[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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[1061] | 37 | #include <duchamp/Outputs/columns.hh> |
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[1064] | 38 | #include <duchamp/Outputs/CatalogueSpecification.hh> |
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[3] | 39 | |
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[570] | 40 | using namespace PixelInfo; |
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| 41 | |
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[378] | 42 | namespace duchamp |
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[3] | 43 | { |
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[258] | 44 | |
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| 45 | |
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[528] | 46 | /// Class to represent a contiguous set of detected voxels. |
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| 47 | /// This is a detected object, which features: |
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| 48 | /// a vector of voxels, average and centroid positions, total & peak fluxes, |
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| 49 | /// the possibility of WCS-calculated parameters (RA, Dec, velocity, |
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| 50 | /// related widths). |
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| 51 | /// Also many functions with which to manipulate the Detections. |
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[258] | 52 | |
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[570] | 53 | class Detection : public Object3D |
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[378] | 54 | { |
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| 55 | public: |
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| 56 | Detection(); |
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[570] | 57 | Detection(const Object3D& o); |
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[378] | 58 | Detection(const Detection& d); |
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| 59 | Detection& operator= (const Detection& d); |
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| 60 | virtual ~Detection(){}; |
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[570] | 61 | void defaultDetection(); |
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[378] | 62 | //------------------------------ |
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| 63 | // These are functions in detection.cc. |
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| 64 | // |
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[258] | 65 | |
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[770] | 66 | friend Detection operator+ (Detection &lhs, Detection &rhs); |
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| 67 | void addDetection(Detection &other); |
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[624] | 68 | |
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[770] | 69 | bool canMerge(Detection &other, Param &par); |
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| 70 | bool isNear(Detection &other, Param &par); |
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| 71 | bool isClose(Detection &other, Param &par); |
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| 72 | |
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[528] | 73 | /// @brief Test whether voxel lists match |
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[417] | 74 | bool voxelListsMatch(std::vector<PixelInfo::Voxel> voxelList); |
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| 75 | |
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[528] | 76 | /// @brief Test whether a voxel list contains all detected voxels |
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[463] | 77 | bool voxelListCovered(std::vector<PixelInfo::Voxel> voxelList); |
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| 78 | |
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[528] | 79 | /// @brief Calculate flux-related parameters of the Detection. |
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[884] | 80 | void calcFluxes(float *fluxArray, size_t *dim); |
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[528] | 81 | /// @brief Calculate flux-related parameters of the Detection. |
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[417] | 82 | void calcFluxes(std::vector<PixelInfo::Voxel> voxelList); |
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[863] | 83 | void calcFluxes(std::map<Voxel,float> &voxelMap); |
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[258] | 84 | |
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[528] | 85 | /// @brief Calculate parameters related to the World Coordinate System. |
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[417] | 86 | // void calcWCSparams(float *fluxArray, long *dim, FitsHeader &head); |
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| 87 | void calcWCSparams(FitsHeader &head); |
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[258] | 88 | |
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[528] | 89 | /// @brief Calculate the integrated flux over the entire Detection. |
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[884] | 90 | void calcIntegFlux(float *fluxArray, size_t *dim, FitsHeader &head); |
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[528] | 91 | /// @brief Calculate the integrated flux over the entire Detection. |
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[884] | 92 | void calcIntegFlux(size_t zdim, std::vector<PixelInfo::Voxel> voxelList, FitsHeader &head); |
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| 93 | void calcIntegFlux(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head); |
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[3] | 94 | |
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[719] | 95 | /// @brief Calculate the 20%-/50%-peak-flux widths in a general fashion |
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[884] | 96 | void calcVelWidths(size_t zdim, float *intSpec, FitsHeader &head); |
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[528] | 97 | /// @brief Calculate the 20%/50% peak flux widths |
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[884] | 98 | void calcVelWidths(float *fluxArray, size_t *dim, FitsHeader &head); |
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[528] | 99 | /// @brief Calculate the 20%/50% peak flux widths |
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[884] | 100 | void calcVelWidths(size_t zdim, std::vector<PixelInfo::Voxel> voxelList, FitsHeader &head); |
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| 101 | void calcVelWidths(size_t zdim, std::map<Voxel,float> voxelMap, FitsHeader &head); |
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[464] | 102 | |
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[1133] | 103 | /// @brief Calculate the spatial (moment-0) shape |
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| 104 | void findShape(float *momentMap, size_t xdim, size_t ydim, FitsHeader &head); |
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| 105 | |
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[528] | 106 | /// @brief Set the values of the axis offsets from the cube. |
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[378] | 107 | void setOffsets(Param &par); |
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[221] | 108 | |
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[528] | 109 | /// @brief Add the offset values to the pixel locations |
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[884] | 110 | void addOffsets(size_t xoff, size_t yoff, size_t zoff){Object3D::addOffsets(xoff,yoff,zoff);}; |
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[378] | 111 | void addOffsets(){ |
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[570] | 112 | Object3D::addOffsets(xSubOffset,ySubOffset,zSubOffset); |
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[498] | 113 | xpeak+=xSubOffset; ypeak+=ySubOffset; zpeak+=zSubOffset; |
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| 114 | xCentroid+=xSubOffset; yCentroid+=ySubOffset; zCentroid+=zSubOffset; |
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[378] | 115 | }; |
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[221] | 116 | |
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[378] | 117 | // |
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| 118 | //--------------------------------- |
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| 119 | // Text Output -- all in Detection/outputDetection.cc |
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| 120 | // |
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[528] | 121 | /// @brief The spectral output label that contains info on the WCS position & velocity. |
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[378] | 122 | std::string outputLabelWCS(); |
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[282] | 123 | |
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[528] | 124 | /// @brief The spectral output label that contains info on the pixel location. |
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[378] | 125 | std::string outputLabelPix(); |
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[221] | 126 | |
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[528] | 127 | /// @brief The spectral output label that contains info on fluxes of the Detection. |
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[378] | 128 | std::string outputLabelFluxes(); |
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[265] | 129 | |
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[528] | 130 | /// @brief The spectral output label that contains info on widths of the Detection. |
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[1133] | 131 | std::string outputLabelWidths(FitsHeader &head); |
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[265] | 132 | |
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[528] | 133 | /// @brief Print all required values for the Detection to a table. |
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[1064] | 134 | void printTableRow(std::ostream &stream, Catalogues::CatalogueSpecification columns, Catalogues::DESTINATION tableType); |
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[441] | 135 | |
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[528] | 136 | /// @brief Print a particular value for the Detection to a table. |
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[1061] | 137 | void printTableEntry(std::ostream &stream, Catalogues::Column column); |
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[440] | 138 | |
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[378] | 139 | //---------------------------------- |
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| 140 | // For plotting routines... in Cubes/drawMomentCutout.cc |
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| 141 | // |
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[528] | 142 | /// @brief Get the location of the spatial borders. |
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[431] | 143 | std::vector<int> getVertexSet(); |
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| 144 | // |
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[528] | 145 | /// @brief Draw spatial borders for a particular Detection. |
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[378] | 146 | void drawBorders(int xoffset, int yoffset); |
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| 147 | // |
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[570] | 148 | |
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[378] | 149 | // |
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| 150 | //---------------------------------- |
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| 151 | // Basic functions |
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| 152 | // |
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[221] | 153 | |
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[528] | 154 | /// @brief Add a single voxel to the pixel list. |
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[570] | 155 | void addPixel(long x, long y, long z){Object3D::addPixel(x,y,z);}; |
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| 156 | |
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[528] | 157 | /// @brief Add a single voxel to the pixel list. |
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[378] | 158 | void addPixel(PixelInfo::Voxel point){ |
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[528] | 159 | /// @brief This one adds the pixel to the pixelArray, and updates the fluxes according to the Voxel's flux information |
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[570] | 160 | Object3D::addPixel(point.getX(),point.getY(),point.getZ()); |
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[378] | 161 | totalFlux += point.getF(); |
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| 162 | if(point.getF()>peakFlux){ |
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| 163 | peakFlux = point.getF(); |
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| 164 | xpeak = point.getX(); ypeak = point.getY(); zpeak = point.getZ(); |
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| 165 | } |
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| 166 | }; |
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[258] | 167 | |
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[528] | 168 | /// @brief How many channels does the Detection have? |
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[570] | 169 | long getNumChannels(){return Object3D::getNumDistinctZ();}; |
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[378] | 170 | |
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[528] | 171 | /// @brief Is there at least the acceptable minimum number of channels in the Detection? |
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[378] | 172 | bool hasEnoughChannels(int minNumber); |
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[258] | 173 | |
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[378] | 174 | //----------------------------------- |
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| 175 | // Basic accessor functions for private members follow... |
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| 176 | // |
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| 177 | long getXOffset(){return xSubOffset;}; |
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| 178 | void setXOffset(long o){xSubOffset = o;}; |
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| 179 | long getYOffset(){return ySubOffset;}; |
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| 180 | void setYOffset(long o){ySubOffset = o;}; |
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| 181 | long getZOffset(){return zSubOffset;}; |
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| 182 | void setZOffset(long o){zSubOffset = o;}; |
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| 183 | // |
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[681] | 184 | bool hasParams(){return haveParams;}; |
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| 185 | // |
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[570] | 186 | float getXcentre(); |
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| 187 | float getYcentre(); |
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| 188 | float getZcentre(); |
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[378] | 189 | float getTotalFlux(){return totalFlux;}; |
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| 190 | void setTotalFlux(float f){totalFlux=f;}; |
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| 191 | double getIntegFlux(){return intFlux;}; |
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| 192 | void setIntegFlux(double f){intFlux=f;}; |
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| 193 | float getPeakFlux(){return peakFlux;}; |
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| 194 | void setPeakFlux(float f){peakFlux=f;}; |
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| 195 | long getXPeak(){return xpeak;}; |
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| 196 | long getYPeak(){return ypeak;}; |
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| 197 | long getZPeak(){return zpeak;}; |
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| 198 | float getPeakSNR(){return peakSNR;}; |
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| 199 | void setPeakSNR(float f){peakSNR = f;}; |
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| 200 | float getXCentroid(){return xCentroid;}; |
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| 201 | float getYCentroid(){return yCentroid;}; |
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| 202 | float getZCentroid(){return zCentroid;}; |
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| 203 | std::string getCentreType(){return centreType;}; |
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| 204 | void setCentreType(std::string s){centreType=s;}; |
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| 205 | bool isNegative(){return negSource;}; |
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| 206 | void setNegative(bool f){negSource = f;}; |
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| 207 | std::string getFlagText(){return flagText;}; |
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| 208 | void setFlagText(std::string s){flagText = s;}; |
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| 209 | void addToFlagText(std::string s){flagText += s;}; |
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| 210 | // |
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[528] | 211 | /// @brief Is the WCS good enough to be used? |
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| 212 | /// \return Detection::flagWCS = True/False |
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[378] | 213 | bool isWCS(){return flagWCS;}; |
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| 214 | bool isSpecOK(){return specOK;}; |
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| 215 | void setSpecOK(bool b){specOK=b;}; |
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| 216 | std::string getName(){return name;}; |
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| 217 | void setName(std::string s){name=s;}; |
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| 218 | std::string getRAs(){return raS;}; |
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| 219 | std::string getDecs(){return decS;}; |
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[950] | 220 | double getRA(){return ra;}; |
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| 221 | double getDec(){return dec;}; |
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| 222 | double getRAWidth(){return raWidth;}; |
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| 223 | double getDecWidth(){return decWidth;}; |
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| 224 | double getMajorAxis(){return majorAxis;}; |
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| 225 | double getMinorAxis(){return minorAxis;}; |
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| 226 | double getPositionAngle(){return posang;}; |
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| 227 | double getVel(){return vel;}; |
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| 228 | double getVelWidth(){return velWidth;}; |
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| 229 | double getVelMin(){return velMin;}; |
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| 230 | double getVelMax(){return velMax;}; |
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| 231 | double getW20(){return w20;}; |
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| 232 | double getV20Min(){return v20min;}; |
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| 233 | double getV20Max(){return v20max;}; |
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| 234 | double getW50(){return w50;}; |
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| 235 | double getV50Min(){return v50min;}; |
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| 236 | double getV50Max(){return v50max;}; |
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[378] | 237 | int getID(){return id;}; |
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| 238 | void setID(int i){id = i;}; |
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| 239 | // |
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| 240 | int getPosPrec(){return posPrec;}; |
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| 241 | void setPosPrec(int i){posPrec=i;}; |
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| 242 | int getXYZPrec(){return xyzPrec;}; |
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| 243 | void setXYZPrec(int i){xyzPrec=i;}; |
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| 244 | int getFintPrec(){return fintPrec;}; |
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| 245 | void setFintPrec(int i){fintPrec=i;}; |
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| 246 | int getFpeakPrec(){return fpeakPrec;}; |
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| 247 | void setFpeakPrec(int i){fpeakPrec=i;}; |
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| 248 | int getVelPrec(){return velPrec;}; |
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| 249 | void setVelPrec(int i){velPrec=i;}; |
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| 250 | int getSNRPrec(){return snrPrec;}; |
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| 251 | void setSNRPrec(int i){snrPrec=i;}; |
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| 252 | // |
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[456] | 253 | protected: |
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[378] | 254 | // Subsection offsets |
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| 255 | long xSubOffset; ///< The x-offset, from subsectioned cube |
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| 256 | long ySubOffset; ///< The y-offset, from subsectioned cube |
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| 257 | long zSubOffset; ///< The z-offset, from subsectioned cube |
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[681] | 258 | bool haveParams; ///< Have the parameters been calculated? |
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[378] | 259 | // Flux related |
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| 260 | float totalFlux; ///< sum of the fluxes of all the pixels |
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[473] | 261 | double intFlux; ///< integrated flux : involves integration over velocity. |
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[378] | 262 | float peakFlux; ///< maximum flux over all the pixels |
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| 263 | long xpeak; ///< x-pixel location of peak flux |
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| 264 | long ypeak; ///< y-pixel location of peak flux |
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| 265 | long zpeak; ///< z-pixel location of peak flux |
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| 266 | float peakSNR; ///< signal-to-noise ratio at peak |
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| 267 | float xCentroid; ///< x-pixel location of centroid |
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| 268 | float yCentroid; ///< y-pixel location of centroid |
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| 269 | float zCentroid; ///< z-pixel location of centroid |
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[473] | 270 | std::string centreType; ///< which type of pixel centre to report: "average", "centroid", or "peak" (flux) |
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[378] | 271 | bool negSource; ///< is the source a negative feature? |
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[473] | 272 | std::string flagText; ///< any warning flags about the quality of the detection. |
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[378] | 273 | // WCS related |
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| 274 | int id; ///< ID -- generally number in list |
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[473] | 275 | std::string name; ///< IAU-style name (based on position) |
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| 276 | bool flagWCS; ///< A flag indicating whether the WCS parameters have been set. |
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| 277 | std::string raS; ///< Right Ascension (or Longitude) of pixel centre in form 12:34:23 |
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| 278 | std::string decS; ///< Declination (or Latitude) of pixel centre, in form -12:23:34 |
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[950] | 279 | double ra; ///< Central Right Ascension in degrees |
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| 280 | double dec; ///< Central Declination in degrees |
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| 281 | double raWidth; ///< Width of detection in RA direction in arcmin |
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| 282 | double decWidth; ///< Width of detection in Dec direction in arcmin |
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| 283 | double majorAxis; ///< Major axis length in arcmin |
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| 284 | double minorAxis; ///< Minor axis length in arcmin |
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| 285 | double posang; ///< Position angle of the major axis, in degrees |
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[378] | 286 | bool specOK; ///< Is the spectral dimension valid? |
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| 287 | std::string specUnits; ///< Units of the spectral dimension |
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[947] | 288 | std::string specType; ///< WCS ctype code for the spectral dimension |
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[378] | 289 | std::string fluxUnits; ///< Units of flux |
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| 290 | std::string intFluxUnits; ///< Units of integrated flux |
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| 291 | std::string lngtype; ///< Type of longitude axis (RA/GLON) |
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| 292 | std::string lattype; ///< Type of latitude axis (DEC/GLAT) |
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[950] | 293 | double vel; ///< Central velocity (from zCentre) |
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| 294 | double velWidth; ///< Full velocity width |
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| 295 | double velMin; ///< Minimum velocity |
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| 296 | double velMax; ///< Maximum velocity |
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| 297 | double v20min; ///< Minimum velocity at 20% of peak flux |
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| 298 | double v20max; ///< Maximum velocity at 20% of peak flux |
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| 299 | double w20; ///< Velocity width at 20% of peak flux |
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| 300 | double v50min; ///< Minimum velocity at 50% of peak flux |
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| 301 | double v50max; ///< Maximum velocity at 50% of peak flux |
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| 302 | double w50; ///< Velocity width at 50% of peak flux |
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[531] | 303 | /// @brief The next six are the precision of values printed in the headers of the spectral plots |
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| 304 | /// @name |
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| 305 | /// @{ |
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[378] | 306 | int posPrec; ///< Precision of WCS positional values |
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[473] | 307 | int xyzPrec; ///< Precision of pixel positional values |
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[378] | 308 | int fintPrec; ///< Precision of F_int/F_tot values |
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| 309 | int fpeakPrec; ///< Precision of F_peak values |
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| 310 | int velPrec; ///< Precision of velocity values. |
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| 311 | int snrPrec; ///< Precision of S/N_max values. |
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[528] | 312 | /// @} |
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[378] | 313 | }; |
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[3] | 314 | |
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[378] | 315 | //========================================================================== |
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[221] | 316 | |
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[378] | 317 | ////////////////////////////////////////////////////// |
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| 318 | // Prototypes for functions that use above classes |
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| 319 | ////////////////////////////////////////////////////// |
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[3] | 320 | |
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[378] | 321 | //---------------- |
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| 322 | // These are in sorting.cc |
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| 323 | // |
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[528] | 324 | /// @brief Sort a list of Detections by Z-pixel value. |
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[378] | 325 | void SortByZ(std::vector <Detection> &inputList); |
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[221] | 326 | |
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[528] | 327 | /// @brief Sort a list of Detections by Velocity. |
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[378] | 328 | void SortByVel(std::vector <Detection> &inputList); |
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[221] | 329 | |
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[571] | 330 | /// @brief Sort a list of Detections by a nominated parameter |
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| 331 | void SortDetections(std::vector <Detection> &inputList, std::string parameter); |
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| 332 | |
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[378] | 333 | //---------------- |
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| 334 | // This is in areClose.cc |
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| 335 | // |
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[770] | 336 | // /// @brief Determine whether two objects are close according to set parameters. |
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| 337 | // bool areClose(Detection &object1, Detection &object2, Param &par); |
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[221] | 338 | |
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[378] | 339 | //---------------- |
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| 340 | // This is in mergeIntoList.cc |
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| 341 | // |
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[528] | 342 | /// @brief Add an object into a list, combining with adjacent objects if need be. |
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[378] | 343 | void mergeIntoList(Detection &object, std::vector <Detection> &objList, |
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| 344 | Param &par); |
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[3] | 345 | |
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[378] | 346 | //---------------- |
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| 347 | // These are in Cubes/Merger.cc |
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| 348 | // |
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[528] | 349 | /// @brief Merge a list of Detections so that all adjacent voxels are in the same Detection. |
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[378] | 350 | void mergeList(std::vector<Detection> &objList, Param &par); |
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[528] | 351 | /// @brief Culls a list of Detections that do not meet minimum requirements. |
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[378] | 352 | void finaliseList(std::vector<Detection> &objList, Param &par); |
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[528] | 353 | /// @brief Manage both the merging and the cleaning up of the list. |
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[378] | 354 | void ObjectMerger(std::vector<Detection> &objList, Param &par); |
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[56] | 355 | |
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[1137] | 356 | // /// @brief Print the header information to a particular table |
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| 357 | // void outputTableHeader(std::ostream &stream, Catalogues::CatalogueSpecification &columns, Catalogues::DESTINATION tableType, bool flagWCS); |
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[439] | 358 | |
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[378] | 359 | } |
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[221] | 360 | |
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[3] | 361 | #endif |
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