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 | // Size and Dimension related |
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48 | long getDimX(); ///< Return X dimension, defaulting to 0. |
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49 | long getDimY(); ///< Return Y dimension, defaulting to 1. |
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50 | long getDimZ(); ///< Return Z dimension, defaulting to 1. |
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51 | long getSize(); ///< Return number of voxels. |
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52 | short int getNumDim(); ///< Return number of dimensions. |
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53 | void getDim(long &x, long &y, long &z); ///< Return first three dimensional axes. |
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54 | |
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55 | // Related to the various arrays |
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56 | void getDimArray(long *output); ///< Return array of dimensional sizes. |
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57 | void getArray(float *output); ///< Return pixel value array. |
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58 | virtual void saveArray(float *input, long size); ///< Save pixel value array. |
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59 | float getPixValue(long pos); ///< Returns the flux value at voxel number pos. |
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60 | void setPixValue(long pos, float f); ///< Sets the value of pixel pos to f. |
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61 | |
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62 | // Related to the object lists |
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63 | Detection getObject(long number); ///< Returns the Detection at position 'number' in the list. |
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64 | void addObject(Detection object); ///< Adds a single detection to the object list. |
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65 | vector <Detection> getObjectList(); ///< Returns the full list of Detections. |
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66 | void addObjectList(vector <Detection> newlist); ///< Adds all objects in a detection list to the object list. |
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67 | void addObjectOffsets(); ///< Add pixel offsets to object coordinates. |
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68 | long getNumObj(); ///< Returns the number of detected objects. |
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69 | void clearDetectionList(); ///< Delete all Detections from the object list. |
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70 | |
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71 | // Parameter list related. |
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72 | int readParam(string paramfile); ///< Read parameters. |
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73 | void showParam(std::ostream &stream); ///< Output the Param set. |
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74 | Param getParam(); ///< Return the Param set. |
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75 | void saveParam(Param newpar); ///< Save a Param set to the Cube. |
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76 | Param& pars(); ///< Provides a reference to the Param set. |
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77 | |
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78 | bool isBlank(int vox); ///< Is the voxel number given by vox a BLANK value? |
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79 | |
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80 | // Statistics |
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81 | StatsContainer<float> getStats(); ///< Returns the StatsContainer. |
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82 | StatsContainer<float>& stats(); ///< Provides a reference to the StatsContainer. |
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83 | void saveStats(StatsContainer<float> newStats); ///< Save a StatsContainer to the Cube. |
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84 | |
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85 | bool isDetection(float value); ///< A detection test for value. |
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86 | bool isDetection(long voxel); ///< A detection test for pixel. |
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87 | |
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88 | friend std::ostream& operator<< (std::ostream& theStream, DataArray &array); |
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89 | ///< Output operator for DataArray. |
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90 | |
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91 | protected: |
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92 | short int numDim; ///< Number of dimensions. |
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93 | long *axisDim; ///< Array of dimensions of cube (ie. how large in each direction). |
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94 | long numPixels; ///< Total number of pixels in cube. |
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95 | float *array; ///< Array of data. |
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96 | vector <Detection> objectList; ///< The list of detected objects. |
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97 | Param par; ///< A parameter list. |
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98 | StatsContainer<float> Stats; ///< The statistics for the DataArray. |
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99 | }; |
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100 | |
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101 | //////////// |
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102 | //// DataArray inline function definitions |
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103 | //////////// |
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104 | |
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105 | inline long DataArray::getDimX(){ if(numDim>0) return this->axisDim[0];else return 0;}; |
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106 | inline long DataArray::getDimY(){ if(numDim>1) return this->axisDim[1];else return 1;}; |
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107 | inline long DataArray::getDimZ(){ if(numDim>2) return this->axisDim[2];else return 1;}; |
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108 | inline long DataArray::getSize(){ return this->numPixels; }; |
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109 | inline short int DataArray::getNumDim(){ return this->numDim; }; |
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110 | |
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111 | inline float DataArray::getPixValue(long pos){ return array[pos]; }; |
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112 | inline void DataArray::setPixValue(long pos, float f){array[pos] = f;}; |
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113 | inline Detection DataArray::getObject(long number){ return objectList[number]; }; |
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114 | inline vector <Detection> DataArray::getObjectList(){ return objectList; }; |
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115 | inline long DataArray::getNumObj(){ return objectList.size(); }; |
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116 | inline void DataArray::clearDetectionList(){ this->objectList.clear(); }; |
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117 | inline int DataArray::readParam(string paramfile){ |
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118 | /** |
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119 | * Uses Param::readParams() to read parameters from a file. |
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120 | * \param paramfile The file to be read. |
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121 | */ |
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122 | return par.readParams(paramfile); }; |
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123 | inline void DataArray::showParam(std::ostream &stream){ stream << this->par; }; |
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124 | inline Param DataArray::getParam(){ return this->par; }; |
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125 | inline void DataArray::saveParam(Param newpar){this->par = newpar;}; |
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126 | inline Param& DataArray::pars(){ Param &rpar = this->par; return rpar; }; |
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127 | inline bool DataArray::isBlank(int vox){ return this->par.isBlank(this->array[vox]); }; |
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128 | inline StatsContainer<float> DataArray::getStats(){ return this->Stats; }; |
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129 | inline StatsContainer<float>& DataArray::stats(){ |
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130 | StatsContainer<float> &rstats = this->Stats; |
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131 | return rstats; |
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132 | }; |
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133 | inline void DataArray::saveStats(StatsContainer<float> newStats){ this->Stats = newStats;}; |
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134 | |
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135 | |
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136 | |
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137 | |
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138 | /****************************************************************/ |
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139 | /** |
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140 | * Definition of an data-cube object (3D): |
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141 | * a DataArray object limited to dim=3 |
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142 | */ |
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143 | |
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144 | class Cube : public DataArray |
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145 | { |
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146 | public: |
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147 | Cube(); ///< Basic Cube constructor. |
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148 | Cube(long nPix); ///< Alternative Cube constructor. |
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149 | Cube(long *dimensions); ///< Alternative Cube constructor. |
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150 | virtual ~Cube(); ///< Basic Cube destructor. |
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151 | |
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152 | // INLINE functions -- definitions included after class declaration. |
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153 | bool isBlank(int vox); ///< Is the voxel number given by vox a BLANK value? |
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154 | bool isBlank(long x, long y, long z); ///< Is the voxel at (x,y,z) a BLANK value? |
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155 | float getPixValue(long pos); ///< Returns the flux value at voxel number pos. |
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156 | float getPixValue(long x, long y, long z); ///< Returns the flux value at voxel (x,y,z). |
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157 | short getDetectMapValue(long pos); ///< Returns the value of the detection map at spatial pixel pos. |
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158 | short getDetectMapValue(long x, long y); ///< Returns the value of the detection map at spatial pixel (x,y). |
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159 | bool isRecon(); ///< Does the Cube::recon array exist? |
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160 | float getReconValue(long pos); ///< Returns the reconstructed flux value at voxel number pos. |
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161 | float getReconValue(long x, long y, long z); ///< Returns the reconstructed flux value at voxel (x,y,z). |
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162 | float getBaselineValue(long pos); ///< Returns the baseline flux value at voxel number pos. |
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163 | float getBaselineValue(long x, long y, long z); ///< Returns the baseline flux value at voxel (x,y,z). |
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164 | void setPixValue(long pos, float f); ///< Sets the value of voxel pos. |
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165 | void setPixValue(long x, long y, long z, float f); ///< Sets the value of voxel (x,y,z). |
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166 | void setDetectMapValue(long pos, short f); ///< Sets the value of the detection map at spatial pixel pos. |
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167 | void setDetectMapValue(long x, long y, short f); ///< Sets the value of the detection map at spatial pixel (x,y). |
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168 | void setReconValue(long pos, float f); ///< Sets the reconstructed flux value of voxel pos. |
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169 | void setReconValue(long x, long y, long z, float f); ///< Sets the reconstructed flux value of voxel (x,y,z). |
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170 | void setReconFlag(bool f); ///< Sets the value of the reconExists flag. |
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171 | vector<Col> getLogCols(); ///< Return the vector of log file columns |
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172 | void setLogCols(vector<Col> C); ///< Set the vector of log file columns |
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173 | vector<Col> getFullCols(); ///< Return the vector of the full output column set. |
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174 | void setFullCols(vector<Col> C); ///< Set the vector of the full output column set. |
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175 | |
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176 | // additional functions -- in Cubes/cubes.cc |
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177 | void initialiseCube(long *dimensions); ///< Allocate memory correctly, with WCS defining the correct axes. |
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178 | int getCube(); ///< Read in a FITS file, with subsection correction. |
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179 | int getopts(int argc, char ** argv); ///< Read in command-line options. |
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180 | void readSavedArrays(); ///< Read in reconstructed & smoothed arrays from FITS files on disk. |
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181 | void saveArray(float *input, long size); ///< Save an external array to the Cube's pixel array |
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182 | void saveRecon(float *input, long size); ///< Save an external array to the Cube's reconstructed array. |
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183 | void getRecon(float *output); ///< Save reconstructed array to an external array. |
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184 | void removeMW(); ///< Set Milky Way channels to zero. |
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185 | // Statistics for cube |
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186 | void setCubeStatsOld(); ///< Calculate the statistics for the Cube (older version). |
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187 | void setCubeStats(); ///< Calculate the statistics for the Cube. |
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188 | int setupFDR(); ///< Set up thresholds for the False Discovery Rate routine. |
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189 | bool isDetection(long x, long y, long z);///< A detection test for a given voxel. |
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190 | // Dealing with the detections |
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191 | void calcObjectWCSparams(); ///< Calculate the WCS parameters for each Cube Detection. |
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192 | void sortDetections(); ///< Sort the list of detections. |
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193 | void updateDetectMap(); ///< Update the map of detected pixels. |
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194 | void updateDetectMap(Detection obj); ///< Update the map of detected pixels for a given Detection. |
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195 | float enclosedFlux(Detection obj); ///< Find the flux enclosed by a Detection. |
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196 | void setupColumns(); ///< Set up the output column definitions for the Cube and its Detection list. |
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197 | bool objAtSpatialEdge(Detection obj); ///< Is the object at the edge of the image? |
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198 | bool objAtSpectralEdge(Detection obj); ///< Is the object at an end of the spectrum? |
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199 | void setObjectFlags(); ///< Set warning flags for the detections. |
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200 | // Graphical plotting of the cube and the detections. |
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201 | void plotBlankEdges(); ///< Draw blank edges of cube. |
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202 | // Dealing with the WCS |
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203 | FitsHeader getHead(); ///< Return the FitsHeader. |
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204 | void setHead(FitsHeader F); ///< Set the FitsHeader. |
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205 | FitsHeader& header(); ///< Provides a reference to the FitsHeader. |
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206 | int wcsToPix(const double *world, double *pix); ///< Convert a point from WCS to Pixel coords. |
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207 | int wcsToPix(const double *world, double *pix, const int npts); ///< Convert a set of points from WCS to Pixel coords. |
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208 | int pixToWCS(const double *pix, double *world); ///< Convert a point from Pixel to WCS coords. |
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209 | int pixToWCS(const double *pix, double *world, const int npts); ///< Convert a set of points from Pixel to WCS coords. |
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210 | |
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211 | // FITS-I/O related functions -- not in cubes.cc |
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212 | // in Cubes/getImage.cc |
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213 | int getCube(string fname); ///< Function to read in FITS file. |
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214 | // in FitsIO/dataIO.cc |
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215 | int getFITSdata(string fname); ///< Function to retrieve FITS data array |
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216 | // in Cubes/saveImage.cc |
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217 | void saveSmoothedCube(); ///< Save Hanning-smoothed array to disk. |
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218 | void saveReconstructedCube(); ///< Save Reconstructed array to disk. |
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219 | // in Cubes/readRecon.cc |
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220 | int readReconCube(); ///< Read in reconstructed array from FITS file. |
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221 | // in Cubes/readSmooth.cc |
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222 | int readSmoothCube(); ///< Read in Hanning-smoothed array from FITS file. |
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223 | |
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224 | // Functions that act on the cube |
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225 | // in Cubes/trimImage.cc |
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226 | void trimCube(); ///< Remove excess BLANK pixels from spatial edge of cube. |
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227 | void unTrimCube(); ///< Replace BLANK pixels to spatial edge of cube. |
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228 | // in Cubes/baseline.cc |
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229 | void removeBaseline(); ///< Removes the baselines from the spectra, and stores in Cube::baseline |
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230 | void replaceBaseline(); ///< Replace the baselines stored in Cube::baseline |
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231 | // in Cubes/invertCube.cc |
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232 | void invert(); ///< Multiply all pixel values by -1. |
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233 | void reInvert(); ///< Undo the inversion, and invert fluxes of all detected objects. |
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234 | |
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235 | // Reconstruction, Searching and Merging functions |
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236 | // in ATrous/ReconSearch.cc |
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237 | void ReconSearch(); ///< Front-end to reconstruction & searching functions. |
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238 | void ReconCube(); ///< Switcher to reconstruction functions |
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239 | void ReconCube1D(); ///< Performs 1-dimensional a trous reconstruction on the Cube. |
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240 | void ReconCube2D(); ///< Performs 2-dimensional a trous reconstruction on the Cube. |
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241 | void ReconCube3D(); ///< Performs 3-dimensional a trous reconstruction on the Cube. |
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242 | // in Cubes/CubicSearch.cc |
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243 | void CubicSearch(); ///< Front-end to the cubic searching routine. |
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244 | // in Cubes/smoothCube.cc |
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245 | void SmoothSearch(); ///< Front-end to the smoothing and searching functions. |
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246 | void SmoothCube(); ///< A function to Hanning-smooth the cube. |
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247 | // in Cubes/Merger.cc |
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248 | void ObjectMerger(); ///< Merge all objects in the detection list so that only distinct ones are left. |
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249 | |
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250 | // Text outputting of detected objects. |
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251 | // in Cubes/detectionIO.cc |
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252 | void outputDetectionsKarma(std::ostream &stream); ///< Output detections to a Karma annotation file. |
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253 | void outputDetectionsVOTable(std::ostream &stream); ///< Output detections to a VOTable. |
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254 | void outputDetectionList(); ///< Output detections to the output file and standard output. |
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255 | void logDetectionList(); ///< Output detections to the log file. |
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256 | void logDetection(Detection obj, int counter); ///< Output a single detection to the log file |
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257 | |
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258 | // in Cubes/plotting.cc |
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259 | void plotDetectionMap(string pgDestination); ///< Plot a spatial map of detections based on number of detected channels. |
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260 | void plotMomentMap(string pgDestination); ///< Plot a spatial map of detections based on 0th moment map of each object. |
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261 | void plotMomentMap(vector<string> pgDestination);///< Plot a spatial map of detections based on 0th moment map of each object to a number of PGPLOT devices. |
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262 | void plotWCSaxes(); ///< Draw WCS axes over a PGPLOT map. |
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263 | |
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264 | // in Cubes/outputSpectra.cc |
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265 | void outputSpectra(); ///< Print spectra of each detected object. |
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266 | void plotSpectrum(Detection obj,Plot::SpectralPlot &plot); ///< Print spectrum of a single object |
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267 | // in Cubes/drawMomentCutout.cc |
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268 | void drawMomentCutout(Detection &object); ///< Draw the 0th moment map for a single object. |
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269 | void drawScale(float xstart,float ystart,float channel); ///< Draw a scale bar indicating angular size of the cutout. |
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270 | void drawFieldEdge(); ///< Draw a yellow line around the edge of the spatial extent of pixels. |
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271 | |
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272 | private: |
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273 | float *recon; ///< reconstructed array - used when doing a trous reconstruction. |
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274 | bool reconExists; ///< flag saying whether there is a reconstruction |
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275 | short *detectMap; ///< "moment map" - x,y locations of detected pixels |
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276 | float *baseline; ///< array of spectral baseline values. |
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277 | |
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278 | bool reconAllocated; ///< have we allocated memory for the recon array? |
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279 | bool baselineAllocated;///< have we allocated memory for the baseline array? |
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280 | |
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281 | FitsHeader head; ///< the WCS and other header information. |
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282 | vector<Col> fullCols; ///< the list of all columns as printed in the results file |
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283 | vector<Col> logCols; ///< the list of columns as printed in the log file |
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284 | |
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285 | }; |
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286 | |
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287 | //////////// |
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288 | //// Cube inline function definitions |
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289 | //////////// |
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290 | |
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291 | inline bool Cube::isBlank(int vox){ return par.isBlank(array[vox]); }; |
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292 | inline bool Cube::isBlank(long x, long y, long z){ return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]); }; |
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293 | inline float Cube::getPixValue(long pos){ return array[pos]; }; |
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294 | inline float Cube::getPixValue(long x, long y, long z){ return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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295 | inline short Cube::getDetectMapValue(long pos){ return detectMap[pos]; }; |
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296 | inline short Cube::getDetectMapValue(long x, long y){ return detectMap[y*axisDim[0]+x]; }; |
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297 | inline bool Cube::isRecon(){ return reconExists; }; |
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298 | inline float Cube::getReconValue(long pos){ return recon[pos]; }; |
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299 | inline float Cube::getReconValue(long x, long y, long z){ return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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300 | inline float Cube::getBaselineValue(long pos){ return baseline[pos]; }; |
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301 | inline float Cube::getBaselineValue(long x, long y, long z){ return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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302 | // these next ones should have checks against array overflow... |
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303 | inline void Cube::setPixValue(long pos, float f){array[pos] = f;}; |
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304 | inline void Cube::setPixValue(long x, long y, long z, float f){ array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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305 | inline void Cube::setDetectMapValue(long pos, short f){ detectMap[pos] = f;}; |
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306 | inline void Cube::setDetectMapValue(long x, long y, short f){ detectMap[y*axisDim[0] + x] = f;}; |
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307 | inline void Cube::setReconValue(long pos, float f){recon[pos] = f;}; |
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308 | inline void Cube::setReconValue(long x, long y, long z, float f){ recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f; }; |
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309 | inline void Cube::setReconFlag(bool f){reconExists = f;}; |
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310 | inline vector<Col> Cube::getLogCols(){return logCols;}; |
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311 | inline void Cube::setLogCols(vector<Col> C){logCols=C;}; |
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312 | inline vector<Col> Cube::getFullCols(){return fullCols;}; |
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313 | inline void Cube::setFullCols(vector<Col> C){fullCols=C;}; |
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314 | inline FitsHeader Cube::getHead(){ return head; }; |
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315 | inline void Cube::setHead(FitsHeader F){}; |
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316 | inline FitsHeader& Cube::header(){ FitsHeader &h = head; return h; }; |
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317 | inline int Cube::wcsToPix(const double *world, double *pix) |
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318 | { |
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319 | /** |
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320 | * Use the WCS in the FitsHeader to convert from WCS to pixel coords for |
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321 | * a single point. |
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322 | * \param world The world coordinates. |
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323 | * \param pix The returned pixel coordinates. |
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324 | */ |
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325 | return this->head.wcsToPix(world,pix); |
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326 | } |
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327 | inline int Cube::wcsToPix(const double *world, double *pix, const int npts) |
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328 | { |
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329 | /** |
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330 | * Use the WCS in the FitsHeader to convert from WCS to pixel coords for |
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331 | * a set of points. |
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332 | * \param world The world coordinates. |
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333 | * \param pix The returned pixel coordinates. |
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334 | * \param npts The number of points being converted. |
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335 | */ |
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336 | return this->head.wcsToPix(world,pix,npts); |
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337 | } |
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338 | inline int Cube::pixToWCS(const double *pix, double *world) |
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339 | { |
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340 | /** |
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341 | * Use the WCS in the FitsHeader to convert from pixel to WCS coords for |
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342 | * a single point. |
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343 | * \param pix The pixel coordinates. |
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344 | * \param world The returned world coordinates. |
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345 | */ |
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346 | return this->head.pixToWCS(pix,world); |
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347 | } |
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348 | inline int Cube::pixToWCS(const double *pix, double *world, const int npts) |
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349 | { |
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350 | /** |
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351 | * Use the WCS in the FitsHeader to convert from pixel to WCS coords for |
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352 | * a set of points. |
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353 | * \param pix The pixel coordinates. |
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354 | * \param world The returned world coordinates. |
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355 | * \param npts The number of points being converted. |
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356 | */ |
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357 | return this->head.pixToWCS(pix,world,npts); |
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358 | } |
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359 | |
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360 | |
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361 | //------------------------------------------------------------------------ |
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362 | |
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363 | /****************************************************************/ |
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364 | /** |
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365 | * A DataArray object limited to two dimensions, and with some additional |
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366 | * special functions. |
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367 | * |
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368 | * It is used primarily for searching a 1- or 2-D array with |
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369 | * lutz_detect() and spectrumDetect(). |
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370 | */ |
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371 | |
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372 | class Image : public DataArray |
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373 | { |
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374 | public: |
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375 | Image(){numPixels=0; numDim=2;}; |
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376 | Image(long nPix); |
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377 | Image(long *dimensions); |
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378 | virtual ~Image(){}; |
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379 | |
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380 | // Defining the array |
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381 | void saveArray(float *input, long size); |
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382 | void extractSpectrum(float *Array, long *dim, long pixel); |
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383 | void extractImage(float *Array, long *dim, long channel); |
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384 | void extractSpectrum(Cube &cube, long pixel); |
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385 | void extractImage(Cube &cube, long channel); |
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386 | // Accessing the data. |
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387 | float getPixValue(long x, long y){return array[y*axisDim[0] + x];}; |
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388 | float getPixValue(long pos){return array[pos];}; |
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389 | // the next few should have checks against array overflow... |
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390 | void setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;}; |
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391 | void setPixValue(long pos, float f){array[pos] = f;}; |
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392 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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393 | bool isBlank(long x,long y){return par.isBlank(array[y*axisDim[0]+x]);}; |
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394 | |
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395 | // Detection-related |
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396 | void lutz_detect(); // in Detection/lutz_detect.cc |
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397 | void spectrumDetect(); // in Detection/spectrumDetect.cc |
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398 | int getMinSize(){return minSize;}; |
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399 | void setMinSize(int i){minSize=i;}; |
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400 | // the rest are in Detection/thresholding_functions.cc |
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401 | bool isDetection(long x, long y){ |
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402 | long voxel = y*axisDim[0] + x; |
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403 | if(isBlank(x,y)) return false; |
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404 | else return Stats.isDetection(array[voxel]); |
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405 | }; |
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406 | |
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407 | void removeMW(); |
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408 | |
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409 | private: |
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410 | int minSize; ///< the minimum number of pixels for a detection to be accepted. |
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411 | }; |
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412 | |
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413 | |
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414 | /****************************************************************/ |
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415 | ////////////////////////////////////////////////////// |
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416 | // Prototypes for functions that use above classes |
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417 | ////////////////////////////////////////////////////// |
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418 | |
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419 | void findSources(Image &image); |
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420 | void findSources(Image &image, float mean, float sigma); |
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421 | |
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422 | vector <Detection> searchReconArray(long *dim, float *originalArray, |
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423 | float *reconArray, Param &par, |
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424 | StatsContainer<float> &stats); |
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425 | vector <Detection> search3DArray(long *dim, float *Array, Param &par, |
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426 | StatsContainer<float> &stats); |
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427 | |
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428 | void growObject(Detection &object, Cube &cube); |
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429 | |
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430 | #endif |
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