[3] | 1 | #include <fstream> |
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| 2 | #include <iostream> |
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| 3 | #include <iomanip> |
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| 4 | #include <vector> |
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[120] | 5 | #include <duchamp.hh> |
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[243] | 6 | #include <PixelMap/Object3D.hh> |
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[3] | 7 | #include <Cubes/cubes.hh> |
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[144] | 8 | #include <Detection/detection.hh> |
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[3] | 9 | #include <ATrous/atrous.hh> |
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| 10 | #include <Utils/utils.hh> |
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[213] | 11 | #include <Utils/feedback.hh> |
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[192] | 12 | #include <Utils/Statistics.hh> |
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[3] | 13 | |
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[252] | 14 | using namespace PixelInfo; |
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| 15 | |
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[103] | 16 | void Cube::ReconSearch() |
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| 17 | { |
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| 18 | /** |
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[220] | 19 | * The Cube is first reconstructed, using Cube::ReconCube(). |
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| 20 | * The statistics of the cube are calculated next. |
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| 21 | * It is then searched, using searchReconArray. |
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| 22 | * The resulting object list is stored in the Cube, and outputted |
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| 23 | * to the log file if the user so requests. |
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[103] | 24 | */ |
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[188] | 25 | |
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| 26 | this->ReconCube(); |
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| 27 | |
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[219] | 28 | if(this->par.isVerbose()) std::cout << " "; |
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| 29 | |
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[212] | 30 | this->setCubeStats(); |
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[189] | 31 | |
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[219] | 32 | if(this->par.isVerbose()) std::cout << " Searching... " << std::flush; |
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[188] | 33 | |
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| 34 | this->objectList = searchReconArray(this->axisDim,this->array, |
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[190] | 35 | this->recon,this->par,this->Stats); |
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[188] | 36 | |
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[248] | 37 | if(this->par.isVerbose()) std::cout << " Updating detection map... " |
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| 38 | << std::flush; |
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[188] | 39 | this->updateDetectMap(); |
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[248] | 40 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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[188] | 41 | |
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[248] | 42 | if(this->par.getFlagLog()){ |
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| 43 | if(this->par.isVerbose()) |
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| 44 | std::cout << " Logging intermediate detections... " << std::flush; |
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| 45 | this->logDetectionList(); |
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| 46 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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| 47 | } |
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| 48 | |
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[188] | 49 | } |
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| 50 | |
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| 51 | ///////////////////////////////////////////////////////////////////////////// |
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| 52 | void Cube::ReconCube() |
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| 53 | { |
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| 54 | /** |
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[220] | 55 | * A front-end to the various reconstruction functions, the choice of |
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| 56 | * which is determined by the use of the reconDim parameter. |
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| 57 | * Differs from ReconSearch only in that no searching is done. |
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[188] | 58 | */ |
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[120] | 59 | int dimRecon = this->par.getReconDim(); |
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[146] | 60 | // Test whether we have eg. an image, but have requested a 3-d |
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| 61 | // reconstruction. |
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| 62 | // If dimension of data array is less than dimRecon, change dimRecon |
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| 63 | // to the dimension of the array. |
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[120] | 64 | int numGoodDim = 0; |
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| 65 | for(int i=0;i<this->numDim;i++) if(this->axisDim[i]>1) numGoodDim++; |
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| 66 | if(numGoodDim<dimRecon) dimRecon = numGoodDim; |
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| 67 | this->par.setReconDim(dimRecon); |
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| 68 | |
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| 69 | switch(dimRecon) |
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[103] | 70 | { |
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[188] | 71 | case 1: this->ReconCube1D(); break; |
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| 72 | case 2: this->ReconCube2D(); break; |
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| 73 | case 3: this->ReconCube3D(); break; |
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[103] | 74 | default: |
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[120] | 75 | if(dimRecon<=0){ |
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| 76 | std::stringstream errmsg; |
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| 77 | errmsg << "reconDim (" << dimRecon |
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| 78 | << ") is less than 1. Performing 1-D reconstruction.\n"; |
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[188] | 79 | duchampWarning("ReconCube", errmsg.str()); |
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[103] | 80 | this->par.setReconDim(1); |
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[188] | 81 | this->ReconCube1D(); |
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[103] | 82 | } |
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[120] | 83 | else if(dimRecon>3){ |
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| 84 | //this probably won't happen with new code above, but just in case... |
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| 85 | std::stringstream errmsg; |
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| 86 | errmsg << "reconDim (" << dimRecon |
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| 87 | << ") is more than 3. Performing 3-D reconstruction.\n"; |
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[188] | 88 | duchampWarning("ReconCube", errmsg.str()); |
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[103] | 89 | this->par.setReconDim(3); |
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[188] | 90 | this->ReconCube3D(); |
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[103] | 91 | } |
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| 92 | break; |
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| 93 | } |
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| 94 | } |
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| 95 | |
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[146] | 96 | ///////////////////////////////////////////////////////////////////////////// |
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[188] | 97 | void Cube::ReconCube1D() |
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[3] | 98 | { |
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[103] | 99 | /** |
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[220] | 100 | * This reconstructs a cube by performing a 1D a trous reconstruction |
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| 101 | * in the spectrum of each spatial pixel. |
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[103] | 102 | */ |
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| 103 | long xySize = this->axisDim[0] * this->axisDim[1]; |
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[188] | 104 | |
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[103] | 105 | long zdim = this->axisDim[2]; |
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[3] | 106 | |
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[187] | 107 | ProgressBar bar; |
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[103] | 108 | if(!this->reconExists){ |
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| 109 | std::cout<<" Reconstructing... "; |
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[187] | 110 | if(par.isVerbose()) bar.init(xySize); |
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[103] | 111 | for(int npix=0; npix<xySize; npix++){ |
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[175] | 112 | |
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[187] | 113 | if( par.isVerbose() ) bar.update(npix+1); |
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[175] | 114 | |
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[103] | 115 | float *spec = new float[zdim]; |
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| 116 | float *newSpec = new float[zdim]; |
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| 117 | for(int z=0;z<zdim;z++) spec[z] = this->array[z*xySize + npix]; |
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| 118 | bool verboseFlag = this->par.isVerbose(); |
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| 119 | this->par.setVerbosity(false); |
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| 120 | atrous1DReconstruct(this->axisDim[2],spec,newSpec,this->par); |
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| 121 | this->par.setVerbosity(verboseFlag); |
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| 122 | for(int z=0;z<zdim;z++) this->recon[z*xySize+npix] = newSpec[z]; |
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[205] | 123 | delete [] spec; |
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| 124 | delete [] newSpec; |
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[3] | 125 | } |
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[103] | 126 | this->reconExists = true; |
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[214] | 127 | bar.fillSpace(" All Done."); |
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[175] | 128 | printSpace(22); |
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[188] | 129 | std::cout << "\n"; |
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[3] | 130 | } |
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[103] | 131 | |
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[3] | 132 | } |
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| 133 | |
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[146] | 134 | ///////////////////////////////////////////////////////////////////////////// |
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[188] | 135 | void Cube::ReconCube2D() |
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[3] | 136 | { |
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[103] | 137 | /** |
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[220] | 138 | * This reconstructs a cube by performing a 2D a trous reconstruction |
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| 139 | * in each spatial image (ie. each channel map) of the cube. |
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[103] | 140 | */ |
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| 141 | long xySize = this->axisDim[0] * this->axisDim[1]; |
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[187] | 142 | ProgressBar bar; |
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[3] | 143 | |
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[103] | 144 | if(!this->reconExists){ |
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| 145 | std::cout<<" Reconstructing... "; |
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[187] | 146 | if(par.isVerbose()) bar.init(this->axisDim[2]); |
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[103] | 147 | for(int z=0;z<this->axisDim[2];z++){ |
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[175] | 148 | |
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[187] | 149 | if( par.isVerbose() ) bar.update((z+1)); |
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[175] | 150 | |
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[103] | 151 | if(!this->par.isInMW(z)){ |
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| 152 | float *im = new float[xySize]; |
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| 153 | float *newIm = new float[xySize]; |
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[146] | 154 | for(int npix=0; npix<xySize; npix++) |
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| 155 | im[npix] = this->array[z*xySize+npix]; |
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[103] | 156 | bool verboseFlag = this->par.isVerbose(); |
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| 157 | this->par.setVerbosity(false); |
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[146] | 158 | atrous2DReconstruct(this->axisDim[0],this->axisDim[1], |
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| 159 | im,newIm,this->par); |
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[103] | 160 | this->par.setVerbosity(verboseFlag); |
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[146] | 161 | for(int npix=0; npix<xySize; npix++) |
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| 162 | this->recon[z*xySize+npix] = newIm[npix]; |
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[205] | 163 | delete [] im; |
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| 164 | delete [] newIm; |
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[3] | 165 | } |
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[103] | 166 | else { |
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[146] | 167 | for(int i=z*xySize; i<(z+1)*xySize; i++) |
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| 168 | this->recon[i] = this->array[i]; |
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[103] | 169 | } |
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[3] | 170 | } |
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[103] | 171 | this->reconExists = true; |
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[214] | 172 | bar.fillSpace(" All Done."); |
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[175] | 173 | printSpace(22); |
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[188] | 174 | std::cout << "\n"; |
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[3] | 175 | } |
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| 176 | } |
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| 177 | |
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[146] | 178 | ///////////////////////////////////////////////////////////////////////////// |
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[188] | 179 | void Cube::ReconCube3D() |
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[3] | 180 | { |
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[103] | 181 | /** |
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[220] | 182 | * This performs a full 3D a trous reconstruction of the cube |
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[103] | 183 | */ |
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[188] | 184 | if(this->axisDim[2]==1) this->ReconCube2D(); |
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[3] | 185 | else { |
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| 186 | |
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[71] | 187 | if(!this->reconExists){ |
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| 188 | std::cout<<" Reconstructing... "<<std::flush; |
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| 189 | atrous3DReconstruct(this->axisDim[0],this->axisDim[1],this->axisDim[2], |
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| 190 | this->array,this->recon,this->par); |
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| 191 | this->reconExists = true; |
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[175] | 192 | std::cout << " All Done."; |
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| 193 | printSpace(22); |
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[188] | 194 | std::cout << "\n"; |
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[71] | 195 | } |
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| 196 | |
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[3] | 197 | } |
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| 198 | } |
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| 199 | |
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[146] | 200 | ///////////////////////////////////////////////////////////////////////////// |
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[232] | 201 | std::vector <Detection> searchReconArray(long *dim, float *originalArray, |
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| 202 | float *reconArray, Param &par, |
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| 203 | StatsContainer<float> &stats) |
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[3] | 204 | { |
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[103] | 205 | /** |
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[220] | 206 | * This searches for objects in a cube that has been reconstructed. |
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[103] | 207 | * |
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[220] | 208 | * The search is conducted first in each spatial pixel (xdim*ydim 1D |
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| 209 | * searches), then in each channel image (zdim 2D searches). |
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| 210 | * The searches are done on the reconstructed array, although the detected |
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| 211 | * objects have fluxes drawn from the corresponding pixels of the original |
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| 212 | * array. |
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[103] | 213 | * |
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[220] | 214 | * \param dim Array of dimension sizes |
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| 215 | * \param originalArray Original, un-reconstructed image array. |
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| 216 | * \param reconArray Reconstructed image array |
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| 217 | * \param par The Param set. |
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| 218 | * \param stats The StatsContainer that defines what a detection is. |
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[103] | 219 | * |
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[220] | 220 | * \return A vector of Detections resulting from the search. |
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[103] | 221 | */ |
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[232] | 222 | std::vector <Detection> outputList; |
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[103] | 223 | long zdim = dim[2]; |
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| 224 | long xySize = dim[0] * dim[1]; |
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[192] | 225 | int num=0; |
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[251] | 226 | ProgressBar bar; |
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[3] | 227 | |
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| 228 | // First search -- in each spectrum. |
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| 229 | if(zdim > 1){ |
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[175] | 230 | if(par.isVerbose()){ |
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| 231 | std::cout << "1D: "; |
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[187] | 232 | bar.init(xySize); |
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[175] | 233 | } |
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[3] | 234 | |
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[251] | 235 | bool *doPixel = new bool[xySize]; |
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| 236 | // doPixel is a bool array to say whether to look in a given spectrum |
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| 237 | for(int npix=0; npix<xySize; npix++){ |
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| 238 | doPixel[npix] = false; |
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| 239 | for(int z=0;z<zdim;z++) { |
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| 240 | doPixel[npix] = doPixel[npix] || |
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| 241 | (!par.isBlank(originalArray[npix]) && !par.isInMW(z)); |
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| 242 | } |
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| 243 | // doPixel[i] is false only when there are no good pixels in spectrum |
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| 244 | // of pixel #i. |
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| 245 | } |
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| 246 | |
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[243] | 247 | long *specdim = new long[2]; |
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| 248 | specdim[0] = zdim; specdim[1]=1; |
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[251] | 249 | Image *spectrum = new Image(specdim); |
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| 250 | delete [] specdim; |
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| 251 | spectrum->saveParam(par); |
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| 252 | spectrum->saveStats(stats); |
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| 253 | spectrum->setMinSize(par.getMinChannels()); |
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| 254 | spectrum->pars().setBeamSize(2.); |
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| 255 | // beam size: for spectrum, only neighbouring channels correlated |
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[3] | 256 | |
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[243] | 257 | for(int y=0; y<dim[1]; y++){ |
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| 258 | for(int x=0; x<dim[0]; x++){ |
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[3] | 259 | |
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[243] | 260 | int npix = y*dim[0] + x; |
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| 261 | if( par.isVerbose() ) bar.update(npix+1); |
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[192] | 262 | |
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[243] | 263 | if(doPixel[npix]){ |
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| 264 | |
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| 265 | spectrum->extractSpectrum(reconArray,dim,npix); |
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| 266 | spectrum->removeMW(); // only works if flagMW is true |
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| 267 | std::vector<Scan> objlist = spectrum->spectrumDetect(); |
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| 268 | num += objlist.size(); |
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| 269 | for(int obj=0;obj<objlist.size();obj++){ |
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| 270 | Detection newObject; |
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[103] | 271 | // Fix up coordinates of each pixel to match original array |
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[243] | 272 | for(int z=objlist[obj].getX();z<=objlist[obj].getXmax();z++) { |
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| 273 | newObject.pixels().addPixel(x,y,z); |
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| 274 | } |
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| 275 | newObject.setOffsets(par); |
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| 276 | mergeIntoList(newObject,outputList,par); |
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[103] | 277 | } |
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[3] | 278 | } |
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[251] | 279 | |
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[3] | 280 | } |
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| 281 | } |
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| 282 | |
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[251] | 283 | delete spectrum; |
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| 284 | delete [] doPixel; |
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| 285 | |
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[175] | 286 | if(par.isVerbose()) { |
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[219] | 287 | bar.fillSpace("Found "); |
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| 288 | std::cout << num <<";" << std::flush; |
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[175] | 289 | } |
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[86] | 290 | } |
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[3] | 291 | |
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| 292 | // Second search -- in each channel |
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[175] | 293 | if(par.isVerbose()){ |
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[219] | 294 | std::cout << " 2D: "; |
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[187] | 295 | bar.init(zdim); |
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[175] | 296 | } |
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[71] | 297 | |
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[146] | 298 | num = 0; |
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| 299 | |
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[251] | 300 | long *imdim = new long[2]; |
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| 301 | imdim[0] = dim[0]; imdim[1] = dim[1]; |
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| 302 | Image *channelImage = new Image(imdim); |
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| 303 | delete [] imdim; |
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| 304 | channelImage->saveParam(par); |
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| 305 | channelImage->saveStats(stats); |
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| 306 | channelImage->setMinSize(par.getMinPix()); |
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| 307 | |
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[86] | 308 | for(int z=0; z<zdim; z++){ // loop over all channels |
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[3] | 309 | |
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[187] | 310 | if( par.isVerbose() ) bar.update(z+1); |
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[3] | 311 | |
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[146] | 312 | if(!par.isInMW(z)){ |
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| 313 | // purpose of this is to ignore the Milky Way channels |
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| 314 | // if we are flagging them |
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| 315 | |
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[53] | 316 | channelImage->extractImage(reconArray,dim,z); |
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[243] | 317 | std::vector<Object2D> objlist = channelImage->lutz_detect(); |
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| 318 | num += objlist.size(); |
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| 319 | for(int obj=0;obj<objlist.size();obj++){ |
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| 320 | Detection newObject; |
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| 321 | newObject.pixels().addChannel(z,objlist[obj]); |
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| 322 | newObject.setOffsets(par); |
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| 323 | mergeIntoList(newObject,outputList,par); |
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[3] | 324 | } |
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[251] | 325 | } |
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| 326 | |
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[3] | 327 | } |
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| 328 | |
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[251] | 329 | delete channelImage; |
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| 330 | |
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[219] | 331 | if(par.isVerbose()){ |
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| 332 | bar.fillSpace("Found "); |
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| 333 | std::cout << num << ".\n"; |
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| 334 | } |
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[86] | 335 | |
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[3] | 336 | |
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| 337 | return outputList; |
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| 338 | } |
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