1 | // ----------------------------------------------------------------------- |
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2 | // cubes.hh: Definitions of the DataArray, Cube and Image classes. |
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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 CUBES_H |
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29 | #define CUBES_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 | |
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35 | #include <duchamp/duchamp.hh> |
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36 | #include <duchamp/param.hh> |
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37 | #include <duchamp/fitsHeader.hh> |
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38 | #include <duchamp/Detection/detection.hh> |
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39 | #include <duchamp/Outputs/columns.hh> |
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40 | #include <duchamp/Outputs/CatalogueSpecification.hh> |
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41 | #include <duchamp/Plotting/SpectralPlot.hh> |
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42 | #include <duchamp/Plotting/CutoutPlot.hh> |
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43 | #include <duchamp/Utils/Statistics.hh> |
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44 | #include <duchamp/Utils/utils.hh> |
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45 | #include <duchamp/PixelMap/Scan.hh> |
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46 | #include <duchamp/PixelMap/Object2D.hh> |
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47 | |
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48 | |
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49 | namespace duchamp |
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50 | { |
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51 | |
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52 | |
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53 | /// @brief Search a reconstructed array for significant detections. |
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54 | std::vector <Detection> searchReconArray(size_t *dim, float *originalArray, float *reconArray, |
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55 | Param &par, Statistics::StatsContainer<float> &stats); |
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56 | std::vector <Detection> searchReconArraySpectral(size_t *dim, float *originalArray, float *reconArray, |
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57 | Param &par, Statistics::StatsContainer<float> &stats); |
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58 | std::vector <Detection> searchReconArraySpatial(size_t *dim, float *originalArray, float *reconArray, |
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59 | Param &par, Statistics::StatsContainer<float> &stats); |
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60 | |
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61 | /// @brief Search a 3-dimensional array for significant detections. |
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62 | std::vector <Detection> search3DArray(size_t *dim, float *Array, Param &par, |
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63 | Statistics::StatsContainer<float> &stats); |
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64 | std::vector <Detection> search3DArraySpectral(size_t *dim, float *Array, Param &par, |
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65 | Statistics::StatsContainer<float> &stats); |
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66 | std::vector <Detection> search3DArraySpatial(size_t *dim, float *Array, Param &par, |
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67 | Statistics::StatsContainer<float> &stats); |
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68 | |
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69 | |
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70 | //========================================================================= |
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71 | |
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72 | /// An enumeration allowing us to refer to a particular array within functions |
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73 | enum ARRAYREF {ARRAY=0, RECON, BASELINE}; |
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74 | |
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75 | |
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76 | /// @brief Base class for the image container. |
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77 | /// |
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78 | /// @details Definition of an n-dimensional data array: array of |
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79 | /// pixel values, size & dimensions array of Detection objects |
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80 | |
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81 | class DataArray |
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82 | { |
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83 | public: |
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84 | DataArray(); ///< Basic DataArray constructor |
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85 | DataArray(short int nDim); ///< Basic nDim-dimensional DataArray constructor |
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86 | DataArray(short int nDim, size_t size);///< Basic nDim-dimensional DataArray constructor, specifying size. |
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87 | DataArray(short int nDim, size_t *dimensions); ///< Basic nDim-dimensional DataArray constructor, specifying size of dimensions. |
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88 | virtual ~DataArray(); ///< Basic DataArray constructor |
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89 | DataArray(const DataArray &d); |
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90 | DataArray& operator=(const DataArray &d); |
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91 | |
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92 | //----------------------------------------- |
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93 | // Obvious inline accessor functions. |
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94 | // |
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95 | size_t getDimX(){if(numDim>0) return axisDim[0];else return 0;}; |
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96 | size_t getDimY(){if(numDim>1) return axisDim[1];else return 1;}; |
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97 | size_t getDimZ(){if(numDim>2) return axisDim[2];else return 1;}; |
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98 | size_t getSize(){ return numPixels; }; |
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99 | size_t getSpatialSize(){if(numDim>1) return axisDim[0]*axisDim[1]; else if(numDim>0) return axisDim[0]; else return 0;}; |
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100 | short int getNumDim(){ return numDim; }; |
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101 | virtual float getPixValue(size_t pos){ return array[pos]; }; |
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102 | virtual void setPixValue(size_t pos, float f){array[pos] = f;}; |
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103 | Detection getObject(size_t number){ return objectList->at(number); }; |
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104 | Detection * pObject(size_t number){ return &(objectList->at(number));}; |
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105 | std::vector <Detection> getObjectList(){ return *objectList; }; |
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106 | std::vector <Detection> *pObjectList(){ return objectList; }; |
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107 | std::vector <Detection> &ObjectList(){ std::vector<Detection> &rlist = *objectList; return rlist; }; |
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108 | size_t getNumObj(){ return objectList->size(); }; |
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109 | |
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110 | /// @brief Delete all objects from the list of detections. |
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111 | void clearDetectionList(){ |
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112 | //objectList->clear(); |
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113 | delete objectList; |
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114 | objectList = new std::vector<Detection>; |
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115 | }; |
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116 | |
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117 | /// @brief Read a parameter set from file. |
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118 | OUTCOME readParam(std::string paramfile){ |
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119 | /// @brief |
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120 | /// Uses Param::readParams() to read parameters from a file. |
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121 | /// \param paramfile The file to be read. |
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122 | |
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123 | return par.readParams(paramfile); |
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124 | }; |
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125 | |
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126 | //----------------------------------------- |
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127 | // Related to the various arrays |
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128 | // |
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129 | /// @brief Return first three dimensional axes. |
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130 | void getDim(size_t &x, size_t &y, size_t &z); |
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131 | /// @brief Return array of dimensional sizes. |
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132 | void getDimArray(size_t *output); |
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133 | size_t * getDimArray(){return axisDim;}; |
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134 | |
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135 | /// @brief Return pixel value array. |
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136 | void getArray(float *output); |
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137 | float * getArray(){return array;}; |
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138 | |
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139 | /// @brief Save pixel value array. |
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140 | virtual void saveArray(float *input, size_t size); |
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141 | |
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142 | //----------------------------------------- |
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143 | // Related to the object lists |
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144 | // |
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145 | /// @brief Adds a single detection to the object list. |
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146 | void addObject(Detection object); |
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147 | |
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148 | /// @brief Adds all objects in a detection list to the object list. |
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149 | void addObjectList(std::vector <Detection> newlist); |
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150 | |
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151 | /// @brief Add pixel offsets to object coordinates. |
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152 | void addObjectOffsets(); |
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153 | |
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154 | //----------------------------------------- |
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155 | // Parameter list related. |
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156 | // |
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157 | /// @brief Output the Param set. |
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158 | void showParam(std::ostream &stream){ stream << par; }; |
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159 | /// @brief Return the Param set. |
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160 | Param getParam(){ return par; }; |
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161 | /// @brief Save a Param set to the Cube. |
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162 | void saveParam(Param &newpar){par = newpar;}; |
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163 | /// @brief Provides a reference to the Param set. |
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164 | Param& pars(){ Param &rpar = par; return rpar; }; |
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165 | /// @brief Is the voxel number given by vox a BLANK value? |
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166 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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167 | |
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168 | // -------------------------------------------- |
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169 | // Statistics |
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170 | // |
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171 | /// @brief Returns the StatsContainer. |
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172 | Statistics::StatsContainer<float> getStats(){ return Stats; }; |
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173 | |
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174 | /// @brief Provides a reference to the StatsContainer. |
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175 | Statistics::StatsContainer<float>& stats(){ |
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176 | Statistics::StatsContainer<float> &rstats = Stats; return rstats; |
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177 | }; |
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178 | |
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179 | /// @brief Save a StatsContainer to the Cube. |
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180 | void saveStats(Statistics::StatsContainer<float> newStats){ Stats = newStats;}; |
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181 | |
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182 | /// @brief A detection test for value. |
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183 | bool isDetection(float value); |
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184 | |
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185 | /// @brief A detection test for pixel. |
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186 | bool isDetection(size_t voxel); |
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187 | |
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188 | |
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189 | /// @brief Output operator for DataArray. |
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190 | friend std::ostream& operator<< (std::ostream& theStream, DataArray &array); |
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191 | |
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192 | |
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193 | protected: |
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194 | short int numDim; ///< Number of dimensions. |
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195 | size_t *axisDim; ///< Array of axis dimensions of cube |
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196 | bool axisDimAllocated; ///< has axisDim been allocated? |
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197 | size_t numPixels; ///< Total number of pixels in cube. |
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198 | float *array; ///< Array of data. |
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199 | bool arrayAllocated; ///< has the array been allocated? |
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200 | std::vector <Detection> *objectList; ///< The list of detected objects. |
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201 | Param par; ///< A parameter list. |
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202 | Statistics::StatsContainer<float> Stats; ///< The statistics for the DataArray. |
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203 | }; |
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204 | |
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205 | |
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206 | |
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207 | //========================================================================= |
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208 | |
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209 | /// @brief Definition of an data-cube object (3D): |
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210 | /// a DataArray object limited to dim=3 |
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211 | |
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212 | class Cube : public DataArray |
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213 | { |
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214 | public: |
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215 | Cube(); ///< Basic Cube constructor. |
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216 | Cube(size_t nPix); ///< Alternative Cube constructor. |
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217 | Cube(size_t *dimensions); ///< Alternative Cube constructor. |
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218 | virtual ~Cube(); ///< Basic Cube destructor. |
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219 | Cube(const Cube &c); ///< Copy constructor |
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220 | Cube& operator=(const Cube &c); ///< Copy operator |
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221 | |
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222 | /// @brief Return a Cube holding only a subsection of the original |
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223 | Cube* slice(Section subsection); |
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224 | |
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225 | |
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226 | short int nondegDim(){return numNondegDim;}; |
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227 | bool is2D(); |
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228 | void checkDim(){head.set2D(is2D());}; |
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229 | void reportMemorySize(std::ostream &theStream, bool allocateArrays); |
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230 | |
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231 | // INLINE functions -- definitions included after class declaration. |
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232 | /// @brief Is the voxel number given by vox a BLANK value? |
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233 | bool isBlank(size_t vox){ return par.isBlank(array[vox]); }; |
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234 | |
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235 | /// @brief Is the voxel at (x,y,z) a BLANK value? |
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236 | bool isBlank(size_t x, size_t y, size_t z){ |
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237 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]); }; |
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238 | |
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239 | /// @brief Return a bool array masking blank pixels: 1=good, 0=blank |
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240 | bool * makeBlankMask(){return par.makeBlankMask(array, numPixels);}; |
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241 | |
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242 | /// @brief Does the Cube::recon array exist? |
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243 | bool isRecon(){ return reconExists; }; |
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244 | |
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245 | float getPixValue(size_t pos){ return array[pos]; }; |
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246 | float getPixValue(size_t x, size_t y, size_t z){ |
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247 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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248 | short getDetectMapValue(size_t pos){ return detectMap[pos]; }; |
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249 | short getDetectMapValue(size_t x, size_t y){ return detectMap[y*axisDim[0]+x]; }; |
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250 | float getReconValue(size_t pos){ return recon[pos]; }; |
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251 | float getReconValue(size_t x, size_t y, size_t z){ |
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252 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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253 | float getBaselineValue(size_t pos){ return baseline[pos]; }; |
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254 | float getBaselineValue(size_t x, size_t y, size_t z){ |
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255 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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256 | void setPixValue(size_t pos, float f){array[pos] = f;}; |
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257 | void setPixValue(size_t x, size_t y, size_t z, float f){ |
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258 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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259 | void setDetectMapValue(size_t pos, short f){ detectMap[pos] = f;}; |
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260 | void setDetectMapValue(size_t x, size_t y, short f){ detectMap[y*axisDim[0] + x] = f;}; |
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261 | void incrementDetectMap(size_t x, size_t y){detectMap[y*axisDim[0]+x]++;}; |
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262 | void incrementDetectMap(size_t pos){detectMap[pos]++;}; |
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263 | void setReconValue(size_t pos, float f){recon[pos] = f;}; |
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264 | void setReconValue(size_t x, size_t y, size_t z, float f){ |
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265 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f; }; |
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266 | void setReconFlag(bool f){reconExists = f;}; |
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267 | |
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268 | Catalogues::CatalogueSpecification getFullCols(){return fullCols;}; |
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269 | Catalogues::CatalogueSpecification *pFullCols(){return &fullCols;}; |
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270 | void setFullCols(Catalogues::CatalogueSpecification C){fullCols=C;}; |
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271 | |
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272 | // additional functions -- in Cubes/cubes.cc |
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273 | /// @brief Allocate memory correctly, with WCS defining the correct axes. |
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274 | OUTCOME initialiseCube(size_t *dimensions, bool allocateArrays=true); |
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275 | OUTCOME initialiseCube(long *dimensions, bool allocateArrays=true); |
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276 | |
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277 | /// @brief Read in a FITS file, with subsection correction. |
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278 | OUTCOME getCube(); |
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279 | /// @brief Read in a FITS file, with subsection correction. |
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280 | OUTCOME getMetadata(); |
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281 | |
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282 | /// @brief Read in command-line options. |
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283 | // int getopts(int argc, char ** argv); |
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284 | int getopts(int argc, char ** argv, std::string progname="Duchamp"){return par.getopts(argc,argv,progname);}; |
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285 | |
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286 | /// @brief Read in reconstructed & smoothed arrays from FITS files on disk. |
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287 | void readSavedArrays(); |
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288 | |
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289 | /// @brief Save an external array to the Cube's pixel array |
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290 | void saveArray(float *input, size_t size); |
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291 | |
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292 | /// @brief Save an external array to the Cube's pixel array |
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293 | void saveArray(std::vector<float> &input); |
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294 | |
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295 | /// @brief Save an external array to the Cube's reconstructed array. |
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296 | void saveRecon(float *input, size_t size); |
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297 | |
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298 | /// @brief Save reconstructed array to an external array. |
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299 | void getRecon(float *output); |
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300 | /// @brief Return the pointer to the reconstructed array. |
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301 | float * getRecon(){return recon; }; |
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302 | |
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303 | /// @brief Save baseline array to an external array. |
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304 | void getBaseline(float *output); |
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305 | /// @brief Return the pointer to the baseline array. |
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306 | float * getBaseline(){return baseline; }; |
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307 | |
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308 | //------------------------ |
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309 | // Statistics for cube |
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310 | // |
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311 | |
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312 | /// @brief Calculate the statistics for the Cube (older version). |
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313 | void setCubeStatsOld(); |
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314 | |
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315 | /// @brief Calculate the statistics for the Cube. |
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316 | void setCubeStats(); |
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317 | |
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318 | /// @brief Set up thresholds for the False Discovery Rate routine. |
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319 | void setupFDR(); |
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320 | /// @brief Set up thresholds for the False Discovery Rate routine using a particular array. |
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321 | void setupFDR(float *input); |
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322 | |
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323 | /// @brief A detection test for a given voxel. |
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324 | bool isDetection(size_t x, size_t y, size_t z); |
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325 | |
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326 | //----------------------------- |
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327 | // Dealing with the detections |
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328 | // |
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329 | |
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330 | /// @brief Get the set of voxels pertaining to the detected objects. |
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331 | std::vector< std::vector<PixelInfo::Voxel> > getObjVoxList(); |
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332 | |
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333 | /// @brief Calculate the object fluxes |
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334 | void calcObjectFluxes(); |
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335 | |
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336 | /// @brief Calculate the WCS parameters for each Cube Detection. |
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337 | void calcObjectWCSparams(); |
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338 | /// @brief Calculate the WCS parameters for each Cube Detection, using flux information in Voxels. |
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339 | void calcObjectWCSparams(std::vector< std::vector<PixelInfo::Voxel> > bigVoxList); |
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340 | void calcObjectWCSparams(std::map<PixelInfo::Voxel,float> &voxelMap); |
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341 | |
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342 | /// @brief Sort the list of detections. |
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343 | void sortDetections(); |
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344 | |
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345 | short *getDetectMap(){return detectMap;}; |
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346 | |
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347 | /// @brief Update the map of detected pixels. |
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348 | void updateDetectMap(); |
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349 | |
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350 | /// @brief Update the map of detected pixels for a given Detection. |
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351 | void updateDetectMap(Detection obj); |
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352 | |
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353 | /// @brief Clear the map of detected pixels. |
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354 | void clearDetectMap(){ |
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355 | for(size_t i=0;i<axisDim[0]*axisDim[1];i++) detectMap[i]=0; |
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356 | }; |
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357 | |
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358 | /// @brief Find the flux enclosed by a Detection. |
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359 | float enclosedFlux(Detection obj); |
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360 | |
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361 | /// @brief Set up the output column definitions for the Cube and its Detection list. |
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362 | void setupColumns(); |
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363 | |
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364 | /// @brief Is the object at the edge of the image? |
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365 | bool objAtSpatialEdge(Detection obj); |
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366 | |
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367 | /// @brief Is the object at an end of the spectrum? |
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368 | bool objAtSpectralEdge(Detection obj); |
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369 | |
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370 | /// @brief Is the object next to or enclosing flagged channels? |
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371 | bool objNextToFlaggedChan(Detection &obj); |
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372 | |
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373 | /// @brief Set warning flags for the detections. |
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374 | void setObjectFlags(); |
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375 | |
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376 | // ---------------------------- |
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377 | // Dealing with the WCS |
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378 | // |
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379 | /// @brief Return the FitsHeader object. |
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380 | FitsHeader getHead(){ return head; }; |
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381 | /// @brief Define the FitsHeader object. |
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382 | void setHead(FitsHeader F){head = F;}; |
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383 | /// @brief Provide a reference to the FitsHeader object. |
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384 | FitsHeader& header(){ FitsHeader &h = head; return h; }; |
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385 | /// @brief Provide a pointer to the FitsHeader object |
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386 | FitsHeader *pHeader(){return &head;}; |
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387 | |
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388 | //------------------------------------------- |
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389 | // FITS-I/O related functions -- not in cubes.cc |
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390 | // |
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391 | /// @brief Function to read in FITS file. |
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392 | OUTCOME getMetadata(std::string fname); // in Cubes/getImage.cc |
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393 | OUTCOME getCube(std::string fname); // in Cubes/getImage.cc |
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394 | |
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395 | /// @brief Convert the flux units to something user-specified. |
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396 | void convertFluxUnits(std::string oldUnit, std::string newUnit, ARRAYREF whichArray=ARRAY); // in Cubes/getImage.cc |
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397 | |
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398 | /// @brief Function to retrieve FITS data array |
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399 | OUTCOME getFITSdata(std::string fname); // in FitsIO/dataIO.cc |
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400 | OUTCOME getFITSdata(); // in FitsIO/dataIO.cc |
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401 | OUTCOME getFITSdata(fitsfile *fptr); // in FitsIO/dataIO.cc |
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402 | |
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403 | OUTCOME writeBasicHeader(fitsfile *fptr, int bitpix, bool is2D=false); |
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404 | |
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405 | /// @brief Handle all the writing to FITS files. |
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406 | void writeToFITS(); |
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407 | |
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408 | /// @brief Save the moment map to a FITS file |
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409 | OUTCOME saveMomentMapImage(); |
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410 | |
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411 | /// @brief Save the moment map mask to a FITS file |
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412 | OUTCOME saveMomentMask(); |
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413 | |
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414 | /// @brief Save a mask array to disk. |
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415 | OUTCOME saveMaskCube(); |
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416 | |
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417 | /// @brief Save Smoothed array to disk. |
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418 | OUTCOME saveSmoothedCube(); |
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419 | |
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420 | /// @brief Save Reconstructed array to disk. |
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421 | OUTCOME saveReconstructedCube(); |
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422 | |
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423 | /// @brief Save baseline array to disk. |
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424 | OUTCOME saveBaselineCube(); |
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425 | |
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426 | //------------------------------------- |
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427 | // Functions that act on the cube |
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428 | // |
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429 | |
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430 | /// @brief Remove excess BLANK pixels from spatial edge of cube. |
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431 | void trimCube(); // in Cubes/trimImage.cc |
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432 | |
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433 | /// @brief Replace BLANK pixels to spatial edge of cube. |
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434 | void unTrimCube(); // in Cubes/trimImage.cc |
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435 | |
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436 | /// @brief Removes the baselines from the spectra, and stores in Cube::baseline |
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437 | void removeBaseline(); // in Cubes/baseline.cc |
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438 | |
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439 | /// @brief Replace the baselines stored in Cube::baseline |
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440 | void replaceBaseline(bool fixObjects=true); // in Cubes/baseline.cc |
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441 | |
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442 | /// @brief Multiply all pixel values by -1. |
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443 | void invert(bool doArrays=true, bool doObjects=true); // in Cubes/invertCube.cc |
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444 | |
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445 | //------------------------------------- |
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446 | // Reconstruction, Searching and Merging functions |
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447 | // |
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448 | // in cubes.cc |
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449 | /// @brief A front-end to all the searching functions |
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450 | void Search(); |
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451 | |
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452 | // in ATrous/ReconSearch.cc |
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453 | /// @brief Front-end to reconstruction & searching functions. |
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454 | void ReconSearch(); |
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455 | /// @brief Switcher to reconstruction functions |
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456 | void ReconCube(); |
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457 | /// @brief Performs 1-dimensional a trous reconstruction on the Cube. |
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458 | void ReconCube1D(); |
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459 | /// @brief Performs 2-dimensional a trous reconstruction on the Cube. |
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460 | void ReconCube2D(); |
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461 | /// @brief Performs 3-dimensional a trous reconstruction on the Cube. |
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462 | void ReconCube3D(); |
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463 | |
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464 | // in Cubes/CubicSearch.cc |
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465 | /// @brief Front-end to the cubic searching routine. |
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466 | void CubicSearch(); |
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467 | |
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468 | // in Cubes/smoothCube.cc |
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469 | /// @brief Smooth the cube with the requested method. |
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470 | void SmoothCube(); |
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471 | /// @brief Front-end to the smoothing and searching functions. |
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472 | void SmoothSearch(); |
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473 | /// @brief A function to spatially smooth the cube and search the result. |
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474 | void SpatialSmoothNSearch(); |
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475 | /// @brief A function to Hanning-smooth the cube. |
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476 | void SpectralSmooth(); |
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477 | /// @brief A function to spatially-smooth the cube. |
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478 | void SpatialSmooth(); |
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479 | |
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480 | void Simple3DSearch(){ |
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481 | /// @brief Basic front-end to the simple 3d searching function -- does |
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482 | /// nothing more. |
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483 | /// |
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484 | /// @details This function just runs the search3DArraySimple function, |
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485 | /// storing the results in the Cube::objectList vector. No stats |
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486 | /// are calculated beforehand, and no logging or detection map |
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487 | /// updating is done. |
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488 | *objectList = search3DArray(axisDim,array,par,Stats); |
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489 | }; |
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490 | |
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491 | void Simple3DSearchRecon(){ |
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492 | /// @brief Basic front-end to the 3d searching function used in the |
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493 | /// reconstruction case -- does nothing more. |
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494 | /// |
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495 | /// @details This function just runs the searchReconArraySimple |
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496 | /// function, storing the results in the Cube::objectList |
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497 | /// vector. No stats are calculated beforehand, and no logging |
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498 | /// or detection map updating is done. The recon array is |
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499 | /// assumed to have been defined already. |
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500 | |
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501 | *objectList = searchReconArray(axisDim,array,recon,par,Stats); |
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502 | }; |
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503 | |
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504 | void Simple3DSearchSmooth(){ |
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505 | /// @brief Basic front-end to the simple 3d searching function |
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506 | /// run on the smoothed array -- does nothing more. |
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507 | /// |
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508 | /// @details This function just runs the search3DArraySimple |
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509 | /// function on the recon array (which contains the smoothed |
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510 | /// array), storing the results in the Cube::objectList |
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511 | /// vector. No stats are calculated beforehand, and no logging |
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512 | /// or detection map updating is done. The recon array is |
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513 | /// assumed to have been defined already. |
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514 | |
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515 | *objectList = search3DArray(axisDim,recon,par,Stats); |
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516 | }; |
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517 | |
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518 | // in Cubes/Merger.cc |
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519 | /// @brief Merge all objects in the detection list so that only distinct ones are left. |
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520 | void ObjectMerger(); |
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521 | /// @brief Grow the sources out to the secondary threshold |
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522 | void growSources(std::vector <Detection> ¤tList); |
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523 | |
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524 | // in Cubes/existingDetections.cc |
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525 | /// @brief Read a previously-created log file to get the detections without searching |
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526 | OUTCOME getExistingDetections(); |
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527 | |
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528 | //------------------------------------- |
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529 | // Text outputting of detected objects. |
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530 | // in Cubes/detectionIO.cc |
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531 | // |
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532 | |
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533 | void outputCatalogue(); |
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534 | |
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535 | /// @brief Set up the output file with parameters and stats. |
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536 | void prepareOutputFile(); |
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537 | |
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538 | /// @brief Write the statistical information to the output file. |
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539 | void outputStats(); |
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540 | |
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541 | /// @brief Prepare the log file for output. |
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542 | void prepareLogFile(int argc, char *argv[]); |
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543 | |
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544 | /// @brief Output detections to the log file. |
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545 | void logDetectionList(bool calcFluxes=true); |
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546 | |
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547 | void logSummary(); |
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548 | |
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549 | /// @brief Write set of detections and metadata to a binary catalogue |
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550 | void writeBinaryCatalogue(); |
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551 | OUTCOME readBinaryCatalogue(); |
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552 | |
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553 | |
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554 | /// @brief Output detections to a Karma annotation file. |
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555 | void outputDetectionsKarma(); |
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556 | |
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557 | /// @brief Output detections to a DS9 annotation file. |
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558 | void outputDetectionsDS9(); |
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559 | |
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560 | /// @brief Output detections to a CASA region file. |
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561 | void outputDetectionsCasa(); |
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562 | |
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563 | /// @brief Write annotation files |
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564 | void outputAnnotations(); |
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565 | |
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566 | /// @brief Output detections to a VOTable. |
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567 | void outputDetectionsVOTable(); |
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568 | |
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569 | |
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570 | // ---------------------------------- |
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571 | // Calculation of overall moment maps |
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572 | |
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573 | /// @brief Return a moment-0 map plus a map of where the object pixels are |
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574 | std::vector<bool> getMomentMap(float *momentMap); |
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575 | /// @brief Return a moment-0 map formatted for logarithmic greyscale plotting, with greyscale limits |
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576 | void getMomentMapForPlot(float *momentMap, float &z1, float &z2); |
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577 | |
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578 | // ---------------------------------- |
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579 | // Graphical plotting of the cube and the detections. |
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580 | // |
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581 | // in Cubes/plotting.cc |
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582 | /// @brief Plot a spatial map of detections based on number of detected channels. |
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583 | void plotDetectionMap(std::string pgDestination); |
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584 | |
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585 | /// @brief Plot a spatial map of detections based on 0th moment map of each object. |
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586 | void plotMomentMap(std::string pgDestination); |
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587 | |
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588 | /// @brief Plot a spatial map of detections based on 0th moment map of each object to a number of PGPLOT devices. |
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589 | void plotMomentMap(std::vector<std::string> pgDestination); |
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590 | |
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591 | /// @brief Draw WCS axes over a PGPLOT map. |
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592 | void plotWCSaxes(){wcsAxes(head.getWCS(),axisDim,DUCHAMP_ID_TEXT_COLOUR,DUCHAMP_WCS_AXIS_COLOUR);}; |
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593 | |
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594 | // in Cubes/outputSpectra.cc |
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595 | /// @brief Print spectra of each detected object. |
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596 | void outputSpectra(); |
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597 | |
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598 | /// @brief Write out text file of all spectra. |
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599 | void writeSpectralData(); |
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600 | |
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601 | /// @brief Print spectrum of a single object |
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602 | void plotSpectrum(int objNum, Plot::SpectralPlot &plot); |
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603 | /// @brief Plot the image cutout for a single object |
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604 | void plotSource(Detection obj, Plot::CutoutPlot &plot); |
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605 | /// @brief Mark channels that have been flagged by the user. |
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606 | void drawFlaggedChannels(Plot::SpectralPlot &plot, double xval, double yval); |
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607 | |
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608 | |
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609 | /// @brief Get the spectral arrays |
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610 | void getSpectralArrays(int objNumber, float *specx, float *specy, float *specRecon, float *specBase); |
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611 | |
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612 | // in Cubes/drawMomentCutout.cc |
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613 | /// @brief Draw the 0th moment map for a single object. |
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614 | void drawMomentCutout(Detection &object); |
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615 | |
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616 | /// @brief Draw a scale bar indicating angular size of the cutout. |
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617 | void drawScale(float xstart,float ystart,float channel); |
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618 | |
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619 | /// @brief Draw a yellow line around the edge of the spatial extent of pixels. |
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620 | void drawFieldEdge(); |
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621 | |
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622 | private: |
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623 | short int numNondegDim; ///< Number of non-degenerate dimensions (ie. with size>1) |
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624 | float *recon; ///< reconstructed array - used when doing a trous reconstruction. |
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625 | bool reconExists; ///< flag saying whether there is a reconstruction |
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626 | short *detectMap; ///< "moment map" - x,y locations of detected pixels |
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627 | float *baseline; ///< array of spectral baseline values. |
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628 | |
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629 | bool reconAllocated; ///< have we allocated memory for the recon array? |
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630 | bool baselineAllocated;///< have we allocated memory for the baseline array? |
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631 | FitsHeader head; ///< the WCS and other header information. |
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632 | Catalogues::CatalogueSpecification fullCols; ///< the list of all columns as printed in the results file |
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633 | }; |
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634 | |
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635 | |
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636 | //============================================================================ |
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637 | |
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638 | /// @brief A DataArray object limited to two dimensions, and with some additional |
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639 | /// special functions. |
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640 | /// |
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641 | /// @details It is used primarily for searching a 1- or 2-D array with |
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642 | /// lutz_detect() and spectrumDetect(). |
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643 | |
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644 | class Image : public DataArray |
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645 | { |
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646 | public: |
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647 | Image(){numPixels=0; numDim=2; minSize=2;}; |
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648 | Image(size_t nPix); |
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649 | Image(size_t *dimensions); |
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650 | virtual ~Image(){}; |
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651 | Image(const Image &i); |
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652 | Image& operator=(const Image &i); |
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653 | |
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654 | //-------------------- |
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655 | // Defining the array |
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656 | // |
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657 | /// @brief Save an external array to the Cube's pixel array |
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658 | void saveArray(float *input, size_t size); |
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659 | |
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660 | /// @brief Extract a spectrum from an array and save to the local pixel array. |
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661 | void extractSpectrum(float *Array, size_t *dim, size_t pixel); |
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662 | |
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663 | /// @brief Extract an image from an array and save to the local pixel array. |
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664 | void extractImage(float *Array, size_t *dim, size_t channel); |
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665 | |
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666 | /// @brief Extract a spectrum from a cube and save to the local pixel array. |
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667 | void extractSpectrum(Cube &cube, size_t pixel); |
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668 | |
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669 | /// @brief Extract an image from a cube and save to the local pixel array. |
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670 | void extractImage(Cube &cube, size_t channel); |
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671 | |
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672 | //-------------------- |
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673 | // Accessing the data. |
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674 | // |
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675 | float getPixValue(size_t pos){ return array[pos]; }; |
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676 | float getPixValue(size_t x, size_t y){return array[y*axisDim[0] + x];}; |
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677 | // the next few should have checks against array overflow... |
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678 | void setPixValue(size_t pos, float f){array[pos] = f;}; |
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679 | void setPixValue(size_t x, size_t y, float f){array[y*axisDim[0] + x] = f;}; |
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680 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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681 | bool isBlank(size_t x,size_t y){return par.isBlank(array[y*axisDim[0]+x]);}; |
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682 | |
---|
683 | //----------------------- |
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684 | // Detection-related |
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685 | // |
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686 | /// @brief Detect objects in a 2-D image |
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687 | std::vector<PixelInfo::Object2D> findSources2D(); |
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688 | |
---|
689 | /// @brief Detect objects in a 1-D spectrum |
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690 | std::vector<PixelInfo::Scan> findSources1D(); |
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691 | |
---|
692 | unsigned int getMinSize(){return minSize;}; |
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693 | void setMinSize(int i){minSize=i;}; |
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694 | |
---|
695 | /// @brief A detection test for a pixel location. |
---|
696 | bool isDetection(size_t x, size_t y){ |
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697 | /// @details Test whether a pixel (x,y) is a statistically |
---|
698 | /// significant detection, according to the set of statistics in |
---|
699 | /// the local StatsContainer object. |
---|
700 | |
---|
701 | size_t voxel = y*axisDim[0] + x; |
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702 | if(isBlank(x,y)) return false; |
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703 | else return Stats.isDetection(array[voxel]); |
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704 | }; |
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705 | |
---|
706 | /// @brief Blank out a set of channels marked as flagged |
---|
707 | void removeFlaggedChannels(); |
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708 | |
---|
709 | private: |
---|
710 | unsigned int minSize; ///< the minimum number of pixels for a detection to be accepted. |
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711 | }; |
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712 | |
---|
713 | |
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714 | } |
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715 | |
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716 | #endif |
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