[300] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // growObject.cc: Grow a detected object down to a lower flux threshold. |
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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 | #include <iostream> |
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| 29 | #include <iomanip> |
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| 30 | #include <vector> |
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[393] | 31 | #include <duchamp/Cubes/cubes.hh> |
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| 32 | #include <duchamp/Utils/utils.hh> |
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| 33 | #include <duchamp/Utils/Statistics.hh> |
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| 34 | #include <duchamp/PixelMap/Voxel.hh> |
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| 35 | #include <duchamp/Detection/detection.hh> |
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[3] | 36 | |
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| 37 | using std::vector; |
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| 38 | using std::setw; |
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| 39 | |
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[258] | 40 | using namespace PixelInfo; |
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[274] | 41 | using namespace Statistics; |
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[258] | 42 | |
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[378] | 43 | namespace duchamp |
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[3] | 44 | { |
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| 45 | |
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[378] | 46 | void growObject(Detection &object, Cube &cube) |
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| 47 | { |
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| 48 | /** |
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| 49 | * A function to grow an object (given by the Detection) by |
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| 50 | * including neighbouring voxels out to some lower threshold than |
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| 51 | * what was previously used in the detection. |
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| 52 | * |
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| 53 | * Each pixel has each of its neighbours examined, and if one of |
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| 54 | * them is not in the object but above the growth threshold, it |
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| 55 | * is added to the object. |
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| 56 | * |
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| 57 | * \param object Object to be grown. |
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| 58 | * \param cube Necessary to see both the Param list, containing |
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| 59 | * the growth threshold, and the actual array of pixel fluxes. |
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| 60 | */ |
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[3] | 61 | |
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| 62 | |
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[378] | 63 | vector <bool> isInObj(cube.getSize(),false); |
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| 64 | bool flagAdj = cube.pars().getFlagAdjacent(); |
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| 65 | int threshS = int(cube.pars().getThreshS()); |
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| 66 | if(flagAdj) threshS = 1; |
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| 67 | int threshV = int(cube.pars().getThreshV()); |
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| 68 | |
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| 69 | for(int i=0;i<object.getSize();i++) { |
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| 70 | Voxel vox = object.getPixel(i); |
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| 71 | long pos = vox.getX() + vox.getY()*cube.getDimX() + |
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| 72 | vox.getZ()*cube.getDimX()*cube.getDimY(); |
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| 73 | isInObj[pos] = true; |
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| 74 | } |
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[3] | 75 | |
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[378] | 76 | StatsContainer<float> growthStats = cube.getStats(); |
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[190] | 77 | |
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[378] | 78 | growthStats.setThresholdSNR(cube.pars().getGrowthCut()); |
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| 79 | growthStats.setUseFDR(false); |
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[190] | 80 | |
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[378] | 81 | for(int pix=0; pix<object.getSize(); pix++){ // for each pixel in the object |
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[3] | 82 | |
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[378] | 83 | for(int xnbr=-1*threshS; xnbr<=1*threshS; xnbr++){ |
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| 84 | for(int ynbr=-1*threshS; ynbr<=1*threshS; ynbr++){ |
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| 85 | for(int znbr=-1*threshV; znbr<=1*threshV; znbr++){ |
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[3] | 86 | |
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[378] | 87 | if((xnbr!=0)||(ynbr!=0)||(znbr!=0)){ |
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| 88 | // ignore when all=0 ie. the current object pixel |
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[3] | 89 | |
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[378] | 90 | Voxel pixnew = object.getPixel(pix); |
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| 91 | long newx = pixnew.getX() + xnbr; |
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| 92 | long newy = pixnew.getY() + ynbr; |
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| 93 | long newz = pixnew.getZ() + znbr; |
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[3] | 94 | |
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[378] | 95 | if((newx<cube.getDimX())&&(newx>=0)&& // x in cube? |
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| 96 | (newy<cube.getDimY())&&(newy>=0)&& // y in cube? |
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| 97 | (newz<cube.getDimZ())&&(newz>=0)&& // z in cube? |
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| 98 | !cube.isBlank(newx,newy,newz) && // pixel not BLANK? |
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| 99 | !cube.pars().isInMW(newz) && // pixel not MW? |
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| 100 | (flagAdj || hypot(xnbr,ynbr)) ){ // pixel not too far? |
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[3] | 101 | |
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[378] | 102 | pixnew.setX(newx); |
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| 103 | pixnew.setY(newy); |
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| 104 | pixnew.setZ(newz); |
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[190] | 105 | |
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[378] | 106 | float flux; |
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| 107 | if(cube.isRecon()) flux = cube.getReconValue(newx,newy,newz); |
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| 108 | else flux = cube.getPixValue(newx,newy,newz); |
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| 109 | pixnew.setF(flux); |
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[3] | 110 | |
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[378] | 111 | long pos = newx + newy * cube.getDimX() + |
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| 112 | newz * cube.getDimX() * cube.getDimY(); |
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| 113 | if( (!isInObj[pos]) && growthStats.isDetection(flux) ){ |
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| 114 | isInObj[pos] = true; |
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| 115 | object.addPixel(pixnew); |
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| 116 | } // end of if |
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[86] | 117 | |
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[378] | 118 | } // end of if clause regarding newx, newy, newz |
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[86] | 119 | |
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[378] | 120 | } // end of if clause regarding xnbr, ynbr, znbr |
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[86] | 121 | |
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[378] | 122 | } // end of znbr loop |
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| 123 | } // end of ynbr loop |
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| 124 | } // end of xnbr loop |
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[86] | 125 | |
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[378] | 126 | } // end of pix loop |
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[86] | 127 | |
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[378] | 128 | object.calcFluxes(cube.getArray(), cube.getDimArray()); |
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[86] | 129 | |
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[378] | 130 | isInObj.clear(); |
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[86] | 131 | |
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[378] | 132 | } |
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| 133 | |
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[86] | 134 | } |
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