[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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[219] | 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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[3] | 37 | |
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| 38 | class DataArray |
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| 39 | { |
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| 40 | public: |
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[220] | 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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[3] | 47 | // Size and Dimension related |
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[220] | 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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[3] | 55 | // Related to the various arrays |
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[220] | 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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[3] | 62 | // Related to the object lists |
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[220] | 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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[3] | 71 | // Parameter list related. |
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[220] | 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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[190] | 80 | // Statistics |
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[220] | 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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[3] | 84 | |
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[220] | 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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[190] | 87 | |
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[220] | 88 | friend std::ostream& operator<< (std::ostream& theStream, DataArray &array); |
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| 89 | ///< Output operator for DataArray. |
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[3] | 90 | |
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| 91 | protected: |
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[219] | 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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[3] | 99 | }; |
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| 100 | |
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[220] | 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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[3] | 138 | /****************************************************************/ |
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[219] | 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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[3] | 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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[220] | 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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[3] | 151 | |
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[220] | 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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[3] | 175 | |
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[220] | 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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[3] | 210 | |
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[220] | 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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[3] | 223 | |
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| 224 | // Functions that act on the cube |
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[220] | 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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[3] | 234 | |
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[220] | 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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[103] | 249 | |
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[3] | 250 | // Text outputting of detected objects. |
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[220] | 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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[3] | 257 | |
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[220] | 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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[3] | 263 | |
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[220] | 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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[3] | 272 | private: |
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[220] | 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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[219] | 277 | |
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[220] | 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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[219] | 280 | |
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[220] | 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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[205] | 284 | |
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[219] | 285 | }; |
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[103] | 286 | |
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[220] | 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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[219] | 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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[3] | 411 | }; |
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| 412 | |
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[219] | 413 | |
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[3] | 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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[190] | 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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[3] | 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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