| 1 | #include <iostream> |
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| 2 | #include <iomanip> |
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| 3 | #include <vector> |
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| 4 | #include <Cubes/cubes.hh> |
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| 5 | #include <Utils/utils.hh> |
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| 6 | #include <Utils/Statistics.hh> |
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| 7 | #include <PixelMap/Voxel.hh> |
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| 8 | #include <Detection/detection.hh> |
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| 9 | |
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| 10 | using std::vector; |
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| 11 | using std::setw; |
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| 12 | |
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| 13 | using namespace PixelInfo; |
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| 14 | |
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| 15 | void growObject(Detection &object, Cube &cube) |
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| 16 | { |
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| 17 | /** |
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| 18 | * A function to grow an object (given by the Detection) by |
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| 19 | * including neighbouring voxels out to some lower threshold than |
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| 20 | * what was previously used in the detection. |
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| 21 | * |
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| 22 | * Each pixel has each of its neighbours examined, and if one of |
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| 23 | * them is not in the object but above the growth threshold, it |
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| 24 | * is added to the object. |
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| 25 | * |
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| 26 | * \param object Object to be grown. |
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| 27 | * \param cube Necessary to see both the Param list, containing the growth |
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| 28 | * threshold, and the actual array of pixel fluxes. |
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| 29 | */ |
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| 30 | |
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| 31 | |
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| 32 | vector <bool> isInObj(cube.getSize(),false); |
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| 33 | float thresh1; |
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| 34 | float thresh2; |
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| 35 | long chanpos; |
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| 36 | |
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| 37 | for(int i=0;i<object.getSize();i++) { |
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| 38 | Voxel vox = object.getPixel(i); |
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| 39 | long pos = vox.getX() + vox.getY()*cube.getDimX() + |
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| 40 | vox.getZ()*cube.getDimX()*cube.getDimY(); |
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| 41 | isInObj[pos] = true; |
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| 42 | } |
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| 43 | |
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| 44 | StatsContainer<float> growthStats = cube.getStats(); |
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| 45 | |
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| 46 | growthStats.setThresholdSNR(cube.pars().getGrowthCut()); |
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| 47 | growthStats.setUseFDR(false); |
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| 48 | |
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| 49 | for(int pix=0; pix<object.getSize(); pix++){ // for each pixel in the object |
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| 50 | |
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| 51 | for(int xnbr=-1; xnbr<=1; xnbr++){ |
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| 52 | for(int ynbr=-1; ynbr<=1; ynbr++){ |
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| 53 | for(int znbr=-1; znbr<=1; znbr++){ |
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| 54 | |
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| 55 | if((xnbr!=0)||(ynbr!=0)||(znbr!=0)){ |
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| 56 | // ignore when all=0 ie. the current object pixel |
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| 57 | |
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| 58 | Voxel pixnew = object.getPixel(pix); |
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| 59 | long newx = pixnew.getX() + xnbr; |
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| 60 | long newy = pixnew.getY() + ynbr; |
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| 61 | long newz = pixnew.getZ() + znbr; |
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| 62 | |
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| 63 | if((newx<cube.getDimX())&&(newx>=0)&& |
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| 64 | (newy<cube.getDimY())&&(newy>=0)&& |
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| 65 | (newz<cube.getDimZ())&&(newz>=0)){ |
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| 66 | |
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| 67 | pixnew.setX(newx); |
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| 68 | pixnew.setY(newy); |
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| 69 | pixnew.setZ(newz); |
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| 70 | |
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| 71 | float flux; |
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| 72 | if(cube.isRecon()) flux = cube.getReconValue(newx,newy,newz); |
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| 73 | else flux = cube.getPixValue(newx,newy,newz); |
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| 74 | pixnew.setF(flux); |
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| 75 | |
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| 76 | long chanpos = newx + newy * cube.getDimX(); |
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| 77 | long pos = newx + newy * cube.getDimX() + |
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| 78 | newz * cube.getDimX() * cube.getDimY(); |
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| 79 | if( (!isInObj[pos]) && growthStats.isDetection(flux) ){ |
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| 80 | isInObj[pos] = true; |
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| 81 | object.addPixel(pixnew); |
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| 82 | } // end of if |
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| 83 | |
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| 84 | } // end of if clause regarding newx, newy, newz |
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| 85 | |
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| 86 | } // end of if clause regarding xnbr, ynbr, znbr |
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| 87 | |
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| 88 | } // end of znbr loop |
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| 89 | } // end of ynbr loop |
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| 90 | } // end of xnbr loop |
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| 91 | |
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| 92 | } // end of pix loop |
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| 93 | |
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| 94 | object.calcFluxes(cube.getArray(), cube.getDimArray()); |
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| 95 | |
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| 96 | isInObj.clear(); |
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| 97 | |
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| 98 | } |
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| 99 | |
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