[3] | 1 | #include <iostream> |
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| 2 | #include <iomanip> |
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| 3 | #include <fstream> |
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| 4 | #include <vector> |
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| 5 | #include <Cubes/cubes.hh> |
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| 6 | #include <Utils/utils.hh> |
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| 7 | |
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[96] | 8 | void Cube::CubicSearch() |
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[3] | 9 | { |
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| 10 | /** |
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| 11 | * Cube::SimpleSearch3D() |
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| 12 | * A front end to the cubic searching routine that does not |
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| 13 | * involve any wavelet reconstruction. |
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| 14 | * Although if baseline-removal is required that is done prior to searching. |
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| 15 | * Once searching is complete, the detection map is updated and |
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| 16 | * the intermediate detections are logged in the log file. |
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| 17 | */ |
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| 18 | |
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[96] | 19 | this->objectList = search3DArray(this->axisDim,this->array,this->par); |
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[3] | 20 | |
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| 21 | this->updateDetectMap(); |
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| 22 | if(this->par.getFlagLog()) this->logDetectionList(); |
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| 23 | |
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| 24 | } |
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| 25 | |
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| 26 | |
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[96] | 27 | vector <Detection> search3DArray(long *dim, float *Array, Param &par) |
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[3] | 28 | { |
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| 29 | /** |
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| 30 | * cubicSearch |
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| 31 | * Takes a dimension array and data array as input (and Parameter set) |
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| 32 | * and searches for detections in a combination of 1D and 2D searches. |
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| 33 | * Returns a vector list of Detections. |
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| 34 | * No reconstruction is assumed to have taken place, so statistics are |
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| 35 | * calculated (using robust methods) from the data array itself. |
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| 36 | */ |
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| 37 | |
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| 38 | vector <Detection> outputList; |
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[96] | 39 | long zdim = dim[2]; |
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| 40 | long xySize = dim[0] * dim[1]; |
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| 41 | long fullSize = zdim * xySize; |
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[3] | 42 | int num = 0; |
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| 43 | |
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| 44 | float blankPixValue = par.getBlankPixVal(); |
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| 45 | bool *isGood = new bool[fullSize]; |
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[96] | 46 | for(int pos=0;pos<fullSize;pos++){ |
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| 47 | isGood[pos] = !par.isBlank(Array[pos]) && !par.isInMW(pos/xySize); |
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| 48 | } |
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| 49 | bool *doChannel = new bool[xySize]; |
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| 50 | int goodSize=0; |
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| 51 | for(int npix=0; npix<xySize; npix++){ |
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| 52 | for(int z=0;z<zdim;z++) if(isGood[z*xySize+npix]) goodSize++; |
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| 53 | if(goodSize==0) doChannel[npix] = false; |
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| 54 | else doChannel[npix] = true; |
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| 55 | } |
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[3] | 56 | |
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| 57 | // FIRST SEARCH -- IN EACH SPECTRUM. |
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| 58 | if(zdim>1){ |
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| 59 | if(par.isVerbose()) std::cout << " 1D: | |" << std::flush; |
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| 60 | |
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| 61 | for(int npix=0; npix<xySize; npix++){ |
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[86] | 62 | |
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[3] | 63 | if( par.isVerbose() && ((100*(npix+1)/xySize)%5 == 0) ){ |
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| 64 | std::cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b|"; |
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| 65 | for(int i=0;i<(100*(npix+1)/xySize)/5;i++) std::cout << "#"; |
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| 66 | for(int i=(100*(npix+1)/xySize)/5;i<20;i++) std::cout << " "; |
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| 67 | std::cout << "|" << std::flush; |
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| 68 | } |
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| 69 | |
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[96] | 70 | if(doChannel[npix]){ |
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| 71 | |
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| 72 | float *spec = new float[zdim]; |
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| 73 | float specMedian,specSigma; |
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| 74 | goodSize=0; |
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| 75 | for(int z=0;z<zdim;z++) |
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| 76 | if(isGood[z*xySize+npix]) spec[goodSize++] = Array[z*xySize+npix]; |
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| 77 | findMedianStats(spec,goodSize,specMedian,specSigma); |
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| 78 | specSigma /= correctionFactor; |
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| 79 | |
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| 80 | |
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| 81 | long *specdim = new long[2]; |
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| 82 | specdim[0] = zdim; specdim[1]=1; |
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| 83 | Image *spectrum = new Image(specdim); |
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| 84 | delete specdim; |
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| 85 | spectrum->saveParam(par); |
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| 86 | spectrum->pars().setBeamSize(2.); // for spectrum, only neighbouring channels correlated |
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| 87 | spectrum->extractSpectrum(Array,dim,npix); |
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| 88 | spectrum->removeMW(); // only works if flagMW is true |
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| 89 | spectrum->setStats(specMedian,specSigma,par.getCut()); |
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| 90 | if(par.getFlagFDR()) spectrum->setupFDR(); |
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| 91 | spectrum->setMinSize(par.getMinChannels()); |
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| 92 | spectrum->spectrumDetect(); |
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| 93 | for(int obj=0;obj<spectrum->getNumObj();obj++){ |
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| 94 | Detection *object = new Detection; |
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| 95 | *object = spectrum->getObject(obj); |
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| 96 | for(int pix=0;pix<object->getSize();pix++) { |
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| 97 | // Fix up coordinates of each pixel to match original array |
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| 98 | object->setZ(pix, object->getX(pix)); |
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| 99 | object->setX(pix, npix%dim[0]); |
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| 100 | object->setY(pix, npix/dim[0]); |
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| 101 | } |
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| 102 | object->addOffsets(par); |
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| 103 | object->calcParams(); |
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| 104 | mergeIntoList(*object,outputList,par); |
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| 105 | delete object; |
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[3] | 106 | } |
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[96] | 107 | delete spectrum; |
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[3] | 108 | } |
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[96] | 109 | } |
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[3] | 110 | |
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| 111 | num = outputList.size(); |
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| 112 | if(par.isVerbose()) |
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| 113 | std::cout <<"\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bFound " << num <<";" << std::flush; |
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| 114 | |
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| 115 | } |
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| 116 | |
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| 117 | // SECOND SEARCH -- IN EACH CHANNEL |
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| 118 | if(par.isVerbose()) std::cout << " 2D: | |" << std::flush; |
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| 119 | |
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| 120 | for(int z=0; z<zdim; z++){ |
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| 121 | |
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| 122 | if( par.isVerbose() && ((100*(z+1)/zdim)%5 == 0) ){ |
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| 123 | std::cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b|"; |
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| 124 | for(int i=0;i<(100*(z+1)/zdim)/5;i++) std::cout << "#"; |
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| 125 | for(int i=(100*(z+1)/zdim)/5;i<20;i++) std::cout << " "; |
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| 126 | std::cout << "|" << std::flush; |
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| 127 | } |
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| 128 | |
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[96] | 129 | if(!par.isInMW(z)){ |
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[3] | 130 | |
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[96] | 131 | float *image = new float[xySize]; |
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| 132 | float imageMedian, imageSigma; |
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| 133 | goodSize=0; |
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| 134 | for(int npix=0; npix<xySize; npix++) |
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| 135 | if(isGood[z*xySize + npix]) image[goodSize++] = Array[z*xySize + npix]; |
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| 136 | findMedianStats(image,goodSize,imageMedian,imageSigma); |
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| 137 | imageSigma /= correctionFactor; |
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| 138 | |
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[3] | 139 | long *imdim = new long[2]; |
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| 140 | imdim[0] = dim[0]; imdim[1] = dim[1]; |
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| 141 | Image *channelImage = new Image(imdim); |
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[86] | 142 | delete imdim; |
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[3] | 143 | channelImage->saveParam(par); |
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[53] | 144 | channelImage->extractImage(Array,dim,z); |
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[96] | 145 | channelImage->setStats(imageMedian,imageSigma,par.getCut()); |
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[3] | 146 | if(par.getFlagFDR()) channelImage->setupFDR(); |
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[13] | 147 | channelImage->setMinSize(par.getMinPix()); |
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[3] | 148 | channelImage->lutz_detect(); |
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| 149 | for(int obj=0;obj<channelImage->getNumObj();obj++){ |
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| 150 | Detection *object = new Detection; |
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| 151 | *object = channelImage->getObject(obj); |
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| 152 | // Fix up coordinates of each pixel to match original array |
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| 153 | for(int pix=0;pix<object->getSize();pix++) object->setZ(pix, z); |
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| 154 | object->addOffsets(par); |
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| 155 | object->calcParams(); |
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| 156 | mergeIntoList(*object,outputList,par); |
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| 157 | delete object; |
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| 158 | } |
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| 159 | delete channelImage; |
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| 160 | } |
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| 161 | |
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| 162 | } |
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| 163 | |
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| 164 | if(par.isVerbose()) |
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[96] | 165 | std::cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bFound " << outputList.size()-num |
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[3] | 166 | << ". " << std::endl << std::flush; |
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| 167 | |
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| 168 | delete [] isGood; |
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| 169 | delete [] doChannel; |
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[86] | 170 | |
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[3] | 171 | return outputList; |
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| 172 | } |
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