[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // param.hh: Definition of the parameter set. |
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| 3 | // ----------------------------------------------------------------------- |
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| 4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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| 5 | // |
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| 6 | // This program is free software; you can redistribute it and/or modify it |
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| 7 | // under the terms of the GNU General Public License as published by the |
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| 8 | // Free Software Foundation; either version 2 of the License, or (at your |
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| 9 | // option) any later version. |
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| 10 | // |
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| 11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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| 12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 14 | // for more details. |
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| 15 | // |
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| 16 | // You should have received a copy of the GNU General Public License |
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| 17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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| 18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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| 19 | // |
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| 20 | // Correspondence concerning Duchamp may be directed to: |
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| 21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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| 22 | // Postal address: Dr. Matthew Whiting |
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| 23 | // Australia Telescope National Facility, CSIRO |
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| 24 | // PO Box 76 |
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| 25 | // Epping NSW 1710 |
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| 26 | // AUSTRALIA |
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| 27 | // ----------------------------------------------------------------------- |
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[3] | 28 | #ifndef PARAM_H |
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| 29 | #define PARAM_H |
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| 30 | |
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| 31 | #include <iostream> |
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| 32 | #include <string> |
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| 33 | #include <vector> |
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[170] | 34 | #include <math.h> |
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[394] | 35 | #include <wcslib/wcs.h> |
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| 36 | #include <wcslib/wcshdr.h> |
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[393] | 37 | #include <duchamp/Utils/Section.hh> |
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| 38 | #include <duchamp/ATrous/filter.hh> |
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[3] | 39 | |
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[378] | 40 | namespace duchamp |
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| 41 | { |
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[221] | 42 | |
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[664] | 43 | /// @brief Write out info on a parameter to e.g. the results file. |
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| 44 | void recordParameters(std::ostream& theStream, std::string paramName, std::string paramDesc, std::string paramValue); |
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[112] | 45 | |
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[664] | 46 | /// @brief A macro to handle streamed output to recordParameters |
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| 47 | #define recordParam(outstream,string1,string2,instream) \ |
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| 48 | do{ \ |
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| 49 | std::ostringstream oss; \ |
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| 50 | oss<<instream; \ |
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| 51 | recordParameters(outstream,string1,string2,oss.str()); \ |
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| 52 | }while(0) |
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| 53 | |
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| 54 | |
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[378] | 55 | class FitsHeader; // foreshadow this so that Param knows it exists |
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[272] | 56 | |
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[572] | 57 | const int numSortingParamOptions = 10; |
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| 58 | const std::string sortingParamOptions[numSortingParamOptions]={"xvalue","yvalue","zvalue","ra","dec","vel","w50","iflux","pflux","snr"}; |
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[571] | 59 | |
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| 60 | |
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[528] | 61 | /// @brief Class to store general parameters. |
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| 62 | /// |
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| 63 | /// @details This is a general repository for parameters that are used by all |
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| 64 | /// functions. This is how the user interacts with the program, as |
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| 65 | /// parameters are read in from disk files through functions in this |
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| 66 | /// class. |
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[272] | 67 | |
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[378] | 68 | class Param |
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| 69 | { |
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| 70 | public: |
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[528] | 71 | /// @brief Default constructor. |
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[378] | 72 | Param(); |
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[272] | 73 | |
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[528] | 74 | /// @brief Copy constructor for Param. |
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[378] | 75 | Param(const Param& p); |
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[309] | 76 | |
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[528] | 77 | /// @brief Assignment operator for Param. |
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[378] | 78 | Param& operator= (const Param& p); |
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[309] | 79 | |
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[528] | 80 | /// @brief Destructor function. |
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[378] | 81 | virtual ~Param(); |
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[266] | 82 | |
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[528] | 83 | /// @brief Define the default values of each parameter. |
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[378] | 84 | void defaultValues(); |
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[221] | 85 | |
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[378] | 86 | //----------------- |
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| 87 | // Functions in param.cc |
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| 88 | // |
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[528] | 89 | /// @brief Parse the command line parameters correctly. |
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[698] | 90 | OUTCOME getopts(int argc, char ** argv, std::string progname="Duchamp"); |
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[221] | 91 | |
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[528] | 92 | /// @brief Read in parameters from a disk file. |
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[698] | 93 | OUTCOME readParams(std::string paramfile); |
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[221] | 94 | |
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[528] | 95 | /// @brief Check the parameter list for inconsistencies |
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[503] | 96 | void checkPars(); |
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| 97 | |
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[528] | 98 | /// @brief Copy certain necessary FITS header parameters from a FitsHeader object |
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[378] | 99 | void copyHeaderInfo(FitsHeader &head); |
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[221] | 100 | |
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[528] | 101 | /// @brief Determine filename in which to save the mask array. |
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[670] | 102 | std::string outputMomentMapFile(); |
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| 103 | |
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| 104 | /// @brief Determine filename in which to save the mask array. |
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[379] | 105 | std::string outputMaskFile(); |
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| 106 | |
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[528] | 107 | /// @brief Determine filename in which to save the smoothed array. |
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[378] | 108 | std::string outputSmoothFile(); |
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[221] | 109 | |
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[528] | 110 | /// @brief Determine filename in which to save the reconstructed array. |
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[378] | 111 | std::string outputReconFile(); |
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[272] | 112 | |
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[528] | 113 | /// @brief Determine filename in which to save the residual array from the atrous reconstruction. |
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[378] | 114 | std::string outputResidFile(); |
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[221] | 115 | |
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[528] | 116 | /// @brief Print the parameter set in a readable fashion. |
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[378] | 117 | friend std::ostream& operator<< ( std::ostream& theStream, Param& par); |
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| 118 | friend class Image; |
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[258] | 119 | |
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[378] | 120 | //------------------ |
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| 121 | // Functions in FitsIO/subsection.cc |
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| 122 | // |
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[528] | 123 | /// @brief Make sure the subsection strings are OK. |
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[698] | 124 | OUTCOME verifySubsection(); |
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[309] | 125 | |
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[528] | 126 | /// @brief Set the correct offset values for each axis |
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[378] | 127 | void setOffsets(struct wcsprm *wcs); |
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[221] | 128 | |
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[528] | 129 | /// @brief Set the correct offset values for each axis |
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[378] | 130 | void setOffsets(struct wcsprm &wcs); |
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[221] | 131 | |
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[378] | 132 | //------------------ |
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| 133 | // These are in param.cc |
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[528] | 134 | /// @brief Is a pixel value a BLANK? |
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[378] | 135 | bool isBlank(float &value); |
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[258] | 136 | |
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[528] | 137 | /// @brief Is a given channel flagged as being in the Milky Way? |
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[378] | 138 | bool isInMW(int z); |
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[275] | 139 | |
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[528] | 140 | /// @brief Is a given pixel position OK for use with stats calculations? |
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[378] | 141 | bool isStatOK(int x, int y, int z); |
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[275] | 142 | |
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[528] | 143 | /// @brief Make a mask array -- an array saying whether each pixel is BLANK or not |
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[378] | 144 | bool *makeBlankMask(float *array, int size); |
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[221] | 145 | |
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[528] | 146 | /// @brief Make a mask array -- an array saying whether each pixel is able to be used for statistics calculations |
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[506] | 147 | bool *makeStatMask(float *array, long *dim); |
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[378] | 148 | |
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| 149 | //-------------------- |
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| 150 | // Basic inline accessor functions |
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| 151 | // |
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| 152 | std::string getImageFile(){return imageFile;}; |
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| 153 | void setImageFile(std::string fname){imageFile = fname;}; |
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| 154 | std::string getFullImageFile(){ |
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| 155 | if(flagSubsection) return imageFile+pixelSec.getSection(); |
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| 156 | else return imageFile; |
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| 157 | }; |
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| 158 | bool getFlagSubsection(){return flagSubsection;}; |
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| 159 | void setFlagSubsection(bool flag){flagSubsection=flag;}; |
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| 160 | std::string getSubsection(){return pixelSec.getSection();}; |
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| 161 | void setSubsection(std::string range){pixelSec.setSection(range);}; |
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| 162 | Section §ion(){Section &rsection = pixelSec; return rsection;}; |
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| 163 | bool getFlagReconExists(){return flagReconExists;}; |
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| 164 | void setFlagReconExists(bool flag){flagReconExists=flag;}; |
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| 165 | std::string getReconFile(){return reconFile;}; |
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| 166 | void setReconFile(std::string file){reconFile = file;}; |
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| 167 | bool getFlagSmoothExists(){return flagSmoothExists;}; |
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| 168 | void setFlagSmoothExists(bool flag){flagSmoothExists=flag;}; |
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| 169 | std::string getSmoothFile(){return smoothFile;}; |
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| 170 | void setSmoothFile(std::string file){smoothFile = file;}; |
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| 171 | // |
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[475] | 172 | bool getFlagUsePrevious(){return usePrevious;}; |
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| 173 | void setFlagUsePrevious(bool flag){usePrevious=flag;}; |
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| 174 | std::string getObjectList(){return objectList;}; |
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| 175 | void setObjectList(std::string s){objectList = s;}; |
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| 176 | std::vector<int> getObjectRequest(); |
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| 177 | std::vector<bool> getObjectChoices(); |
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| 178 | std::vector<bool> getObjectChoices(int numObjects); |
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| 179 | // |
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[378] | 180 | bool getFlagLog(){return flagLog;}; |
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| 181 | void setFlagLog(bool flag){flagLog=flag;}; |
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| 182 | std::string getLogFile(){return logFile;}; |
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| 183 | void setLogFile(std::string fname){logFile = fname;}; |
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| 184 | std::string getOutFile(){return outFile;}; |
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| 185 | void setOutFile(std::string fname){outFile = fname;}; |
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| 186 | bool getFlagSeparateHeader(){return flagSeparateHeader;}; |
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| 187 | void setFlagSeparateHeader(bool b){flagSeparateHeader=b;}; |
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| 188 | std::string getHeaderFile(){return headerFile;}; |
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| 189 | void setHeaderFile(std::string s){headerFile=s;}; |
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| 190 | std::string getSpectraFile(){return spectraFile;}; |
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| 191 | void setSpectraFile(std::string fname){spectraFile = fname;}; |
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[424] | 192 | bool getFlagTextSpectra(){return flagTextSpectra;}; |
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| 193 | void setFlagTextSpectra(bool b){flagTextSpectra = b;}; |
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| 194 | std::string getSpectraTextFile(){return spectraTextFile;}; |
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| 195 | void setSpectraTextFile(std::string fname){spectraTextFile = fname;}; |
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[670] | 196 | bool getFlagOutputMomentMap(){return flagOutputMomentMap;}; |
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| 197 | void setFlagOutputMomentMap(bool flag){flagOutputMomentMap=flag;}; |
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| 198 | std::string getFileOutputMomentMap(){return fileOutputMomentMap;}; |
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| 199 | void setFileOutputMomentMap(std::string s){fileOutputMomentMap=s;}; |
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[379] | 200 | bool getFlagOutputMask(){return flagOutputMask;}; |
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| 201 | void setFlagOutputMask(bool flag){flagOutputMask=flag;}; |
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[525] | 202 | std::string getFileOutputMask(){return fileOutputMask;}; |
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| 203 | void setFileOutputMask(std::string s){fileOutputMask=s;}; |
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[521] | 204 | bool getFlagMaskWithObjectNum(){return flagMaskWithObjectNum;}; |
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| 205 | void setFlagMaskWithObjectNum(bool flag){flagMaskWithObjectNum=flag;}; |
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[378] | 206 | bool getFlagOutputSmooth(){return flagOutputSmooth;}; |
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| 207 | void setFlagOutputSmooth(bool flag){flagOutputSmooth=flag;}; |
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[525] | 208 | std::string getFileOutputSmooth(){return fileOutputSmooth;}; |
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| 209 | void setFileOutputSmooth(std::string s){fileOutputSmooth=s;}; |
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[378] | 210 | bool getFlagOutputRecon(){return flagOutputRecon;}; |
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| 211 | void setFlagOutputRecon(bool flag){flagOutputRecon=flag;}; |
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[525] | 212 | std::string getFileOutputRecon(){return fileOutputRecon;}; |
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| 213 | void setFileOutputRecon(std::string s){fileOutputRecon=s;}; |
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[378] | 214 | bool getFlagOutputResid(){return flagOutputResid;}; |
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| 215 | void setFlagOutputResid(bool flag){flagOutputResid=flag;}; |
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[525] | 216 | std::string getFileOutputResid(){return fileOutputResid;}; |
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| 217 | void setFileOutputResid(std::string s){fileOutputResid=s;}; |
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[378] | 218 | bool getFlagVOT(){return flagVOT;}; |
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| 219 | void setFlagVOT(bool flag){flagVOT=flag;}; |
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| 220 | std::string getVOTFile(){return votFile;}; |
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| 221 | void setVOTFile(std::string fname){votFile = fname;}; |
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| 222 | bool getFlagKarma(){return flagKarma;}; |
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| 223 | void setFlagKarma(bool flag){flagKarma=flag;}; |
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[446] | 224 | std::string getAnnotationType(){return annotationType;}; |
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| 225 | void setAnnotationType(std::string s){annotationType=s;}; |
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[378] | 226 | std::string getKarmaFile(){return karmaFile;}; |
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| 227 | void setKarmaFile(std::string fname){karmaFile = fname;}; |
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| 228 | bool getFlagMaps(){return flagMaps;}; |
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| 229 | void setFlagMaps(bool flag){flagMaps=flag;}; |
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| 230 | std::string getDetectionMap(){return detectionMap;}; |
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| 231 | void setDetectionMap(std::string fname){detectionMap = fname;}; |
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| 232 | std::string getMomentMap(){return momentMap;}; |
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| 233 | void setMomentMap(std::string fname){momentMap = fname;}; |
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| 234 | bool getFlagXOutput(){return flagXOutput;}; |
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| 235 | void setFlagXOutput(bool b){flagXOutput=b;}; |
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[438] | 236 | int getPrecFlux(){return precFlux;}; |
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| 237 | void setPrecFlux(int i){precFlux=i;}; |
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| 238 | int getPrecVel(){return precVel;}; |
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| 239 | void setPrecVel(int i){precVel=i;}; |
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| 240 | int getPrecSNR(){return precSNR;}; |
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| 241 | void setPrecSNR(int i){precSNR=i;}; |
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[378] | 242 | // |
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| 243 | bool getFlagNegative(){return flagNegative;}; |
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| 244 | void setFlagNegative(bool flag){flagNegative=flag;}; |
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| 245 | bool getFlagBlankPix(){return flagBlankPix;}; |
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| 246 | void setFlagBlankPix(bool flag){flagBlankPix=flag;}; |
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| 247 | float getBlankPixVal(){return blankPixValue;}; |
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| 248 | void setBlankPixVal(float v){blankPixValue=v;}; |
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| 249 | int getBlankKeyword(){return blankKeyword;}; |
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| 250 | void setBlankKeyword(int v){blankKeyword=v;}; |
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| 251 | float getBscaleKeyword(){return bscaleKeyword;}; |
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| 252 | void setBscaleKeyword(float v){bscaleKeyword=v;}; |
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| 253 | float getBzeroKeyword(){return bzeroKeyword;}; |
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| 254 | void setBzeroKeyword(float v){bzeroKeyword=v;}; |
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| 255 | bool getFlagMW(){return flagMW;}; |
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| 256 | void setFlagMW(bool flag){flagMW=flag;}; |
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[673] | 257 | int getMaxMW(){return maxMW - zSubOffset;}; |
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[378] | 258 | void setMaxMW(int m){maxMW=m;}; |
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[673] | 259 | int getMinMW(){return minMW - zSubOffset;}; |
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[378] | 260 | void setMinMW(int m){minMW=m;}; |
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[662] | 261 | void setBeamSize(float s){areaBeam = s;}; |
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| 262 | float getBeamSize(){return areaBeam;}; |
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| 263 | void setBeamFWHM(float s){fwhmBeam = s;}; |
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| 264 | float getBeamFWHM(){return fwhmBeam;}; |
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[378] | 265 | bool getFlagUsingBeam(){return flagUsingBeam;}; |
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| 266 | void setFlagUsingBeam(bool b){flagUsingBeam=b;}; |
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[434] | 267 | std::string getNewFluxUnits(){return newFluxUnits;}; |
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[686] | 268 | void setNewFluxUnits(std::string s){newFluxUnits=s;}; |
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| 269 | std::string getSearchType(){return searchType;}; |
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| 270 | void setSearchType(std::string s){searchType=s;}; |
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[378] | 271 | // |
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| 272 | bool getFlagTrim(){return flagTrim;}; |
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| 273 | void setFlagTrim(bool b){flagTrim=b;}; |
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| 274 | bool getFlagCubeTrimmed(){return hasBeenTrimmed;}; |
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| 275 | void setFlagCubeTrimmed(bool flag){hasBeenTrimmed = flag;}; |
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| 276 | long getBorderLeft(){return borderLeft;}; |
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| 277 | void setBorderLeft(long b){borderLeft = b;}; |
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| 278 | long getBorderRight(){return borderRight;}; |
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| 279 | void setBorderRight(long b){borderRight = b;}; |
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| 280 | long getBorderBottom(){return borderBottom;}; |
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| 281 | void setBorderBottom(long b){borderBottom = b;}; |
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| 282 | long getBorderTop(){return borderTop;}; |
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| 283 | void setBorderTop(long b){borderTop = b;}; |
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| 284 | // |
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| 285 | long getXOffset(){return xSubOffset;}; |
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| 286 | void setXOffset(long o){xSubOffset = o;}; |
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| 287 | long getYOffset(){return ySubOffset;}; |
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| 288 | void setYOffset(long o){ySubOffset = o;}; |
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| 289 | long getZOffset(){return zSubOffset;}; |
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| 290 | void setZOffset(long o){zSubOffset = o;}; |
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| 291 | // |
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[537] | 292 | unsigned int getMinPix(){return minPix;}; |
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[378] | 293 | void setMinPix(int m){minPix=m;}; |
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| 294 | // |
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| 295 | bool getFlagGrowth(){return flagGrowth;}; |
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| 296 | void setFlagGrowth(bool flag){flagGrowth=flag;}; |
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| 297 | float getGrowthCut(){return growthCut;}; |
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| 298 | void setGrowthCut(float c){growthCut=c;}; |
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[461] | 299 | float getGrowthThreshold(){return growthThreshold;}; |
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| 300 | void setGrowthThreshold(float f){growthThreshold=f;}; |
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| 301 | bool getFlagUserGrowthThreshold(){return flagUserGrowthThreshold;}; |
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| 302 | void setFlagUserGrowthThreshold(bool b){flagUserGrowthThreshold=b;}; |
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[378] | 303 | // |
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| 304 | bool getFlagFDR(){return flagFDR;}; |
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| 305 | void setFlagFDR(bool flag){flagFDR=flag;}; |
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| 306 | float getAlpha(){return alphaFDR;}; |
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| 307 | void setAlpha(float a){alphaFDR=a;}; |
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[543] | 308 | int getFDRnumCorChan(){return FDRnumCorChan;}; |
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| 309 | void setFDRnumCorChan(int i){FDRnumCorChan=i;}; |
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[378] | 310 | // |
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| 311 | bool getFlagBaseline(){return flagBaseline;}; |
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| 312 | void setFlagBaseline(bool flag){flagBaseline = flag;}; |
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| 313 | // |
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| 314 | bool getFlagStatSec(){return flagStatSec;}; |
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| 315 | void setFlagStatSec(bool flag){flagStatSec=flag;}; |
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| 316 | std::string getStatSec(){return statSec.getSection();}; |
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| 317 | void setStatSec(std::string range){statSec.setSection(range);}; |
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[385] | 318 | bool getFlagRobustStats(){return flagRobustStats;}; |
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| 319 | void setFlagRobustStats(bool flag){flagRobustStats=flag;}; |
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[378] | 320 | float getCut(){return snrCut;}; |
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| 321 | void setCut(float c){snrCut=c;}; |
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| 322 | float getThreshold(){return threshold;}; |
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| 323 | void setThreshold(float f){threshold=f;}; |
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| 324 | bool getFlagUserThreshold(){return flagUserThreshold;}; |
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| 325 | void setFlagUserThreshold(bool b){flagUserThreshold=b;}; |
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| 326 | // |
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| 327 | bool getFlagSmooth(){return flagSmooth;}; |
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| 328 | void setFlagSmooth(bool b){flagSmooth=b;}; |
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| 329 | std::string getSmoothType(){return smoothType;}; |
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| 330 | void setSmoothType(std::string s){smoothType=s;}; |
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| 331 | int getHanningWidth(){return hanningWidth;}; |
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| 332 | void setHanningWidth(int f){hanningWidth=f;}; |
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| 333 | void setKernMaj(float f){kernMaj=f;}; |
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| 334 | float getKernMaj(){return kernMaj;}; |
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| 335 | void setKernMin(float f){kernMin=f;}; |
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| 336 | float getKernMin(){return kernMin;}; |
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| 337 | void setKernPA(float f){kernPA=f;}; |
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| 338 | float getKernPA(){return kernPA;}; |
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| 339 | // |
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| 340 | bool getFlagATrous(){return flagATrous;}; |
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| 341 | void setFlagATrous(bool flag){flagATrous=flag;}; |
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| 342 | int getReconDim(){return reconDim;}; |
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| 343 | void setReconDim(int i){reconDim=i;}; |
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| 344 | int getMinScale(){return scaleMin;}; |
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| 345 | void setMinScale(int s){scaleMin=s;}; |
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| 346 | int getMaxScale(){return scaleMax;}; |
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| 347 | void setMaxScale(int s){scaleMax=s;}; |
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| 348 | float getAtrousCut(){return snrRecon;}; |
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| 349 | void setAtrousCut(float c){snrRecon=c;}; |
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| 350 | int getFilterCode(){return filterCode;}; |
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| 351 | void setFilterCode(int c){filterCode=c;}; |
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| 352 | std::string getFilterName(){return reconFilter.getName();}; |
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| 353 | Filter& filter(){ Filter &rfilter = reconFilter; return rfilter; }; |
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| 354 | // |
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| 355 | bool getFlagAdjacent(){return flagAdjacent;}; |
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| 356 | void setFlagAdjacent(bool flag){flagAdjacent=flag;}; |
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| 357 | float getThreshS(){return threshSpatial;}; |
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| 358 | void setThreshS(float t){threshSpatial=t;}; |
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| 359 | float getThreshV(){return threshVelocity;}; |
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| 360 | void setThreshV(float t){threshVelocity=t;}; |
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| 361 | int getMinChannels(){return minChannels;}; |
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| 362 | void setMinChannels(int n){minChannels=n;}; |
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[721] | 363 | unsigned int getMinVoxels(){return minVoxels;}; |
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| 364 | void setMinVoxels(unsigned int n){minVoxels=n;}; |
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[672] | 365 | bool getFlagRejectBeforeMerge(){return flagRejectBeforeMerge;}; |
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| 366 | void setFlagRejectBeforeMerge(bool flag){flagRejectBeforeMerge=flag;}; |
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[691] | 367 | bool getFlagTwoStageMerging(){return flagTwoStageMerging;}; |
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| 368 | void setFlagTwoStageMerging(bool flag){flagTwoStageMerging=flag;}; |
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[378] | 369 | // |
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| 370 | std::string getSpectralMethod(){return spectralMethod;}; |
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| 371 | void setSpectralMethod(std::string s){spectralMethod=s;}; |
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| 372 | std::string getSpectralUnits(){return spectralUnits;}; |
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| 373 | void setSpectralUnits(std::string s){spectralUnits=s;}; |
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| 374 | std::string getPixelCentre(){return pixelCentre;}; |
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| 375 | void setPixelCentre(std::string s){pixelCentre=s;}; |
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[571] | 376 | std::string getSortingParam(){return sortingParam;}; |
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| 377 | void setSortingParam(std::string s){sortingParam=s;}; |
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[378] | 378 | bool drawBorders(){return borders;}; |
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| 379 | void setDrawBorders(bool f){borders=f;}; |
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| 380 | bool drawBlankEdge(){return blankEdge;}; |
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| 381 | void setDrawBlankEdge(bool f){blankEdge=f;}; |
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| 382 | |
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[528] | 383 | /// @brief Are we in verbose mode? |
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[378] | 384 | bool isVerbose(){return verbose;}; |
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| 385 | void setVerbosity(bool f){verbose=f;}; |
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[3] | 386 | |
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[378] | 387 | private: |
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| 388 | // Input files |
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[528] | 389 | std::string imageFile; ///< The image to be analysed. |
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| 390 | bool flagSubsection; ///< Whether we just want a subsection of the image |
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| 391 | Section pixelSec; ///< The Section object storing the pixel subsection information. |
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| 392 | bool flagReconExists; ///< The reconstructed array is in a FITS file on disk. |
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| 393 | std::string reconFile; ///< The FITS file containing the reconstructed array. |
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| 394 | bool flagSmoothExists;///< The smoothed array is in a FITS file. |
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| 395 | std::string smoothFile; ///< The FITS file containing the smoothed array. |
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[71] | 396 | |
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[528] | 397 | bool usePrevious; ///< Whether to read the detections from a previously-created log file |
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| 398 | std::string objectList; ///< List of objects to re-plot |
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[475] | 399 | |
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[378] | 400 | // Output files |
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[528] | 401 | bool flagLog; ///< Should we do the intermediate logging? |
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| 402 | std::string logFile; ///< Where the intermediate logging goes. |
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| 403 | std::string outFile; ///< Where the final results get put. |
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| 404 | bool flagSeparateHeader;///< Should the header information(parameters & statistics) be written to a separate file to the table ofresults? |
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| 405 | std::string headerFile; ///< Where the header information to go with the results table should be written. |
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| 406 | std::string spectraFile; ///< Where the spectra are displayed |
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| 407 | bool flagTextSpectra; ///< Should a text file with all spectra be written? |
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| 408 | std::string spectraTextFile; ///< Where the text spectra are written. |
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[670] | 409 | bool flagOutputMomentMap; ///< Should the moment map image be written to a FITS file? |
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| 410 | std::string fileOutputMomentMap; ///< The name of the moment map FITS file |
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[528] | 411 | bool flagOutputMask; ///< Should the mask image be written? |
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| 412 | std::string fileOutputMask; ///< The name of the mask image. |
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| 413 | bool flagMaskWithObjectNum;///< Should the mask values be labeled with the object ID (or just 1)? |
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| 414 | bool flagOutputSmooth;///< Should the smoothed cube be written? |
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| 415 | std::string fileOutputSmooth;///< The name of the smoothed cube file |
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| 416 | bool flagOutputRecon; ///< Should the reconstructed cube be written to a FITS file? |
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[525] | 417 | std::string fileOutputRecon; ///< The name of the reconstructed cube file |
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[528] | 418 | bool flagOutputResid; ///< Should the residuals from the reconstruction be written to a FITS file? |
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[525] | 419 | std::string fileOutputResid; ///< The name of the residual cube file |
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[528] | 420 | bool flagVOT; ///< Should we save results in VOTable format? |
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| 421 | std::string votFile; ///< Where the VOTable goes. |
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| 422 | bool flagKarma; ///< Should we save results in Karma annotation format? |
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| 423 | std::string karmaFile; ///< Where the Karma annotation file goes. |
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| 424 | std::string annotationType; ///< Should the annoations be circles or borders? |
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| 425 | bool flagMaps; ///< Should we produce detection and moment maps in postscript form? |
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| 426 | std::string detectionMap; ///< The name of the detection map (postscript file). |
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| 427 | std::string momentMap; ///< The name of the 0th moment map (ps file). |
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| 428 | bool flagXOutput; ///< Should there be an xwindows output of the detection map? |
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| 429 | int precFlux; ///< The desired precision for flux values. |
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| 430 | int precVel; ///< The desired precision for velocity/frequency values. |
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| 431 | int precSNR; ///< The desired precision for the SNR values. |
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[3] | 432 | |
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[378] | 433 | // Cube related parameters |
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[528] | 434 | bool flagNegative; ///< Are we going to search for negative features? |
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| 435 | bool flagBlankPix; ///< A flag that indicates whether there are pixels defined as BLANK and whether we need to remove & ignore them in processing. |
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| 436 | float blankPixValue; ///< Pixel value that is considered BLANK. |
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| 437 | int blankKeyword; ///< The FITS header keyword BLANK. |
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| 438 | float bscaleKeyword; ///< The FITS header keyword BSCALE. |
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| 439 | float bzeroKeyword; ///< The FITS header keyword BZERO. |
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| 440 | std::string newFluxUnits; ///< The user-requested flux units, to replace BUNIT. |
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[475] | 441 | |
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[385] | 442 | // Milky-Way parameters |
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[528] | 443 | bool flagMW; ///< A flag that indicates whether to ignore the Milky Way channels. |
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| 444 | int maxMW; ///< Last Milky Way channel |
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| 445 | int minMW; ///< First Milky Way channel |
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[475] | 446 | |
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[378] | 447 | // Trim-related |
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[528] | 448 | bool flagTrim; ///< Does the user want the cube trimmed? |
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| 449 | bool hasBeenTrimmed; ///< Has the cube been trimmed of excess BLANKs around the edge? |
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| 450 | long borderLeft; ///< The number of BLANK pixels trimmed from the left of the cube; |
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| 451 | long borderRight; ///< The number trimmed from the Right of the cube; |
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| 452 | long borderBottom; ///< The number trimmed from the Bottom of the cube; |
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| 453 | long borderTop; ///< The number trimmed from the Top of the cube; |
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[475] | 454 | |
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[378] | 455 | // Subsection offsets |
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[528] | 456 | long *offsets; ///< The array of offsets for each FITS axis. |
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| 457 | long sizeOffsets; ///< The size of the offsets array. |
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| 458 | long xSubOffset; ///< The subsection's x-axis offset |
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| 459 | long ySubOffset; ///< The subsection's y-axis offset |
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| 460 | long zSubOffset; ///< The subsection's z-axis offset |
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[475] | 461 | |
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[378] | 462 | // Baseline related |
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[528] | 463 | bool flagBaseline; ///< Whether to do baseline subtraction before reconstruction and/or searching. |
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[475] | 464 | |
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[378] | 465 | // Detection-related |
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[528] | 466 | int minPix; ///< Minimum number of pixels for a detected object to be counted |
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[662] | 467 | float areaBeam; ///< Size (area) of the beam in pixels. |
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| 468 | float fwhmBeam; ///< FWHM of the beam in pixels. |
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[528] | 469 | bool flagUsingBeam; ///< If true, we are using the numPixBeam parameter, otherwise we use the value in the FITS header. |
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[686] | 470 | std::string searchType; ///< How to do the search: by channel map or by spectrum |
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[475] | 471 | |
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[378] | 472 | // Object growth |
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[528] | 473 | bool flagGrowth; ///< Are we growing objects once they are found? |
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| 474 | float growthCut; ///< The SNR that we are growing objects down to. |
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| 475 | bool flagUserGrowthThreshold; ///< Whether the user has manually defined a growth threshold |
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| 476 | float growthThreshold; ///< The threshold for growing objects down to |
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[475] | 477 | |
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[378] | 478 | // FDR analysis |
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[528] | 479 | bool flagFDR; ///< Should the FDR method be used? |
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| 480 | float alphaFDR; ///< Alpha value for FDR detection algorithm |
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[543] | 481 | int FDRnumCorChan; ///< Number of correlated channels, used in the FDR algorithm |
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[475] | 482 | |
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[378] | 483 | // Basic detection |
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[528] | 484 | bool flagStatSec; ///< Whether we just want to use a subsection of the image to calculate the statistics. |
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| 485 | Section statSec; ///< The Section object storing the statistics subsection information. |
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| 486 | bool flagRobustStats; ///< Whether to use robust statistics. |
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| 487 | float snrCut; ///< How many sigma above mean is a detection when sigma-clipping |
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| 488 | float threshold; ///< What the threshold is (when sigma-clipping). |
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| 489 | bool flagUserThreshold;///< Whether the user has defined a threshold of their own. |
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[475] | 490 | |
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[378] | 491 | // Smoothing of the cube |
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[528] | 492 | bool flagSmooth; ///< Should the cube be smoothed before searching? |
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| 493 | std::string smoothType; ///< The type of smoothing to be done. |
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| 494 | int hanningWidth; ///< Width for hanning smoothing. |
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| 495 | float kernMaj; ///< Semi-Major axis of gaussian smoothing kernel |
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| 496 | float kernMin; ///< Semi-Minor axis of gaussian smoothing kernel |
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| 497 | float kernPA; ///< Position angle of gaussian smoothing kernel, in degrees east of north (i.e. anticlockwise). |
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[475] | 498 | |
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[378] | 499 | // A trous reconstruction parameters |
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| 500 | bool flagATrous; ///< Are we using the a trous reconstruction? |
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[475] | 501 | int reconDim; ///< How many dimensions to use for the reconstruction? |
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[378] | 502 | int scaleMin; ///< Min scale used in a trous reconstruction |
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| 503 | int scaleMax; ///< Max scale used in a trous reconstruction |
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[475] | 504 | float snrRecon; ///< SNR cutoff used in a trous reconstruction (only wavelet coefficients that survive this threshold are kept) |
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[378] | 505 | Filter reconFilter; ///< The filter used for reconstructions. |
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[475] | 506 | int filterCode; ///< The code number for the filter to be used (saves having to parse names) |
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| 507 | std::string filterName; ///< The code number converted into a name, for outputting purposes. |
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[3] | 508 | |
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[378] | 509 | // Volume-merging parameters |
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[475] | 510 | bool flagAdjacent; ///< Whether to use the adjacent criterion for judging if objects are to be merged. |
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| 511 | float threshSpatial; ///< Maximum spatial separation between objects |
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| 512 | float threshVelocity; ///< Maximum channels separation between objects |
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[378] | 513 | int minChannels; ///< Minimum no. of channels to make an object |
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[721] | 514 | unsigned int minVoxels; ///< Minimum no. of voxels required in an object |
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[672] | 515 | bool flagRejectBeforeMerge; ///< Whether to reject sources before merging |
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[691] | 516 | bool flagTwoStageMerging; ///< Whether to do a partial merge when the objects are found, via the mergeIntoList function. |
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[385] | 517 | |
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[378] | 518 | // Input-Output related |
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[475] | 519 | std::string spectralMethod; ///< A string indicating choice of spectral plotting method: choices are "peak" (default) or "sum" |
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| 520 | std::string spectralUnits; ///< A string indicating what units the spectral axis should be quoted in. |
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| 521 | std::string pixelCentre;///< A string indicating which type of centre to give the results in: "average", "centroid", or "peak"(flux). |
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[571] | 522 | std::string sortingParam; ///< A string indicating the parameter to sort the detection list on. |
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[475] | 523 | bool borders; ///< Whether to draw a border around the individual pixels of a detection in the spectral display |
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| 524 | bool blankEdge; ///< Whether to draw a border around the BLANK pixel region in the moment maps and cutout images |
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| 525 | bool verbose; ///< Whether to use maximum verbosity -- use progress indicators in the reconstruction & merging steps. |
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[3] | 526 | |
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[378] | 527 | }; |
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[3] | 528 | |
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[378] | 529 | //=========================================================================== |
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[221] | 530 | |
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[3] | 531 | |
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[528] | 532 | /// @brief Convert a string to lowercase. |
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[378] | 533 | std::string makelower( std::string s ); |
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[103] | 534 | |
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[378] | 535 | } |
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[3] | 536 | #endif |
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