[300] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // detection.hh: Definition of the Detection class. |
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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 DETECTION_H |
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| 29 | #define DETECTION_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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[393] | 34 | #include <duchamp/param.hh> |
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| 35 | #include <duchamp/PixelMap/Voxel.hh> |
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| 36 | #include <duchamp/PixelMap/Object3D.hh> |
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| 37 | #include <duchamp/Detection/columns.hh> |
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[3] | 38 | |
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[378] | 39 | namespace duchamp |
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[3] | 40 | { |
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[258] | 41 | |
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| 42 | |
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[528] | 43 | /// Class to represent a contiguous set of detected voxels. |
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| 44 | /// This is a detected object, which features: |
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| 45 | /// a vector of voxels, average and centroid positions, total & peak fluxes, |
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| 46 | /// the possibility of WCS-calculated parameters (RA, Dec, velocity, |
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| 47 | /// related widths). |
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| 48 | /// Also many functions with which to manipulate the Detections. |
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[258] | 49 | |
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[378] | 50 | class Detection |
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| 51 | { |
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| 52 | public: |
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| 53 | Detection(); |
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| 54 | Detection(const Detection& d); |
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| 55 | Detection& operator= (const Detection& d); |
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| 56 | virtual ~Detection(){}; |
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| 57 | //------------------------------ |
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| 58 | // These are functions in detection.cc. |
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| 59 | // |
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[528] | 60 | /// @brief Add all voxels of one object to another. |
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[378] | 61 | friend Detection operator+ (Detection lhs, Detection rhs); |
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| 62 | friend Detection operator+= (Detection lhs, Detection rhs){ |
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| 63 | lhs = lhs + rhs; |
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| 64 | return lhs; |
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| 65 | } |
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[258] | 66 | |
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[528] | 67 | /// @brief Provides a reference to the pixel array. |
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[378] | 68 | PixelInfo::Object3D& pixels(){ |
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| 69 | PixelInfo::Object3D &rpix = this->pixelArray; |
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| 70 | return rpix; |
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| 71 | }; |
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[258] | 72 | |
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[528] | 73 | /// @brief Calculate basic parameters of the Detection. |
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[378] | 74 | void calcParams(){pixelArray.calcParams();}; |
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[258] | 75 | |
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[528] | 76 | /// @brief Test whether voxel lists match |
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[417] | 77 | bool voxelListsMatch(std::vector<PixelInfo::Voxel> voxelList); |
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| 78 | |
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[528] | 79 | /// @brief Test whether a voxel list contains all detected voxels |
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[463] | 80 | bool voxelListCovered(std::vector<PixelInfo::Voxel> voxelList); |
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| 81 | |
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[528] | 82 | /// @brief Calculate flux-related parameters of the Detection. |
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[378] | 83 | void calcFluxes(float *fluxArray, long *dim); |
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[528] | 84 | /// @brief Calculate flux-related parameters of the Detection. |
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[417] | 85 | void calcFluxes(std::vector<PixelInfo::Voxel> voxelList); |
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[258] | 86 | |
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[528] | 87 | /// @brief Calculate parameters related to the World Coordinate System. |
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[417] | 88 | // void calcWCSparams(float *fluxArray, long *dim, FitsHeader &head); |
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| 89 | void calcWCSparams(FitsHeader &head); |
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[258] | 90 | |
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[528] | 91 | /// @brief Calculate the integrated flux over the entire Detection. |
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[378] | 92 | void calcIntegFlux(float *fluxArray, long *dim, FitsHeader &head); |
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[528] | 93 | /// @brief Calculate the integrated flux over the entire Detection. |
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[417] | 94 | void calcIntegFlux(std::vector<PixelInfo::Voxel> voxelList, FitsHeader &head); |
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[3] | 95 | |
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[528] | 96 | /// @brief Calculate the 20%/50% peak flux widths |
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[464] | 97 | void calcVelWidths(float *fluxArray, long *dim, FitsHeader &head); |
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[528] | 98 | /// @brief Calculate the 20%/50% peak flux widths |
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[464] | 99 | void calcVelWidths(std::vector<PixelInfo::Voxel> voxelList, FitsHeader &head); |
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| 100 | |
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[528] | 101 | /// @brief Set the values of the axis offsets from the cube. |
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[378] | 102 | void setOffsets(Param &par); |
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[221] | 103 | |
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[528] | 104 | /// @brief Add the offset values to the pixel locations |
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[378] | 105 | void addOffsets(){ |
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| 106 | pixelArray.addOffsets(xSubOffset,ySubOffset,zSubOffset); |
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[498] | 107 | xpeak+=xSubOffset; ypeak+=ySubOffset; zpeak+=zSubOffset; |
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| 108 | xCentroid+=xSubOffset; yCentroid+=ySubOffset; zCentroid+=zSubOffset; |
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[378] | 109 | }; |
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[221] | 110 | |
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[378] | 111 | // |
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| 112 | friend std::ostream& operator<< ( std::ostream& theStream, Detection& obj); |
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| 113 | //--------------------------------- |
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| 114 | // Text Output -- all in Detection/outputDetection.cc |
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| 115 | // |
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[528] | 116 | /// @brief The spectral output label that contains info on the WCS position & velocity. |
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[378] | 117 | std::string outputLabelWCS(); |
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[282] | 118 | |
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[528] | 119 | /// @brief The spectral output label that contains info on the pixel location. |
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[378] | 120 | std::string outputLabelPix(); |
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[221] | 121 | |
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[528] | 122 | /// @brief The spectral output label that contains info on fluxes of the Detection. |
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[378] | 123 | std::string outputLabelFluxes(); |
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[265] | 124 | |
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[528] | 125 | /// @brief The spectral output label that contains info on widths of the Detection. |
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[378] | 126 | std::string outputLabelWidths(); |
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[265] | 127 | |
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[528] | 128 | /// @brief Print all required values for the Detection to a table. |
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[440] | 129 | void printTableRow(std::ostream &stream, std::vector<Column::Col> columns, std::string tableType); |
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[441] | 130 | |
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[528] | 131 | /// @brief Print a particular value for the Detection to a table. |
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[440] | 132 | void printTableEntry(std::ostream &stream, Column::Col column); |
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| 133 | |
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[378] | 134 | //---------------------------------- |
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| 135 | // For plotting routines... in Cubes/drawMomentCutout.cc |
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| 136 | // |
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[528] | 137 | /// @brief Get the location of the spatial borders. |
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[431] | 138 | std::vector<int> getVertexSet(); |
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| 139 | // |
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[528] | 140 | /// @brief Draw spatial borders for a particular Detection. |
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[378] | 141 | void drawBorders(int xoffset, int yoffset); |
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| 142 | // |
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[528] | 143 | /// @brief Sort the pixels by central z-value. |
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[378] | 144 | void SortByZ(){pixelArray.order();}; |
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| 145 | // |
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| 146 | //---------------------------------- |
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| 147 | // Basic functions |
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| 148 | // |
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[528] | 149 | /// @brief Delete all pixel information from Detection. Does not clear other parameters. |
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[378] | 150 | // void clearDetection(){this->pix.clear();}; |
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[221] | 151 | |
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[528] | 152 | /// @brief Add a single voxel to the pixel list. |
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[378] | 153 | void addPixel(long x, long y, long z){pixelArray.addPixel(x,y,z);}; |
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[528] | 154 | /// @brief Add a single voxel to the pixel list. |
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[378] | 155 | void addPixel(PixelInfo::Voxel point){ |
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[528] | 156 | /// @brief This one adds the pixel to the pixelArray, and updates the fluxes according to the Voxel's flux information |
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[378] | 157 | pixelArray.addPixel(point); |
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| 158 | totalFlux += point.getF(); |
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| 159 | if(point.getF()>peakFlux){ |
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| 160 | peakFlux = point.getF(); |
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| 161 | xpeak = point.getX(); ypeak = point.getY(); zpeak = point.getZ(); |
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| 162 | } |
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| 163 | }; |
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[258] | 164 | |
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[528] | 165 | /// @brief Return a single voxel. |
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[378] | 166 | PixelInfo::Voxel getPixel(int i){return pixelArray.getPixel(i);}; |
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[258] | 167 | |
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[528] | 168 | /// @brief Return the set of voxels. |
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[418] | 169 | std::vector<PixelInfo::Voxel> getPixelSet(){return pixelArray.getPixelSet();}; |
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| 170 | |
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[528] | 171 | /// @brief How many voxels are in the Detection? |
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[538] | 172 | unsigned int getSize(){return pixelArray.getSize();}; |
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[378] | 173 | |
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[528] | 174 | /// @brief How many distinct spatial pixels are there? |
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[538] | 175 | unsigned int getSpatialSize(){return pixelArray.getSpatialSize();}; |
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[378] | 176 | |
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[528] | 177 | /// @brief How many channels does the Detection have? |
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[378] | 178 | long getNumChannels(){return pixelArray.getNumDistinctZ();}; |
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| 179 | |
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[528] | 180 | /// @brief Is there at least the acceptable minimum number of channels in the Detection? |
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[378] | 181 | bool hasEnoughChannels(int minNumber); |
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[258] | 182 | |
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[378] | 183 | //----------------------------------- |
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| 184 | // Basic accessor functions for private members follow... |
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| 185 | // |
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| 186 | long getXOffset(){return xSubOffset;}; |
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| 187 | void setXOffset(long o){xSubOffset = o;}; |
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| 188 | long getYOffset(){return ySubOffset;}; |
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| 189 | void setYOffset(long o){ySubOffset = o;}; |
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| 190 | long getZOffset(){return zSubOffset;}; |
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| 191 | void setZOffset(long o){zSubOffset = o;}; |
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| 192 | // |
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| 193 | float getXcentre(){ |
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| 194 | if(centreType=="peak") return xpeak; |
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| 195 | else if(centreType=="average") return pixelArray.getXcentre(); |
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| 196 | else return xCentroid; |
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| 197 | }; |
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| 198 | float getYcentre(){ |
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| 199 | if(centreType=="peak") return ypeak; |
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| 200 | else if(centreType=="average") return pixelArray.getYcentre(); |
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| 201 | else return yCentroid; |
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| 202 | }; |
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| 203 | float getZcentre(){ |
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| 204 | if(centreType=="peak") return zpeak; |
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| 205 | else if(centreType=="average") return pixelArray.getZcentre(); |
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| 206 | else return zCentroid; |
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| 207 | }; |
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| 208 | float getXAverage(){return pixelArray.getXcentre();}; |
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| 209 | float getYAverage(){return pixelArray.getYcentre();}; |
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| 210 | float getZAverage(){return pixelArray.getZcentre();}; |
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| 211 | float getTotalFlux(){return totalFlux;}; |
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| 212 | void setTotalFlux(float f){totalFlux=f;}; |
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| 213 | double getIntegFlux(){return intFlux;}; |
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| 214 | void setIntegFlux(double f){intFlux=f;}; |
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| 215 | float getPeakFlux(){return peakFlux;}; |
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| 216 | void setPeakFlux(float f){peakFlux=f;}; |
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| 217 | long getXPeak(){return xpeak;}; |
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| 218 | long getYPeak(){return ypeak;}; |
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| 219 | long getZPeak(){return zpeak;}; |
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| 220 | float getPeakSNR(){return peakSNR;}; |
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| 221 | void setPeakSNR(float f){peakSNR = f;}; |
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| 222 | float getXCentroid(){return xCentroid;}; |
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| 223 | float getYCentroid(){return yCentroid;}; |
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| 224 | float getZCentroid(){return zCentroid;}; |
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| 225 | std::string getCentreType(){return centreType;}; |
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| 226 | void setCentreType(std::string s){centreType=s;}; |
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| 227 | bool isNegative(){return negSource;}; |
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| 228 | void setNegative(bool f){negSource = f;}; |
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| 229 | std::string getFlagText(){return flagText;}; |
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| 230 | void setFlagText(std::string s){flagText = s;}; |
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| 231 | void addToFlagText(std::string s){flagText += s;}; |
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| 232 | // |
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| 233 | long getXmin(){return pixelArray.getXmin();}; |
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| 234 | long getYmin(){return pixelArray.getYmin();}; |
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| 235 | long getZmin(){return pixelArray.getZmin();}; |
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| 236 | long getXmax(){return pixelArray.getXmax();}; |
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| 237 | long getYmax(){return pixelArray.getYmax();}; |
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| 238 | long getZmax(){return pixelArray.getZmax();}; |
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| 239 | // |
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[528] | 240 | /// @brief Is the WCS good enough to be used? |
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| 241 | /// \return Detection::flagWCS = True/False |
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[378] | 242 | bool isWCS(){return flagWCS;}; |
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| 243 | bool isSpecOK(){return specOK;}; |
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| 244 | void setSpecOK(bool b){specOK=b;}; |
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| 245 | std::string getName(){return name;}; |
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| 246 | void setName(std::string s){name=s;}; |
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| 247 | std::string getRAs(){return raS;}; |
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| 248 | std::string getDecs(){return decS;}; |
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| 249 | float getRA(){return ra;}; |
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| 250 | float getDec(){return dec;}; |
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| 251 | float getRAWidth(){return raWidth;}; |
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| 252 | float getDecWidth(){return decWidth;}; |
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[473] | 253 | float getMajorAxis(){return majorAxis;}; |
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| 254 | float getMinorAxis(){return minorAxis;}; |
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| 255 | float getPositionAngle(){return posang;}; |
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[378] | 256 | float getVel(){return vel;}; |
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| 257 | float getVelWidth(){return velWidth;}; |
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| 258 | float getVelMin(){return velMin;}; |
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| 259 | float getVelMax(){return velMax;}; |
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[463] | 260 | float getW20(){return w20;}; |
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| 261 | float getV20Min(){return v20min;}; |
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| 262 | float getV20Max(){return v20max;}; |
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| 263 | float getW50(){return w50;}; |
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| 264 | float getV50Min(){return v50min;}; |
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| 265 | float getV50Max(){return v50max;}; |
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[378] | 266 | int getID(){return id;}; |
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| 267 | void setID(int i){id = i;}; |
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| 268 | // |
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| 269 | int getPosPrec(){return posPrec;}; |
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| 270 | void setPosPrec(int i){posPrec=i;}; |
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| 271 | int getXYZPrec(){return xyzPrec;}; |
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| 272 | void setXYZPrec(int i){xyzPrec=i;}; |
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| 273 | int getFintPrec(){return fintPrec;}; |
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| 274 | void setFintPrec(int i){fintPrec=i;}; |
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| 275 | int getFpeakPrec(){return fpeakPrec;}; |
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| 276 | void setFpeakPrec(int i){fpeakPrec=i;}; |
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| 277 | int getVelPrec(){return velPrec;}; |
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| 278 | void setVelPrec(int i){velPrec=i;}; |
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| 279 | int getSNRPrec(){return snrPrec;}; |
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| 280 | void setSNRPrec(int i){snrPrec=i;}; |
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| 281 | // |
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[456] | 282 | protected: |
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[378] | 283 | PixelInfo::Object3D pixelArray; ///< The pixel locations |
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| 284 | // Subsection offsets |
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| 285 | long xSubOffset; ///< The x-offset, from subsectioned cube |
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| 286 | long ySubOffset; ///< The y-offset, from subsectioned cube |
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| 287 | long zSubOffset; ///< The z-offset, from subsectioned cube |
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| 288 | // Flux related |
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| 289 | float totalFlux; ///< sum of the fluxes of all the pixels |
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[473] | 290 | double intFlux; ///< integrated flux : involves integration over velocity. |
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[378] | 291 | float peakFlux; ///< maximum flux over all the pixels |
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| 292 | long xpeak; ///< x-pixel location of peak flux |
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| 293 | long ypeak; ///< y-pixel location of peak flux |
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| 294 | long zpeak; ///< z-pixel location of peak flux |
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| 295 | float peakSNR; ///< signal-to-noise ratio at peak |
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| 296 | float xCentroid; ///< x-pixel location of centroid |
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| 297 | float yCentroid; ///< y-pixel location of centroid |
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| 298 | float zCentroid; ///< z-pixel location of centroid |
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[473] | 299 | std::string centreType; ///< which type of pixel centre to report: "average", "centroid", or "peak" (flux) |
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[378] | 300 | bool negSource; ///< is the source a negative feature? |
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[473] | 301 | std::string flagText; ///< any warning flags about the quality of the detection. |
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[378] | 302 | // WCS related |
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| 303 | int id; ///< ID -- generally number in list |
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[473] | 304 | std::string name; ///< IAU-style name (based on position) |
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| 305 | bool flagWCS; ///< A flag indicating whether the WCS parameters have been set. |
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| 306 | std::string raS; ///< Right Ascension (or Longitude) of pixel centre in form 12:34:23 |
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| 307 | std::string decS; ///< Declination (or Latitude) of pixel centre, in form -12:23:34 |
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| 308 | float ra; ///< Central Right Ascension in degrees |
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| 309 | float dec; ///< Central Declination in degrees |
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| 310 | float raWidth; ///< Width of detection in RA direction in arcmin |
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| 311 | float decWidth; ///< Width of detection in Dec direction in arcmin |
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| 312 | float majorAxis; ///< Major axis length in arcmin |
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| 313 | float minorAxis; ///< Minor axis length in arcmin |
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| 314 | float posang; ///< Position angle of the major axis, in degrees |
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[378] | 315 | bool specOK; ///< Is the spectral dimension valid? |
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| 316 | std::string specUnits; ///< Units of the spectral dimension |
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| 317 | std::string fluxUnits; ///< Units of flux |
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| 318 | std::string intFluxUnits; ///< Units of integrated flux |
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| 319 | std::string lngtype; ///< Type of longitude axis (RA/GLON) |
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| 320 | std::string lattype; ///< Type of latitude axis (DEC/GLAT) |
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[473] | 321 | float vel; ///< Central velocity (from zCentre) |
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[378] | 322 | float velWidth; ///< Full velocity width |
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| 323 | float velMin; ///< Minimum velocity |
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| 324 | float velMax; ///< Maximum velocity |
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[473] | 325 | float v20min; ///< Minimum velocity at 20% of peak flux |
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| 326 | float v20max; ///< Maximum velocity at 20% of peak flux |
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| 327 | float w20; ///< Velocity width at 20% of peak flux |
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| 328 | float v50min; ///< Minimum velocity at 50% of peak flux |
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| 329 | float v50max; ///< Maximum velocity at 50% of peak flux |
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| 330 | float w50; ///< Velocity width at 50% of peak flux |
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[531] | 331 | /// @brief The next six are the precision of values printed in the headers of the spectral plots |
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| 332 | /// @name |
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| 333 | /// @{ |
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[378] | 334 | int posPrec; ///< Precision of WCS positional values |
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[473] | 335 | int xyzPrec; ///< Precision of pixel positional values |
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[378] | 336 | int fintPrec; ///< Precision of F_int/F_tot values |
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| 337 | int fpeakPrec; ///< Precision of F_peak values |
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| 338 | int velPrec; ///< Precision of velocity values. |
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| 339 | int snrPrec; ///< Precision of S/N_max values. |
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[528] | 340 | /// @} |
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[378] | 341 | }; |
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[3] | 342 | |
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[378] | 343 | //========================================================================== |
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[221] | 344 | |
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[378] | 345 | ////////////////////////////////////////////////////// |
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| 346 | // Prototypes for functions that use above classes |
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| 347 | ////////////////////////////////////////////////////// |
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[3] | 348 | |
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[378] | 349 | //---------------- |
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| 350 | // These are in sorting.cc |
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| 351 | // |
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[528] | 352 | /// @brief Sort a list of Detections by Z-pixel value. |
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[378] | 353 | void SortByZ(std::vector <Detection> &inputList); |
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[221] | 354 | |
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[528] | 355 | /// @brief Sort a list of Detections by Velocity. |
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[378] | 356 | void SortByVel(std::vector <Detection> &inputList); |
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[221] | 357 | |
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[378] | 358 | //---------------- |
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| 359 | // This is in areClose.cc |
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| 360 | // |
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[528] | 361 | /// @brief Determine whether two objects are close according to set parameters. |
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[378] | 362 | bool areClose(Detection &object1, Detection &object2, Param &par); |
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[221] | 363 | |
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[378] | 364 | //---------------- |
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| 365 | // This is in mergeIntoList.cc |
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| 366 | // |
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[528] | 367 | /// @brief Add an object into a list, combining with adjacent objects if need be. |
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[378] | 368 | void mergeIntoList(Detection &object, std::vector <Detection> &objList, |
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| 369 | Param &par); |
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[3] | 370 | |
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[378] | 371 | //---------------- |
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| 372 | // These are in Cubes/Merger.cc |
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| 373 | // |
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[528] | 374 | /// @brief Merge a list of Detections so that all adjacent voxels are in the same Detection. |
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[378] | 375 | void mergeList(std::vector<Detection> &objList, Param &par); |
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[528] | 376 | /// @brief Culls a list of Detections that do not meet minimum requirements. |
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[378] | 377 | void finaliseList(std::vector<Detection> &objList, Param &par); |
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[528] | 378 | /// @brief Manage both the merging and the cleaning up of the list. |
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[378] | 379 | void ObjectMerger(std::vector<Detection> &objList, Param &par); |
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[56] | 380 | |
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[528] | 381 | /// @brief Print the header information to a particular table |
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[439] | 382 | void outputTableHeader(std::ostream &stream, std::vector<Column::Col> columns, std::string tableType, bool flagWCS); |
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| 383 | |
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[378] | 384 | } |
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[221] | 385 | |
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[3] | 386 | #endif |
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