1 | // ----------------------------------------------------------------------- |
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2 | // detection.hh: Definition of the Detection class. |
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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 | #ifndef DETECTION_H |
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29 | #define DETECTION_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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34 | #include <duchamp/param.hh> |
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35 | #include <duchamp/PixelMap/Voxel.hh> |
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36 | #include <duchamp/PixelMap/Object3D.hh> |
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37 | #include <duchamp/Outputs/columns.hh> |
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38 | #include <duchamp/Outputs/CatalogueSpecification.hh> |
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39 | |
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40 | using namespace PixelInfo; |
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41 | |
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42 | namespace duchamp |
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43 | { |
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44 | |
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45 | |
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46 | /// Class to represent a contiguous set of detected voxels. |
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47 | /// This is a detected object, which features: |
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48 | /// a vector of voxels, average and centroid positions, total & peak fluxes, |
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49 | /// the possibility of WCS-calculated parameters (RA, Dec, velocity, |
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50 | /// related widths). |
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51 | /// Also many functions with which to manipulate the Detections. |
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52 | |
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53 | class Detection : public Object3D |
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54 | { |
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55 | public: |
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56 | Detection(); |
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57 | Detection(const Object3D& o); |
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58 | Detection(const Detection& d); |
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59 | Detection& operator= (const Detection& d); |
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60 | virtual ~Detection(){}; |
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61 | void defaultDetection(); |
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62 | //------------------------------ |
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63 | // These are functions in detection.cc. |
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64 | // |
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65 | |
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66 | friend Detection operator+ (Detection &lhs, Detection &rhs); |
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67 | void addDetection(Detection &other); |
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68 | |
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69 | bool canMerge(Detection &other, Param &par); |
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70 | bool isNear(Detection &other, Param &par); |
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71 | bool isClose(Detection &other, Param &par); |
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72 | |
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73 | /// @brief Test whether voxel lists match |
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74 | bool voxelListsMatch(std::vector<PixelInfo::Voxel> voxelList); |
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75 | |
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76 | /// @brief Test whether a voxel list contains all detected voxels |
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77 | bool voxelListCovered(std::vector<PixelInfo::Voxel> voxelList); |
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78 | |
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79 | /// @brief Calculate flux-related parameters of the Detection. |
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80 | void calcFluxes(float *fluxArray, size_t *dim); |
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81 | /// @brief Calculate flux-related parameters of the Detection. |
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82 | void calcFluxes(std::vector<PixelInfo::Voxel> voxelList); |
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83 | void calcFluxes(std::map<Voxel,float> &voxelMap); |
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84 | |
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85 | /// @brief Invert the source's flux values |
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86 | void invert(); |
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87 | |
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88 | /// @brief Calculate parameters related to the World Coordinate System. |
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89 | // void calcWCSparams(float *fluxArray, long *dim, FitsHeader &head); |
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90 | void calcWCSparams(FitsHeader &head); |
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91 | |
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92 | /// @brief Calculate the integrated flux over the entire Detection. |
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93 | void calcIntegFlux(float *fluxArray, size_t *dim, FitsHeader &head); |
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94 | /// @brief Calculate the integrated flux over the entire Detection. |
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95 | void calcIntegFlux(size_t zdim, std::vector<PixelInfo::Voxel> voxelList, FitsHeader &head); |
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96 | void calcIntegFlux(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head); |
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97 | |
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98 | /// @brief Calculate the 20%-/50%-peak-flux widths in a general fashion |
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99 | void calcVelWidths(size_t zdim, float *intSpec, FitsHeader &head); |
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100 | /// @brief Calculate the 20%/50% peak flux widths |
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101 | void calcVelWidths(float *fluxArray, size_t *dim, FitsHeader &head); |
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102 | /// @brief Calculate the 20%/50% peak flux widths |
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103 | void calcVelWidths(size_t zdim, std::vector<PixelInfo::Voxel> voxelList, FitsHeader &head); |
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104 | void calcVelWidths(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head); |
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105 | |
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106 | /// @brief Calculate the spatial (moment-0) shape |
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107 | void findShape(const float *momentMap, const size_t *dim, FitsHeader &head); |
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108 | |
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109 | /// @brief Set the values of the axis offsets from the cube. |
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110 | void setOffsets(Param &par); |
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111 | |
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112 | /// @brief Add the offset values to the pixel locations |
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113 | void addOffsets(size_t xoff, size_t yoff, size_t zoff){ |
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114 | Object3D::addOffsets(xoff,yoff,zoff); |
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115 | xpeak+=xoff; ypeak+=yoff; zpeak+=zoff; |
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116 | xCentroid+=xoff; yCentroid+=yoff; zCentroid+=zoff; |
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117 | }; |
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118 | void addOffsets(){ |
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119 | Object3D::addOffsets(xSubOffset,ySubOffset,zSubOffset); |
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120 | xpeak+=xSubOffset; ypeak+=ySubOffset; zpeak+=zSubOffset; |
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121 | xCentroid+=xSubOffset; yCentroid+=ySubOffset; zCentroid+=zSubOffset; |
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122 | }; |
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123 | |
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124 | // |
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125 | //--------------------------------- |
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126 | // Text Output -- all in Detection/outputDetection.cc |
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127 | // |
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128 | /// @brief The spectral output label that contains info on the WCS position & velocity. |
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129 | std::string outputLabelWCS(); |
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130 | |
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131 | /// @brief The spectral output label that contains info on the pixel location. |
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132 | std::string outputLabelPix(); |
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133 | |
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134 | /// @brief The spectral output label that contains info on fluxes of the Detection. |
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135 | std::string outputLabelFluxes(); |
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136 | |
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137 | /// @brief The spectral output label that contains info on widths of the Detection. |
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138 | std::string outputLabelWidths(FitsHeader &head); |
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139 | |
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140 | /// @brief Print all required values for the Detection to a table. |
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141 | void printTableRow(std::ostream &stream, Catalogues::CatalogueSpecification columns, Catalogues::DESTINATION tableType); |
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142 | |
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143 | /// @brief Print a particular value for the Detection to a table. |
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144 | void printTableEntry(std::ostream &stream, Catalogues::Column column); |
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145 | |
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146 | //---------------------------------- |
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147 | // For plotting routines... in Cubes/drawMomentCutout.cc |
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148 | // |
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149 | /// @brief Get the location of the spatial borders. |
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150 | std::vector<int> getVertexSet(); |
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151 | // |
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152 | /// @brief Draw spatial borders for a particular Detection. |
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153 | void drawBorders(int xoffset, int yoffset); |
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154 | // |
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155 | |
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156 | // |
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157 | //---------------------------------- |
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158 | // Basic functions |
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159 | // |
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160 | |
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161 | /// @brief Add a single voxel to the pixel list. |
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162 | void addPixel(long x, long y, long z){Object3D::addPixel(x,y,z);}; |
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163 | |
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164 | /// @brief Add a single voxel to the pixel list. |
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165 | void addPixel(PixelInfo::Voxel point){ |
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166 | /// @brief This one adds the pixel to the pixelArray, and updates the fluxes according to the Voxel's flux information |
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167 | Object3D::addPixel(point.getX(),point.getY(),point.getZ()); |
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168 | totalFlux += point.getF(); |
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169 | if(point.getF()>peakFlux){ |
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170 | peakFlux = point.getF(); |
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171 | xpeak = point.getX(); ypeak = point.getY(); zpeak = point.getZ(); |
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172 | } |
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173 | }; |
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174 | |
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175 | /// @brief How many channels does the Detection have? |
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176 | size_t getNumChannels(){return Object3D::getNumDistinctZ();}; |
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177 | |
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178 | /// @brief Is there at least the acceptable minimum number of channels in the Detection? |
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179 | bool hasEnoughChannels(int minNumber); |
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180 | |
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181 | //----------------------------------- |
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182 | // Basic accessor functions for private members follow... |
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183 | // |
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184 | long getXOffset(){return xSubOffset;}; |
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185 | void setXOffset(long o){xSubOffset = o;}; |
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186 | long getYOffset(){return ySubOffset;}; |
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187 | void setYOffset(long o){ySubOffset = o;}; |
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188 | long getZOffset(){return zSubOffset;}; |
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189 | void setZOffset(long o){zSubOffset = o;}; |
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190 | // |
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191 | bool hasParams(){return haveParams;}; |
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192 | // |
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193 | float getXcentre(); |
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194 | float getYcentre(); |
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195 | float getZcentre(); |
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196 | float getTotalFlux(){return totalFlux;}; |
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197 | void setTotalFlux(float f){totalFlux=f;}; |
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198 | float getTotalFluxError(){return eTotalFlux;}; |
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199 | void setTotalFluxError(float f){eTotalFlux=f;}; |
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200 | double getIntegFlux(){return intFlux;}; |
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201 | void setIntegFlux(double f){intFlux=f;}; |
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202 | double getIntegFluxError(){return eIntFlux;}; |
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203 | void setIntegFluxError(double d){eIntFlux=d;}; |
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204 | float getPeakFlux(){return peakFlux;}; |
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205 | void setPeakFlux(float f){peakFlux=f;}; |
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206 | long getXPeak(){return xpeak;}; |
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207 | long getYPeak(){return ypeak;}; |
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208 | long getZPeak(){return zpeak;}; |
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209 | float getPeakSNR(){return peakSNR;}; |
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210 | void setPeakSNR(float f){peakSNR = f;}; |
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211 | float getXCentroid(){return xCentroid;}; |
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212 | float getYCentroid(){return yCentroid;}; |
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213 | float getZCentroid(){return zCentroid;}; |
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214 | std::string getCentreType(){return centreType;}; |
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215 | void setCentreType(std::string s){centreType=s;}; |
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216 | bool isNegative(){return negSource;}; |
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217 | void setNegative(bool f){negSource = f;}; |
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218 | std::string getFlagText(){return flagText;}; |
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219 | void setFlagText(std::string s){flagText = s;}; |
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220 | void addToFlagText(std::string s){flagText += s;}; |
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221 | // |
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222 | /// @brief Is the WCS good enough to be used? |
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223 | /// \return Detection::flagWCS = True/False |
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224 | bool isWCS(){return flagWCS;}; |
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225 | bool isSpecOK(){return specOK;}; |
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226 | void setSpecOK(bool b){specOK=b;}; |
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227 | std::string getName(){return name;}; |
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228 | void setName(std::string s){name=s;}; |
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229 | std::string getRAs(){return raS;}; |
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230 | std::string getDecs(){return decS;}; |
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231 | double getRA(){return ra;}; |
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232 | double getDec(){return dec;}; |
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233 | double getRAWidth(){return raWidth;}; |
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234 | double getDecWidth(){return decWidth;}; |
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235 | double getMajorAxis(){return majorAxis;}; |
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236 | double getMinorAxis(){return minorAxis;}; |
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237 | double getPositionAngle(){return posang;}; |
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238 | double getVel(){return vel;}; |
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239 | double getVelWidth(){return velWidth;}; |
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240 | double getVelMin(){return velMin;}; |
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241 | double getVelMax(){return velMax;}; |
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242 | double getW20(){return w20;}; |
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243 | double getV20Min(){return v20min;}; |
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244 | double getV20Max(){return v20max;}; |
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245 | double getW50(){return w50;}; |
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246 | double getV50Min(){return v50min;}; |
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247 | double getV50Max(){return v50max;}; |
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248 | int getID(){return id;}; |
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249 | void setID(int i){id = i;}; |
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250 | // |
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251 | int getPosPrec(){return posPrec;}; |
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252 | void setPosPrec(int i){posPrec=i;}; |
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253 | int getXYZPrec(){return xyzPrec;}; |
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254 | void setXYZPrec(int i){xyzPrec=i;}; |
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255 | int getFintPrec(){return fintPrec;}; |
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256 | void setFintPrec(int i){fintPrec=i;}; |
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257 | int getFpeakPrec(){return fpeakPrec;}; |
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258 | void setFpeakPrec(int i){fpeakPrec=i;}; |
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259 | int getVelPrec(){return velPrec;}; |
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260 | void setVelPrec(int i){velPrec=i;}; |
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261 | int getSNRPrec(){return snrPrec;}; |
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262 | void setSNRPrec(int i){snrPrec=i;}; |
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263 | // |
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264 | protected: |
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265 | // Subsection offsets |
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266 | long xSubOffset; ///< The x-offset, from subsectioned cube |
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267 | long ySubOffset; ///< The y-offset, from subsectioned cube |
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268 | long zSubOffset; ///< The z-offset, from subsectioned cube |
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269 | bool haveParams; ///< Have the parameters been calculated? |
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270 | // Flux related |
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271 | float totalFlux; ///< sum of the fluxes of all the pixels |
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272 | float eTotalFlux; ///< error on the total flux |
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273 | double intFlux; ///< integrated flux : involves integration over velocity. |
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274 | double eIntFlux; ///< error on the integrated flux |
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275 | float peakFlux; ///< maximum flux over all the pixels |
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276 | long xpeak; ///< x-pixel location of peak flux |
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277 | long ypeak; ///< y-pixel location of peak flux |
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278 | long zpeak; ///< z-pixel location of peak flux |
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279 | float peakSNR; ///< signal-to-noise ratio at peak |
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280 | float xCentroid; ///< x-pixel location of centroid |
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281 | float yCentroid; ///< y-pixel location of centroid |
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282 | float zCentroid; ///< z-pixel location of centroid |
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283 | std::string centreType; ///< which type of pixel centre to report: "average", "centroid", or "peak" (flux) |
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284 | bool negSource; ///< is the source a negative feature? |
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285 | std::string flagText; ///< any warning flags about the quality of the detection. |
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286 | // WCS related |
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287 | int id; ///< ID -- generally number in list |
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288 | std::string name; ///< IAU-style name (based on position) |
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289 | bool flagWCS; ///< A flag indicating whether the WCS parameters have been set. |
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290 | std::string raS; ///< Right Ascension (or Longitude) of pixel centre in form 12:34:23 |
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291 | std::string decS; ///< Declination (or Latitude) of pixel centre, in form -12:23:34 |
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292 | double ra; ///< Central Right Ascension in degrees |
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293 | double dec; ///< Central Declination in degrees |
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294 | double raWidth; ///< Width of detection in RA direction in arcmin |
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295 | double decWidth; ///< Width of detection in Dec direction in arcmin |
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296 | double majorAxis; ///< Major axis length in arcmin |
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297 | double minorAxis; ///< Minor axis length in arcmin |
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298 | double posang; ///< Position angle of the major axis, in degrees |
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299 | bool specOK; ///< Is the spectral dimension valid? |
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300 | std::string specUnits; ///< Units of the spectral dimension |
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301 | std::string specType; ///< WCS ctype code for the spectral dimension |
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302 | std::string fluxUnits; ///< Units of flux |
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303 | std::string intFluxUnits; ///< Units of integrated flux |
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304 | std::string lngtype; ///< Type of longitude axis (RA/GLON) |
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305 | std::string lattype; ///< Type of latitude axis (DEC/GLAT) |
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306 | double vel; ///< Central velocity (from zCentre) |
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307 | double velWidth; ///< Full velocity width |
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308 | double velMin; ///< Minimum velocity |
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309 | double velMax; ///< Maximum velocity |
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310 | double v20min; ///< Minimum velocity at 20% of peak flux |
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311 | double v20max; ///< Maximum velocity at 20% of peak flux |
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312 | double w20; ///< Velocity width at 20% of peak flux |
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313 | double v50min; ///< Minimum velocity at 50% of peak flux |
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314 | double v50max; ///< Maximum velocity at 50% of peak flux |
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315 | double w50; ///< Velocity width at 50% of peak flux |
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316 | /// @brief The next six are the precision of values printed in the headers of the spectral plots |
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317 | /// @name |
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318 | /// @{ |
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319 | int posPrec; ///< Precision of WCS positional values |
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320 | int xyzPrec; ///< Precision of pixel positional values |
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321 | int fintPrec; ///< Precision of F_int/F_tot values |
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322 | int fpeakPrec; ///< Precision of F_peak values |
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323 | int velPrec; ///< Precision of velocity values. |
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324 | int snrPrec; ///< Precision of S/N_max values. |
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325 | /// @} |
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326 | }; |
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327 | |
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328 | //========================================================================== |
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329 | |
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330 | ////////////////////////////////////////////////////// |
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331 | // Prototypes for functions that use above classes |
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332 | ////////////////////////////////////////////////////// |
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333 | |
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334 | //---------------- |
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335 | // These are in sorting.cc |
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336 | // |
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337 | /// @brief Sort a list of Detections by Z-pixel value. |
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338 | void SortByZ(std::vector <Detection> &inputList); |
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339 | |
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340 | /// @brief Sort a list of Detections by Velocity. |
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341 | void SortByVel(std::vector <Detection> &inputList); |
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342 | |
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343 | /// @brief Sort a list of Detections by a nominated parameter |
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344 | void SortDetections(std::vector <Detection> &inputList, std::string parameter); |
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345 | |
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346 | //---------------- |
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347 | // This is in areClose.cc |
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348 | // |
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349 | // /// @brief Determine whether two objects are close according to set parameters. |
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350 | // bool areClose(Detection &object1, Detection &object2, Param &par); |
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351 | |
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352 | //---------------- |
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353 | // This is in mergeIntoList.cc |
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354 | // |
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355 | /// @brief Add an object into a list, combining with adjacent objects if need be. |
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356 | void mergeIntoList(Detection &object, std::vector <Detection> &objList, |
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357 | Param &par); |
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358 | |
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359 | //---------------- |
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360 | // These are in Cubes/Merger.cc |
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361 | // |
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362 | /// @brief Merge a list of Detections so that all adjacent voxels are in the same Detection. |
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363 | void mergeList(std::vector<Detection> &objList, Param &par); |
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364 | /// @brief Culls a list of Detections that do not meet minimum requirements. |
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365 | void finaliseList(std::vector<Detection> &objList, Param &par); |
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366 | /// @brief Manage both the merging and the cleaning up of the list. |
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367 | void ObjectMerger(std::vector<Detection> &objList, Param &par); |
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368 | |
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369 | // /// @brief Print the header information to a particular table |
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370 | // void outputTableHeader(std::ostream &stream, Catalogues::CatalogueSpecification &columns, Catalogues::DESTINATION tableType, bool flagWCS); |
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371 | |
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372 | } |
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373 | |
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374 | #endif |
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