[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // cubes.hh: Definitions of the DataArray, Cube and Image classes. |
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| 3 | // ----------------------------------------------------------------------- |
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| 4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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| 5 | // |
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| 6 | // This program is free software; you can redistribute it and/or modify it |
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| 7 | // under the terms of the GNU General Public License as published by the |
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| 8 | // Free Software Foundation; either version 2 of the License, or (at your |
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| 9 | // option) any later version. |
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| 10 | // |
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| 11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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| 12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 14 | // for more details. |
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| 15 | // |
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| 16 | // You should have received a copy of the GNU General Public License |
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| 17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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| 18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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| 19 | // |
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| 20 | // Correspondence concerning Duchamp may be directed to: |
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| 21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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| 22 | // Postal address: Dr. Matthew Whiting |
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| 23 | // Australia Telescope National Facility, CSIRO |
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| 24 | // PO Box 76 |
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| 25 | // Epping NSW 1710 |
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| 26 | // AUSTRALIA |
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| 27 | // ----------------------------------------------------------------------- |
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[3] | 28 | #ifndef CUBES_H |
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| 29 | #define CUBES_H |
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| 30 | |
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| 31 | #include <iostream> |
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| 32 | #include <string> |
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| 33 | #include <vector> |
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| 34 | |
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[459] | 35 | #include <duchamp/duchamp.hh> |
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[393] | 36 | #include <duchamp/param.hh> |
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| 37 | #include <duchamp/fitsHeader.hh> |
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| 38 | #include <duchamp/Detection/detection.hh> |
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| 39 | #include <duchamp/Detection/columns.hh> |
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| 40 | #include <duchamp/Cubes/plots.hh> |
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| 41 | #include <duchamp/Utils/Statistics.hh> |
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| 42 | #include <duchamp/PixelMap/Scan.hh> |
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| 43 | #include <duchamp/PixelMap/Object2D.hh> |
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[3] | 44 | |
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| 45 | |
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[378] | 46 | namespace duchamp |
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| 47 | { |
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[290] | 48 | |
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| 49 | |
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[528] | 50 | /// @brief Search a reconstructed array for significant detections. |
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[686] | 51 | std::vector <Detection> searchReconArray(long *dim, float *originalArray, float *reconArray, |
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| 52 | Param &par, Statistics::StatsContainer<float> &stats); |
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| 53 | std::vector <Detection> searchReconArraySpectral(long *dim, float *originalArray, float *reconArray, |
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| 54 | Param &par, Statistics::StatsContainer<float> &stats); |
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| 55 | std::vector <Detection> searchReconArraySpatial(long *dim, float *originalArray, float *reconArray, |
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| 56 | Param &par, Statistics::StatsContainer<float> &stats); |
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[3] | 57 | |
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[528] | 58 | /// @brief Search a 3-dimensional array for significant detections. |
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[686] | 59 | std::vector <Detection> search3DArray(long *dim, float *Array, Param &par, |
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| 60 | Statistics::StatsContainer<float> &stats); |
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| 61 | std::vector <Detection> search3DArraySpectral(long *dim, float *Array, Param &par, |
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| 62 | Statistics::StatsContainer<float> &stats); |
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| 63 | std::vector <Detection> search3DArraySpatial(long *dim, float *Array, Param &par, |
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| 64 | Statistics::StatsContainer<float> &stats); |
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[220] | 65 | |
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[528] | 66 | //========================================================================= |
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[220] | 67 | |
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[528] | 68 | /// @brief Base class for the image container. |
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| 69 | /// |
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| 70 | /// @details Definition of an n-dimensional data array: array of |
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| 71 | /// pixel values, size & dimensions array of Detection objects |
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| 72 | |
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[378] | 73 | class DataArray |
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| 74 | { |
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| 75 | public: |
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| 76 | DataArray(); ///< Basic DataArray constructor |
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| 77 | DataArray(short int nDim); ///< Basic nDim-dimensional DataArray constructor |
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| 78 | DataArray(short int nDim, long size);///< Basic nDim-dimensional DataArray constructor, specifying size. |
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| 79 | DataArray(short int nDim, long *dimensions); ///< Basic nDim-dimensional DataArray constructor, specifying size of dimensions. |
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| 80 | virtual ~DataArray(); ///< Basic DataArray constructor |
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[736] | 81 | DataArray(const DataArray &d); |
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| 82 | DataArray& operator=(const DataArray &d); |
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[222] | 83 | |
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[378] | 84 | //----------------------------------------- |
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| 85 | // Obvious inline accessor functions. |
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| 86 | // |
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| 87 | long getDimX(){if(numDim>0) return axisDim[0];else return 0;}; |
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| 88 | long getDimY(){if(numDim>1) return axisDim[1];else return 1;}; |
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| 89 | long getDimZ(){if(numDim>2) return axisDim[2];else return 1;}; |
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| 90 | long getSize(){ return numPixels; }; |
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| 91 | short int getNumDim(){ return numDim; }; |
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| 92 | virtual float getPixValue(long pos){ return array[pos]; }; |
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| 93 | virtual void setPixValue(long pos, float f){array[pos] = f;}; |
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| 94 | Detection getObject(long number){ return objectList->at(number); }; |
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[424] | 95 | Detection * pObject(long number){ return &(objectList->at(number));}; |
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[378] | 96 | std::vector <Detection> getObjectList(){ return *objectList; }; |
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[387] | 97 | std::vector <Detection> *pObjectList(){ return objectList; }; |
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| 98 | std::vector <Detection> &ObjectList(){ std::vector<Detection> &rlist = *objectList; return rlist; }; |
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[378] | 99 | long getNumObj(){ return objectList->size(); }; |
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[222] | 100 | |
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[528] | 101 | /// @brief Delete all objects from the list of detections. |
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[378] | 102 | void clearDetectionList(){ |
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| 103 | //objectList->clear(); |
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| 104 | delete objectList; |
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| 105 | objectList = new std::vector<Detection>; |
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| 106 | }; |
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[220] | 107 | |
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[528] | 108 | /// @brief Read a parameter set from file. |
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[700] | 109 | OUTCOME readParam(std::string paramfile){ |
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[528] | 110 | /// @brief |
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[531] | 111 | /// Uses Param::readParams() to read parameters from a file. |
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| 112 | /// \param paramfile The file to be read. |
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[528] | 113 | |
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[378] | 114 | return par.readParams(paramfile); |
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| 115 | }; |
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[222] | 116 | |
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[378] | 117 | //----------------------------------------- |
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| 118 | // Related to the various arrays |
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| 119 | // |
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[528] | 120 | /// @brief Return first three dimensional axes. |
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[378] | 121 | void getDim(long &x, long &y, long &z); |
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[528] | 122 | /// @brief Return array of dimensional sizes. |
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[378] | 123 | void getDimArray(long *output); |
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| 124 | long * getDimArray(){return axisDim;}; |
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[222] | 125 | |
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[528] | 126 | /// @brief Return pixel value array. |
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[378] | 127 | void getArray(float *output); |
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| 128 | float * getArray(){return array;}; |
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[220] | 129 | |
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[528] | 130 | /// @brief Save pixel value array. |
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[378] | 131 | virtual void saveArray(float *input, long size); |
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[258] | 132 | |
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[378] | 133 | //----------------------------------------- |
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| 134 | // Related to the object lists |
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| 135 | // |
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[528] | 136 | /// @brief Adds a single detection to the object list. |
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[378] | 137 | void addObject(Detection object); |
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[222] | 138 | |
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[528] | 139 | /// @brief Adds all objects in a detection list to the object list. |
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[378] | 140 | void addObjectList(std::vector <Detection> newlist); |
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[220] | 141 | |
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[528] | 142 | /// @brief Add pixel offsets to object coordinates. |
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[378] | 143 | void addObjectOffsets(); |
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[3] | 144 | |
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[378] | 145 | //----------------------------------------- |
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| 146 | // Parameter list related. |
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| 147 | // |
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[528] | 148 | /// @brief Output the Param set. |
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[378] | 149 | void showParam(std::ostream &stream){ stream << par; }; |
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[528] | 150 | /// @brief Return the Param set. |
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[378] | 151 | Param getParam(){ return par; }; |
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[528] | 152 | /// @brief Save a Param set to the Cube. |
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[378] | 153 | void saveParam(Param &newpar){par = newpar;}; |
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[528] | 154 | /// @brief Provides a reference to the Param set. |
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[378] | 155 | Param& pars(){ Param &rpar = par; return rpar; }; |
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[528] | 156 | /// @brief Is the voxel number given by vox a BLANK value? |
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[741] | 157 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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[378] | 158 | |
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| 159 | // -------------------------------------------- |
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| 160 | // Statistics |
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| 161 | // |
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[528] | 162 | /// @brief Returns the StatsContainer. |
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[378] | 163 | Statistics::StatsContainer<float> getStats(){ return Stats; }; |
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| 164 | |
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[528] | 165 | /// @brief Provides a reference to the StatsContainer. |
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[378] | 166 | Statistics::StatsContainer<float>& stats(){ |
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| 167 | Statistics::StatsContainer<float> &rstats = Stats; return rstats; |
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| 168 | }; |
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[258] | 169 | |
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[528] | 170 | /// @brief Save a StatsContainer to the Cube. |
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[378] | 171 | void saveStats(Statistics::StatsContainer<float> newStats){ Stats = newStats;}; |
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[190] | 172 | |
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[528] | 173 | /// @brief A detection test for value. |
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[378] | 174 | bool isDetection(float value); |
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[222] | 175 | |
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[528] | 176 | /// @brief A detection test for pixel. |
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[378] | 177 | bool isDetection(long voxel); |
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[222] | 178 | |
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| 179 | |
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[528] | 180 | /// @brief Output operator for DataArray. |
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[378] | 181 | friend std::ostream& operator<< (std::ostream& theStream, DataArray &array); |
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[222] | 182 | |
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[3] | 183 | |
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[378] | 184 | protected: |
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| 185 | short int numDim; ///< Number of dimensions. |
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[443] | 186 | long *axisDim; ///< Array of axis dimensions of cube |
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| 187 | bool axisDimAllocated; ///< has axisDim been allocated? |
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[378] | 188 | long numPixels; ///< Total number of pixels in cube. |
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| 189 | float *array; ///< Array of data. |
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[444] | 190 | bool arrayAllocated; ///< has the array been allocated? |
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[378] | 191 | std::vector <Detection> *objectList; ///< The list of detected objects. |
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| 192 | Param par; ///< A parameter list. |
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| 193 | Statistics::StatsContainer<float> Stats; ///< The statistics for the DataArray. |
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| 194 | }; |
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[3] | 195 | |
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[220] | 196 | |
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| 197 | |
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[378] | 198 | //========================================================================= |
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[220] | 199 | |
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[528] | 200 | /// @brief Definition of an data-cube object (3D): |
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| 201 | /// a DataArray object limited to dim=3 |
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[3] | 202 | |
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[378] | 203 | class Cube : public DataArray |
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| 204 | { |
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| 205 | public: |
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| 206 | Cube(); ///< Basic Cube constructor. |
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| 207 | Cube(long nPix); ///< Alternative Cube constructor. |
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| 208 | Cube(long *dimensions); ///< Alternative Cube constructor. |
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| 209 | virtual ~Cube(); ///< Basic Cube destructor. |
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[736] | 210 | Cube(const Cube &c); ///< Copy constructor |
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| 211 | Cube& operator=(const Cube &c); ///< Copy operator |
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[3] | 212 | |
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[513] | 213 | bool is2D(); |
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| 214 | void checkDim(){head.set2D(is2D());}; |
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[758] | 215 | void reportMemorySize(std::ostream &theStream, bool allocateArrays); |
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[513] | 216 | |
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[378] | 217 | // INLINE functions -- definitions included after class declaration. |
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[528] | 218 | /// @brief Is the voxel number given by vox a BLANK value? |
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[378] | 219 | bool isBlank(int vox){ return par.isBlank(array[vox]); }; |
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[3] | 220 | |
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[528] | 221 | /// @brief Is the voxel at (x,y,z) a BLANK value? |
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[378] | 222 | bool isBlank(long x, long y, long z){ |
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| 223 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]); }; |
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[222] | 224 | |
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[528] | 225 | /// @brief Return a bool array masking blank pixels: 1=good, 0=blank |
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[463] | 226 | bool * makeBlankMask(){return par.makeBlankMask(array, numPixels);}; |
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| 227 | |
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[528] | 228 | /// @brief Does the Cube::recon array exist? |
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[378] | 229 | bool isRecon(){ return reconExists; }; |
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[222] | 230 | |
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[378] | 231 | float getPixValue(long pos){ return array[pos]; }; |
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| 232 | float getPixValue(long x, long y, long z){ |
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| 233 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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| 234 | short getDetectMapValue(long pos){ return detectMap[pos]; }; |
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| 235 | short getDetectMapValue(long x, long y){ return detectMap[y*axisDim[0]+x]; }; |
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| 236 | float getReconValue(long pos){ return recon[pos]; }; |
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| 237 | float getReconValue(long x, long y, long z){ |
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| 238 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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| 239 | float getBaselineValue(long pos){ return baseline[pos]; }; |
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| 240 | float getBaselineValue(long x, long y, long z){ |
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| 241 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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[419] | 242 | void setPixValue(long pos, float f){array[pos] = f;}; |
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[378] | 243 | void setPixValue(long x, long y, long z, float f){ |
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| 244 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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| 245 | void setDetectMapValue(long pos, short f){ detectMap[pos] = f;}; |
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| 246 | void setDetectMapValue(long x, long y, short f){ detectMap[y*axisDim[0] + x] = f;}; |
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[739] | 247 | void incrementDetectMap(long x, long y){detectMap[y*axisDim[0]+x]++;}; |
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| 248 | void incrementDetectMap(long pos){detectMap[pos]++;}; |
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[378] | 249 | void setReconValue(long pos, float f){recon[pos] = f;}; |
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| 250 | void setReconValue(long x, long y, long z, float f){ |
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| 251 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f; }; |
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| 252 | void setReconFlag(bool f){reconExists = f;}; |
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[222] | 253 | |
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[378] | 254 | std::vector<Column::Col> getLogCols(){return logCols;}; |
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| 255 | void setLogCols(std::vector<Column::Col> C){logCols=C;}; |
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| 256 | std::vector<Column::Col> getFullCols(){return fullCols;}; |
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| 257 | void setFullCols(std::vector<Column::Col> C){fullCols=C;}; |
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[222] | 258 | |
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[378] | 259 | // additional functions -- in Cubes/cubes.cc |
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[528] | 260 | /// @brief Allocate memory correctly, with WCS defining the correct axes. |
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[679] | 261 | OUTCOME initialiseCube(long *dimensions, bool allocateArrays=true); |
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[222] | 262 | |
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[528] | 263 | /// @brief Read in a FITS file, with subsection correction. |
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[698] | 264 | OUTCOME getCube(); |
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[528] | 265 | /// @brief Read in a FITS file, with subsection correction. |
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[698] | 266 | OUTCOME getMetadata(); |
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[222] | 267 | |
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[528] | 268 | /// @brief Read in command-line options. |
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[378] | 269 | // int getopts(int argc, char ** argv); |
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[474] | 270 | int getopts(int argc, char ** argv, std::string progname="Duchamp"){return par.getopts(argc,argv,progname);}; |
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[222] | 271 | |
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[528] | 272 | /// @brief Read in reconstructed & smoothed arrays from FITS files on disk. |
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[378] | 273 | void readSavedArrays(); |
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[222] | 274 | |
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[528] | 275 | /// @brief Save an external array to the Cube's pixel array |
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[378] | 276 | void saveArray(float *input, long size); |
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[222] | 277 | |
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[528] | 278 | /// @brief Save an external array to the Cube's pixel array |
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[491] | 279 | void saveArray(std::vector<float> &input); |
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| 280 | |
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[528] | 281 | /// @brief Save an external array to the Cube's reconstructed array. |
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[378] | 282 | void saveRecon(float *input, long size); |
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[222] | 283 | |
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[528] | 284 | /// @brief Save reconstructed array to an external array. |
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[378] | 285 | void getRecon(float *output); |
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[387] | 286 | float * getRecon(){return recon; }; |
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[222] | 287 | |
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[528] | 288 | /// @brief Set Milky Way channels to zero. |
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[378] | 289 | void removeMW(); |
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[222] | 290 | |
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[378] | 291 | //------------------------ |
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| 292 | // Statistics for cube |
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| 293 | // |
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[222] | 294 | |
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[528] | 295 | /// @brief Calculate the statistics for the Cube (older version). |
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[378] | 296 | void setCubeStatsOld(); |
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[222] | 297 | |
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[528] | 298 | /// @brief Calculate the statistics for the Cube. |
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[378] | 299 | void setCubeStats(); |
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[222] | 300 | |
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[528] | 301 | /// @brief Set up thresholds for the False Discovery Rate routine. |
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[378] | 302 | void setupFDR(); |
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[531] | 303 | /// @brief Set up thresholds for the False Discovery Rate routine using a particular array. |
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[378] | 304 | void setupFDR(float *input); |
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[222] | 305 | |
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[528] | 306 | /// @brief A detection test for a given voxel. |
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[378] | 307 | bool isDetection(long x, long y, long z); |
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[222] | 308 | |
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[378] | 309 | //----------------------------- |
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| 310 | // Dealing with the detections |
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| 311 | // |
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[659] | 312 | |
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| 313 | /// @brief Get the set of voxels pertaining to the detected objects. |
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| 314 | std::vector< std::vector<PixelInfo::Voxel> > getObjVoxList(); |
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[222] | 315 | |
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[528] | 316 | /// @brief Calculate the object fluxes |
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[420] | 317 | void calcObjectFluxes(); |
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| 318 | |
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[528] | 319 | /// @brief Calculate the WCS parameters for each Cube Detection. |
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[378] | 320 | void calcObjectWCSparams(); |
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[528] | 321 | /// @brief Calculate the WCS parameters for each Cube Detection, using flux information in Voxels. |
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[418] | 322 | void calcObjectWCSparams(std::vector< std::vector<PixelInfo::Voxel> > bigVoxList); |
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[863] | 323 | void calcObjectWCSparams(std::map<PixelInfo::Voxel,float> &voxelMap); |
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| 324 | |
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[528] | 325 | /// @brief Sort the list of detections. |
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[378] | 326 | void sortDetections(); |
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[222] | 327 | |
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[528] | 328 | /// @brief Update the map of detected pixels. |
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[378] | 329 | void updateDetectMap(); |
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[222] | 330 | |
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[528] | 331 | /// @brief Update the map of detected pixels for a given Detection. |
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[378] | 332 | void updateDetectMap(Detection obj); |
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[222] | 333 | |
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[528] | 334 | /// @brief Clear the map of detected pixels. |
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[378] | 335 | void clearDetectMap(){ |
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| 336 | for(int i=0;i<axisDim[0]*axisDim[1];i++) detectMap[i]=0; |
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| 337 | }; |
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[290] | 338 | |
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[528] | 339 | /// @brief Find the flux enclosed by a Detection. |
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[378] | 340 | float enclosedFlux(Detection obj); |
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[222] | 341 | |
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[531] | 342 | /// @brief Set up the output column definitions for the Cube and its Detection list. |
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[378] | 343 | void setupColumns(); |
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[222] | 344 | |
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[528] | 345 | /// @brief Is the object at the edge of the image? |
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[378] | 346 | bool objAtSpatialEdge(Detection obj); |
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[222] | 347 | |
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[528] | 348 | /// @brief Is the object at an end of the spectrum? |
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[378] | 349 | bool objAtSpectralEdge(Detection obj); |
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[222] | 350 | |
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[528] | 351 | /// @brief Set warning flags for the detections. |
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[378] | 352 | void setObjectFlags(); |
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[222] | 353 | |
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[378] | 354 | // ---------------------------- |
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| 355 | // Dealing with the WCS |
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| 356 | // |
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[528] | 357 | /// @brief Return the FitsHeader object. |
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[378] | 358 | FitsHeader getHead(){ return head; }; |
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[528] | 359 | /// @brief Define the FitsHeader object. |
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[378] | 360 | void setHead(FitsHeader F){head = F;}; |
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[528] | 361 | /// @brief Provide a reference to the FitsHeader object. |
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[378] | 362 | FitsHeader& header(){ FitsHeader &h = head; return h; }; |
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[3] | 363 | |
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[528] | 364 | /// @brief Convert a point from WCS to Pixel coords. |
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[378] | 365 | int wcsToPix(const double *world, double *pix); |
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[222] | 366 | |
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[528] | 367 | /// @brief Convert a set of points from WCS to Pixel coords. |
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[378] | 368 | int wcsToPix(const double *world, double *pix, const int npts); |
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[222] | 369 | |
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[528] | 370 | /// @brief Convert a point from Pixel to WCS coords. |
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[378] | 371 | int pixToWCS(const double *pix, double *world); |
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[222] | 372 | |
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[528] | 373 | /// @brief Convert a set of points from Pixel to WCS coords. |
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[378] | 374 | int pixToWCS(const double *pix, double *world, const int npts); |
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[222] | 375 | |
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[378] | 376 | //------------------------------------------- |
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| 377 | // FITS-I/O related functions -- not in cubes.cc |
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| 378 | // |
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[528] | 379 | /// @brief Function to read in FITS file. |
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[698] | 380 | OUTCOME getMetadata(std::string fname); // in Cubes/getImage.cc |
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| 381 | OUTCOME getCube(std::string fname); // in Cubes/getImage.cc |
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[3] | 382 | |
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[528] | 383 | /// @brief Convert the flux units to something user-specified. |
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[434] | 384 | void convertFluxUnits(); // in Cubes/getImage.cc |
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| 385 | |
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[528] | 386 | /// @brief Function to retrieve FITS data array |
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[698] | 387 | OUTCOME getFITSdata(std::string fname); // in FitsIO/dataIO.cc |
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[222] | 388 | |
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[670] | 389 | /// @brief Save the moment map to a FITS file |
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[695] | 390 | OUTCOME saveMomentMapImage(); |
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[670] | 391 | |
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[528] | 392 | /// @brief Save a mask array to disk. |
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[695] | 393 | OUTCOME saveMaskCube(); // in Cubes/saveImage.cc |
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[379] | 394 | |
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[528] | 395 | /// @brief Save Smoothed array to disk. |
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[695] | 396 | OUTCOME saveSmoothedCube(); // in Cubes/saveImage.cc |
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[258] | 397 | |
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[528] | 398 | /// @brief Save Reconstructed array to disk. |
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[695] | 399 | OUTCOME saveReconstructedCube(); // in Cubes/saveImage.cc |
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[222] | 400 | |
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[528] | 401 | /// @brief Read in reconstructed array from FITS file. |
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[698] | 402 | OUTCOME readReconCube(); // in Cubes/readRecon.cc |
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[222] | 403 | |
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[528] | 404 | /// @brief Read in Hanning-smoothed array from FITS file. |
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[698] | 405 | OUTCOME readSmoothCube(); // in Cubes/readSmooth.cc |
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[222] | 406 | |
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[378] | 407 | //------------------------------------- |
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| 408 | // Functions that act on the cube |
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| 409 | // |
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[3] | 410 | |
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[528] | 411 | /// @brief Remove excess BLANK pixels from spatial edge of cube. |
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[378] | 412 | void trimCube(); // in Cubes/trimImage.cc |
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[222] | 413 | |
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[528] | 414 | /// @brief Replace BLANK pixels to spatial edge of cube. |
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[378] | 415 | void unTrimCube(); // in Cubes/trimImage.cc |
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[222] | 416 | |
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[528] | 417 | /// @brief Removes the baselines from the spectra, and stores in Cube::baseline |
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[378] | 418 | void removeBaseline(); // in Cubes/baseline.cc |
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[222] | 419 | |
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[528] | 420 | /// @brief Replace the baselines stored in Cube::baseline |
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[378] | 421 | void replaceBaseline(); // in Cubes/baseline.cc |
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[222] | 422 | |
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[528] | 423 | /// @brief Multiply all pixel values by -1. |
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[378] | 424 | void invert(); // in Cubes/invertCube.cc |
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[222] | 425 | |
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[528] | 426 | /// @brief Undo the inversion, and invert fluxes of all detected objects. |
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[378] | 427 | void reInvert(); // in Cubes/invertCube.cc |
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[222] | 428 | |
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[378] | 429 | //------------------------------------- |
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| 430 | // Reconstruction, Searching and Merging functions |
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| 431 | // |
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[729] | 432 | // in cubes.cc |
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| 433 | /// @brief A front-end to all the searching functions |
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[834] | 434 | void Search(); |
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[729] | 435 | |
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[378] | 436 | // in ATrous/ReconSearch.cc |
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[528] | 437 | /// @brief Front-end to reconstruction & searching functions. |
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[378] | 438 | void ReconSearch(); |
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[528] | 439 | /// @brief Switcher to reconstruction functions |
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[378] | 440 | void ReconCube(); |
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[528] | 441 | /// @brief Performs 1-dimensional a trous reconstruction on the Cube. |
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[378] | 442 | void ReconCube1D(); |
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[528] | 443 | /// @brief Performs 2-dimensional a trous reconstruction on the Cube. |
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[378] | 444 | void ReconCube2D(); |
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[528] | 445 | /// @brief Performs 3-dimensional a trous reconstruction on the Cube. |
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[378] | 446 | void ReconCube3D(); |
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[222] | 447 | |
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[378] | 448 | // in Cubes/CubicSearch.cc |
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[528] | 449 | /// @brief Front-end to the cubic searching routine. |
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[378] | 450 | void CubicSearch(); |
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[222] | 451 | |
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[378] | 452 | // in Cubes/smoothCube.cc |
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[528] | 453 | /// @brief Smooth the cube with the requested method. |
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[378] | 454 | void SmoothCube(); |
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[528] | 455 | /// @brief Front-end to the smoothing and searching functions. |
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[378] | 456 | void SmoothSearch(); |
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[528] | 457 | /// @brief A function to spatially smooth the cube and search the result. |
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[378] | 458 | void SpatialSmoothNSearch(); |
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[528] | 459 | /// @brief A function to Hanning-smooth the cube. |
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[378] | 460 | void SpectralSmooth(); |
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[528] | 461 | /// @brief A function to spatially-smooth the cube. |
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[378] | 462 | void SpatialSmooth(); |
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[222] | 463 | |
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[378] | 464 | void Simple3DSearch(){ |
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[528] | 465 | /// @brief Basic front-end to the simple 3d searching function -- does |
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| 466 | /// nothing more. |
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| 467 | /// |
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| 468 | /// @details This function just runs the search3DArraySimple function, |
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| 469 | /// storing the results in the Cube::objectList vector. No stats |
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| 470 | /// are calculated beforehand, and no logging or detection map |
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| 471 | /// updating is done. |
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[686] | 472 | *objectList = search3DArray(axisDim,array,par,Stats); |
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[378] | 473 | }; |
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[290] | 474 | |
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[378] | 475 | void Simple3DSearchRecon(){ |
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[528] | 476 | /// @brief Basic front-end to the 3d searching function used in the |
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| 477 | /// reconstruction case -- does nothing more. |
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| 478 | /// |
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| 479 | /// @details This function just runs the searchReconArraySimple |
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| 480 | /// function, storing the results in the Cube::objectList |
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| 481 | /// vector. No stats are calculated beforehand, and no logging |
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| 482 | /// or detection map updating is done. The recon array is |
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| 483 | /// assumed to have been defined already. |
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| 484 | |
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[686] | 485 | *objectList = searchReconArray(axisDim,array,recon,par,Stats); |
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[378] | 486 | }; |
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[290] | 487 | |
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[378] | 488 | void Simple3DSearchSmooth(){ |
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[528] | 489 | /// @brief Basic front-end to the simple 3d searching function |
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| 490 | /// run on the smoothed array -- does nothing more. |
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| 491 | /// |
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| 492 | /// @details This function just runs the search3DArraySimple |
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| 493 | /// function on the recon array (which contains the smoothed |
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| 494 | /// array), storing the results in the Cube::objectList |
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| 495 | /// vector. No stats are calculated beforehand, and no logging |
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| 496 | /// or detection map updating is done. The recon array is |
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| 497 | /// assumed to have been defined already. |
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| 498 | |
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[686] | 499 | *objectList = search3DArray(axisDim,recon,par,Stats); |
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[378] | 500 | }; |
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[290] | 501 | |
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[378] | 502 | // in Cubes/Merger.cc |
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[531] | 503 | /// @brief Merge all objects in the detection list so that only distinct ones are left. |
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[378] | 504 | void ObjectMerger(); |
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[103] | 505 | |
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[475] | 506 | // in Cubes/existingDetections.cc |
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[528] | 507 | /// @brief Read a previously-created log file to get the detections without searching |
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[698] | 508 | OUTCOME getExistingDetections(); |
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[475] | 509 | |
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[378] | 510 | //------------------------------------- |
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| 511 | // Text outputting of detected objects. |
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| 512 | // in Cubes/detectionIO.cc |
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| 513 | // |
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[528] | 514 | /// @brief Set up the output file with parameters and stats. |
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[378] | 515 | void prepareOutputFile(); |
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[3] | 516 | |
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[528] | 517 | /// @brief Write the statistical information to the output file. |
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[378] | 518 | void outputStats(); |
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[222] | 519 | |
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[528] | 520 | /// @brief Output detections to the output file and standard output. |
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[378] | 521 | void outputDetectionList(); |
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[222] | 522 | |
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[528] | 523 | /// @brief Prepare the log file for output. |
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[418] | 524 | void prepareLogFile(int argc, char *argv[]); |
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| 525 | |
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[528] | 526 | /// @brief Output detections to the log file. |
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[659] | 527 | void logDetectionList(bool calcFluxes=true); |
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[222] | 528 | |
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[528] | 529 | /// @brief Output a single detection to the log file. |
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[378] | 530 | void logDetection(Detection obj, int counter); |
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[222] | 531 | |
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[528] | 532 | /// @brief Output detections to a Karma annotation file. |
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[378] | 533 | void outputDetectionsKarma(std::ostream &stream); |
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[222] | 534 | |
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[528] | 535 | /// @brief Output detections to a VOTable. |
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[378] | 536 | void outputDetectionsVOTable(std::ostream &stream); |
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[275] | 537 | |
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[668] | 538 | |
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[378] | 539 | // ---------------------------------- |
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[668] | 540 | // Calculation of overall moment maps |
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| 541 | |
---|
| 542 | /// @brief Return a moment-0 map plus a map of where the object pixels are |
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[693] | 543 | void getMomentMap(float *momentMap, std::vector<bool> &detectedPixels); |
---|
[668] | 544 | /// @brief Return a moment-0 map formatted for logarithmic greyscale plotting, with greyscale limits |
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[693] | 545 | void getMomentMapForPlot(float *momentMap, float &z1, float &z2); |
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[668] | 546 | |
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| 547 | // ---------------------------------- |
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[378] | 548 | // Graphical plotting of the cube and the detections. |
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| 549 | // |
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| 550 | // in Cubes/plotting.cc |
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[531] | 551 | /// @brief Plot a spatial map of detections based on number of detected channels. |
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[378] | 552 | void plotDetectionMap(std::string pgDestination); |
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[3] | 553 | |
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[531] | 554 | /// @brief Plot a spatial map of detections based on 0th moment map of each object. |
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[378] | 555 | void plotMomentMap(std::string pgDestination); |
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[222] | 556 | |
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[531] | 557 | /// @brief Plot a spatial map of detections based on 0th moment map of each object to a number of PGPLOT devices. |
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[378] | 558 | void plotMomentMap(std::vector<std::string> pgDestination); |
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[222] | 559 | |
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[528] | 560 | /// @brief Draw WCS axes over a PGPLOT map. |
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[581] | 561 | void plotWCSaxes(){duchamp::plotWCSaxes(head.getWCS(),axisDim);}; |
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[222] | 562 | |
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[378] | 563 | // in Cubes/outputSpectra.cc |
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[528] | 564 | /// @brief Print spectra of each detected object. |
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[378] | 565 | void outputSpectra(); |
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[222] | 566 | |
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[528] | 567 | /// @brief Write out text file of all spectra. |
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[424] | 568 | void writeSpectralData(); |
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| 569 | |
---|
[528] | 570 | /// @brief Print spectrum of a single object |
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[424] | 571 | void plotSpectrum(int objNum, Plot::SpectralPlot &plot); |
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[528] | 572 | /// @brief Plot the image cutout for a single object |
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[378] | 573 | void plotSource(Detection obj, Plot::CutoutPlot &plot); |
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[222] | 574 | |
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[528] | 575 | /// @brief Get the spectral arrays |
---|
[424] | 576 | void getSpectralArrays(int objNumber, float *specx, float *specy, float *specRecon, float *specBase); |
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| 577 | |
---|
[378] | 578 | // in Cubes/drawMomentCutout.cc |
---|
[528] | 579 | /// @brief Draw the 0th moment map for a single object. |
---|
[378] | 580 | void drawMomentCutout(Detection &object); |
---|
[220] | 581 | |
---|
[528] | 582 | /// @brief Draw a scale bar indicating angular size of the cutout. |
---|
[378] | 583 | void drawScale(float xstart,float ystart,float channel); |
---|
[222] | 584 | |
---|
[531] | 585 | /// @brief Draw a yellow line around the edge of the spatial extent of pixels. |
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[378] | 586 | void drawFieldEdge(); |
---|
[222] | 587 | |
---|
[378] | 588 | private: |
---|
[528] | 589 | float *recon; ///< reconstructed array - used when doing a trous reconstruction. |
---|
| 590 | bool reconExists; ///< flag saying whether there is a reconstruction |
---|
| 591 | short *detectMap; ///< "moment map" - x,y locations of detected pixels |
---|
| 592 | float *baseline; ///< array of spectral baseline values. |
---|
[219] | 593 | |
---|
[528] | 594 | bool reconAllocated; ///< have we allocated memory for the recon array? |
---|
| 595 | bool baselineAllocated;///< have we allocated memory for the baseline array? |
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| 596 | FitsHeader head; ///< the WCS and other header information. |
---|
| 597 | std::vector<Column::Col> fullCols; ///< the list of all columns as printed in the results file |
---|
| 598 | std::vector<Column::Col> logCols; ///< the list of columns as printed in the log file |
---|
[205] | 599 | |
---|
[378] | 600 | }; |
---|
[103] | 601 | |
---|
[378] | 602 | //////////// |
---|
| 603 | //// Cube inline function definitions |
---|
| 604 | //////////// |
---|
[220] | 605 | |
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[378] | 606 | inline int Cube::wcsToPix(const double *world, double *pix) |
---|
| 607 | { |
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[528] | 608 | /// @brief Use the WCS in the FitsHeader to convert from WCS to pixel coords for |
---|
| 609 | /// a single point. |
---|
| 610 | /// \param world The world coordinates. |
---|
| 611 | /// \param pix The returned pixel coordinates. |
---|
| 612 | /// |
---|
[378] | 613 | return this->head.wcsToPix(world,pix); |
---|
| 614 | } |
---|
| 615 | inline int Cube::wcsToPix(const double *world, double *pix, const int npts) |
---|
| 616 | { |
---|
[528] | 617 | /// @brief Use the WCS in the FitsHeader to convert from WCS to pixel coords for |
---|
| 618 | /// a set of points. |
---|
| 619 | /// \param world The world coordinates. |
---|
| 620 | /// \param pix The returned pixel coordinates. |
---|
| 621 | /// \param npts The number of points being converted. |
---|
| 622 | |
---|
[378] | 623 | return this->head.wcsToPix(world,pix,npts); |
---|
| 624 | } |
---|
| 625 | inline int Cube::pixToWCS(const double *pix, double *world) |
---|
| 626 | { |
---|
[528] | 627 | /// @brief Use the WCS in the FitsHeader to convert from pixel to WCS coords for |
---|
| 628 | /// a single point. |
---|
| 629 | /// \param pix The pixel coordinates. |
---|
| 630 | /// \param world The returned world coordinates. |
---|
| 631 | |
---|
[378] | 632 | return this->head.pixToWCS(pix,world); |
---|
| 633 | } |
---|
| 634 | inline int Cube::pixToWCS(const double *pix, double *world, const int npts) |
---|
| 635 | { |
---|
[528] | 636 | /// @brief Use the WCS in the FitsHeader to convert from pixel to WCS coords for |
---|
| 637 | /// a set of points. |
---|
| 638 | /// \param pix The pixel coordinates. |
---|
| 639 | /// \param world The returned world coordinates. |
---|
| 640 | /// \param npts The number of points being converted. |
---|
| 641 | |
---|
[378] | 642 | return this->head.pixToWCS(pix,world,npts); |
---|
| 643 | } |
---|
[220] | 644 | |
---|
| 645 | |
---|
[378] | 646 | //============================================================================ |
---|
[220] | 647 | |
---|
[528] | 648 | /// @brief A DataArray object limited to two dimensions, and with some additional |
---|
| 649 | /// special functions. |
---|
| 650 | /// |
---|
| 651 | /// @details It is used primarily for searching a 1- or 2-D array with |
---|
| 652 | /// lutz_detect() and spectrumDetect(). |
---|
[219] | 653 | |
---|
[378] | 654 | class Image : public DataArray |
---|
| 655 | { |
---|
| 656 | public: |
---|
[732] | 657 | Image(){numPixels=0; numDim=2; minSize=2;}; |
---|
[378] | 658 | Image(long nPix); |
---|
| 659 | Image(long *dimensions); |
---|
| 660 | virtual ~Image(){}; |
---|
[736] | 661 | Image(const Image &i); |
---|
| 662 | Image& operator=(const Image &i); |
---|
[219] | 663 | |
---|
[378] | 664 | //-------------------- |
---|
| 665 | // Defining the array |
---|
| 666 | // |
---|
[528] | 667 | /// @brief Save an external array to the Cube's pixel array |
---|
[378] | 668 | void saveArray(float *input, long size); |
---|
[222] | 669 | |
---|
[528] | 670 | /// @brief Extract a spectrum from an array and save to the local pixel array. |
---|
[378] | 671 | void extractSpectrum(float *Array, long *dim, long pixel); |
---|
[222] | 672 | |
---|
[528] | 673 | /// @brief Extract an image from an array and save to the local pixel array. |
---|
[378] | 674 | void extractImage(float *Array, long *dim, long channel); |
---|
[222] | 675 | |
---|
[528] | 676 | /// @brief Extract a spectrum from a cube and save to the local pixel array. |
---|
[378] | 677 | void extractSpectrum(Cube &cube, long pixel); |
---|
[222] | 678 | |
---|
[528] | 679 | /// @brief Extract an image from a cube and save to the local pixel array. |
---|
[378] | 680 | void extractImage(Cube &cube, long channel); |
---|
[222] | 681 | |
---|
[378] | 682 | //-------------------- |
---|
| 683 | // Accessing the data. |
---|
| 684 | // |
---|
| 685 | float getPixValue(long pos){ return array[pos]; }; |
---|
| 686 | float getPixValue(long x, long y){return array[y*axisDim[0] + x];}; |
---|
| 687 | // the next few should have checks against array overflow... |
---|
[419] | 688 | void setPixValue(long pos, float f){array[pos] = f;}; |
---|
[378] | 689 | void setPixValue(long x, long y, float f){array[y*axisDim[0] + x] = f;}; |
---|
| 690 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
---|
| 691 | bool isBlank(long x,long y){return par.isBlank(array[y*axisDim[0]+x]);}; |
---|
[219] | 692 | |
---|
[378] | 693 | //----------------------- |
---|
| 694 | // Detection-related |
---|
| 695 | // |
---|
[528] | 696 | /// @brief Detect objects in a 2-D image |
---|
[582] | 697 | std::vector<PixelInfo::Object2D> findSources2D(); |
---|
[222] | 698 | |
---|
[528] | 699 | /// @brief Detect objects in a 1-D spectrum |
---|
[582] | 700 | std::vector<PixelInfo::Scan> findSources1D(); |
---|
[222] | 701 | |
---|
[577] | 702 | unsigned int getMinSize(){return minSize;}; |
---|
| 703 | void setMinSize(int i){minSize=i;}; |
---|
[222] | 704 | |
---|
[528] | 705 | /// @brief A detection test for a pixel location. |
---|
[378] | 706 | bool isDetection(long x, long y){ |
---|
[528] | 707 | /// @details Test whether a pixel (x,y) is a statistically |
---|
| 708 | /// significant detection, according to the set of statistics in |
---|
| 709 | /// the local StatsContainer object. |
---|
| 710 | |
---|
[378] | 711 | long voxel = y*axisDim[0] + x; |
---|
| 712 | if(isBlank(x,y)) return false; |
---|
| 713 | else return Stats.isDetection(array[voxel]); |
---|
| 714 | }; |
---|
[219] | 715 | |
---|
[528] | 716 | /// @brief Blank out a set of channels marked as being Milky Way channels |
---|
[378] | 717 | void removeMW(); |
---|
[258] | 718 | |
---|
[378] | 719 | private: |
---|
[577] | 720 | unsigned int minSize; ///< the minimum number of pixels for a detection to be accepted. |
---|
[378] | 721 | }; |
---|
[3] | 722 | |
---|
[219] | 723 | |
---|
[378] | 724 | } |
---|
| 725 | |
---|
[3] | 726 | #endif |
---|