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