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