[525] | 194 | std::string getFileOutputResid(){return fileOutputResid;}; |
---|
| 195 | void setFileOutputResid(std::string s){fileOutputResid=s;}; |
---|
[378] | 196 | bool getFlagVOT(){return flagVOT;}; |
---|
| 197 | void setFlagVOT(bool flag){flagVOT=flag;}; |
---|
| 198 | std::string getVOTFile(){return votFile;}; |
---|
| 199 | void setVOTFile(std::string fname){votFile = fname;}; |
---|
| 200 | bool getFlagKarma(){return flagKarma;}; |
---|
| 201 | void setFlagKarma(bool flag){flagKarma=flag;}; |
---|
[446] | 202 | std::string getAnnotationType(){return annotationType;}; |
---|
| 203 | void setAnnotationType(std::string s){annotationType=s;}; |
---|
[378] | 204 | std::string getKarmaFile(){return karmaFile;}; |
---|
| 205 | void setKarmaFile(std::string fname){karmaFile = fname;}; |
---|
| 206 | bool getFlagMaps(){return flagMaps;}; |
---|
| 207 | void setFlagMaps(bool flag){flagMaps=flag;}; |
---|
| 208 | std::string getDetectionMap(){return detectionMap;}; |
---|
| 209 | void setDetectionMap(std::string fname){detectionMap = fname;}; |
---|
| 210 | std::string getMomentMap(){return momentMap;}; |
---|
| 211 | void setMomentMap(std::string fname){momentMap = fname;}; |
---|
| 212 | bool getFlagXOutput(){return flagXOutput;}; |
---|
| 213 | void setFlagXOutput(bool b){flagXOutput=b;}; |
---|
[438] | 214 | int getPrecFlux(){return precFlux;}; |
---|
| 215 | void setPrecFlux(int i){precFlux=i;}; |
---|
| 216 | int getPrecVel(){return precVel;}; |
---|
| 217 | void setPrecVel(int i){precVel=i;}; |
---|
| 218 | int getPrecSNR(){return precSNR;}; |
---|
| 219 | void setPrecSNR(int i){precSNR=i;}; |
---|
[378] | 220 | // |
---|
| 221 | bool getFlagNegative(){return flagNegative;}; |
---|
| 222 | void setFlagNegative(bool flag){flagNegative=flag;}; |
---|
| 223 | bool getFlagBlankPix(){return flagBlankPix;}; |
---|
| 224 | void setFlagBlankPix(bool flag){flagBlankPix=flag;}; |
---|
| 225 | float getBlankPixVal(){return blankPixValue;}; |
---|
| 226 | void setBlankPixVal(float v){blankPixValue=v;}; |
---|
| 227 | int getBlankKeyword(){return blankKeyword;}; |
---|
| 228 | void setBlankKeyword(int v){blankKeyword=v;}; |
---|
| 229 | float getBscaleKeyword(){return bscaleKeyword;}; |
---|
| 230 | void setBscaleKeyword(float v){bscaleKeyword=v;}; |
---|
| 231 | float getBzeroKeyword(){return bzeroKeyword;}; |
---|
| 232 | void setBzeroKeyword(float v){bzeroKeyword=v;}; |
---|
| 233 | bool getFlagMW(){return flagMW;}; |
---|
| 234 | void setFlagMW(bool flag){flagMW=flag;}; |
---|
| 235 | int getMaxMW(){return maxMW;}; |
---|
| 236 | void setMaxMW(int m){maxMW=m;}; |
---|
| 237 | int getMinMW(){return minMW;}; |
---|
| 238 | void setMinMW(int m){minMW=m;}; |
---|
| 239 | void setBeamSize(float s){numPixBeam = s;}; |
---|
| 240 | float getBeamSize(){return numPixBeam;}; |
---|
| 241 | bool getFlagUsingBeam(){return flagUsingBeam;}; |
---|
| 242 | void setFlagUsingBeam(bool b){flagUsingBeam=b;}; |
---|
[434] | 243 | std::string getNewFluxUnits(){return newFluxUnits;}; |
---|
| 244 | void setNewFluxUnits(std::string s){newFluxUnits=s;}; |
---|
[378] | 245 | // |
---|
| 246 | bool getFlagTrim(){return flagTrim;}; |
---|
| 247 | void setFlagTrim(bool b){flagTrim=b;}; |
---|
| 248 | bool getFlagCubeTrimmed(){return hasBeenTrimmed;}; |
---|
| 249 | void setFlagCubeTrimmed(bool flag){hasBeenTrimmed = flag;}; |
---|
| 250 | long getBorderLeft(){return borderLeft;}; |
---|
| 251 | void setBorderLeft(long b){borderLeft = b;}; |
---|
| 252 | long getBorderRight(){return borderRight;}; |
---|
| 253 | void setBorderRight(long b){borderRight = b;}; |
---|
| 254 | long getBorderBottom(){return borderBottom;}; |
---|
| 255 | void setBorderBottom(long b){borderBottom = b;}; |
---|
| 256 | long getBorderTop(){return borderTop;}; |
---|
| 257 | void setBorderTop(long b){borderTop = b;}; |
---|
| 258 | // |
---|
| 259 | long getXOffset(){return xSubOffset;}; |
---|
| 260 | void setXOffset(long o){xSubOffset = o;}; |
---|
| 261 | long getYOffset(){return ySubOffset;}; |
---|
| 262 | void setYOffset(long o){ySubOffset = o;}; |
---|
| 263 | long getZOffset(){return zSubOffset;}; |
---|
| 264 | void setZOffset(long o){zSubOffset = o;}; |
---|
| 265 | // |
---|
[537] | 266 | unsigned int getMinPix(){return minPix;}; |
---|
[378] | 267 | void setMinPix(int m){minPix=m;}; |
---|
| 268 | // |
---|
| 269 | bool getFlagGrowth(){return flagGrowth;}; |
---|
| 270 | void setFlagGrowth(bool flag){flagGrowth=flag;}; |
---|
| 271 | float getGrowthCut(){return growthCut;}; |
---|
| 272 | void setGrowthCut(float c){growthCut=c;}; |
---|
[461] | 273 | float getGrowthThreshold(){return growthThreshold;}; |
---|
| 274 | void setGrowthThreshold(float f){growthThreshold=f;}; |
---|
| 275 | bool getFlagUserGrowthThreshold(){return flagUserGrowthThreshold;}; |
---|
| 276 | void setFlagUserGrowthThreshold(bool b){flagUserGrowthThreshold=b;}; |
---|
[378] | 277 | // |
---|
| 278 | bool getFlagFDR(){return flagFDR;}; |
---|
| 279 | void setFlagFDR(bool flag){flagFDR=flag;}; |
---|
| 280 | float getAlpha(){return alphaFDR;}; |
---|
| 281 | void setAlpha(float a){alphaFDR=a;}; |
---|
| 282 | // |
---|
| 283 | bool getFlagBaseline(){return flagBaseline;}; |
---|
| 284 | void setFlagBaseline(bool flag){flagBaseline = flag;}; |
---|
| 285 | // |
---|
| 286 | bool getFlagStatSec(){return flagStatSec;}; |
---|
| 287 | void setFlagStatSec(bool flag){flagStatSec=flag;}; |
---|
| 288 | std::string getStatSec(){return statSec.getSection();}; |
---|
| 289 | void setStatSec(std::string range){statSec.setSection(range);}; |
---|
[385] | 290 | bool getFlagRobustStats(){return flagRobustStats;}; |
---|
| 291 | void setFlagRobustStats(bool flag){flagRobustStats=flag;}; |
---|
[378] | 292 | float getCut(){return snrCut;}; |
---|
| 293 | void setCut(float c){snrCut=c;}; |
---|
| 294 | float getThreshold(){return threshold;}; |
---|
| 295 | void setThreshold(float f){threshold=f;}; |
---|
| 296 | bool getFlagUserThreshold(){return flagUserThreshold;}; |
---|
| 297 | void setFlagUserThreshold(bool b){flagUserThreshold=b;}; |
---|
| 298 | // |
---|
| 299 | bool getFlagSmooth(){return flagSmooth;}; |
---|
| 300 | void setFlagSmooth(bool b){flagSmooth=b;}; |
---|
| 301 | std::string getSmoothType(){return smoothType;}; |
---|
| 302 | void setSmoothType(std::string s){smoothType=s;}; |
---|
| 303 | int getHanningWidth(){return hanningWidth;}; |
---|
| 304 | void setHanningWidth(int f){hanningWidth=f;}; |
---|
| 305 | void setKernMaj(float f){kernMaj=f;}; |
---|
| 306 | float getKernMaj(){return kernMaj;}; |
---|
| 307 | void setKernMin(float f){kernMin=f;}; |
---|
| 308 | float getKernMin(){return kernMin;}; |
---|
| 309 | void setKernPA(float f){kernPA=f;}; |
---|
| 310 | float getKernPA(){return kernPA;}; |
---|
| 311 | // |
---|
| 312 | bool getFlagATrous(){return flagATrous;}; |
---|
| 313 | void setFlagATrous(bool flag){flagATrous=flag;}; |
---|
| 314 | int getReconDim(){return reconDim;}; |
---|
| 315 | void setReconDim(int i){reconDim=i;}; |
---|
| 316 | int getMinScale(){return scaleMin;}; |
---|
| 317 | void setMinScale(int s){scaleMin=s;}; |
---|
| 318 | int getMaxScale(){return scaleMax;}; |
---|
| 319 | void setMaxScale(int s){scaleMax=s;}; |
---|
| 320 | float getAtrousCut(){return snrRecon;}; |
---|
| 321 | void setAtrousCut(float c){snrRecon=c;}; |
---|
| 322 | int getFilterCode(){return filterCode;}; |
---|
| 323 | void setFilterCode(int c){filterCode=c;}; |
---|
| 324 | std::string getFilterName(){return reconFilter.getName();}; |
---|
| 325 | Filter& filter(){ Filter &rfilter = reconFilter; return rfilter; }; |
---|
| 326 | // |
---|
| 327 | bool getFlagAdjacent(){return flagAdjacent;}; |
---|
| 328 | void setFlagAdjacent(bool flag){flagAdjacent=flag;}; |
---|
| 329 | float getThreshS(){return threshSpatial;}; |
---|
| 330 | void setThreshS(float t){threshSpatial=t;}; |
---|
| 331 | float getThreshV(){return threshVelocity;}; |
---|
| 332 | void setThreshV(float t){threshVelocity=t;}; |
---|
| 333 | int getMinChannels(){return minChannels;}; |
---|
| 334 | void setMinChannels(int n){minChannels=n;}; |
---|
| 335 | // |
---|
| 336 | std::string getSpectralMethod(){return spectralMethod;}; |
---|
| 337 | void setSpectralMethod(std::string s){spectralMethod=s;}; |
---|
| 338 | std::string getSpectralUnits(){return spectralUnits;}; |
---|
| 339 | void setSpectralUnits(std::string s){spectralUnits=s;}; |
---|
| 340 | std::string getPixelCentre(){return pixelCentre;}; |
---|
| 341 | void setPixelCentre(std::string s){pixelCentre=s;}; |
---|
| 342 | bool drawBorders(){return borders;}; |
---|
| 343 | void setDrawBorders(bool f){borders=f;}; |
---|
| 344 | bool drawBlankEdge(){return blankEdge;}; |
---|
| 345 | void setDrawBlankEdge(bool f){blankEdge=f;}; |
---|
| 346 | |
---|
[528] | 347 | /// @brief Are we in verbose mode? |
---|
[378] | 348 | bool isVerbose(){return verbose;}; |
---|
| 349 | void setVerbosity(bool f){verbose=f;}; |
---|
[3] | 350 | |
---|
[378] | 351 | private: |
---|
| 352 | // Input files |
---|
[528] | 353 | std::string imageFile; ///< The image to be analysed. |
---|
| 354 | bool flagSubsection; ///< Whether we just want a subsection of the image |
---|
| 355 | Section pixelSec; ///< The Section object storing the pixel subsection information. |
---|
| 356 | bool flagReconExists; ///< The reconstructed array is in a FITS file on disk. |
---|
| 357 | std::string reconFile; ///< The FITS file containing the reconstructed array. |
---|
| 358 | bool flagSmoothExists;///< The smoothed array is in a FITS file. |
---|
| 359 | std::string smoothFile; ///< The FITS file containing the smoothed array. |
---|
[71] | 360 | |
---|
[528] | 361 | bool usePrevious; ///< Whether to read the detections from a previously-created log file |
---|
| 362 | std::string objectList; ///< List of objects to re-plot |
---|
[475] | 363 | |
---|
[378] | 364 | // Output files |
---|
[528] | 365 | bool flagLog; ///< Should we do the intermediate logging? |
---|
| 366 | std::string logFile; ///< Where the intermediate logging goes. |
---|
| 367 | std::string outFile; ///< Where the final results get put. |
---|
| 368 | bool flagSeparateHeader;///< Should the header information(parameters & statistics) be written to a separate file to the table ofresults? |
---|
| 369 | std::string headerFile; ///< Where the header information to go with the results table should be written. |
---|
| 370 | std::string spectraFile; ///< Where the spectra are displayed |
---|
| 371 | bool flagTextSpectra; ///< Should a text file with all spectra be written? |
---|
| 372 | std::string spectraTextFile; ///< Where the text spectra are written. |
---|
| 373 | bool flagOutputMask; ///< Should the mask image be written? |
---|
| 374 | std::string fileOutputMask; ///< The name of the mask image. |
---|
| 375 | bool flagMaskWithObjectNum;///< Should the mask values be labeled with the object ID (or just 1)? |
---|
| 376 | bool flagOutputSmooth;///< Should the smoothed cube be written? |
---|
| 377 | std::string fileOutputSmooth;///< The name of the smoothed cube file |
---|
| 378 | bool flagOutputRecon; ///< Should the reconstructed cube be written to a FITS file? |
---|
[525] | 379 | std::string fileOutputRecon; ///< The name of the reconstructed cube file |
---|
[528] | 380 | bool flagOutputResid; ///< Should the residuals from the reconstruction be written to a FITS file? |
---|
[525] | 381 | std::string fileOutputResid; ///< The name of the residual cube file |
---|
[528] | 382 | bool flagVOT; ///< Should we save results in VOTable format? |
---|
| 383 | std::string votFile; ///< Where the VOTable goes. |
---|
| 384 | bool flagKarma; ///< Should we save results in Karma annotation format? |
---|
| 385 | std::string karmaFile; ///< Where the Karma annotation file goes. |
---|
| 386 | std::string annotationType; ///< Should the annoations be circles or borders? |
---|
| 387 | bool flagMaps; ///< Should we produce detection and moment maps in postscript form? |
---|
| 388 | std::string detectionMap; ///< The name of the detection map (postscript file). |
---|
| 389 | std::string momentMap; ///< The name of the 0th moment map (ps file). |
---|
| 390 | bool flagXOutput; ///< Should there be an xwindows output of the detection map? |
---|
| 391 | int precFlux; ///< The desired precision for flux values. |
---|
| 392 | int precVel; ///< The desired precision for velocity/frequency values. |
---|
| 393 | int precSNR; ///< The desired precision for the SNR values. |
---|
[3] | 394 | |
---|
[378] | 395 | // Cube related parameters |
---|
[528] | 396 | bool flagNegative; ///< Are we going to search for negative features? |
---|
| 397 | bool flagBlankPix; ///< A flag that indicates whether there are pixels defined as BLANK and whether we need to remove & ignore them in processing. |
---|
| 398 | float blankPixValue; ///< Pixel value that is considered BLANK. |
---|
| 399 | int blankKeyword; ///< The FITS header keyword BLANK. |
---|
| 400 | float bscaleKeyword; ///< The FITS header keyword BSCALE. |
---|
| 401 | float bzeroKeyword; ///< The FITS header keyword BZERO. |
---|
| 402 | std::string newFluxUnits; ///< The user-requested flux units, to replace BUNIT. |
---|
[475] | 403 | |
---|
[385] | 404 | // Milky-Way parameters |
---|
[528] | 405 | bool flagMW; ///< A flag that indicates whether to ignore the Milky Way channels. |
---|
| 406 | int maxMW; ///< Last Milky Way channel |
---|
| 407 | int minMW; ///< First Milky Way channel |
---|
[475] | 408 | |
---|
[378] | 409 | // Trim-related |
---|
[528] | 410 | bool flagTrim; ///< Does the user want the cube trimmed? |
---|
| 411 | bool hasBeenTrimmed; ///< Has the cube been trimmed of excess BLANKs around the edge? |
---|
| 412 | long borderLeft; ///< The number of BLANK pixels trimmed from the left of the cube; |
---|
| 413 | long borderRight; ///< The number trimmed from the Right of the cube; |
---|
| 414 | long borderBottom; ///< The number trimmed from the Bottom of the cube; |
---|
| 415 | long borderTop; ///< The number trimmed from the Top of the cube; |
---|
[475] | 416 | |
---|
[378] | 417 | // Subsection offsets |
---|
[528] | 418 | long *offsets; ///< The array of offsets for each FITS axis. |
---|
| 419 | long sizeOffsets; ///< The size of the offsets array. |
---|
| 420 | long xSubOffset; ///< The subsection's x-axis offset |
---|
| 421 | long ySubOffset; ///< The subsection's y-axis offset |
---|
| 422 | long zSubOffset; ///< The subsection's z-axis offset |
---|
[475] | 423 | |
---|
[378] | 424 | // Baseline related |
---|
[528] | 425 | bool flagBaseline; ///< Whether to do baseline subtraction before reconstruction and/or searching. |
---|
[475] | 426 | |
---|
[378] | 427 | // Detection-related |
---|
[528] | 428 | int minPix; ///< Minimum number of pixels for a detected object to be counted |
---|
| 429 | float numPixBeam; ///< Size (area) of the beam in pixels. |
---|
| 430 | bool flagUsingBeam; ///< If true, we are using the numPixBeam parameter, otherwise we use the value in the FITS header. |
---|
[475] | 431 | |
---|
[378] | 432 | // Object growth |
---|
[528] | 433 | bool flagGrowth; ///< Are we growing objects once they are found? |
---|
| 434 | float growthCut; ///< The SNR that we are growing objects down to. |
---|
| 435 | bool flagUserGrowthThreshold; ///< Whether the user has manually defined a growth threshold |
---|
| 436 | float growthThreshold; ///< The threshold for growing objects down to |
---|
[475] | 437 | |
---|
[378] | 438 | // FDR analysis |
---|
[528] | 439 | bool flagFDR; ///< Should the FDR method be used? |
---|
| 440 | float alphaFDR; ///< Alpha value for FDR detection algorithm |
---|
[475] | 441 | |
---|
[378] | 442 | // Basic detection |
---|
[528] | 443 | bool flagStatSec; ///< Whether we just want to use a subsection of the image to calculate the statistics. |
---|
| 444 | Section statSec; ///< The Section object storing the statistics subsection information. |
---|
| 445 | bool flagRobustStats; ///< Whether to use robust statistics. |
---|
| 446 | float snrCut; ///< How many sigma above mean is a detection when sigma-clipping |
---|
| 447 | float threshold; ///< What the threshold is (when sigma-clipping). |
---|
| 448 | bool flagUserThreshold;///< Whether the user has defined a threshold of their own. |
---|
[475] | 449 | |
---|
[378] | 450 | // Smoothing of the cube |
---|
[528] | 451 | bool flagSmooth; ///< Should the cube be smoothed before searching? |
---|
| 452 | std::string smoothType; ///< The type of smoothing to be done. |
---|
| 453 | int hanningWidth; ///< Width for hanning smoothing. |
---|
| 454 | float kernMaj; ///< Semi-Major axis of gaussian smoothing kernel |
---|
| 455 | float kernMin; ///< Semi-Minor axis of gaussian smoothing kernel |
---|
| 456 | float kernPA; ///< Position angle of gaussian smoothing kernel, in degrees east of north (i.e. anticlockwise). |
---|
[475] | 457 | |
---|
[378] | 458 | // A trous reconstruction parameters |
---|
| 459 | bool flagATrous; ///< Are we using the a trous reconstruction? |
---|
[475] | 460 | int reconDim; ///< How many dimensions to use for the reconstruction? |
---|
[378] | 461 | int scaleMin; ///< Min scale used in a trous reconstruction |
---|
| 462 | int scaleMax; ///< Max scale used in a trous reconstruction |
---|
[475] | 463 | float snrRecon; ///< SNR cutoff used in a trous reconstruction (only wavelet coefficients that survive this threshold are kept) |
---|
[378] | 464 | Filter reconFilter; ///< The filter used for reconstructions. |
---|
[475] | 465 | int filterCode; ///< The code number for the filter to be used (saves having to parse names) |
---|
| 466 | std::string filterName; ///< The code number converted into a name, for outputting purposes. |
---|
[3] | 467 | |
---|
[378] | 468 | // Volume-merging parameters |
---|
[475] | 469 | bool flagAdjacent; ///< Whether to use the adjacent criterion for judging if objects are to be merged. |
---|
| 470 | float threshSpatial; ///< Maximum spatial separation between objects |
---|
| 471 | float threshVelocity; ///< Maximum channels separation between objects |
---|
[378] | 472 | int minChannels; ///< Minimum no. of channels to make an object |
---|
[385] | 473 | |
---|
[378] | 474 | // Input-Output related |
---|
[475] | 475 | std::string spectralMethod; ///< A string indicating choice of spectral plotting method: choices are "peak" (default) or "sum" |
---|
| 476 | std::string spectralUnits; ///< A string indicating what units the spectral axis should be quoted in. |
---|
| 477 | std::string pixelCentre;///< A string indicating which type of centre to give the results in: "average", "centroid", or "peak"(flux). |
---|
| 478 | bool borders; ///< Whether to draw a border around the individual pixels of a detection in the spectral display |
---|
| 479 | bool blankEdge; ///< Whether to draw a border around the BLANK pixel region in the moment maps and cutout images |
---|
| 480 | bool verbose; ///< Whether to use maximum verbosity -- use progress indicators in the reconstruction & merging steps. |
---|
[3] | 481 | |
---|
[378] | 482 | }; |
---|
[3] | 483 | |
---|
[378] | 484 | //=========================================================================== |
---|
[221] | 485 | |
---|
[3] | 486 | |
---|
[528] | 487 | /// @brief Convert a string to lowercase. |
---|
[378] | 488 | std::string makelower( std::string s ); |
---|
[103] | 489 | |
---|
[378] | 490 | } |
---|
[3] | 491 | #endif |
---|