[3] | 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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[103] | 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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[190] | 20 | #ifndef STATS_H |
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| 21 | #include <Utils/Statistics.hh> |
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| 22 | #endif |
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[3] | 23 | |
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| 24 | using std::string; |
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| 25 | using std::vector; |
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[103] | 26 | using namespace Column; |
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[190] | 27 | using namespace Statistics; |
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[3] | 28 | |
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| 29 | /****************************************************************/ |
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| 30 | ///////////////////////////////////////////////////////////// |
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| 31 | //// Definition of an n-dimensional data array: |
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| 32 | //// array of pixel values, size & dimensions |
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| 33 | //// array of Detection objects |
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| 34 | ///////////////////////////////////////////////////////////// |
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| 35 | |
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| 36 | |
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| 37 | class DataArray |
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| 38 | { |
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| 39 | public: |
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| 40 | DataArray(){numDim=0; numPixels=0;}; |
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| 41 | DataArray(short int nDim){numDim=nDim; numPixels=0;}; |
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| 42 | DataArray(short int nDim, long size); |
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| 43 | DataArray(short int nDim, long *dimensions); |
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[137] | 44 | virtual ~DataArray(); |
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[3] | 45 | // Size and Dimension related |
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[190] | 46 | long getDimX(){if(numDim>0) return axisDim[0];else return 0;}; |
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| 47 | long getDimY(){if(numDim>1) return axisDim[1];else return 1;}; |
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| 48 | long getDimZ(){if(numDim>2) return axisDim[2];else return 1;}; |
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| 49 | void getDim(long &x, long &y, long &z); |
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| 50 | long getSize(){return numPixels;}; |
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| 51 | short int getNumDim(){return numDim;}; |
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[3] | 52 | // Related to the various arrays |
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[204] | 53 | void getDimArray(long *output); |
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| 54 | void getArray(float *output); |
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| 55 | virtual void saveArray(float *input, long size); |
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| 56 | float getPixValue(long pos){return array[pos];}; |
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| 57 | void setPixValue(long pos, float f){array[pos] = f;}; |
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[3] | 58 | // Related to the object lists |
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[204] | 59 | Detection getObject(long number){return objectList[number];}; |
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| 60 | void addObject(Detection object); |
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[205] | 61 | // adds a single detection to the object list |
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[204] | 62 | vector <Detection> getObjectList(){return objectList;}; |
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| 63 | void addObjectList(vector <Detection> newlist); |
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[205] | 64 | // adds all objects in a detection list to the object list |
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[204] | 65 | void addObjectOffsets(); |
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| 66 | long getNumObj(){return objectList.size();}; |
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| 67 | void clearDetectionList(){this->objectList.clear();}; |
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[3] | 68 | // Parameter list related. |
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[204] | 69 | int readParam(string paramfile){ |
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[160] | 70 | return par.readParams(paramfile);}; |
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[204] | 71 | void showParam(std::ostream &stream){stream << par;}; |
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| 72 | Param getParam(){return par;}; |
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| 73 | void saveParam(Param newpar){par = newpar;}; |
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| 74 | Param& pars(){Param &rpar = par; return rpar;}; |
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| 75 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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[190] | 76 | // Statistics |
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| 77 | StatsContainer<float> getStats(){return Stats;}; |
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| 78 | StatsContainer<float>& stats(){ |
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| 79 | StatsContainer<float> &rstats = Stats; |
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| 80 | return rstats; |
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| 81 | }; |
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| 82 | void saveStats(StatsContainer<float> newStats){ |
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| 83 | Stats = newStats; |
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| 84 | }; |
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[3] | 85 | |
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[190] | 86 | bool isDetection(float value){ |
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| 87 | if(par.isBlank(value)) return false; |
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| 88 | else return Stats.isDetection(value); |
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| 89 | }; |
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| 90 | |
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[3] | 91 | friend std::ostream& operator<< ( std::ostream& theStream, DataArray &array); |
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| 92 | |
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| 93 | protected: |
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[190] | 94 | short int numDim; // number of dimensions. |
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| 95 | long *axisDim; // array of dimensions of cube |
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| 96 | // (ie. how large in each direction). |
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| 97 | long numPixels; // total number of pixels in cube |
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| 98 | float *array; // array of data |
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| 99 | vector <Detection> objectList; // the list of detected objects |
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| 100 | Param par; // a parameter list. |
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| 101 | StatsContainer<float> Stats; // The statistics for the dataArray |
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[3] | 102 | }; |
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| 103 | |
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| 104 | |
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| 105 | /****************************************************************/ |
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| 106 | ///////////////////////////////////////////////////////////// |
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| 107 | //// Definition of an image object (2D): |
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| 108 | //// a DataArray object |
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| 109 | //// arrays for: probability values (for FDR) |
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| 110 | //// mask image to indicate location of objects |
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| 111 | //// detected objects |
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| 112 | //// statistics information |
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| 113 | ///////////////////////////////////////////////////////////// |
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| 114 | |
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[117] | 115 | class Cube; |
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[3] | 116 | class Image : public DataArray |
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| 117 | { |
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| 118 | public: |
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[205] | 119 | Image(){numPixels=0; numDim=2;}; |
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[3] | 120 | Image(long nPix); |
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| 121 | Image(long *dimensions); |
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[205] | 122 | virtual ~Image(){}; |
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[3] | 123 | |
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[53] | 124 | // Defining the array |
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[3] | 125 | void saveArray(float *input, long size); |
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[53] | 126 | void extractSpectrum(float *Array, long *dim, long pixel); |
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| 127 | void extractImage(float *Array, long *dim, long channel); |
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[117] | 128 | void extractSpectrum(Cube &cube, long pixel); |
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| 129 | void extractImage(Cube &cube, long channel); |
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[106] | 130 | // Accessing the data. |
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[3] | 131 | float getPixValue(long x, long y){return array[y*axisDim[0] + x];}; |
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| 132 | float getPixValue(long pos){return array[pos];}; |
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| 133 | // the next few should have checks against array overflow... |
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| 134 | void setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;}; |
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| 135 | void setPixValue(long pos, float f){array[pos] = f;}; |
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[103] | 136 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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[155] | 137 | bool isBlank(long x,long y){return par.isBlank(array[y*axisDim[0]+x]);}; |
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[3] | 138 | |
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| 139 | // Detection-related |
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[155] | 140 | void lutz_detect(); // in Detection/lutz_detect.cc |
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| 141 | void spectrumDetect(); // in Detection/spectrumDetect.cc |
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[190] | 142 | int getMinSize(){return minSize;}; |
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| 143 | void setMinSize(int i){minSize=i;}; |
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[155] | 144 | // the rest are in Detection/thresholding_functions.cc |
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[190] | 145 | bool isDetection(long x, long y){ |
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| 146 | long voxel = y*axisDim[0] + x; |
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[192] | 147 | if(isBlank(x,y)) return false; |
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| 148 | else return Stats.isDetection(array[voxel]); |
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| 149 | }; |
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[3] | 150 | |
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[103] | 151 | void removeMW(); |
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[3] | 152 | |
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| 153 | private: |
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[155] | 154 | int minSize; // the minimum number of pixels for a detection |
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| 155 | // to be accepted. |
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[3] | 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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[205] | 167 | Cube(){ |
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| 168 | numPixels=0; numDim=3; |
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| 169 | reconExists = false; reconAllocated = false; baselineAllocated = false; |
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| 170 | }; |
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[3] | 171 | Cube(long nPix); |
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| 172 | Cube(long *dimensions); |
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[187] | 173 | virtual ~Cube(); |
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[3] | 174 | |
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[155] | 175 | // additional accessor functions |
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| 176 | // -- in Cubes/cubes.cc unless otherwise specified. |
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[3] | 177 | |
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| 178 | int getCube(string fname); |
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[106] | 179 | int getCube(){ |
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| 180 | // a front-end to the getCube function, that does subsection checks |
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| 181 | // assumes the Param is setup properly |
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[129] | 182 | string fname = par.getImageFile(); |
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[164] | 183 | if(par.getFlagSubsection()) fname+=par.getSubsection(); |
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[129] | 184 | return getCube(fname); |
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[106] | 185 | }; |
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[160] | 186 | int getFITSdata(string fname); // in FitsIO/dataIO.cc |
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[136] | 187 | void initialiseCube(long *dimensions); // in cubes.cc |
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| 188 | int getopts(int argc, char ** argv); // in cubes.cc |
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[208] | 189 | void readSavedArrays(); // in cubes.cc |
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| 190 | void saveSmoothedCube(); // in saveImage.cc |
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| 191 | void saveReconstructedCube(); // in saveImage.cc |
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| 192 | int readReconCube(); // in readRecon.cc |
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| 193 | int readSmoothCube(); // in readSmooth.cc |
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[3] | 194 | |
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[87] | 195 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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| 196 | bool isBlank(long x, long y, long z){ |
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| 197 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]);}; |
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[3] | 198 | float getPixValue(long pos){return array[pos];}; |
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| 199 | float getPixValue(long x, long y, long z){ |
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| 200 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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| 201 | short getDetectMapValue(long pos){return detectMap[pos];}; |
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[155] | 202 | short getDetectMapValue(long x, long y){return detectMap[y*axisDim[0]+x];}; |
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[3] | 203 | bool isRecon(){return reconExists;}; |
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| 204 | float getReconValue(long pos){return recon[pos];}; |
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| 205 | float getReconValue(long x, long y, long z){ |
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| 206 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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| 207 | float getBaselineValue(long pos){return baseline[pos];}; |
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| 208 | float getBaselineValue(long x, long y, long z){ |
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| 209 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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| 210 | // these should have checks against array overflow... |
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| 211 | void setPixValue(long pos, float f){array[pos] = f;}; |
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| 212 | void setPixValue(long x, long y, long z, float f){ |
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| 213 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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| 214 | void setDetectMapValue(long pos, short f){detectMap[pos] = f;}; |
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| 215 | void setDetectMapValue(long x, long y, short f){ |
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| 216 | detectMap[y*axisDim[0] + x] = f;}; |
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| 217 | void setReconValue(long pos, float f){recon[pos] = f;}; |
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| 218 | void setReconValue(long x, long y, long z, float f){ |
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| 219 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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| 220 | void setReconFlag(bool f){reconExists = f;}; |
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| 221 | void saveArray(float *input, long size); |
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| 222 | void saveRecon(float *input, long size); |
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| 223 | void getRecon(float *output); |
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| 224 | |
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[144] | 225 | vector<Col> getLogCols(){return logCols;}; |
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| 226 | void setLogCols(vector<Col> C){logCols=C;}; |
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| 227 | vector<Col> getFullCols(){return fullCols;}; |
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| 228 | void setFullCols(vector<Col> C){fullCols=C;}; |
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[141] | 229 | |
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[3] | 230 | // Statistics for cube |
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[205] | 231 | void setCubeStatsOld(); // in Cubes/cubes.cc |
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[86] | 232 | void setCubeStats(); // in Cubes/cubes.cc |
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[190] | 233 | int setupFDR(); |
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| 234 | bool isDetection(long x, long y, long z){ |
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| 235 | long voxel = z*axisDim[0]*axisDim[1] + y*axisDim[0] + x; |
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| 236 | return DataArray::isDetection(array[voxel]); |
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| 237 | }; |
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[3] | 238 | |
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| 239 | // Functions that act on the cube |
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[86] | 240 | void removeMW(); // in Cubes/cubes.cc |
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| 241 | void trimCube(); // in Cubes/trimImage.cc |
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| 242 | void unTrimCube(); // in Cubes/trimImage.cc |
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[3] | 243 | void removeBaseline(); // in ATrous/baselineSubtract.cc |
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| 244 | void replaceBaseline(); // in ATrous/baselineSubtract.cc |
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[60] | 245 | void invert(); // in Cubes/invertCube.cc |
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| 246 | void reInvert(); // in Cubes/invertCube.cc |
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[3] | 247 | |
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| 248 | // Reconstruction and Searching functions |
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[103] | 249 | void ReconSearch(); // in ATrous/ReconSearch.cc |
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[188] | 250 | void ReconCube(); // in ATrous/ReconSearch.cc |
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| 251 | void ReconCube1D(); // in ATrous/ReconSearch.cc |
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| 252 | void ReconCube2D(); // in ATrous/ReconSearch.cc |
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| 253 | void ReconCube3D(); // in ATrous/ReconSearch.cc |
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[103] | 254 | void CubicSearch(); // in Cubes/CubicSearch.cc |
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[201] | 255 | void SmoothSearch(); // in Cubes/smoothCube.cc |
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| 256 | void SmoothCube(); // in Cubes/smoothCube.cc |
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[3] | 257 | |
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| 258 | // Dealing with the WCS |
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[103] | 259 | FitsHeader getHead(){return head;}; |
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| 260 | void setHead(FitsHeader F){head=F;}; |
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| 261 | FitsHeader& header(){FitsHeader &h = head; return h;}; |
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| 262 | int wcsToPix(const double *world, double *pix){ |
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| 263 | return this->head.wcsToPix(world,pix);} |
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| 264 | int wcsToPix(const double *world, double *pix, const int npts){ |
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| 265 | return this->head.wcsToPix(world,pix,npts);} |
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| 266 | int pixToWCS(const double *pix, double *world){ |
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| 267 | return this->head.pixToWCS(pix,world);} |
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| 268 | int pixToWCS(const double *pix, double *world, const int npts){ |
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| 269 | return this->head.pixToWCS(pix,world,npts);} |
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| 270 | |
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[3] | 271 | // Dealing with the detections |
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| 272 | void ObjectMerger(); // in Cubes/Merger.cc |
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| 273 | void calcObjectWCSparams(); |
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| 274 | void sortDetections(); |
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| 275 | void updateDetectMap(); |
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| 276 | void updateDetectMap(Detection obj); |
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[87] | 277 | void setObjectFlags(); |
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| 278 | float enclosedFlux(Detection obj); |
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[192] | 279 | bool objAtSpatialEdge(Detection obj); |
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| 280 | bool objAtSpectralEdge(Detection obj); |
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[87] | 281 | |
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[3] | 282 | // Text outputting of detected objects. |
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[142] | 283 | // the next five in Cubes/detectionIO.cc |
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| 284 | void outputDetectionsKarma(std::ostream &stream); |
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| 285 | void outputDetectionsVOTable(std::ostream &stream); |
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| 286 | void outputDetectionList(); |
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| 287 | void logDetectionList(); |
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| 288 | void logDetection(Detection obj, int counter); |
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| 289 | void setupColumns(); // in Cubes/cubes.cc |
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[3] | 290 | |
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[129] | 291 | // Graphical plotting of the cube and the detections. |
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[142] | 292 | void plotBlankEdges(); // in Cubes/cubes.cc |
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| 293 | // the next three in Cubes/plotting.cc |
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| 294 | void plotDetectionMap(string pgDestination); |
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| 295 | void plotMomentMap(string pgDestination); |
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[203] | 296 | void plotMomentMap(vector<string> pgDestination); |
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[142] | 297 | void plotWCSaxes(); |
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| 298 | // the next two in Cubes/outputSpectra.cc |
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[155] | 299 | void outputSpectra(); |
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[142] | 300 | void plotSpectrum(Detection obj,Plot::SpectralPlot &plot); |
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| 301 | // the next three in Cubes/drawMomentCutout.cc |
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| 302 | void drawMomentCutout(Detection &object); |
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| 303 | void drawScale(float xstart,float ystart,float channel); |
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| 304 | void drawFieldEdge(); |
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[3] | 305 | |
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| 306 | private: |
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[155] | 307 | float *recon; // reconstructed array -- used when doing a trous |
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| 308 | // reconstruction. |
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[3] | 309 | bool reconExists; // flag saying whether there is a reconstruction |
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| 310 | short *detectMap; // "moment map" -- x,y locations of detected pixels |
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| 311 | float *baseline; // array of spectral baseline values. |
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[205] | 312 | |
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| 313 | bool reconAllocated; // have we allocated memory for the recon array? |
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| 314 | bool baselineAllocated;// have we allocated memory for the baseline array? |
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[103] | 315 | |
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| 316 | FitsHeader head; // the WCS and other header information. |
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[155] | 317 | vector<Col> fullCols; // the list of all columns as printed in the |
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| 318 | // results file |
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[144] | 319 | vector<Col> logCols; // the list of columns as printed in the log file |
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[103] | 320 | |
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[3] | 321 | }; |
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| 322 | |
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| 323 | /****************************************************************/ |
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| 324 | ////////////////////////////////////////////////////// |
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| 325 | // Prototypes for functions that use above classes |
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| 326 | ////////////////////////////////////////////////////// |
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| 327 | |
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| 328 | void findSources(Image &image); |
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| 329 | void findSources(Image &image, float mean, float sigma); |
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| 330 | |
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[190] | 331 | vector <Detection> searchReconArray(long *dim, float *originalArray, |
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| 332 | float *reconArray, Param &par, |
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| 333 | StatsContainer<float> &stats); |
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| 334 | vector <Detection> search3DArray(long *dim, float *Array, Param &par, |
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| 335 | StatsContainer<float> &stats); |
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[3] | 336 | |
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| 337 | void growObject(Detection &object, Cube &cube); |
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| 338 | |
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| 339 | #endif |
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