[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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[1061] | 39 | #include <duchamp/Outputs/columns.hh> |
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[1064] | 40 | #include <duchamp/Outputs/CatalogueSpecification.hh> |
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[1242] | 41 | #include <duchamp/Plotting/SpectralPlot.hh> |
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| 42 | #include <duchamp/Plotting/CutoutPlot.hh> |
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[393] | 43 | #include <duchamp/Utils/Statistics.hh> |
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[1250] | 44 | #include <duchamp/Utils/utils.hh> |
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[393] | 45 | #include <duchamp/PixelMap/Scan.hh> |
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| 46 | #include <duchamp/PixelMap/Object2D.hh> |
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[3] | 47 | |
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| 48 | |
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[378] | 49 | namespace duchamp |
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| 50 | { |
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[290] | 51 | |
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| 52 | |
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[528] | 53 | /// @brief Search a reconstructed array for significant detections. |
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[884] | 54 | std::vector <Detection> searchReconArray(size_t *dim, float *originalArray, float *reconArray, |
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[686] | 55 | Param &par, Statistics::StatsContainer<float> &stats); |
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[884] | 56 | std::vector <Detection> searchReconArraySpectral(size_t *dim, float *originalArray, float *reconArray, |
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[686] | 57 | Param &par, Statistics::StatsContainer<float> &stats); |
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[884] | 58 | std::vector <Detection> searchReconArraySpatial(size_t *dim, float *originalArray, float *reconArray, |
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[686] | 59 | Param &par, Statistics::StatsContainer<float> &stats); |
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[3] | 60 | |
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[528] | 61 | /// @brief Search a 3-dimensional array for significant detections. |
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[884] | 62 | std::vector <Detection> search3DArray(size_t *dim, float *Array, Param &par, |
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[686] | 63 | Statistics::StatsContainer<float> &stats); |
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[884] | 64 | std::vector <Detection> search3DArraySpectral(size_t *dim, float *Array, Param &par, |
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[686] | 65 | Statistics::StatsContainer<float> &stats); |
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[884] | 66 | std::vector <Detection> search3DArraySpatial(size_t *dim, float *Array, Param &par, |
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[686] | 67 | Statistics::StatsContainer<float> &stats); |
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[220] | 68 | |
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[1242] | 69 | |
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[528] | 70 | //========================================================================= |
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[220] | 71 | |
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[899] | 72 | /// An enumeration allowing us to refer to a particular array within functions |
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| 73 | enum ARRAYREF {ARRAY=0, RECON, BASELINE}; |
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| 74 | |
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| 75 | |
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[528] | 76 | /// @brief Base class for the image container. |
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| 77 | /// |
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| 78 | /// @details Definition of an n-dimensional data array: array of |
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| 79 | /// pixel values, size & dimensions array of Detection objects |
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| 80 | |
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[378] | 81 | class DataArray |
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| 82 | { |
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| 83 | public: |
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| 84 | DataArray(); ///< Basic DataArray constructor |
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| 85 | DataArray(short int nDim); ///< Basic nDim-dimensional DataArray constructor |
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[884] | 86 | DataArray(short int nDim, size_t size);///< Basic nDim-dimensional DataArray constructor, specifying size. |
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| 87 | DataArray(short int nDim, size_t *dimensions); ///< Basic nDim-dimensional DataArray constructor, specifying size of dimensions. |
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[378] | 88 | virtual ~DataArray(); ///< Basic DataArray constructor |
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[736] | 89 | DataArray(const DataArray &d); |
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| 90 | DataArray& operator=(const DataArray &d); |
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[222] | 91 | |
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[378] | 92 | //----------------------------------------- |
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| 93 | // Obvious inline accessor functions. |
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| 94 | // |
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[884] | 95 | size_t getDimX(){if(numDim>0) return axisDim[0];else return 0;}; |
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| 96 | size_t getDimY(){if(numDim>1) return axisDim[1];else return 1;}; |
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| 97 | size_t getDimZ(){if(numDim>2) return axisDim[2];else return 1;}; |
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| 98 | size_t getSize(){ return numPixels; }; |
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[1120] | 99 | size_t getSpatialSize(){if(numDim>1) return axisDim[0]*axisDim[1]; else if(numDim>0) return axisDim[0]; else return 0;}; |
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[378] | 100 | short int getNumDim(){ return numDim; }; |
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[884] | 101 | virtual float getPixValue(size_t pos){ return array[pos]; }; |
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| 102 | virtual void setPixValue(size_t pos, float f){array[pos] = f;}; |
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| 103 | Detection getObject(size_t number){ return objectList->at(number); }; |
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| 104 | Detection * pObject(size_t number){ return &(objectList->at(number));}; |
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[378] | 105 | std::vector <Detection> getObjectList(){ return *objectList; }; |
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[387] | 106 | std::vector <Detection> *pObjectList(){ return objectList; }; |
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| 107 | std::vector <Detection> &ObjectList(){ std::vector<Detection> &rlist = *objectList; return rlist; }; |
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[884] | 108 | size_t getNumObj(){ return objectList->size(); }; |
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[222] | 109 | |
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[528] | 110 | /// @brief Delete all objects from the list of detections. |
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[378] | 111 | void clearDetectionList(){ |
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| 112 | //objectList->clear(); |
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| 113 | delete objectList; |
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| 114 | objectList = new std::vector<Detection>; |
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| 115 | }; |
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[220] | 116 | |
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[528] | 117 | /// @brief Read a parameter set from file. |
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[700] | 118 | OUTCOME readParam(std::string paramfile){ |
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[528] | 119 | /// @brief |
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[531] | 120 | /// Uses Param::readParams() to read parameters from a file. |
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| 121 | /// \param paramfile The file to be read. |
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[528] | 122 | |
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[378] | 123 | return par.readParams(paramfile); |
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| 124 | }; |
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[222] | 125 | |
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[378] | 126 | //----------------------------------------- |
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| 127 | // Related to the various arrays |
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| 128 | // |
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[528] | 129 | /// @brief Return first three dimensional axes. |
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[884] | 130 | void getDim(size_t &x, size_t &y, size_t &z); |
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[528] | 131 | /// @brief Return array of dimensional sizes. |
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[884] | 132 | void getDimArray(size_t *output); |
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| 133 | size_t * getDimArray(){return axisDim;}; |
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[222] | 134 | |
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[528] | 135 | /// @brief Return pixel value array. |
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[378] | 136 | void getArray(float *output); |
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| 137 | float * getArray(){return array;}; |
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[220] | 138 | |
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[528] | 139 | /// @brief Save pixel value array. |
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[884] | 140 | virtual void saveArray(float *input, size_t size); |
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[258] | 141 | |
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[378] | 142 | //----------------------------------------- |
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| 143 | // Related to the object lists |
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| 144 | // |
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[528] | 145 | /// @brief Adds a single detection to the object list. |
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[1429] | 146 | void addObject(Detection &object); |
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[222] | 147 | |
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[528] | 148 | /// @brief Adds all objects in a detection list to the object list. |
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[1429] | 149 | void addObjectList(std::vector <Detection> &newlist); |
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[220] | 150 | |
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[1429] | 151 | /// @brief Merge an object into the list |
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| 152 | void mergeIntoList(Detection &object); |
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| 153 | |
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| 154 | |
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[528] | 155 | /// @brief Add pixel offsets to object coordinates. |
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[378] | 156 | void addObjectOffsets(); |
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[3] | 157 | |
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[378] | 158 | //----------------------------------------- |
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| 159 | // Parameter list related. |
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| 160 | // |
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[528] | 161 | /// @brief Output the Param set. |
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[378] | 162 | void showParam(std::ostream &stream){ stream << par; }; |
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[528] | 163 | /// @brief Return the Param set. |
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[378] | 164 | Param getParam(){ return par; }; |
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[528] | 165 | /// @brief Save a Param set to the Cube. |
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[378] | 166 | void saveParam(Param &newpar){par = newpar;}; |
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[528] | 167 | /// @brief Provides a reference to the Param set. |
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[378] | 168 | Param& pars(){ Param &rpar = par; return rpar; }; |
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[528] | 169 | /// @brief Is the voxel number given by vox a BLANK value? |
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[741] | 170 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
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[378] | 171 | |
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| 172 | // -------------------------------------------- |
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| 173 | // Statistics |
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| 174 | // |
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[528] | 175 | /// @brief Returns the StatsContainer. |
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[378] | 176 | Statistics::StatsContainer<float> getStats(){ return Stats; }; |
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| 177 | |
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[528] | 178 | /// @brief Provides a reference to the StatsContainer. |
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[378] | 179 | Statistics::StatsContainer<float>& stats(){ |
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| 180 | Statistics::StatsContainer<float> &rstats = Stats; return rstats; |
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| 181 | }; |
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[258] | 182 | |
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[528] | 183 | /// @brief Save a StatsContainer to the Cube. |
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[378] | 184 | void saveStats(Statistics::StatsContainer<float> newStats){ Stats = newStats;}; |
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[190] | 185 | |
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[528] | 186 | /// @brief A detection test for value. |
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[378] | 187 | bool isDetection(float value); |
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[222] | 188 | |
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[528] | 189 | /// @brief A detection test for pixel. |
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[884] | 190 | bool isDetection(size_t voxel); |
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[222] | 191 | |
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| 192 | |
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[528] | 193 | /// @brief Output operator for DataArray. |
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[378] | 194 | friend std::ostream& operator<< (std::ostream& theStream, DataArray &array); |
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[222] | 195 | |
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[3] | 196 | |
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[378] | 197 | protected: |
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| 198 | short int numDim; ///< Number of dimensions. |
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[884] | 199 | size_t *axisDim; ///< Array of axis dimensions of cube |
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[443] | 200 | bool axisDimAllocated; ///< has axisDim been allocated? |
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[884] | 201 | size_t numPixels; ///< Total number of pixels in cube. |
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[378] | 202 | float *array; ///< Array of data. |
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[444] | 203 | bool arrayAllocated; ///< has the array been allocated? |
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[378] | 204 | std::vector <Detection> *objectList; ///< The list of detected objects. |
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| 205 | Param par; ///< A parameter list. |
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| 206 | Statistics::StatsContainer<float> Stats; ///< The statistics for the DataArray. |
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| 207 | }; |
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[3] | 208 | |
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[220] | 209 | |
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| 210 | |
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[378] | 211 | //========================================================================= |
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[220] | 212 | |
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[528] | 213 | /// @brief Definition of an data-cube object (3D): |
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| 214 | /// a DataArray object limited to dim=3 |
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[3] | 215 | |
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[378] | 216 | class Cube : public DataArray |
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| 217 | { |
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| 218 | public: |
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| 219 | Cube(); ///< Basic Cube constructor. |
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[884] | 220 | Cube(size_t nPix); ///< Alternative Cube constructor. |
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| 221 | Cube(size_t *dimensions); ///< Alternative Cube constructor. |
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[378] | 222 | virtual ~Cube(); ///< Basic Cube destructor. |
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[736] | 223 | Cube(const Cube &c); ///< Copy constructor |
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| 224 | Cube& operator=(const Cube &c); ///< Copy operator |
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[3] | 225 | |
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[877] | 226 | /// @brief Return a Cube holding only a subsection of the original |
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[878] | 227 | Cube* slice(Section subsection); |
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[877] | 228 | |
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| 229 | |
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[977] | 230 | short int nondegDim(){return numNondegDim;}; |
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[513] | 231 | bool is2D(); |
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| 232 | void checkDim(){head.set2D(is2D());}; |
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[758] | 233 | void reportMemorySize(std::ostream &theStream, bool allocateArrays); |
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[513] | 234 | |
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[378] | 235 | // INLINE functions -- definitions included after class declaration. |
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[528] | 236 | /// @brief Is the voxel number given by vox a BLANK value? |
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[884] | 237 | bool isBlank(size_t vox){ return par.isBlank(array[vox]); }; |
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[3] | 238 | |
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[528] | 239 | /// @brief Is the voxel at (x,y,z) a BLANK value? |
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[884] | 240 | bool isBlank(size_t x, size_t y, size_t z){ |
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[378] | 241 | return par.isBlank(array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]); }; |
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[222] | 242 | |
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[528] | 243 | /// @brief Return a bool array masking blank pixels: 1=good, 0=blank |
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[1393] | 244 | std::vector<bool> makeBlankMask(){return par.makeBlankMask(array, numPixels);}; |
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[463] | 245 | |
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[528] | 246 | /// @brief Does the Cube::recon array exist? |
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[378] | 247 | bool isRecon(){ return reconExists; }; |
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[222] | 248 | |
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[884] | 249 | float getPixValue(size_t pos){ return array[pos]; }; |
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| 250 | float getPixValue(size_t x, size_t y, size_t z){ |
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[378] | 251 | return array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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[884] | 252 | short getDetectMapValue(size_t pos){ return detectMap[pos]; }; |
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| 253 | short getDetectMapValue(size_t x, size_t y){ return detectMap[y*axisDim[0]+x]; }; |
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| 254 | float getReconValue(size_t pos){ return recon[pos]; }; |
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| 255 | float getReconValue(size_t x, size_t y, size_t z){ |
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[378] | 256 | return recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x];}; |
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[884] | 257 | float getBaselineValue(size_t pos){ return baseline[pos]; }; |
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| 258 | float getBaselineValue(size_t x, size_t y, size_t z){ |
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[378] | 259 | return baseline[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x]; }; |
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[884] | 260 | void setPixValue(size_t pos, float f){array[pos] = f;}; |
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| 261 | void setPixValue(size_t x, size_t y, size_t z, float f){ |
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[378] | 262 | array[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f;}; |
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[884] | 263 | void setDetectMapValue(size_t pos, short f){ detectMap[pos] = f;}; |
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| 264 | void setDetectMapValue(size_t x, size_t y, short f){ detectMap[y*axisDim[0] + x] = f;}; |
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| 265 | void incrementDetectMap(size_t x, size_t y){detectMap[y*axisDim[0]+x]++;}; |
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| 266 | void incrementDetectMap(size_t pos){detectMap[pos]++;}; |
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| 267 | void setReconValue(size_t pos, float f){recon[pos] = f;}; |
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| 268 | void setReconValue(size_t x, size_t y, size_t z, float f){ |
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[378] | 269 | recon[z*axisDim[0]*axisDim[1] + y*axisDim[0] + x] = f; }; |
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| 270 | void setReconFlag(bool f){reconExists = f;}; |
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[222] | 271 | |
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[1064] | 272 | Catalogues::CatalogueSpecification getFullCols(){return fullCols;}; |
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| 273 | Catalogues::CatalogueSpecification *pFullCols(){return &fullCols;}; |
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| 274 | void setFullCols(Catalogues::CatalogueSpecification C){fullCols=C;}; |
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[222] | 275 | |
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[378] | 276 | // additional functions -- in Cubes/cubes.cc |
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[528] | 277 | /// @brief Allocate memory correctly, with WCS defining the correct axes. |
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[884] | 278 | OUTCOME initialiseCube(size_t *dimensions, bool allocateArrays=true); |
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[679] | 279 | OUTCOME initialiseCube(long *dimensions, bool allocateArrays=true); |
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[222] | 280 | |
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[528] | 281 | /// @brief Read in a FITS file, with subsection correction. |
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[698] | 282 | OUTCOME getCube(); |
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[528] | 283 | /// @brief Read in a FITS file, with subsection correction. |
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[698] | 284 | OUTCOME getMetadata(); |
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[222] | 285 | |
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[528] | 286 | /// @brief Read in command-line options. |
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[378] | 287 | // int getopts(int argc, char ** argv); |
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[474] | 288 | int getopts(int argc, char ** argv, std::string progname="Duchamp"){return par.getopts(argc,argv,progname);}; |
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[222] | 289 | |
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[528] | 290 | /// @brief Read in reconstructed & smoothed arrays from FITS files on disk. |
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[378] | 291 | void readSavedArrays(); |
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[222] | 292 | |
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[528] | 293 | /// @brief Save an external array to the Cube's pixel array |
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[884] | 294 | void saveArray(float *input, size_t size); |
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[222] | 295 | |
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[528] | 296 | /// @brief Save an external array to the Cube's pixel array |
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[491] | 297 | void saveArray(std::vector<float> &input); |
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| 298 | |
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[528] | 299 | /// @brief Save an external array to the Cube's reconstructed array. |
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[884] | 300 | void saveRecon(float *input, size_t size); |
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[222] | 301 | |
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[528] | 302 | /// @brief Save reconstructed array to an external array. |
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[378] | 303 | void getRecon(float *output); |
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[1120] | 304 | /// @brief Return the pointer to the reconstructed array. |
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[387] | 305 | float * getRecon(){return recon; }; |
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[222] | 306 | |
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[1120] | 307 | /// @brief Save baseline array to an external array. |
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| 308 | void getBaseline(float *output); |
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| 309 | /// @brief Return the pointer to the baseline array. |
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| 310 | float * getBaseline(){return baseline; }; |
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| 311 | |
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[378] | 312 | //------------------------ |
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| 313 | // Statistics for cube |
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| 314 | // |
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[222] | 315 | |
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[528] | 316 | /// @brief Calculate the statistics for the Cube (older version). |
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[378] | 317 | void setCubeStatsOld(); |
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[222] | 318 | |
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[528] | 319 | /// @brief Calculate the statistics for the Cube. |
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[378] | 320 | void setCubeStats(); |
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[222] | 321 | |
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[528] | 322 | /// @brief Set up thresholds for the False Discovery Rate routine. |
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[378] | 323 | void setupFDR(); |
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[531] | 324 | /// @brief Set up thresholds for the False Discovery Rate routine using a particular array. |
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[378] | 325 | void setupFDR(float *input); |
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[222] | 326 | |
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[528] | 327 | /// @brief A detection test for a given voxel. |
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[884] | 328 | bool isDetection(size_t x, size_t y, size_t z); |
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[222] | 329 | |
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[378] | 330 | //----------------------------- |
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| 331 | // Dealing with the detections |
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| 332 | // |
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[659] | 333 | |
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| 334 | /// @brief Get the set of voxels pertaining to the detected objects. |
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| 335 | std::vector< std::vector<PixelInfo::Voxel> > getObjVoxList(); |
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[222] | 336 | |
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[528] | 337 | /// @brief Calculate the object fluxes |
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[420] | 338 | void calcObjectFluxes(); |
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| 339 | |
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[528] | 340 | /// @brief Calculate the WCS parameters for each Cube Detection. |
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[378] | 341 | void calcObjectWCSparams(); |
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[528] | 342 | /// @brief Calculate the WCS parameters for each Cube Detection, using flux information in Voxels. |
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[418] | 343 | void calcObjectWCSparams(std::vector< std::vector<PixelInfo::Voxel> > bigVoxList); |
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[863] | 344 | void calcObjectWCSparams(std::map<PixelInfo::Voxel,float> &voxelMap); |
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| 345 | |
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[528] | 346 | /// @brief Sort the list of detections. |
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[378] | 347 | void sortDetections(); |
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[222] | 348 | |
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[1051] | 349 | short *getDetectMap(){return detectMap;}; |
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| 350 | |
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[528] | 351 | /// @brief Update the map of detected pixels. |
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[378] | 352 | void updateDetectMap(); |
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[222] | 353 | |
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[528] | 354 | /// @brief Update the map of detected pixels for a given Detection. |
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[378] | 355 | void updateDetectMap(Detection obj); |
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[222] | 356 | |
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[528] | 357 | /// @brief Clear the map of detected pixels. |
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[378] | 358 | void clearDetectMap(){ |
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[884] | 359 | for(size_t i=0;i<axisDim[0]*axisDim[1];i++) detectMap[i]=0; |
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[378] | 360 | }; |
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[290] | 361 | |
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[528] | 362 | /// @brief Find the flux enclosed by a Detection. |
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[378] | 363 | float enclosedFlux(Detection obj); |
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[222] | 364 | |
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[531] | 365 | /// @brief Set up the output column definitions for the Cube and its Detection list. |
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[378] | 366 | void setupColumns(); |
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[222] | 367 | |
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[528] | 368 | /// @brief Is the object at the edge of the image? |
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[378] | 369 | bool objAtSpatialEdge(Detection obj); |
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[222] | 370 | |
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[528] | 371 | /// @brief Is the object at an end of the spectrum? |
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[378] | 372 | bool objAtSpectralEdge(Detection obj); |
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[222] | 373 | |
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[1242] | 374 | /// @brief Is the object next to or enclosing flagged channels? |
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| 375 | bool objNextToFlaggedChan(Detection &obj); |
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| 376 | |
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[528] | 377 | /// @brief Set warning flags for the detections. |
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[378] | 378 | void setObjectFlags(); |
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[222] | 379 | |
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[378] | 380 | // ---------------------------- |
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| 381 | // Dealing with the WCS |
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| 382 | // |
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[528] | 383 | /// @brief Return the FitsHeader object. |
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[378] | 384 | FitsHeader getHead(){ return head; }; |
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[528] | 385 | /// @brief Define the FitsHeader object. |
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[378] | 386 | void setHead(FitsHeader F){head = F;}; |
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[528] | 387 | /// @brief Provide a reference to the FitsHeader object. |
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[378] | 388 | FitsHeader& header(){ FitsHeader &h = head; return h; }; |
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[1156] | 389 | /// @brief Provide a pointer to the FitsHeader object |
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| 390 | FitsHeader *pHeader(){return &head;}; |
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[3] | 391 | |
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[378] | 392 | //------------------------------------------- |
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| 393 | // FITS-I/O related functions -- not in cubes.cc |
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| 394 | // |
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[528] | 395 | /// @brief Function to read in FITS file. |
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[698] | 396 | OUTCOME getMetadata(std::string fname); // in Cubes/getImage.cc |
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| 397 | OUTCOME getCube(std::string fname); // in Cubes/getImage.cc |
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[3] | 398 | |
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[528] | 399 | /// @brief Convert the flux units to something user-specified. |
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[899] | 400 | void convertFluxUnits(std::string oldUnit, std::string newUnit, ARRAYREF whichArray=ARRAY); // in Cubes/getImage.cc |
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[434] | 401 | |
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[528] | 402 | /// @brief Function to retrieve FITS data array |
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[698] | 403 | OUTCOME getFITSdata(std::string fname); // in FitsIO/dataIO.cc |
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[971] | 404 | OUTCOME getFITSdata(); // in FitsIO/dataIO.cc |
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| 405 | OUTCOME getFITSdata(fitsfile *fptr); // in FitsIO/dataIO.cc |
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[222] | 406 | |
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[902] | 407 | OUTCOME writeBasicHeader(fitsfile *fptr, int bitpix, bool is2D=false); |
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[900] | 408 | |
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[1120] | 409 | /// @brief Handle all the writing to FITS files. |
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| 410 | void writeToFITS(); |
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| 411 | |
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[1179] | 412 | /// @brief Save the moment map to a FITS file |
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| 413 | OUTCOME saveMomentMapImage(); |
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| 414 | |
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| 415 | /// @brief Save the moment map mask to a FITS file |
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| 416 | OUTCOME saveMomentMask(); |
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| 417 | |
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| 418 | /// @brief Save a mask array to disk. |
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| 419 | OUTCOME saveMaskCube(); |
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| 420 | |
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| 421 | /// @brief Save Smoothed array to disk. |
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| 422 | OUTCOME saveSmoothedCube(); |
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| 423 | |
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| 424 | /// @brief Save Reconstructed array to disk. |
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| 425 | OUTCOME saveReconstructedCube(); |
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| 426 | |
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| 427 | /// @brief Save baseline array to disk. |
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| 428 | OUTCOME saveBaselineCube(); |
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| 429 | |
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| 430 | //------------------------------------- |
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[378] | 431 | // Functions that act on the cube |
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| 432 | // |
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[3] | 433 | |
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[528] | 434 | /// @brief Remove excess BLANK pixels from spatial edge of cube. |
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[378] | 435 | void trimCube(); // in Cubes/trimImage.cc |
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[222] | 436 | |
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[528] | 437 | /// @brief Replace BLANK pixels to spatial edge of cube. |
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[378] | 438 | void unTrimCube(); // in Cubes/trimImage.cc |
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[222] | 439 | |
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[528] | 440 | /// @brief Removes the baselines from the spectra, and stores in Cube::baseline |
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[378] | 441 | void removeBaseline(); // in Cubes/baseline.cc |
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[222] | 442 | |
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[528] | 443 | /// @brief Replace the baselines stored in Cube::baseline |
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[1361] | 444 | void replaceBaseline(bool fixObjects=true); // in Cubes/baseline.cc |
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[222] | 445 | |
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[528] | 446 | /// @brief Multiply all pixel values by -1. |
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[1361] | 447 | void invert(bool doArrays=true, bool doObjects=true); // in Cubes/invertCube.cc |
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[222] | 448 | |
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[378] | 449 | //------------------------------------- |
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| 450 | // Reconstruction, Searching and Merging functions |
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| 451 | // |
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[729] | 452 | // in cubes.cc |
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| 453 | /// @brief A front-end to all the searching functions |
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[834] | 454 | void Search(); |
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[729] | 455 | |
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[378] | 456 | // in ATrous/ReconSearch.cc |
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[528] | 457 | /// @brief Front-end to reconstruction & searching functions. |
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[378] | 458 | void ReconSearch(); |
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[528] | 459 | /// @brief Switcher to reconstruction functions |
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[378] | 460 | void ReconCube(); |
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[528] | 461 | /// @brief Performs 1-dimensional a trous reconstruction on the Cube. |
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[378] | 462 | void ReconCube1D(); |
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[528] | 463 | /// @brief Performs 2-dimensional a trous reconstruction on the Cube. |
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[378] | 464 | void ReconCube2D(); |
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[528] | 465 | /// @brief Performs 3-dimensional a trous reconstruction on the Cube. |
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[378] | 466 | void ReconCube3D(); |
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[222] | 467 | |
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[378] | 468 | // in Cubes/CubicSearch.cc |
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[528] | 469 | /// @brief Front-end to the cubic searching routine. |
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[378] | 470 | void CubicSearch(); |
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[222] | 471 | |
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[378] | 472 | // in Cubes/smoothCube.cc |
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[528] | 473 | /// @brief Smooth the cube with the requested method. |
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[378] | 474 | void SmoothCube(); |
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[528] | 475 | /// @brief Front-end to the smoothing and searching functions. |
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[378] | 476 | void SmoothSearch(); |
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[528] | 477 | /// @brief A function to spatially smooth the cube and search the result. |
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[378] | 478 | void SpatialSmoothNSearch(); |
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[528] | 479 | /// @brief A function to Hanning-smooth the cube. |
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[378] | 480 | void SpectralSmooth(); |
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[528] | 481 | /// @brief A function to spatially-smooth the cube. |
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[378] | 482 | void SpatialSmooth(); |
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[222] | 483 | |
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[378] | 484 | void Simple3DSearch(){ |
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[528] | 485 | /// @brief Basic front-end to the simple 3d searching function -- does |
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| 486 | /// nothing more. |
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| 487 | /// |
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| 488 | /// @details This function just runs the search3DArraySimple function, |
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| 489 | /// storing the results in the Cube::objectList vector. No stats |
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| 490 | /// are calculated beforehand, and no logging or detection map |
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| 491 | /// updating is done. |
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[686] | 492 | *objectList = search3DArray(axisDim,array,par,Stats); |
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[378] | 493 | }; |
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[290] | 494 | |
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[378] | 495 | void Simple3DSearchRecon(){ |
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[528] | 496 | /// @brief Basic front-end to the 3d searching function used in the |
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| 497 | /// reconstruction case -- does nothing more. |
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| 498 | /// |
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| 499 | /// @details This function just runs the searchReconArraySimple |
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| 500 | /// function, storing the results in the Cube::objectList |
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| 501 | /// vector. No stats are calculated beforehand, and no logging |
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| 502 | /// or detection map updating is done. The recon array is |
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| 503 | /// assumed to have been defined already. |
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| 504 | |
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[686] | 505 | *objectList = searchReconArray(axisDim,array,recon,par,Stats); |
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[378] | 506 | }; |
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[290] | 507 | |
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[378] | 508 | void Simple3DSearchSmooth(){ |
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[528] | 509 | /// @brief Basic front-end to the simple 3d searching function |
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| 510 | /// run on the smoothed array -- does nothing more. |
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| 511 | /// |
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| 512 | /// @details This function just runs the search3DArraySimple |
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| 513 | /// function on the recon array (which contains the smoothed |
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| 514 | /// array), storing the results in the Cube::objectList |
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| 515 | /// vector. No stats are calculated beforehand, and no logging |
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| 516 | /// or detection map updating is done. The recon array is |
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| 517 | /// assumed to have been defined already. |
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| 518 | |
---|
[686] | 519 | *objectList = search3DArray(axisDim,recon,par,Stats); |
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[378] | 520 | }; |
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[290] | 521 | |
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[378] | 522 | // in Cubes/Merger.cc |
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[531] | 523 | /// @brief Merge all objects in the detection list so that only distinct ones are left. |
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[378] | 524 | void ObjectMerger(); |
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[1056] | 525 | /// @brief Grow the sources out to the secondary threshold |
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| 526 | void growSources(std::vector <Detection> ¤tList); |
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| 527 | |
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[475] | 528 | // in Cubes/existingDetections.cc |
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[528] | 529 | /// @brief Read a previously-created log file to get the detections without searching |
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[698] | 530 | OUTCOME getExistingDetections(); |
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[475] | 531 | |
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[378] | 532 | //------------------------------------- |
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| 533 | // Text outputting of detected objects. |
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| 534 | // in Cubes/detectionIO.cc |
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| 535 | // |
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[1049] | 536 | |
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| 537 | void outputCatalogue(); |
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| 538 | |
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[528] | 539 | /// @brief Set up the output file with parameters and stats. |
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[378] | 540 | void prepareOutputFile(); |
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[3] | 541 | |
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[528] | 542 | /// @brief Write the statistical information to the output file. |
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[378] | 543 | void outputStats(); |
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[222] | 544 | |
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[528] | 545 | /// @brief Prepare the log file for output. |
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[418] | 546 | void prepareLogFile(int argc, char *argv[]); |
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| 547 | |
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[528] | 548 | /// @brief Output detections to the log file. |
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[659] | 549 | void logDetectionList(bool calcFluxes=true); |
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[222] | 550 | |
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[1049] | 551 | void logSummary(); |
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| 552 | |
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[1146] | 553 | /// @brief Write set of detections and metadata to a binary catalogue |
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| 554 | void writeBinaryCatalogue(); |
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| 555 | OUTCOME readBinaryCatalogue(); |
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| 556 | |
---|
| 557 | |
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[528] | 558 | /// @brief Output detections to a Karma annotation file. |
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[1074] | 559 | void outputDetectionsKarma(); |
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[222] | 560 | |
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[1077] | 561 | /// @brief Output detections to a DS9 annotation file. |
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| 562 | void outputDetectionsDS9(); |
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| 563 | |
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[1126] | 564 | /// @brief Output detections to a CASA region file. |
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| 565 | void outputDetectionsCasa(); |
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| 566 | |
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[1077] | 567 | /// @brief Write annotation files |
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| 568 | void outputAnnotations(); |
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| 569 | |
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[528] | 570 | /// @brief Output detections to a VOTable. |
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[1048] | 571 | void outputDetectionsVOTable(); |
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[275] | 572 | |
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[668] | 573 | |
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[378] | 574 | // ---------------------------------- |
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[668] | 575 | // Calculation of overall moment maps |
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| 576 | |
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| 577 | /// @brief Return a moment-0 map plus a map of where the object pixels are |
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[946] | 578 | std::vector<bool> getMomentMap(float *momentMap); |
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[668] | 579 | /// @brief Return a moment-0 map formatted for logarithmic greyscale plotting, with greyscale limits |
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[693] | 580 | void getMomentMapForPlot(float *momentMap, float &z1, float &z2); |
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[668] | 581 | |
---|
| 582 | // ---------------------------------- |
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[378] | 583 | // Graphical plotting of the cube and the detections. |
---|
| 584 | // |
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| 585 | // in Cubes/plotting.cc |
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[531] | 586 | /// @brief Plot a spatial map of detections based on number of detected channels. |
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[378] | 587 | void plotDetectionMap(std::string pgDestination); |
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[3] | 588 | |
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[531] | 589 | /// @brief Plot a spatial map of detections based on 0th moment map of each object. |
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[378] | 590 | void plotMomentMap(std::string pgDestination); |
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[222] | 591 | |
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[531] | 592 | /// @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] | 593 | void plotMomentMap(std::vector<std::string> pgDestination); |
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[222] | 594 | |
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[528] | 595 | /// @brief Draw WCS axes over a PGPLOT map. |
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[1250] | 596 | void plotWCSaxes(){wcsAxes(head.getWCS(),axisDim,DUCHAMP_ID_TEXT_COLOUR,DUCHAMP_WCS_AXIS_COLOUR);}; |
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[222] | 597 | |
---|
[378] | 598 | // in Cubes/outputSpectra.cc |
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[528] | 599 | /// @brief Print spectra of each detected object. |
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[378] | 600 | void outputSpectra(); |
---|
[222] | 601 | |
---|
[528] | 602 | /// @brief Write out text file of all spectra. |
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[424] | 603 | void writeSpectralData(); |
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| 604 | |
---|
[528] | 605 | /// @brief Print spectrum of a single object |
---|
[424] | 606 | void plotSpectrum(int objNum, Plot::SpectralPlot &plot); |
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[528] | 607 | /// @brief Plot the image cutout for a single object |
---|
[378] | 608 | void plotSource(Detection obj, Plot::CutoutPlot &plot); |
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[1242] | 609 | /// @brief Mark channels that have been flagged by the user. |
---|
| 610 | void drawFlaggedChannels(Plot::SpectralPlot &plot, double xval, double yval); |
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[222] | 611 | |
---|
[1242] | 612 | |
---|
[528] | 613 | /// @brief Get the spectral arrays |
---|
[424] | 614 | void getSpectralArrays(int objNumber, float *specx, float *specy, float *specRecon, float *specBase); |
---|
| 615 | |
---|
[378] | 616 | // in Cubes/drawMomentCutout.cc |
---|
[528] | 617 | /// @brief Draw the 0th moment map for a single object. |
---|
[378] | 618 | void drawMomentCutout(Detection &object); |
---|
[220] | 619 | |
---|
[528] | 620 | /// @brief Draw a scale bar indicating angular size of the cutout. |
---|
[378] | 621 | void drawScale(float xstart,float ystart,float channel); |
---|
[222] | 622 | |
---|
[531] | 623 | /// @brief Draw a yellow line around the edge of the spatial extent of pixels. |
---|
[378] | 624 | void drawFieldEdge(); |
---|
[222] | 625 | |
---|
[378] | 626 | private: |
---|
[977] | 627 | short int numNondegDim; ///< Number of non-degenerate dimensions (ie. with size>1) |
---|
[528] | 628 | float *recon; ///< reconstructed array - used when doing a trous reconstruction. |
---|
| 629 | bool reconExists; ///< flag saying whether there is a reconstruction |
---|
| 630 | short *detectMap; ///< "moment map" - x,y locations of detected pixels |
---|
| 631 | float *baseline; ///< array of spectral baseline values. |
---|
[219] | 632 | |
---|
[528] | 633 | bool reconAllocated; ///< have we allocated memory for the recon array? |
---|
| 634 | bool baselineAllocated;///< have we allocated memory for the baseline array? |
---|
| 635 | FitsHeader head; ///< the WCS and other header information. |
---|
[1064] | 636 | Catalogues::CatalogueSpecification fullCols; ///< the list of all columns as printed in the results file |
---|
[378] | 637 | }; |
---|
[103] | 638 | |
---|
[220] | 639 | |
---|
[378] | 640 | //============================================================================ |
---|
[220] | 641 | |
---|
[528] | 642 | /// @brief A DataArray object limited to two dimensions, and with some additional |
---|
| 643 | /// special functions. |
---|
| 644 | /// |
---|
| 645 | /// @details It is used primarily for searching a 1- or 2-D array with |
---|
| 646 | /// lutz_detect() and spectrumDetect(). |
---|
[219] | 647 | |
---|
[378] | 648 | class Image : public DataArray |
---|
| 649 | { |
---|
| 650 | public: |
---|
[732] | 651 | Image(){numPixels=0; numDim=2; minSize=2;}; |
---|
[884] | 652 | Image(size_t nPix); |
---|
| 653 | Image(size_t *dimensions); |
---|
[378] | 654 | virtual ~Image(){}; |
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[736] | 655 | Image(const Image &i); |
---|
| 656 | Image& operator=(const Image &i); |
---|
[219] | 657 | |
---|
[378] | 658 | //-------------------- |
---|
| 659 | // Defining the array |
---|
| 660 | // |
---|
[528] | 661 | /// @brief Save an external array to the Cube's pixel array |
---|
[884] | 662 | void saveArray(float *input, size_t size); |
---|
[222] | 663 | |
---|
[528] | 664 | /// @brief Extract a spectrum from an array and save to the local pixel array. |
---|
[884] | 665 | void extractSpectrum(float *Array, size_t *dim, size_t pixel); |
---|
[222] | 666 | |
---|
[528] | 667 | /// @brief Extract an image from an array and save to the local pixel array. |
---|
[884] | 668 | void extractImage(float *Array, size_t *dim, size_t channel); |
---|
[222] | 669 | |
---|
[528] | 670 | /// @brief Extract a spectrum from a cube and save to the local pixel array. |
---|
[884] | 671 | void extractSpectrum(Cube &cube, size_t pixel); |
---|
[222] | 672 | |
---|
[528] | 673 | /// @brief Extract an image from a cube and save to the local pixel array. |
---|
[884] | 674 | void extractImage(Cube &cube, size_t channel); |
---|
[222] | 675 | |
---|
[378] | 676 | //-------------------- |
---|
| 677 | // Accessing the data. |
---|
| 678 | // |
---|
[884] | 679 | float getPixValue(size_t pos){ return array[pos]; }; |
---|
| 680 | float getPixValue(size_t x, size_t y){return array[y*axisDim[0] + x];}; |
---|
[378] | 681 | // the next few should have checks against array overflow... |
---|
[884] | 682 | void setPixValue(size_t pos, float f){array[pos] = f;}; |
---|
| 683 | void setPixValue(size_t x, size_t y, float f){array[y*axisDim[0] + x] = f;}; |
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[378] | 684 | bool isBlank(int vox){return par.isBlank(array[vox]);}; |
---|
[884] | 685 | bool isBlank(size_t x,size_t y){return par.isBlank(array[y*axisDim[0]+x]);}; |
---|
[219] | 686 | |
---|
[378] | 687 | //----------------------- |
---|
| 688 | // Detection-related |
---|
| 689 | // |
---|
[528] | 690 | /// @brief Detect objects in a 2-D image |
---|
[582] | 691 | std::vector<PixelInfo::Object2D> findSources2D(); |
---|
[222] | 692 | |
---|
[528] | 693 | /// @brief Detect objects in a 1-D spectrum |
---|
[582] | 694 | std::vector<PixelInfo::Scan> findSources1D(); |
---|
[222] | 695 | |
---|
[577] | 696 | unsigned int getMinSize(){return minSize;}; |
---|
| 697 | void setMinSize(int i){minSize=i;}; |
---|
[222] | 698 | |
---|
[528] | 699 | /// @brief A detection test for a pixel location. |
---|
[884] | 700 | bool isDetection(size_t x, size_t y){ |
---|
[528] | 701 | /// @details Test whether a pixel (x,y) is a statistically |
---|
| 702 | /// significant detection, according to the set of statistics in |
---|
| 703 | /// the local StatsContainer object. |
---|
| 704 | |
---|
[884] | 705 | size_t voxel = y*axisDim[0] + x; |
---|
[378] | 706 | if(isBlank(x,y)) return false; |
---|
| 707 | else return Stats.isDetection(array[voxel]); |
---|
| 708 | }; |
---|
[219] | 709 | |
---|
[1242] | 710 | /// @brief Blank out a set of channels marked as flagged |
---|
| 711 | void removeFlaggedChannels(); |
---|
[258] | 712 | |
---|
[378] | 713 | private: |
---|
[577] | 714 | unsigned int minSize; ///< the minimum number of pixels for a detection to be accepted. |
---|
[378] | 715 | }; |
---|
[3] | 716 | |
---|
[219] | 717 | |
---|
[378] | 718 | } |
---|
| 719 | |
---|
[3] | 720 | #endif |
---|