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 | #include <wcs.h> |
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8 | |
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9 | #ifndef PARAM_H |
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10 | #include <param.hh> |
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11 | #endif |
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12 | #ifndef DETECTION_H |
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13 | #include <Detection/detection.hh> |
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14 | #endif |
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15 | |
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16 | using std::string; |
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17 | using std::vector; |
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18 | |
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19 | /****************************************************************/ |
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20 | ///////////////////////////////////////////////////////////// |
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21 | //// Definition of an n-dimensional data array: |
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22 | //// array of pixel values, size & dimensions |
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23 | //// array of Detection objects |
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24 | ///////////////////////////////////////////////////////////// |
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25 | |
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26 | |
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27 | class DataArray |
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28 | { |
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29 | public: |
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30 | DataArray(){numDim=0; numPixels=0;}; |
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31 | DataArray(short int nDim){numDim=nDim; numPixels=0;}; |
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32 | DataArray(short int nDim, long size); |
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33 | DataArray(short int nDim, long *dimensions); |
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34 | virtual ~DataArray(){}; |
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35 | // Size and Dimension related |
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36 | long getDimX(){if(numDim>0) return axisDim[0]; else return 0;}; |
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37 | long getDimY(){if(numDim>1) return axisDim[1]; else return 1;}; |
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38 | long getDimZ(){if(numDim>2) return axisDim[2]; else return 1;}; |
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39 | void getDim(long &x, long &y, long &z); |
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40 | long getSize(){return numPixels;}; |
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41 | short int getNumDim(){return numDim;}; |
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42 | // Related to the various arrays |
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43 | void getDimArray(long *output); |
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44 | void getArray(float *output); |
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45 | virtual void saveArray(float *input, long size); |
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46 | float getPixValue(long pos){return array[pos];}; |
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47 | void setPixValue(long pos, float f){array[pos] = f;}; |
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48 | // Related to the object lists |
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49 | Detection getObject(long number){return objectList[number];}; |
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50 | void addObject(Detection object); |
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51 | // adds a single detection to the object list |
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52 | vector <Detection> getObjectList(){return objectList;}; |
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53 | void addObjectList(vector <Detection> newlist); |
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54 | // adds all objects in a detection list to the object list |
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55 | long getNumObj(){return objectList.size();}; |
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56 | void clearDetectionList(){this->objectList.clear();}; |
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57 | // Parameter list related. |
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58 | void readParam(string ¶mfile){par.readParams(paramfile);}; |
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59 | void showParam(std::ostream &stream){stream << par;}; |
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60 | Param getParam(){return par;}; |
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61 | void saveParam(Param newpar){par = newpar;}; |
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62 | Param& pars(){Param &rpar = par; return rpar;}; |
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63 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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64 | |
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65 | friend std::ostream& operator<< ( std::ostream& theStream, DataArray &array); |
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66 | |
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67 | |
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68 | protected: |
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69 | short int numDim; // number of dimensions. |
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70 | long *axisDim; // array of dimensions of cube |
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71 | // (ie. how large in each direction). |
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72 | long numPixels; // total number of pixels in cube |
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73 | float *array; // array of data |
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74 | vector <Detection> objectList; // the list of detected objects in the image |
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75 | Param par; // a parameter list. |
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76 | }; |
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77 | |
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78 | |
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79 | /****************************************************************/ |
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80 | ///////////////////////////////////////////////////////////// |
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81 | //// Definition of an image object (2D): |
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82 | //// a DataArray object |
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83 | //// arrays for: probability values (for FDR) |
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84 | //// mask image to indicate location of objects |
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85 | //// detected objects |
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86 | //// statistics information |
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87 | ///////////////////////////////////////////////////////////// |
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88 | |
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89 | class Image : public DataArray |
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90 | { |
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91 | public: |
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92 | Image(){ |
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93 | numPixels=0; |
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94 | numDim=2;}; |
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95 | Image(long nPix); |
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96 | Image(long *dimensions); |
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97 | virtual ~Image(){}; |
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98 | |
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99 | // Defining the array |
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100 | void saveArray(float *input, long size); |
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101 | void extractSpectrum(float *Array, long *dim, long pixel); |
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102 | void extractImage(float *Array, long *dim, long channel); |
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103 | // Accessing the data. |
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104 | float getPixValue(long x, long y){return array[y*axisDim[0] + x];}; |
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105 | float getPixValue(long pos){return array[pos];}; |
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106 | float getPValue(long pos){return pValue[pos];}; |
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107 | float getPValue(long x, long y){return pValue[y*axisDim[0] + x];}; |
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108 | short int getMaskValue(long pos){return mask[pos];}; |
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109 | short int getMaskValue(long x, long y){return mask[y*axisDim[0] + x];}; |
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110 | // the next few should have checks against array overflow... |
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111 | void setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;}; |
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112 | void setPixValue(long pos, float f){array[pos] = f;}; |
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113 | void setPValue(long pos, float p){pValue[pos] = p;}; |
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114 | void setPValue(long x, long y, float p){pValue[y*axisDim[0] + x] = p;}; |
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115 | void setMaskValue(long pos, short int m){mask[pos] = m;}; |
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116 | void setMaskValue(long x, long y, short int m){mask[y*axisDim[0] + x] = m;}; |
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117 | // Stats-related |
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118 | void setStats(float m, float s, float c){mean=m; sigma=s; cutLevel=c;}; |
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119 | void findStats(int code); |
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120 | float getMean(){return mean;}; |
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121 | void setMean(float m){mean=m;}; |
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122 | float getSigma(){return sigma;}; |
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123 | void setSigma(float s){sigma=s;}; |
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124 | float getCut(){return cutLevel;}; |
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125 | void setCut(float c){cutLevel=c;}; |
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126 | float getPCut(){return pCutLevel;}; |
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127 | void setPCut(float p){pCutLevel = p;}; |
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128 | float getAlpha(){return alpha;}; |
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129 | void setAlpha(float a){alpha = a;}; |
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130 | int getMinSize(){return minSize;}; |
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131 | void setMinSize(int s){minSize = s;}; |
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132 | |
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133 | void maskObject(Detection &object); |
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134 | |
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135 | // Detection-related |
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136 | void lutz_detect(); // in Detection/lutz_detect.cc |
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137 | void spectrumDetect(); // in Detection/spectrumDetect.cc |
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138 | int setupFDR(); // in Detection/thresholding_functions.cc |
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139 | bool isDetection(float value); // in Detection/thresholding_functions.cc |
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140 | bool isDetection(long x, long y); // in Detection/thresholding_functions.cc |
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141 | bool isDetectionFDR(float pvalue); // in Detection/thresholding_functions.cc |
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142 | |
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143 | |
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144 | private: |
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145 | float *pValue; // the array of p-values for each pixel |
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146 | // --> used by FDR method |
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147 | short int *mask; // a mask image indicating where objects are |
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148 | |
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149 | float mean; // the mean background level of the image |
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150 | float sigma; // the standard deviation of the background in the image |
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151 | float cutLevel; // the limiting value (in sigmas above the mean) for |
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152 | // a pixel to be called a detection. |
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153 | float alpha; // used by FDR routine -- significance level |
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154 | float pCutLevel; // the limiting P-value for the FDR analysis |
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155 | int minSize; // the minimum number of pixels for a detection to be accepted. |
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156 | }; |
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157 | |
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158 | /****************************************************************/ |
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159 | ///////////////////////////////////////////////////////////// |
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160 | //// Definition of an data-cube object (3D): |
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161 | //// a DataArray object limited to dim=3 |
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162 | ///////////////////////////////////////////////////////////// |
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163 | |
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164 | class Cube : public DataArray |
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165 | { |
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166 | public: |
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167 | Cube(){numPixels=0; numDim=3; flagWCS=false;}; |
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168 | Cube(long nPix); |
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169 | Cube(long *dimensions); |
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170 | virtual ~Cube(){}; // destructor |
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171 | |
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172 | // additional accessor functions -- in Cubes/cubes.cc unless otherwise specified. |
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173 | |
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174 | int getCube(string fname); |
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175 | void initialiseCube(long *dimensions); |
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176 | void saveReconstructedCube(); |
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177 | int readReconCube(); |
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178 | |
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179 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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180 | bool isBlank(long x, long y, long z){ |
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181 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]);}; |
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182 | float getPixValue(long pos){return array[pos];}; |
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183 | float getPixValue(long x, long y, long z){ |
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184 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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185 | short getDetectMapValue(long pos){return detectMap[pos];}; |
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186 | short getDetectMapValue(long x, long y){return detectMap[y*axisDim[0] + x];}; |
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187 | bool isRecon(){return reconExists;}; |
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188 | float getReconValue(long pos){return recon[pos];}; |
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189 | float getReconValue(long x, long y, long z){ |
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190 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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191 | float getBaselineValue(long pos){return baseline[pos];}; |
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192 | float getBaselineValue(long x, long y, long z){ |
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193 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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194 | // these should have checks against array overflow... |
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195 | void setPixValue(long pos, float f){array[pos] = f;}; |
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196 | void setPixValue(long x, long y, long z, float f){ |
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197 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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198 | void setDetectMapValue(long pos, short f){detectMap[pos] = f;}; |
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199 | void setDetectMapValue(long x, long y, short f){ |
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200 | detectMap[y*axisDim[0] + x] = f;}; |
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201 | void setReconValue(long pos, float f){recon[pos] = f;}; |
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202 | void setReconValue(long x, long y, long z, float f){ |
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203 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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204 | void setReconFlag(bool f){reconExists = f;}; |
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205 | void saveArray(float *input, long size); |
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206 | void saveRecon(float *input, long size); |
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207 | void getRecon(float *output); |
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208 | |
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209 | // Statistics for cube |
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210 | float getSpecMean(int pixel){return specMean[pixel];}; |
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211 | float getSpecSigma(int pixel){return specSigma[pixel];}; |
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212 | float getChanMean(int channel){return chanMean[channel];}; |
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213 | float getChanSigma(int channel){return chanSigma[channel];}; |
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214 | void setCubeStats(); // in Cubes/cubes.cc |
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215 | |
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216 | // Functions that act on the cube |
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217 | void removeMW(); // in Cubes/cubes.cc |
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218 | void trimCube(); // in Cubes/trimImage.cc |
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219 | void unTrimCube(); // in Cubes/trimImage.cc |
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220 | void removeBaseline(); // in ATrous/baselineSubtract.cc |
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221 | void replaceBaseline(); // in ATrous/baselineSubtract.cc |
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222 | void invert(); // in Cubes/invertCube.cc |
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223 | void reInvert(); // in Cubes/invertCube.cc |
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224 | |
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225 | // Reconstruction and Searching functions |
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226 | void ReconSearch1D(); // in ATrous/ReconSearch.cc |
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227 | void ReconSearch2D(); // in ATrous/ReconSearch.cc |
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228 | void ReconSearch3D(); // in ATrous/ReconSearch.cc |
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229 | void SimpleSearch3D(); // in Cubes/CubicSearch.cc |
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230 | |
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231 | // Dealing with the WCS |
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232 | bool isWCS(){return flagWCS;}; |
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233 | void setWCS(wcsprm *w); |
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234 | wcsprm *getWCS(); |
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235 | void setNWCS(int n){nwcs = n;}; |
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236 | int getNWCS(){return nwcs;}; |
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237 | void setBUnit(char *s){bunit = s;}; |
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238 | string getBUnit(){return bunit;}; |
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239 | |
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240 | // Dealing with the detections |
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241 | void ObjectMerger(); // in Cubes/Merger.cc |
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242 | void calcObjectWCSparams(); |
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243 | void sortDetections(); |
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244 | void updateDetectMap(); |
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245 | void updateDetectMap(Detection obj); |
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246 | void setObjectFlags(); |
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247 | float enclosedFlux(Detection obj); |
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248 | bool objAtEdge(Detection obj); |
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249 | |
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250 | // Text outputting of detected objects. |
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251 | void outputDetectionsKarma(std::ostream &stream); // in Cubes/detectionIO.cc |
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252 | void outputDetectionsVOTable(std::ostream &stream); // in Cubes/detectionIO.cc |
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253 | void outputDetectionList(); // in Cubes/detectionIO.cc |
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254 | void logDetectionList(); // in Cubes/detectionIO.cc |
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255 | void logDetection(Detection obj, int counter); // in Cubes/detectionIO.cc |
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256 | |
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257 | // Graphical plotting of detections. |
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258 | void plotDetectionMap(string pgDestination); // in Cubes/plotting.cc |
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259 | void plotMomentMap(string pgDestination); // in Cubes/plotting.cc |
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260 | void plotWCSaxes(); // in Cubes/plotting.cc |
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261 | void outputSpectra(); // in Cubes/outputSpectra.cc |
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262 | void drawScale(float xstart, float ystart, float channel, float scaleLength); |
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263 | // in Cubes/drawMomentCutout.cc |
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264 | |
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265 | |
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266 | private: |
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267 | float *recon; // reconstructed array -- used when doing a trous reconstruction. |
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268 | bool reconExists; // flag saying whether there is a reconstruction |
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269 | short *detectMap; // "moment map" -- x,y locations of detected pixels |
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270 | float *baseline; // array of spectral baseline values. |
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271 | |
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272 | float *specMean; // array of means for each spectrum in cube |
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273 | float *specSigma; // array of sigmas for each spectrum in cube |
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274 | float *chanMean; // array of means for each channel map in cube |
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275 | float *chanSigma; // array of sigmas for each channel map in cube |
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276 | |
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277 | bool flagWCS; // a flag indicating whether there is a valid WCS present. |
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278 | wcsprm *wcs; // the WCS parameters for the cube -- a struct from wcslib |
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279 | int nwcs; // number of WCS parameters |
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280 | string bunit; // The header keyword BUNIT -- the units of brightness in the FITS file. |
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281 | }; |
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282 | |
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283 | /****************************************************************/ |
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284 | ////////////////////////////////////////////////////// |
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285 | // Prototypes for functions that use above classes |
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286 | ////////////////////////////////////////////////////// |
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287 | |
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288 | DataArray getImage(string fname, short int maxdim); |
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289 | Image getImage(string fname); |
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290 | |
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291 | void findSources(Image &image); |
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292 | void findSources(Image &image, float mean, float sigma); |
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293 | |
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294 | vector <Detection> reconSearch(long *dim,float *originalArray,float *reconArray, Param &par); |
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295 | vector <Detection> cubicSearch(long *dim, float *Array, Param &par); |
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296 | vector <Detection> cubicSearchNMerge(long *dim, float *Array, Param &par); |
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297 | |
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298 | void growObject(Detection &object, Image &image); |
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299 | void growObject(Detection &object, Cube &cube); |
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300 | |
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301 | void drawMomentCutout(Cube &cube, Detection &object); |
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302 | |
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303 | #endif |
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