[440] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // VOTable.cc: Output of the detected objects to a VOTable |
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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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| 28 | |
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| 29 | #include <iostream> |
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| 30 | #include <sstream> |
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| 31 | #include <fstream> |
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| 32 | #include <iomanip> |
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| 33 | #include <string> |
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| 34 | #include <vector> |
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| 35 | #include <time.h> |
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| 36 | #include <duchamp/Cubes/VOTable.hh> |
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| 37 | #include <duchamp/param.hh> |
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| 38 | #include <duchamp/fitsHeader.hh> |
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| 39 | #include <duchamp/Cubes/cubes.hh> |
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| 40 | #include <duchamp/Detection/detection.hh> |
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| 41 | #include <duchamp/Detection/columns.hh> |
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[733] | 42 | #include <duchamp/Utils/utils.hh> |
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[912] | 43 | #include <duchamp/Utils/VOParam.hh> |
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[733] | 44 | |
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[440] | 45 | namespace duchamp |
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| 46 | { |
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| 47 | |
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| 48 | using namespace Column; |
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| 49 | std::string fixUnitsVOT(std::string oldstring) |
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| 50 | { |
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[528] | 51 | /// @details |
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| 52 | /// Fix a string containing units to make it acceptable for a VOTable. |
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| 53 | /// |
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| 54 | /// This function makes the provided units string acceptable |
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| 55 | /// according to the standard found at |
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| 56 | /// http://vizier.u-strasbg.fr/doc/catstd-3.2.htx |
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| 57 | /// This should then be able to convert the units used in the text |
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| 58 | /// table to units suitable for putting in a VOTable. |
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| 59 | /// |
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| 60 | /// Specifically, it removes any square brackets [] from the |
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| 61 | /// start/end of the string, and replaces blank spaces (representing |
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| 62 | /// multiplication) with a '.' (full stop). |
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| 63 | /// |
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| 64 | /// \param oldstring Input unit string to be fixed |
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| 65 | /// \return String with fixed units |
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[440] | 66 | |
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| 67 | std::string newstring; |
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[623] | 68 | for(size_t i=0;i<oldstring.size();i++){ |
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[440] | 69 | if((oldstring[i]!='[')&&(oldstring[i]!=']')){ |
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| 70 | if(oldstring[i]==' ') newstring += '.'; |
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| 71 | else newstring += oldstring[i]; |
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| 72 | } |
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| 73 | } |
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| 74 | return newstring; |
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| 75 | } |
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| 76 | |
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| 77 | |
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| 78 | void VOField::define(std::string i, std::string n, std::string U, std::string u, std::string d, std::string r, int w, int p) |
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| 79 | { |
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[528] | 80 | /// @details |
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| 81 | /// A basic definition function, defining each parameter individually. |
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| 82 | /// \param i The ID parameter |
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| 83 | /// \param n The name parameter |
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| 84 | /// \param U The UCD |
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| 85 | /// \param u The units (fixed by fixUnits()) |
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| 86 | /// \param d The datatype |
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| 87 | /// \param r The ref |
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| 88 | /// \param w The width |
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| 89 | /// \param p The precision |
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| 90 | |
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[440] | 91 | this->ID = i; |
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| 92 | this->name = n; |
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| 93 | this->UCD = U; |
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| 94 | this->unit = fixUnitsVOT(u); |
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| 95 | this->datatype = d; |
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| 96 | this->ref = r; |
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| 97 | this->width = w; |
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| 98 | this->precision = p; |
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| 99 | } |
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| 100 | |
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| 101 | void VOField::define(Column::Col column, std::string i, std::string U, std::string d, std::string r) |
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| 102 | { |
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[528] | 103 | /// @details |
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| 104 | /// Another definition function, using the information in a Column::Col object for some parameters. |
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| 105 | /// \param column A Column::Col object, used for name, unit, width & precision |
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| 106 | /// \param i The ID parameter |
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| 107 | /// \param U The UCD |
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| 108 | /// \param d The datatype |
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| 109 | /// \param r The ref |
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| 110 | |
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[440] | 111 | this->ID = i; |
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| 112 | this->name = column.getName(); |
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| 113 | this->UCD = U; |
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| 114 | this->unit = fixUnitsVOT(column.getUnits()); |
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| 115 | this->datatype = d; |
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| 116 | this->ref = r; |
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| 117 | this->width = column.getWidth(); |
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| 118 | this->precision = column.getPrecision(); |
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| 119 | } |
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| 120 | |
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| 121 | void VOField::define(Column::Col column) |
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| 122 | { |
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[528] | 123 | /// @details |
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| 124 | /// A more useful definition function, using the Column::COLNAME |
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| 125 | /// key to specify particular values for each of the parameters for |
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| 126 | /// different columns. |
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| 127 | /// \param column A Column::Col object of a particular type. The |
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| 128 | /// column.getType() function is used to decide which call to |
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| 129 | /// VOField::define(Column::Col column, std::string i, std::string |
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| 130 | /// U, std::string d, std::string r) to use |
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| 131 | |
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[440] | 132 | switch(column.getType()) |
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| 133 | { |
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| 134 | case NUM: |
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| 135 | this->define(column,"col01","meta.id","int",""); |
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| 136 | break; |
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| 137 | case NAME: |
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| 138 | this->define(column,"col02","meta.id;meta.main","char",""); |
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| 139 | break; |
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| 140 | case RAJD: |
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| 141 | this->define(column,"col03","","float","J2000"); |
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| 142 | break; |
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| 143 | case DECJD: |
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| 144 | this->define(column,"col04","","float","J2000"); |
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| 145 | break; |
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| 146 | case VEL: |
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| 147 | this->define(column,"col05","phys.veloc;src.dopplerVeloc","float",""); |
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| 148 | break; |
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| 149 | case WRA: |
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| 150 | this->define(column,"col06","","float","J2000"); |
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| 151 | break; |
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| 152 | case WDEC: |
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| 153 | this->define(column,"col07","","float","J2000"); |
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| 154 | break; |
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[512] | 155 | case W50: |
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[440] | 156 | this->define(column,"col08","phys.veloc;src.dopplerVeloc;spect.line.width","float",""); |
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| 157 | break; |
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[512] | 158 | case W20: |
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| 159 | this->define(column,"col09","phys.veloc;src.dopplerVeloc;spect.line.width","float",""); |
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| 160 | break; |
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| 161 | case WVEL: |
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| 162 | this->define(column,"col10","phys.veloc;src.dopplerVeloc;spect.line.width","float",""); |
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| 163 | break; |
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[440] | 164 | case FINT: |
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[512] | 165 | this->define(column,"col11","phot.flux;spect.line.intensity","float",""); |
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[440] | 166 | this->name = "Integrated_Flux"; |
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| 167 | break; |
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| 168 | case FTOT: |
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[512] | 169 | this->define(column,"col11","phot.flux;spect.line.intensity","float",""); |
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[440] | 170 | this->name = "Total_Flux"; |
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| 171 | break; |
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| 172 | case FPEAK: |
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[512] | 173 | this->define(column,"col12","phot.flux;spect.line.intensity","float",""); |
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[440] | 174 | this->name = "Peak_Flux"; |
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| 175 | break; |
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| 176 | case SNRPEAK: |
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[512] | 177 | this->define(column,"col13","phot.flux;stat.snr","float",""); |
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[440] | 178 | break; |
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| 179 | case FLAG: |
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[512] | 180 | this->define(column,"col14","meta.code.qual","char",""); |
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[440] | 181 | break; |
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| 182 | case XAV: |
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[512] | 183 | this->define(column,"col15","pos.cartesian.x","float",""); |
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[440] | 184 | break; |
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| 185 | case YAV: |
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[512] | 186 | this->define(column,"col16","pos.cartesian.y","float",""); |
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[440] | 187 | break; |
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| 188 | case ZAV: |
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[512] | 189 | this->define(column,"col17","pos.cartesian.z","float",""); |
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[440] | 190 | break; |
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| 191 | case XCENT: |
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[512] | 192 | this->define(column,"col18","pos.cartesian.x","float",""); |
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[440] | 193 | this->name = "X_Centroid"; |
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| 194 | break; |
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| 195 | case YCENT: |
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[512] | 196 | this->define(column,"col19","pos.cartesian.y","float",""); |
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[440] | 197 | this->name = "Y_Centroid"; |
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| 198 | break; |
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| 199 | case ZCENT: |
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[512] | 200 | this->define(column,"col20","pos.cartesian.z","float",""); |
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[440] | 201 | this->name = "Z_Centroid"; |
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| 202 | break; |
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| 203 | case XPEAK: |
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[512] | 204 | this->define(column,"col21","pos.cartesian.x","int",""); |
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[440] | 205 | break; |
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| 206 | case YPEAK: |
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[512] | 207 | this->define(column,"col22","pos.cartesian.y","int",""); |
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[440] | 208 | break; |
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| 209 | case ZPEAK: |
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[512] | 210 | this->define(column,"col23","pos.cartesian.z","int",""); |
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[440] | 211 | break; |
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| 212 | default: |
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| 213 | break; |
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| 214 | }; |
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| 215 | } |
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| 216 | |
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| 217 | void VOField::printField(std::ostream &stream) |
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| 218 | { |
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[528] | 219 | /// @details |
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| 220 | /// Print the Field entry with appropriate formatting. |
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| 221 | /// \param stream The output stream to send the text to. |
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| 222 | |
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[440] | 223 | stream << "<FIELD name=\"" <<this->name |
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| 224 | << "\" ID=\"" << this->ID |
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| 225 | << "\" ucd=\"" << this->UCD; |
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| 226 | if(this->ref!="") stream << "\" ref=\"" << this->ref; |
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| 227 | stream << "\" datatype=\"" << this->datatype; |
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| 228 | stream << "\" unit=\"" << this->unit; |
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| 229 | if(datatype=="char") |
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| 230 | stream << "\" arraysize=\"" << this->width; |
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| 231 | else{ |
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| 232 | stream << "\" width=\"" << this->width; |
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| 233 | if(datatype=="float" || datatype=="double") |
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| 234 | stream << "\" precision=\"" << this->precision; |
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| 235 | } |
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| 236 | stream << "\"/>\n"; |
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| 237 | |
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| 238 | } |
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| 239 | |
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| 240 | |
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| 241 | |
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| 242 | //------------------------------------------------ |
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| 243 | |
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| 244 | |
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[912] | 245 | // template <class T> void VOParam::define(std::string n, std::string U, std::string d, T v, int w, std::string u) |
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| 246 | // { |
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| 247 | // /// @details |
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| 248 | // /// A basic definition function, defining each parameter |
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| 249 | // /// individually. The value (v) is written to a stringstream, and |
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| 250 | // /// from there stored as a string. |
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| 251 | // /// \param n The name |
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| 252 | // /// \param U The UCD |
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| 253 | // /// \param d The datatype |
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| 254 | // /// \param v The value |
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| 255 | // /// \param w The width |
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| 256 | // /// \param u The units |
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[528] | 257 | |
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[912] | 258 | // this->name = n; |
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| 259 | // this->UCD = U; |
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| 260 | // this->datatype = d; |
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| 261 | // this->width = w; |
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| 262 | // std::stringstream ss; |
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| 263 | // ss << v; |
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| 264 | // this->value = ss.str(); |
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| 265 | // this->units = u; |
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| 266 | // } |
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| 267 | // template void VOParam::define<int>(std::string n, std::string U, std::string d, int v, int w, std::string u); |
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| 268 | // template void VOParam::define<long>(std::string n, std::string U, std::string d, long v, int w, std::string u); |
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| 269 | // template void VOParam::define<float>(std::string n, std::string U, std::string d, float v, int w, std::string u); |
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| 270 | // template void VOParam::define<double>(std::string n, std::string U, std::string d, double v, int w, std::string u); |
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| 271 | // template void VOParam::define<std::string>(std::string n, std::string U, std::string d, std::string v, int w, std::string u); |
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[440] | 272 | |
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[912] | 273 | // void VOParam::printParam(std::ostream &stream) |
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| 274 | // { |
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| 275 | // /// @details |
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| 276 | // /// Print the Param entry with appropriate formatting. |
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| 277 | // /// \param stream The output stream to send the text to. |
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[528] | 278 | |
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[912] | 279 | // stream << "<PARAM name=\"" <<this->name |
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| 280 | // << "\" ucd=\"" << this->UCD |
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| 281 | // << "\" datatype=\"" << this->datatype; |
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| 282 | // if(this->units!="") |
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| 283 | // stream << "\" units=\"" << this->units; |
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| 284 | // if(this->width!=0){ |
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| 285 | // if(datatype=="char") |
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| 286 | // stream << "\" arraysize=\"" << this->width; |
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| 287 | // else |
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| 288 | // stream << "\" width=\"" << this->width; |
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| 289 | // } |
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| 290 | // stream << "\" value=\"" << this->value |
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| 291 | // << "\"/>\n"; |
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| 292 | // } |
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[440] | 293 | |
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[912] | 294 | // //------------------------------------------------ |
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[440] | 295 | |
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| 296 | |
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| 297 | |
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| 298 | void Cube::outputDetectionsVOTable(std::ostream &stream) |
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| 299 | { |
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[528] | 300 | /// @details |
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| 301 | /// Prints to a stream (provided) the list of detected objects in the cube |
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| 302 | /// in a VOTable format. |
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| 303 | /// Uses WCS information and assumes WCS parameters have been calculated for each |
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| 304 | /// detected object. |
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| 305 | /// \param stream The output stream to send the text to. |
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[441] | 306 | |
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[440] | 307 | stream<<"<?xml version=\"1.0\"?>\n"; |
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| 308 | stream<<"<VOTABLE version=\"1.1\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n"; |
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| 309 | stream<<" xsi:noNamespaceSchemaLocation=\"http://www.ivoa.net/xml/VOTable/VOTable/v1.1\">\n"; |
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| 310 | |
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| 311 | stream<<" <COOSYS ID=\"J2000\" equinox=\"J2000.\" epoch=\"J2000.\" system=\"eq_FK5\"/>\n"; |
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| 312 | stream<<" <RESOURCE name=\"Duchamp Output\">\n"; |
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| 313 | stream<<" <TABLE name=\"Detections\">\n"; |
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| 314 | stream<<" <DESCRIPTION>Detected sources and parameters from running the Duchamp source finder.</DESCRIPTION>\n"; |
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| 315 | |
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| 316 | // PARAM section -- parts that are not entry-specific ie. apply to whole dataset |
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| 317 | std::vector<VOParam> paramList; |
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| 318 | std::vector<VOParam>::iterator param; |
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| 319 | VOParam singleParam; |
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| 320 | |
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| 321 | std::string fname = this->par.getImageFile(); |
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| 322 | if(this->par.getFlagSubsection()) fname+=this->par.getSubsection(); |
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| 323 | |
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[912] | 324 | singleParam = VOParam("FITS file","meta.file;meta.fits","char",fname,fname.size(),""); |
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[440] | 325 | paramList.push_back(singleParam); |
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| 326 | if(this->par.getFlagFDR()) |
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[912] | 327 | singleParam = VOParam("FDR Significance","stat.param","float",this->par.getAlpha(),0,""); |
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[440] | 328 | else |
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[912] | 329 | singleParam = VOParam("Threshold (SNR)","stat.snr","float",this->par.getCut(),0,""); |
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[440] | 330 | paramList.push_back(singleParam); |
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[912] | 331 | singleParam = VOParam("Flux Threshold","phot.flux;stat.min","float",this->Stats.getThreshold(),0,this->head.getFluxUnits()); |
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[512] | 332 | paramList.push_back(singleParam); |
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[440] | 333 | |
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| 334 | if(this->par.getFlagATrous()){ |
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| 335 | std::string note = "The a trous reconstruction method was used, with the following parameters."; |
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[912] | 336 | singleParam = VOParam("ATrous note","meta.note","char",note,note.size(),""); |
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[440] | 337 | paramList.push_back(singleParam); |
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[912] | 338 | singleParam = VOParam("ATrous Dimension","meta.code;stat","int",this->par.getReconDim(),0,""); |
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[440] | 339 | paramList.push_back(singleParam); |
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[912] | 340 | singleParam = VOParam("ATrous Threshold","stat.snr","float",this->par.getAtrousCut(),0,""); |
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[440] | 341 | paramList.push_back(singleParam); |
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[912] | 342 | singleParam = VOParam("ATrous Minimum Scale","stat.param","int",this->par.getMinScale(),0,""); |
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[440] | 343 | paramList.push_back(singleParam); |
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[912] | 344 | singleParam = VOParam("ATrous Filter","meta.code;stat","char",this->par.getFilterName(),this->par.getFilterName().size(),""); |
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[440] | 345 | paramList.push_back(singleParam); |
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| 346 | } |
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| 347 | if(this->par.getFlagSmooth()){ |
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| 348 | if(this->par.getSmoothType()=="spectral"){ |
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| 349 | std::string note = "The cube was smoothed spectrally with a Hanning filter, with the following parameters."; |
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[912] | 350 | singleParam = VOParam("Smoothing note","meta.note","char",note,note.size(),""); |
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[440] | 351 | paramList.push_back(singleParam); |
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[912] | 352 | singleParam = VOParam("Hanning filter width","meta.code;stat","int",this->par.getHanningWidth(),0,""); |
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[440] | 353 | paramList.push_back(singleParam); |
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| 354 | } |
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| 355 | else if(this->par.getSmoothType()=="spatial"){ |
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| 356 | std::string note = "The cube was smoothed spatially with a Gaussian kernel, with the following parameters."; |
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[912] | 357 | singleParam = VOParam("Smoothing note","meta.note","char",note,note.size(),""); |
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[440] | 358 | paramList.push_back(singleParam); |
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[912] | 359 | singleParam = VOParam("Gaussian kernel major-axis FWHM","meta.code;stat","int",this->par.getKernMaj(),0,""); |
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[440] | 360 | paramList.push_back(singleParam); |
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[912] | 361 | singleParam = VOParam("Gaussian kernel minor-axis FWHM","meta.code;stat","int",this->par.getKernMin(),0,""); |
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[440] | 362 | paramList.push_back(singleParam); |
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[912] | 363 | singleParam = VOParam("Gaussian kernel position angle","meta.code;stat","int",this->par.getKernPA(),0,""); |
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[440] | 364 | paramList.push_back(singleParam); |
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| 365 | } |
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| 366 | } |
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| 367 | |
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| 368 | for(param=paramList.begin();param<paramList.end();param++){ |
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| 369 | stream << " "; |
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| 370 | param->printParam(stream); |
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| 371 | } |
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| 372 | |
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| 373 | |
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[461] | 374 | if(this->fullCols.size()==0) this->setupColumns(); |
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| 375 | // in case cols haven't been set -- need the column names |
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| 376 | |
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[440] | 377 | std::string posUCD[4]; |
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| 378 | if(makelower(this->fullCols[Column::RAJD].getName())=="ra"){ |
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| 379 | posUCD[0] = "pos.eq.ra;meta.main"; |
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| 380 | posUCD[2] = "phys.angSize;pos.eq.ra"; |
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| 381 | } |
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| 382 | else{ |
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| 383 | posUCD[0] = "pos.galactic.lat;meta.main"; |
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| 384 | posUCD[2] = "phys.angSize;pos.galactic.lat"; |
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| 385 | } |
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| 386 | if(makelower(this->fullCols[DECJD].getName())=="dec"){ |
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| 387 | posUCD[1] = "pos.eq.dec;meta.main"; |
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| 388 | posUCD[3] = "phys.angSize;pos.eq.dec"; |
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| 389 | } |
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| 390 | else{ |
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| 391 | posUCD[1] = "pos.galactic.lon;meta.main"; |
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| 392 | posUCD[3] = "phys.angSize;pos.galactic.lon"; |
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| 393 | } |
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| 394 | |
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| 395 | std::vector<Column::Col>::iterator col; |
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| 396 | for(col=this->fullCols.begin();col<this->fullCols.end();col++){ |
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| 397 | |
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| 398 | if(col->doCol("votable",this->head.isSpecOK())){ |
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| 399 | VOField field; |
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| 400 | field.define(*col); |
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| 401 | if(col->getType()==RAJD) field.setUCD(posUCD[0]); |
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| 402 | if(col->getType()==WRA) field.setUCD(posUCD[1]); |
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| 403 | if(col->getType()==DECJD) field.setUCD(posUCD[2]); |
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| 404 | if(col->getType()==WDEC) field.setUCD(posUCD[3]); |
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| 405 | stream << " "; |
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| 406 | field.printField(stream); |
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| 407 | } |
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| 408 | |
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| 409 | } |
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| 410 | |
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| 411 | stream<<" <DATA>\n" |
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| 412 | <<" <TABLEDATA>\n"; |
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| 413 | |
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| 414 | stream.setf(std::ios::fixed); |
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| 415 | |
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| 416 | std::vector<Detection>::iterator obj; |
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| 417 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
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| 418 | |
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| 419 | stream<<" <TR>\n"; |
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| 420 | stream<<" "; |
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| 421 | std::vector<Column::Col>::iterator col; |
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| 422 | for(col=this->fullCols.begin();col<this->fullCols.end();col++){ |
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| 423 | if(col->doCol("votable",this->head.isSpecOK())){ |
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| 424 | stream<<"<TD>"; |
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| 425 | obj->printTableEntry(stream, *col); |
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| 426 | stream<<"</TD>"; |
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| 427 | } |
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| 428 | } |
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| 429 | stream<<"\n"; |
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| 430 | stream<<" </TR>\n"; |
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| 431 | |
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| 432 | } |
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| 433 | |
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| 434 | stream<<" </TABLEDATA>\n"; |
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| 435 | stream<<" </DATA>\n"; |
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| 436 | stream<<" </TABLE>\n"; |
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| 437 | stream<<" </RESOURCE>\n"; |
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| 438 | stream<<"</VOTABLE>\n"; |
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| 439 | resetiosflags(std::ios::fixed); |
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| 440 | |
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| 441 | } |
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| 442 | |
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| 443 | |
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| 444 | |
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| 445 | |
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| 446 | } |
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