1 | #ifndef CUBES_H |
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2 | #define CUBES_H |
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3 | |
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4 | #include <iostream> |
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5 | #include <string> |
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6 | #include <vector> |
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7 | |
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8 | #ifndef PARAM_H |
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9 | #include <param.hh> |
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10 | #endif |
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11 | #ifndef DETECTION_H |
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12 | #include <Detection/detection.hh> |
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13 | #endif |
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14 | #ifndef COLUMNS_H |
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15 | #include <Detection/columns.hh> |
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16 | #endif |
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17 | #ifndef PLOTS_H |
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18 | #include <Cubes/plots.hh> |
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19 | #endif |
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20 | #ifndef STATS_H |
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21 | #include <Utils/Statistics.hh> |
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22 | #endif |
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23 | |
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24 | using std::string; |
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25 | using std::vector; |
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26 | using namespace Column; |
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27 | using namespace Statistics; |
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28 | |
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29 | /****************************************************************/ |
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30 | /** |
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31 | * Base class for the image container. |
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32 | * |
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33 | * Definition of an n-dimensional data array: |
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34 | * array of pixel values, size & dimensions |
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35 | * array of Detection objects |
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36 | */ |
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37 | |
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38 | class DataArray |
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39 | { |
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40 | public: |
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41 | DataArray(); ///< Basic DataArray constructor |
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42 | DataArray(short int nDim); ///< Basic nDim-dimensional DataArray constructor |
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43 | DataArray(short int nDim, long size);///< Basic nDim-dimensional DataArray constructor, specifying size. |
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44 | DataArray(short int nDim, long *dimensions); ///< Basic nDim-dimensional DataArray constructor, specifying size of dimensions. |
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45 | virtual ~DataArray(); ///< Basic DataArray constructor |
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46 | |
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47 | //----------------------------------------- |
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48 | // Obvious inline accessor functions. |
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49 | // |
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50 | long getDimX(){if(numDim>0) return this->axisDim[0];else return 0;}; |
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51 | long getDimY(){if(numDim>1) return this->axisDim[1];else return 1;}; |
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52 | long getDimZ(){if(numDim>2) return this->axisDim[2];else return 1;}; |
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53 | long getSize(){ return this->numPixels; }; |
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54 | short int getNumDim(){ return this->numDim; }; |
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55 | virtual float getPixValue(long pos){ return array[pos]; }; |
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56 | virtual void setPixValue(long pos, float f){array[pos] = f;};; |
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57 | Detection getObject(long number){ return objectList[number]; }; |
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58 | vector <Detection> getObjectList(){ return objectList; }; |
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59 | long getNumObj(){ return objectList.size(); }; |
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60 | |
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61 | /** Delete all objects from the list of detections. */ |
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62 | void clearDetectionList(){ this->objectList.clear(); }; |
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63 | |
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64 | /** Read a parameter set from file. */ |
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65 | int readParam(string paramfile){ |
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66 | /** |
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67 | * Uses Param::readParams() to read parameters from a file. |
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68 | * \param paramfile The file to be read. |
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69 | */ |
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70 | return par.readParams(paramfile); }; |
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71 | |
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72 | //----------------------------------------- |
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73 | // Related to the various arrays |
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74 | // |
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75 | /** Return first three dimensional axes. */ |
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76 | void getDim(long &x, long &y, long &z); |
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77 | /** Return array of dimensional sizes.*/ |
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78 | void getDimArray(long *output); |
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79 | |
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80 | /** Return pixel value array. */ |
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81 | void getArray(float *output); |
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82 | |
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83 | /** Save pixel value array. */ |
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84 | virtual void saveArray(float *input, long size); |
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85 | |
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86 | //----------------------------------------- |
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87 | // Related to the object lists |
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88 | // |
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89 | /** Adds a single detection to the object list.*/ |
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90 | void addObject(Detection object); |
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91 | |
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92 | /** Adds all objects in a detection list to the object list. */ |
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93 | void addObjectList(vector <Detection> newlist); |
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94 | /** Add pixel offsets to object coordinates. */ |
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95 | void addObjectOffsets(); |
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96 | |
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97 | //----------------------------------------- |
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98 | // Parameter list related. |
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99 | // |
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100 | /** Output the Param set.*/ |
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101 | void showParam(std::ostream &stream){ stream << this->par; }; |
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102 | /** Return the Param set.*/ |
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103 | Param getParam(){ return this->par; }; |
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104 | /** Save a Param set to the Cube.*/ |
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105 | void saveParam(Param newpar){this->par = newpar;}; |
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106 | /** Provides a reference to the Param set.*/ |
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107 | Param& pars(){ Param &rpar = this->par; return rpar; }; |
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108 | /** Is the voxel number given by vox a BLANK value?*/ |
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109 | bool isBlank(int vox); |
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110 | |
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111 | // -------------------------------------------- |
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112 | // Statistics |
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113 | // |
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114 | /** Returns the StatsContainer. */ |
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115 | StatsContainer<float> getStats(){ return this->Stats; }; |
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116 | |
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117 | /** Provides a reference to the StatsContainer. */ |
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118 | StatsContainer<float>& stats(){ StatsContainer<float> &rstats = this->Stats; return rstats;}; |
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119 | /** Save a StatsContainer to the Cube. */ |
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120 | void saveStats(StatsContainer<float> newStats){ this->Stats = newStats;}; |
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121 | |
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122 | /** A detection test for value. */ |
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123 | bool isDetection(float value); |
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124 | |
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125 | /** A detection test for pixel. */ |
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126 | bool isDetection(long voxel); |
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127 | |
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128 | |
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129 | /** Output operator for DataArray.*/ |
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130 | friend std::ostream& operator<< (std::ostream& theStream, DataArray &array); |
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131 | |
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132 | |
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133 | protected: |
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134 | short int numDim; ///< Number of dimensions. |
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135 | long *axisDim; ///< Array of dimensions of cube (ie. how large in each direction). |
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136 | long numPixels; ///< Total number of pixels in cube. |
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137 | float *array; ///< Array of data. |
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138 | vector <Detection> objectList; ///< The list of detected objects. |
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139 | Param par; ///< A parameter list. |
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140 | StatsContainer<float> Stats; ///< The statistics for the DataArray. |
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141 | }; |
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142 | |
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143 | |
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144 | |
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145 | //=============================================================================== |
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146 | |
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147 | /** |
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148 | * Definition of an data-cube object (3D): |
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149 | * a DataArray object limited to dim=3 |
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150 | */ |
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151 | |
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152 | class Cube : public DataArray |
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153 | { |
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154 | public: |
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155 | Cube(); ///< Basic Cube constructor. |
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156 | Cube(long nPix); ///< Alternative Cube constructor. |
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157 | Cube(long *dimensions); ///< Alternative Cube constructor. |
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158 | virtual ~Cube(); ///< Basic Cube destructor. |
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159 | |
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160 | // INLINE functions -- definitions included after class declaration. |
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161 | /** Is the voxel number given by vox a BLANK value? */ |
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162 | bool isBlank(int vox){ return par.isBlank(array[vox]); }; |
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163 | |
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164 | /** Is the voxel at (x,y,z) a BLANK value? */ |
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165 | bool isBlank(long x, long y, long z){ |
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166 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]); }; |
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167 | |
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168 | /** Does the Cube::recon array exist? */ |
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169 | bool isRecon(){ return reconExists; }; |
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170 | |
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171 | float getPixValue(long pos){ return array[pos]; }; |
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172 | float getPixValue(long x, long y, long z){ |
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173 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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174 | short getDetectMapValue(long pos){ return detectMap[pos]; }; |
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175 | short getDetectMapValue(long x, long y){ return detectMap[y*axisDim[0]+x]; }; |
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176 | float getReconValue(long pos){ return recon[pos]; }; |
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177 | float getReconValue(long x, long y, long z){ |
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178 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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179 | float getBaselineValue(long pos){ return baseline[pos]; }; |
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180 | float getBaselineValue(long x, long y, long z){ |
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181 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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182 | void setPixValue(long pos, float f){array[pos] = f;};; |
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183 | void setPixValue(long x, long y, long z, float f){ |
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184 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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185 | void setDetectMapValue(long pos, short f){ detectMap[pos] = f;}; |
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186 | void setDetectMapValue(long x, long y, short f){ detectMap[y*axisDim[0] + x] = f;}; |
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187 | void setReconValue(long pos, float f){recon[pos] = f;}; |
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188 | void setReconValue(long x, long y, long z, float f){ |
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189 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f; }; |
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190 | void setReconFlag(bool f){reconExists = f;}; |
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191 | |
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192 | vector<Col> getLogCols(){return logCols;}; |
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193 | void setLogCols(vector<Col> C){logCols=C;}; |
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194 | vector<Col> getFullCols(){return fullCols;}; |
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195 | void setFullCols(vector<Col> C){fullCols=C;}; |
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196 | |
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197 | // additional functions -- in Cubes/cubes.cc |
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198 | /** Allocate memory correctly, with WCS defining the correct axes. */ |
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199 | void initialiseCube(long *dimensions); |
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200 | |
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201 | /** Read in a FITS file, with subsection correction. */ |
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202 | int getCube(); |
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203 | |
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204 | /** Read in command-line options. */ |
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205 | int getopts(int argc, char ** argv); |
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206 | |
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207 | /** Read in reconstructed & smoothed arrays from FITS files on disk. */ |
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208 | void readSavedArrays(); |
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209 | |
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210 | /** Save an external array to the Cube's pixel array */ |
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211 | void saveArray(float *input, long size); |
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212 | |
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213 | /** Save an external array to the Cube's reconstructed array. */ |
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214 | void saveRecon(float *input, long size); |
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215 | |
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216 | /** Save reconstructed array to an external array. */ |
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217 | void getRecon(float *output); |
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218 | |
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219 | /** Set Milky Way channels to zero. */ |
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220 | void removeMW(); |
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221 | |
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222 | //------------------------ |
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223 | // Statistics for cube |
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224 | // |
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225 | |
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226 | /** Calculate the statistics for the Cube (older version). */ |
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227 | void setCubeStatsOld(); |
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228 | |
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229 | /** Calculate the statistics for the Cube. */ |
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230 | void setCubeStats(); |
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231 | |
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232 | /** Set up thresholds for the False Discovery Rate routine. */ |
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233 | int setupFDR(); |
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234 | |
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235 | /** A detection test for a given voxel. */ |
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236 | bool isDetection(long x, long y, long z); |
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237 | |
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238 | //----------------------------- |
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239 | // Dealing with the detections |
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240 | // |
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241 | |
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242 | /** Calculate the WCS parameters for each Cube Detection. */ |
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243 | void calcObjectWCSparams(); |
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244 | |
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245 | /** Sort the list of detections. */ |
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246 | void sortDetections(); |
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247 | |
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248 | /** Update the map of detected pixels. */ |
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249 | void updateDetectMap(); |
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250 | |
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251 | /** Update the map of detected pixels for a given Detection. */ |
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252 | void updateDetectMap(Detection obj); |
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253 | |
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254 | /** Find the flux enclosed by a Detection. */ |
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255 | float enclosedFlux(Detection obj); |
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256 | |
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257 | /** Set up the output column definitions for the Cube and its Detection list. */ |
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258 | void setupColumns(); |
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259 | |
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260 | /** Is the object at the edge of the image? */ |
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261 | bool objAtSpatialEdge(Detection obj); |
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262 | |
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263 | /** Is the object at an end of the spectrum? */ |
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264 | bool objAtSpectralEdge(Detection obj); |
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265 | |
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266 | /** Set warning flags for the detections. */ |
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267 | void setObjectFlags(); |
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268 | |
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269 | // ---------------------------- |
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270 | // Dealing with the WCS |
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271 | // |
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272 | FitsHeader getHead(){ return head; }; |
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273 | void setHead(FitsHeader F){head = F;}; |
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274 | FitsHeader& header(){ FitsHeader &h = head; return h; }; |
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275 | |
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276 | /** Convert a point from WCS to Pixel coords. */ |
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277 | int wcsToPix(const double *world, double *pix); |
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278 | |
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279 | /** Convert a set of points from WCS to Pixel coords. */ |
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280 | int wcsToPix(const double *world, double *pix, const int npts); |
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281 | |
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282 | /** Convert a point from Pixel to WCS coords. */ |
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283 | int pixToWCS(const double *pix, double *world); |
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284 | |
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285 | /** Convert a set of points from Pixel to WCS coords. */ |
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286 | int pixToWCS(const double *pix, double *world, const int npts); |
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287 | |
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288 | //------------------------------------------- |
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289 | // FITS-I/O related functions -- not in cubes.cc |
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290 | // |
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291 | /** Function to read in FITS file.*/ |
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292 | int getCube(string fname); // in Cubes/getImage.cc |
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293 | |
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294 | /** Function to retrieve FITS data array */ |
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295 | int getFITSdata(string fname); // in FitsIO/dataIO.cc |
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296 | |
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297 | /** Save Hanning-smoothed array to disk.*/ |
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298 | void saveSmoothedCube(); // in Cubes/saveImage.cc |
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299 | /** Save Reconstructed array to disk. */ |
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300 | void saveReconstructedCube(); // in Cubes/saveImage.cc |
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301 | |
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302 | /** Read in reconstructed array from FITS file. */ |
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303 | int readReconCube(); // in Cubes/readRecon.cc |
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304 | |
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305 | /** Read in Hanning-smoothed array from FITS file. */ |
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306 | int readSmoothCube(); // in Cubes/readSmooth.cc |
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307 | |
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308 | //------------------------------------- |
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309 | // Functions that act on the cube |
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310 | // |
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311 | |
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312 | /** Remove excess BLANK pixels from spatial edge of cube. */ |
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313 | void trimCube(); // in Cubes/trimImage.cc |
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314 | |
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315 | /** Replace BLANK pixels to spatial edge of cube. */ |
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316 | void unTrimCube(); // in Cubes/trimImage.cc |
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317 | |
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318 | /** Removes the baselines from the spectra, and stores in Cube::baseline */ |
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319 | void removeBaseline(); // in Cubes/baseline.cc |
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320 | |
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321 | /** Replace the baselines stored in Cube::baseline */ |
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322 | void replaceBaseline(); // in Cubes/baseline.cc |
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323 | |
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324 | /** Multiply all pixel values by -1. */ |
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325 | void invert(); // in Cubes/invertCube.cc |
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326 | |
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327 | /** Undo the inversion, and invert fluxes of all detected objects. */ |
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328 | void reInvert(); // in Cubes/invertCube.cc |
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329 | |
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330 | //------------------------------------- |
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331 | // Reconstruction, Searching and Merging functions |
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332 | // |
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333 | // in ATrous/ReconSearch.cc |
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334 | /** Switcher to reconstruction functions */ |
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335 | void ReconCube(); |
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336 | |
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337 | /** Front-end to reconstruction & searching functions.*/ |
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338 | void ReconSearch(); |
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339 | /** Performs 1-dimensional a trous reconstruction on the Cube. */ |
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340 | void ReconCube1D(); |
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341 | /** Performs 2-dimensional a trous reconstruction on the Cube. */ |
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342 | void ReconCube2D(); |
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343 | /** Performs 3-dimensional a trous reconstruction on the Cube. */ |
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344 | void ReconCube3D(); |
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345 | |
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346 | // in Cubes/CubicSearch.cc |
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347 | /** Front-end to the cubic searching routine. */ |
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348 | void CubicSearch(); |
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349 | |
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350 | // in Cubes/smoothCube.cc |
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351 | /** Front-end to the smoothing and searching functions. */ |
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352 | void SmoothSearch(); |
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353 | /** A function to Hanning-smooth the cube. */ |
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354 | void SmoothCube(); |
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355 | |
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356 | // in Cubes/Merger.cc |
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357 | /** Merge all objects in the detection list so that only distinct ones are left. */ |
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358 | void ObjectMerger(); |
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359 | |
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360 | //------------------------------------- |
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361 | // Text outputting of detected objects. |
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362 | // in Cubes/detectionIO.cc |
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363 | // |
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364 | /** Output detections to a Karma annotation file. */ |
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365 | void outputDetectionsKarma(std::ostream &stream); |
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366 | |
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367 | /** Output detections to a VOTable. */ |
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368 | void outputDetectionsVOTable(std::ostream &stream); |
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369 | |
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370 | /** Output detections to the output file and standard output. */ |
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371 | void outputDetectionList(); |
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372 | |
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373 | /** Output detections to the log file. */ |
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374 | void logDetectionList(); |
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375 | |
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376 | /** Output a single detection to the log file. */ |
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377 | void logDetection(Detection obj, int counter); |
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378 | |
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379 | |
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380 | // ---------------------------------- |
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381 | // Graphical plotting of the cube and the detections. |
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382 | // |
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383 | /** Draw blank edges of cube. */ |
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384 | void plotBlankEdges(); // in cubes.cc |
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385 | |
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386 | // in Cubes/plotting.cc |
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387 | /** Plot a spatial map of detections based on number of detected channels. */ |
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388 | void plotDetectionMap(string pgDestination); |
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389 | |
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390 | /** Plot a spatial map of detections based on 0th moment map of each object. */ |
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391 | void plotMomentMap(string pgDestination); |
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392 | |
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393 | /** Plot a spatial map of detections based on 0th moment map of each object to a number of PGPLOT devices. */ |
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394 | void plotMomentMap(vector<string> pgDestination); |
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395 | |
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396 | /** Draw WCS axes over a PGPLOT map. */ |
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397 | void plotWCSaxes(); |
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398 | |
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399 | // in Cubes/outputSpectra.cc |
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400 | /** Print spectra of each detected object. */ |
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401 | void outputSpectra(); |
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402 | |
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403 | /** Print spectrum of a single object */ |
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404 | void plotSpectrum(Detection obj,Plot::SpectralPlot &plot); |
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405 | |
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406 | // in Cubes/drawMomentCutout.cc |
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407 | /** Draw the 0th moment map for a single object. */ |
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408 | void drawMomentCutout(Detection &object); |
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409 | |
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410 | /** Draw a scale bar indicating angular size of the cutout. */ |
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411 | void drawScale(float xstart,float ystart,float channel); |
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412 | |
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413 | /** Draw a yellow line around the edge of the spatial extent of pixels. */ |
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414 | void drawFieldEdge(); |
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415 | |
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416 | private: |
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417 | float *recon; ///< reconstructed array - used when doing a trous reconstruction. |
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418 | bool reconExists; ///< flag saying whether there is a reconstruction |
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419 | short *detectMap; ///< "moment map" - x,y locations of detected pixels |
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420 | float *baseline; ///< array of spectral baseline values. |
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421 | |
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422 | bool reconAllocated; ///< have we allocated memory for the recon array? |
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423 | bool baselineAllocated;///< have we allocated memory for the baseline array? |
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424 | |
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425 | FitsHeader head; ///< the WCS and other header information. |
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426 | vector<Col> fullCols; ///< the list of all columns as printed in the results file |
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427 | vector<Col> logCols; ///< the list of columns as printed in the log file |
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428 | |
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429 | }; |
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430 | |
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431 | //////////// |
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432 | //// Cube inline function definitions |
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433 | //////////// |
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434 | |
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435 | inline int Cube::wcsToPix(const double *world, double *pix) |
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436 | { |
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437 | /** |
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438 | * Use the WCS in the FitsHeader to convert from WCS to pixel coords for |
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439 | * a single point. |
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440 | * \param world The world coordinates. |
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441 | * \param pix The returned pixel coordinates. |
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442 | */ |
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443 | return this->head.wcsToPix(world,pix); |
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444 | } |
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445 | inline int Cube::wcsToPix(const double *world, double *pix, const int npts) |
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446 | { |
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447 | /** |
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448 | * Use the WCS in the FitsHeader to convert from WCS to pixel coords for |
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449 | * a set of points. |
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450 | * \param world The world coordinates. |
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451 | * \param pix The returned pixel coordinates. |
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452 | * \param npts The number of points being converted. |
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453 | */ |
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454 | return this->head.wcsToPix(world,pix,npts); |
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455 | } |
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456 | inline int Cube::pixToWCS(const double *pix, double *world) |
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457 | { |
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458 | /** |
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459 | * Use the WCS in the FitsHeader to convert from pixel to WCS coords for |
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460 | * a single point. |
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461 | * \param pix The pixel coordinates. |
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462 | * \param world The returned world coordinates. |
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463 | */ |
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464 | return this->head.pixToWCS(pix,world); |
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465 | } |
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466 | inline int Cube::pixToWCS(const double *pix, double *world, const int npts) |
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467 | { |
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468 | /** |
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469 | * Use the WCS in the FitsHeader to convert from pixel to WCS coords for |
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470 | * a set of points. |
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471 | * \param pix The pixel coordinates. |
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472 | * \param world The returned world coordinates. |
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473 | * \param npts The number of points being converted. |
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474 | */ |
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475 | return this->head.pixToWCS(pix,world,npts); |
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476 | } |
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477 | |
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478 | |
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479 | //=============================================================================== |
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480 | |
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481 | /** |
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482 | * A DataArray object limited to two dimensions, and with some additional |
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483 | * special functions. |
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484 | * |
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485 | * It is used primarily for searching a 1- or 2-D array with |
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486 | * lutz_detect() and spectrumDetect(). |
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487 | */ |
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488 | |
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489 | class Image : public DataArray |
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490 | { |
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491 | public: |
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492 | Image(){numPixels=0; numDim=2;}; |
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493 | Image(long nPix); |
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494 | Image(long *dimensions); |
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495 | virtual ~Image(){}; |
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496 | |
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497 | // Defining the array |
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498 | /** Save an external array to the Cube's pixel array */ |
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499 | void saveArray(float *input, long size); |
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500 | |
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501 | /** Extract a spectrum from an array and save to the local pixel array. */ |
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502 | void extractSpectrum(float *Array, long *dim, long pixel); |
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503 | |
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504 | /** Extract an image from an array and save to the local pixel array. */ |
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505 | void extractImage(float *Array, long *dim, long channel); |
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506 | |
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507 | /** Extract a spectrum from a cube and save to the local pixel array. */ |
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508 | void extractSpectrum(Cube &cube, long pixel); |
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509 | |
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510 | /** Extract an image from a cube and save to the local pixel array. */ |
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511 | void extractImage(Cube &cube, long channel); |
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512 | |
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513 | //-------------------- |
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514 | // Accessing the data. |
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515 | float getPixValue(long pos){ return array[pos]; }; |
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516 | float getPixValue(long x, long y){return array[y*axisDim[0] + x];}; |
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517 | // the next few should have checks against array overflow... |
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518 | void setPixValue(long pos, float f){array[pos] = f;};; |
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519 | void setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;}; |
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520 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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521 | bool isBlank(long x,long y){return par.isBlank(array[y*axisDim[0]+x]);}; |
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522 | |
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523 | //----------------------- |
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524 | // Detection-related |
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525 | /** Detect objects in a 2-D image */ |
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526 | void lutz_detect(); // in Detection/lutz_detect.cc |
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527 | |
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528 | /** Detect objects in a 1-D spectrum */ |
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529 | void spectrumDetect(); // in Detection/spectrumDetect.cc |
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530 | |
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531 | int getMinSize(){return minSize;}; |
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532 | void setMinSize(int i){minSize=i;}; |
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533 | // the rest are in Detection/thresholding_functions.cc |
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534 | |
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535 | /** A detection test for a pixel location. */ |
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536 | bool isDetection(long x, long y){ |
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537 | /** |
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538 | * Test whether a pixel (x,y) is a statistically significant detection, |
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539 | * according to the set of statistics in the local StatsContainer object. |
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540 | */ |
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541 | long voxel = y*axisDim[0] + x; |
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542 | if(isBlank(x,y)) return false; |
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543 | else return Stats.isDetection(array[voxel]); |
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544 | }; |
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545 | |
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546 | /** Blank out a set of channels marked as being Milky Way channels */ |
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547 | void removeMW(); |
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548 | |
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549 | private: |
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550 | int minSize; ///< the minimum number of pixels for a detection to be accepted. |
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551 | }; |
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552 | |
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553 | |
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554 | /****************************************************************/ |
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555 | ////////////////////////////////////////////////////// |
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556 | // Prototypes for functions that use above classes |
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557 | ////////////////////////////////////////////////////// |
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558 | |
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559 | /** Search a reconstructed array for significant detections. */ |
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560 | vector <Detection> searchReconArray(long *dim, float *originalArray, |
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561 | float *reconArray, Param &par, |
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562 | StatsContainer<float> &stats); |
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563 | |
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564 | /** Search a 3-dimensional array for significant detections. */ |
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565 | vector <Detection> search3DArray(long *dim, float *Array, Param &par, |
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566 | StatsContainer<float> &stats); |
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567 | |
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568 | /** Grow an object to a lower threshold */ |
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569 | void growObject(Detection &object, Cube &cube); |
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570 | |
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571 | /** Draw the edge of the BLANK region on a map.*/ |
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572 | void drawBlankEdges(float *dataArray, int xdim, int ydim, Param &par); |
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573 | |
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574 | #endif |
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