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 | |
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21 | using std::string; |
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22 | using std::vector; |
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23 | using namespace Column; |
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24 | |
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25 | /****************************************************************/ |
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26 | ///////////////////////////////////////////////////////////// |
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27 | //// Definition of an n-dimensional data array: |
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28 | //// array of pixel values, size & dimensions |
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29 | //// array of Detection objects |
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30 | ///////////////////////////////////////////////////////////// |
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31 | |
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32 | |
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33 | class DataArray |
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34 | { |
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35 | public: |
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36 | DataArray(){numDim=0; numPixels=0;}; |
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37 | DataArray(short int nDim){numDim=nDim; numPixels=0;}; |
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38 | DataArray(short int nDim, long size); |
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39 | DataArray(short int nDim, long *dimensions); |
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40 | virtual ~DataArray(); |
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41 | // Size and Dimension related |
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42 | long getDimX(){if(numDim>0) return axisDim[0];else return 0;}; |
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43 | long getDimY(){if(numDim>1) return axisDim[1];else return 1;}; |
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44 | long getDimZ(){if(numDim>2) return axisDim[2];else return 1;}; |
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45 | void getDim(long &x, long &y, long &z); |
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46 | long getSize(){return numPixels;}; |
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47 | short int getNumDim(){return numDim;}; |
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48 | // Related to the various arrays |
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49 | void getDimArray(long *output); |
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50 | void getArray(float *output); |
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51 | virtual void saveArray(float *input, long size); |
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52 | float getPixValue(long pos){return array[pos];}; |
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53 | void setPixValue(long pos, float f){array[pos] = f;}; |
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54 | // Related to the object lists |
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55 | Detection getObject(long number){return objectList[number];}; |
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56 | void addObject(Detection object); |
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57 | // adds a single detection to the object list |
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58 | vector <Detection> getObjectList(){return objectList;}; |
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59 | void addObjectList(vector <Detection> newlist); |
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60 | // adds all objects in a detection list to the object list |
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61 | void addObjectOffsets(); |
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62 | long getNumObj(){return objectList.size();}; |
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63 | void clearDetectionList(){this->objectList.clear();}; |
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64 | // Parameter list related. |
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65 | int readParam(string paramfile){ |
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66 | return par.readParams(paramfile);}; |
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67 | void showParam(std::ostream &stream){stream << par;}; |
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68 | Param getParam(){return par;}; |
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69 | void saveParam(Param newpar){par = newpar;}; |
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70 | Param& pars(){Param &rpar = par; return rpar;}; |
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71 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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72 | |
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73 | friend std::ostream& operator<< ( std::ostream& theStream, DataArray &array); |
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74 | |
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75 | |
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76 | protected: |
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77 | short int numDim; // number of dimensions. |
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78 | long *axisDim; // array of dimensions of cube |
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79 | // (ie. how large in each direction). |
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80 | long numPixels; // total number of pixels in cube |
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81 | float *array; // array of data |
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82 | vector <Detection> objectList; // the list of detected objects in the image |
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83 | Param par; // a parameter list. |
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84 | }; |
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85 | |
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86 | |
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87 | /****************************************************************/ |
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88 | ///////////////////////////////////////////////////////////// |
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89 | //// Definition of an image object (2D): |
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90 | //// a DataArray object |
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91 | //// arrays for: probability values (for FDR) |
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92 | //// mask image to indicate location of objects |
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93 | //// detected objects |
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94 | //// statistics information |
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95 | ///////////////////////////////////////////////////////////// |
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96 | |
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97 | class Cube; |
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98 | class Image : public DataArray |
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99 | { |
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100 | public: |
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101 | Image(){ |
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102 | numPixels=0; |
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103 | numDim=2;}; |
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104 | Image(long nPix); |
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105 | Image(long *dimensions); |
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106 | virtual ~Image(); |
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107 | |
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108 | // Defining the array |
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109 | void saveArray(float *input, long size); |
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110 | void extractSpectrum(float *Array, long *dim, long pixel); |
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111 | void extractImage(float *Array, long *dim, long channel); |
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112 | void extractSpectrum(Cube &cube, long pixel); |
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113 | void extractImage(Cube &cube, long channel); |
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114 | // Accessing the data. |
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115 | float getPixValue(long x, long y){return array[y*axisDim[0] + x];}; |
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116 | float getPixValue(long pos){return array[pos];}; |
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117 | float getPValue(long pos){return pValue[pos];}; |
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118 | float getPValue(long x, long y){return pValue[y*axisDim[0] + x];}; |
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119 | short int getMaskValue(long pos){return mask[pos];}; |
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120 | short int getMaskValue(long x, long y){return mask[y*axisDim[0] + x];}; |
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121 | // the next few should have checks against array overflow... |
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122 | void setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;}; |
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123 | void setPixValue(long pos, float f){array[pos] = f;}; |
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124 | void setPValue(long pos, float p){pValue[pos] = p;}; |
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125 | void setPValue(long x, long y, float p){pValue[y*axisDim[0] + x] = p;}; |
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126 | void setMaskValue(long pos, short int m){mask[pos] = m;}; |
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127 | void setMaskValue(long x, long y, short int m){mask[y*axisDim[0]+x]=m;}; |
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128 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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129 | bool isBlank(long x,long y){return par.isBlank(array[y*axisDim[0]+x]);}; |
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130 | // Stats-related |
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131 | void setStats(float m, float s, float c){mean=m; sigma=s; cutLevel=c;}; |
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132 | void findStats(int code); |
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133 | float getMean(){return mean;}; |
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134 | void setMean(float m){mean=m;}; |
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135 | float getSigma(){return sigma;}; |
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136 | void setSigma(float s){sigma=s;}; |
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137 | float getCut(){return cutLevel;}; |
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138 | void setCut(float c){cutLevel=c;}; |
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139 | float getPCut(){return pCutLevel;}; |
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140 | void setPCut(float p){pCutLevel = p;}; |
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141 | float getAlpha(){return alpha;}; |
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142 | void setAlpha(float a){alpha = a;}; |
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143 | int getMinSize(){return minSize;}; |
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144 | void setMinSize(int s){minSize = s;}; |
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145 | |
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146 | void maskObject(Detection &object); |
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147 | |
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148 | // Detection-related |
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149 | void lutz_detect(); // in Detection/lutz_detect.cc |
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150 | void spectrumDetect(); // in Detection/spectrumDetect.cc |
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151 | // the rest are in Detection/thresholding_functions.cc |
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152 | int setupFDR(); |
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153 | bool isDetection(float value); |
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154 | bool isDetection(long x, long y); |
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155 | bool isDetectionFDR(float pvalue); |
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156 | |
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157 | void removeMW(); |
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158 | |
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159 | private: |
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160 | float *pValue; // the array of p-values for each pixel |
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161 | // --> used by FDR method |
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162 | short int *mask; // a mask image indicating where objects are |
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163 | |
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164 | float mean; // the mean background level of the image |
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165 | float sigma; // the standard deviation of the image's background |
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166 | float cutLevel; // the limiting value (in sigmas above the mean) for |
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167 | // a pixel to be called a detection. |
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168 | float alpha; // used by FDR routine -- significance level |
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169 | float pCutLevel; // the limiting P-value for the FDR analysis |
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170 | int minSize; // the minimum number of pixels for a detection |
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171 | // to be accepted. |
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172 | }; |
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173 | |
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174 | /****************************************************************/ |
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175 | ///////////////////////////////////////////////////////////// |
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176 | //// Definition of an data-cube object (3D): |
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177 | //// a DataArray object limited to dim=3 |
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178 | ///////////////////////////////////////////////////////////// |
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179 | |
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180 | class Cube : public DataArray |
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181 | { |
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182 | public: |
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183 | Cube(){numPixels=0; numDim=3; reconExists = false;}; |
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184 | Cube(long nPix); |
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185 | Cube(long *dimensions); |
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186 | virtual ~Cube(); |
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187 | |
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188 | // additional accessor functions |
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189 | // -- in Cubes/cubes.cc unless otherwise specified. |
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190 | |
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191 | int getCube(string fname); |
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192 | int getCube(){ |
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193 | // a front-end to the getCube function, that does subsection checks |
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194 | // assumes the Param is setup properly |
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195 | string fname = par.getImageFile(); |
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196 | if(par.getFlagSubsection()) fname+=par.getSubsection(); |
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197 | return getCube(fname); |
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198 | }; |
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199 | int getFITSdata(string fname); // in FitsIO/dataIO.cc |
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200 | void initialiseCube(long *dimensions); // in cubes.cc |
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201 | int getopts(int argc, char ** argv); // in cubes.cc |
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202 | void saveReconstructedCube(); |
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203 | int readReconCube(); |
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204 | |
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205 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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206 | bool isBlank(long x, long y, long z){ |
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207 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]);}; |
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208 | float getPixValue(long pos){return array[pos];}; |
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209 | float getPixValue(long x, long y, long z){ |
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210 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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211 | short getDetectMapValue(long pos){return detectMap[pos];}; |
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212 | short getDetectMapValue(long x, long y){return detectMap[y*axisDim[0]+x];}; |
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213 | bool isRecon(){return reconExists;}; |
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214 | float getReconValue(long pos){return recon[pos];}; |
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215 | float getReconValue(long x, long y, long z){ |
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216 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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217 | float getBaselineValue(long pos){return baseline[pos];}; |
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218 | float getBaselineValue(long x, long y, long z){ |
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219 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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220 | // these should have checks against array overflow... |
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221 | void setPixValue(long pos, float f){array[pos] = f;}; |
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222 | void setPixValue(long x, long y, long z, float f){ |
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223 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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224 | void setDetectMapValue(long pos, short f){detectMap[pos] = f;}; |
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225 | void setDetectMapValue(long x, long y, short f){ |
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226 | detectMap[y*axisDim[0] + x] = f;}; |
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227 | void setReconValue(long pos, float f){recon[pos] = f;}; |
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228 | void setReconValue(long x, long y, long z, float f){ |
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229 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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230 | void setReconFlag(bool f){reconExists = f;}; |
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231 | void saveArray(float *input, long size); |
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232 | void saveRecon(float *input, long size); |
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233 | void getRecon(float *output); |
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234 | |
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235 | vector<Col> getLogCols(){return logCols;}; |
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236 | void setLogCols(vector<Col> C){logCols=C;}; |
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237 | vector<Col> getFullCols(){return fullCols;}; |
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238 | void setFullCols(vector<Col> C){fullCols=C;}; |
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239 | |
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240 | |
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241 | // Statistics for cube |
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242 | float getSpecMean(int pixel){return specMean[pixel];}; |
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243 | float getSpecSigma(int pixel){return specSigma[pixel];}; |
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244 | float getChanMean(int channel){return chanMean[channel];}; |
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245 | float getChanSigma(int channel){return chanSigma[channel];}; |
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246 | void setCubeStats(); // in Cubes/cubes.cc |
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247 | |
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248 | // Functions that act on the cube |
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249 | void removeMW(); // in Cubes/cubes.cc |
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250 | void trimCube(); // in Cubes/trimImage.cc |
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251 | void unTrimCube(); // in Cubes/trimImage.cc |
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252 | void removeBaseline(); // in ATrous/baselineSubtract.cc |
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253 | void replaceBaseline(); // in ATrous/baselineSubtract.cc |
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254 | void invert(); // in Cubes/invertCube.cc |
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255 | void reInvert(); // in Cubes/invertCube.cc |
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256 | |
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257 | // Reconstruction and Searching functions |
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258 | void ReconSearch(); // in ATrous/ReconSearch.cc |
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259 | void ReconSearch1D(); // in ATrous/ReconSearch.cc |
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260 | void ReconSearch2D(); // in ATrous/ReconSearch.cc |
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261 | void ReconSearch3D(); // in ATrous/ReconSearch.cc |
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262 | void CubicSearch(); // in Cubes/CubicSearch.cc |
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263 | |
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264 | // Dealing with the WCS |
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265 | FitsHeader getHead(){return head;}; |
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266 | void setHead(FitsHeader F){head=F;}; |
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267 | FitsHeader& header(){FitsHeader &h = head; return h;}; |
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268 | int wcsToPix(const double *world, double *pix){ |
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269 | return this->head.wcsToPix(world,pix);} |
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270 | int wcsToPix(const double *world, double *pix, const int npts){ |
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271 | return this->head.wcsToPix(world,pix,npts);} |
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272 | int pixToWCS(const double *pix, double *world){ |
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273 | return this->head.pixToWCS(pix,world);} |
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274 | int pixToWCS(const double *pix, double *world, const int npts){ |
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275 | return this->head.pixToWCS(pix,world,npts);} |
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276 | |
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277 | // Dealing with the detections |
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278 | void ObjectMerger(); // in Cubes/Merger.cc |
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279 | void calcObjectWCSparams(); |
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280 | void sortDetections(); |
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281 | void updateDetectMap(); |
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282 | void updateDetectMap(Detection obj); |
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283 | void setObjectFlags(); |
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284 | float enclosedFlux(Detection obj); |
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285 | bool objAtEdge(Detection obj); |
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286 | |
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287 | // Text outputting of detected objects. |
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288 | // the next five in Cubes/detectionIO.cc |
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289 | void outputDetectionsKarma(std::ostream &stream); |
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290 | void outputDetectionsVOTable(std::ostream &stream); |
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291 | void outputDetectionList(); |
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292 | void logDetectionList(); |
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293 | void logDetection(Detection obj, int counter); |
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294 | void setupColumns(); // in Cubes/cubes.cc |
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295 | |
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296 | // Graphical plotting of the cube and the detections. |
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297 | void plotBlankEdges(); // in Cubes/cubes.cc |
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298 | // the next three in Cubes/plotting.cc |
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299 | void plotDetectionMap(string pgDestination); |
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300 | void plotMomentMap(string pgDestination); |
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301 | void plotWCSaxes(); |
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302 | // the next two in Cubes/outputSpectra.cc |
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303 | void outputSpectra(); |
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304 | void plotSpectrum(Detection obj,Plot::SpectralPlot &plot); |
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305 | // the next three in Cubes/drawMomentCutout.cc |
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306 | void drawMomentCutout(Detection &object); |
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307 | void drawScale(float xstart,float ystart,float channel); |
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308 | void drawFieldEdge(); |
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309 | |
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310 | private: |
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311 | float *recon; // reconstructed array -- used when doing a trous |
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312 | // reconstruction. |
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313 | bool reconExists; // flag saying whether there is a reconstruction |
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314 | short *detectMap; // "moment map" -- x,y locations of detected pixels |
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315 | float *baseline; // array of spectral baseline values. |
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316 | |
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317 | float *specMean; // array of means for each spectrum in cube |
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318 | float *specSigma; // array of sigmas for each spectrum in cube |
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319 | float *chanMean; // array of means for each channel map in cube |
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320 | float *chanSigma; // array of sigmas for each channel map in cube |
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321 | |
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322 | FitsHeader head; // the WCS and other header information. |
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323 | vector<Col> fullCols; // the list of all columns as printed in the |
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324 | // results file |
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325 | vector<Col> logCols; // the list of columns as printed in the log file |
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326 | |
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327 | }; |
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328 | |
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329 | /****************************************************************/ |
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330 | ////////////////////////////////////////////////////// |
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331 | // Prototypes for functions that use above classes |
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332 | ////////////////////////////////////////////////////// |
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333 | |
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334 | DataArray getImage(string fname, short int maxdim); |
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335 | Image getImage(string fname); |
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336 | |
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337 | void findSources(Image &image); |
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338 | void findSources(Image &image, float mean, float sigma); |
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339 | |
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340 | vector <Detection> searchReconArray(long *dim,float *originalArray, |
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341 | float *reconArray, Param &par); |
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342 | vector <Detection> search3DArray(long *dim, float *Array, Param &par); |
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343 | |
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344 | void growObject(Detection &object, Image &image); |
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345 | void growObject(Detection &object, Cube &cube); |
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346 | |
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347 | #endif |
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