[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // ReconSearch.cc: Searching a wavelet-reconstructed cube. |
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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 <fstream> |
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| 29 | #include <iostream> |
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| 30 | #include <iomanip> |
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| 31 | #include <vector> |
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[393] | 32 | #include <duchamp/duchamp.hh> |
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| 33 | #include <duchamp/PixelMap/Object3D.hh> |
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| 34 | #include <duchamp/Cubes/cubes.hh> |
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| 35 | #include <duchamp/Detection/detection.hh> |
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| 36 | #include <duchamp/ATrous/atrous.hh> |
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| 37 | #include <duchamp/Utils/utils.hh> |
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| 38 | #include <duchamp/Utils/feedback.hh> |
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| 39 | #include <duchamp/Utils/Statistics.hh> |
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[3] | 40 | |
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[258] | 41 | using namespace PixelInfo; |
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[274] | 42 | using namespace Statistics; |
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[258] | 43 | |
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[378] | 44 | namespace duchamp |
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[103] | 45 | { |
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[285] | 46 | |
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[378] | 47 | void Cube::ReconSearch() |
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| 48 | { |
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| 49 | /** |
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| 50 | * The Cube is first reconstructed, using Cube::ReconCube(). |
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| 51 | * The statistics of the cube are calculated next. |
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| 52 | * It is then searched, using searchReconArray. |
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| 53 | * The resulting object list is stored in the Cube, and outputted |
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| 54 | * to the log file if the user so requests. |
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| 55 | */ |
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| 56 | |
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| 57 | if(!this->par.getFlagATrous()){ |
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| 58 | duchampWarning("ReconSearch", |
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| 59 | "You've requested a reconSearch, but not allocated space for the reconstructed array.\nDoing the basic CubicSearch.\n"); |
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| 60 | this->CubicSearch(); |
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| 61 | } |
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| 62 | else { |
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[188] | 63 | |
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[378] | 64 | this->ReconCube(); |
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[188] | 65 | |
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[378] | 66 | if(this->par.isVerbose()) std::cout << " "; |
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[219] | 67 | |
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[378] | 68 | this->setCubeStats(); |
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[189] | 69 | |
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[378] | 70 | if(this->par.isVerbose()) std::cout << " Searching... " << std::flush; |
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[188] | 71 | |
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[378] | 72 | *this->objectList = searchReconArraySimple(this->axisDim,this->array, |
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| 73 | this->recon, |
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| 74 | this->par,this->Stats); |
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| 75 | // this->objectList = searchReconArray(this->axisDim,this->array, |
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| 76 | // this->recon,this->par,this->Stats); |
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[188] | 77 | |
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[378] | 78 | if(this->par.isVerbose()) std::cout << " Updating detection map... " |
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| 79 | << std::flush; |
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| 80 | this->updateDetectMap(); |
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[285] | 81 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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| 82 | |
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[378] | 83 | if(this->par.getFlagLog()){ |
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| 84 | if(this->par.isVerbose()) |
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| 85 | std::cout << " Logging intermediate detections... " << std::flush; |
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| 86 | this->logDetectionList(); |
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| 87 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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| 88 | } |
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[188] | 89 | |
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[378] | 90 | } |
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[285] | 91 | } |
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[120] | 92 | |
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[378] | 93 | ///////////////////////////////////////////////////////////////////////////// |
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| 94 | void Cube::ReconCube() |
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| 95 | { |
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| 96 | /** |
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| 97 | * A front-end to the various reconstruction functions, the choice of |
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| 98 | * which is determined by the use of the reconDim parameter. |
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| 99 | * Differs from ReconSearch only in that no searching is done. |
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| 100 | */ |
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| 101 | int dimRecon = this->par.getReconDim(); |
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| 102 | // Test whether we have eg. an image, but have requested a 3-d |
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| 103 | // reconstruction. |
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| 104 | // If dimension of data array is less than dimRecon, change dimRecon |
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| 105 | // to the dimension of the array. |
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| 106 | int numGoodDim = this->head.getNumAxes(); |
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| 107 | if(numGoodDim<dimRecon){ |
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| 108 | dimRecon = numGoodDim; |
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| 109 | this->par.setReconDim(dimRecon); |
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| 110 | std::stringstream errmsg; |
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| 111 | errmsg << "You requested a " << dimRecon << "-dimensional reconstruction," |
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| 112 | << " but the FITS file is only " << numGoodDim << "-dimensional.\n" |
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| 113 | << "Changing reconDim to " << numGoodDim << ".\n"; |
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| 114 | duchampWarning("Reconstruction",errmsg.str()); |
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[103] | 115 | } |
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| 116 | |
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[378] | 117 | switch(dimRecon) |
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| 118 | { |
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| 119 | case 1: this->ReconCube1D(); break; |
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| 120 | case 2: this->ReconCube2D(); break; |
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| 121 | case 3: this->ReconCube3D(); break; |
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| 122 | default: |
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| 123 | if(dimRecon<=0){ |
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| 124 | std::stringstream errmsg; |
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| 125 | errmsg << "reconDim (" << dimRecon |
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| 126 | << ") is less than 1. Performing 1-D reconstruction.\n"; |
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| 127 | duchampWarning("Reconstruction", errmsg.str()); |
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| 128 | this->par.setReconDim(1); |
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| 129 | this->ReconCube1D(); |
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| 130 | } |
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| 131 | else if(dimRecon>3){ |
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| 132 | //this probably won't happen with new code above, but just in case... |
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| 133 | std::stringstream errmsg; |
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| 134 | errmsg << "reconDim (" << dimRecon |
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| 135 | << ") is more than 3. Performing 3-D reconstruction.\n"; |
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| 136 | duchampWarning("Reconstruction", errmsg.str()); |
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| 137 | this->par.setReconDim(3); |
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| 138 | this->ReconCube3D(); |
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| 139 | } |
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| 140 | break; |
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| 141 | } |
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[3] | 142 | } |
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[103] | 143 | |
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[378] | 144 | ///////////////////////////////////////////////////////////////////////////// |
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| 145 | void Cube::ReconCube1D() |
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| 146 | { |
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| 147 | /** |
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| 148 | * This reconstructs a cube by performing a 1D a trous reconstruction |
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| 149 | * in the spectrum of each spatial pixel. |
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| 150 | */ |
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| 151 | long xySize = this->axisDim[0] * this->axisDim[1]; |
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[3] | 152 | |
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[378] | 153 | long zdim = this->axisDim[2]; |
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[3] | 154 | |
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[378] | 155 | ProgressBar bar; |
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| 156 | if(!this->reconExists){ |
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| 157 | std::cout<<" Reconstructing... "; |
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| 158 | if(par.isVerbose()) bar.init(xySize); |
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| 159 | for(int npix=0; npix<xySize; npix++){ |
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[175] | 160 | |
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[378] | 161 | if( par.isVerbose() ) bar.update(npix+1); |
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[175] | 162 | |
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[378] | 163 | float *spec = new float[zdim]; |
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| 164 | float *newSpec = new float[zdim]; |
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| 165 | for(int z=0;z<zdim;z++) spec[z] = this->array[z*xySize + npix]; |
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[103] | 166 | bool verboseFlag = this->par.isVerbose(); |
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| 167 | this->par.setVerbosity(false); |
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[378] | 168 | atrous1DReconstruct(this->axisDim[2],spec,newSpec,this->par); |
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[103] | 169 | this->par.setVerbosity(verboseFlag); |
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[378] | 170 | for(int z=0;z<zdim;z++) this->recon[z*xySize+npix] = newSpec[z]; |
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| 171 | delete [] spec; |
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| 172 | delete [] newSpec; |
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[3] | 173 | } |
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[378] | 174 | this->reconExists = true; |
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| 175 | bar.fillSpace(" All Done."); |
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| 176 | printSpace(22); |
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| 177 | std::cout << "\n"; |
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[3] | 178 | } |
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[378] | 179 | |
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[3] | 180 | } |
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| 181 | |
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[378] | 182 | ///////////////////////////////////////////////////////////////////////////// |
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| 183 | void Cube::ReconCube2D() |
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| 184 | { |
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| 185 | /** |
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| 186 | * This reconstructs a cube by performing a 2D a trous reconstruction |
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| 187 | * in each spatial image (ie. each channel map) of the cube. |
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| 188 | */ |
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| 189 | long xySize = this->axisDim[0] * this->axisDim[1]; |
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| 190 | ProgressBar bar; |
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| 191 | bool useBar = (this->axisDim[2]>1); |
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[3] | 192 | |
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[71] | 193 | if(!this->reconExists){ |
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[378] | 194 | std::cout<<" Reconstructing... "; |
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| 195 | if(useBar&&par.isVerbose()) bar.init(this->axisDim[2]); |
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| 196 | for(int z=0;z<this->axisDim[2];z++){ |
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| 197 | |
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| 198 | if( par.isVerbose() && useBar ) bar.update((z+1)); |
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| 199 | |
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| 200 | if(!this->par.isInMW(z)){ |
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| 201 | float *im = new float[xySize]; |
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| 202 | float *newIm = new float[xySize]; |
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| 203 | for(int npix=0; npix<xySize; npix++) |
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| 204 | im[npix] = this->array[z*xySize+npix]; |
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| 205 | bool verboseFlag = this->par.isVerbose(); |
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| 206 | this->par.setVerbosity(false); |
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| 207 | atrous2DReconstruct(this->axisDim[0],this->axisDim[1], |
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| 208 | im,newIm,this->par); |
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| 209 | this->par.setVerbosity(verboseFlag); |
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| 210 | for(int npix=0; npix<xySize; npix++) |
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| 211 | this->recon[z*xySize+npix] = newIm[npix]; |
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| 212 | delete [] im; |
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| 213 | delete [] newIm; |
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| 214 | } |
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| 215 | else { |
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| 216 | for(int i=z*xySize; i<(z+1)*xySize; i++) |
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| 217 | this->recon[i] = this->array[i]; |
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| 218 | } |
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| 219 | } |
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[71] | 220 | this->reconExists = true; |
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[378] | 221 | if(useBar) bar.fillSpace(" All Done."); |
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[175] | 222 | printSpace(22); |
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[188] | 223 | std::cout << "\n"; |
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[71] | 224 | } |
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[3] | 225 | } |
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| 226 | |
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[378] | 227 | ///////////////////////////////////////////////////////////////////////////// |
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| 228 | void Cube::ReconCube3D() |
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| 229 | { |
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| 230 | /** |
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| 231 | * This performs a full 3D a trous reconstruction of the cube |
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| 232 | */ |
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| 233 | if(this->axisDim[2]==1) this->ReconCube2D(); |
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| 234 | else { |
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[3] | 235 | |
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[378] | 236 | if(!this->reconExists){ |
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| 237 | std::cout<<" Reconstructing... "<<std::flush; |
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| 238 | atrous3DReconstruct(this->axisDim[0],this->axisDim[1],this->axisDim[2], |
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| 239 | this->array,this->recon,this->par); |
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| 240 | this->reconExists = true; |
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| 241 | std::cout << " All Done."; |
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| 242 | printSpace(22); |
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| 243 | std::cout << "\n"; |
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| 244 | } |
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| 245 | |
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[175] | 246 | } |
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[378] | 247 | } |
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[3] | 248 | |
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[378] | 249 | ///////////////////////////////////////////////////////////////////////////// |
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| 250 | std::vector <Detection> searchReconArray(long *dim, float *originalArray, |
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| 251 | float *reconArray, Param &par, |
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| 252 | StatsContainer<float> &stats) |
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| 253 | { |
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| 254 | /** |
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| 255 | * This searches for objects in a cube that has been reconstructed. |
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| 256 | * |
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| 257 | * The search is conducted first in each spatial pixel (xdim*ydim 1D |
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| 258 | * searches), then in each channel image (zdim 2D searches). |
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| 259 | * The searches are done on the reconstructed array, although the detected |
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| 260 | * objects have fluxes drawn from the corresponding pixels of the original |
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| 261 | * array. |
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| 262 | * |
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| 263 | * \param dim Array of dimension sizes |
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| 264 | * \param originalArray Original, un-reconstructed image array. |
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| 265 | * \param reconArray Reconstructed image array |
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| 266 | * \param par The Param set. |
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| 267 | * \param stats The StatsContainer that defines what a detection is. |
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| 268 | * |
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| 269 | * \return A vector of Detections resulting from the search. |
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| 270 | */ |
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| 271 | std::vector <Detection> outputList; |
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| 272 | long zdim = dim[2]; |
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| 273 | long xySize = dim[0] * dim[1]; |
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| 274 | int num=0; |
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| 275 | ProgressBar bar; |
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| 276 | |
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| 277 | // First search -- in each spectrum. |
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| 278 | if(zdim > 1){ |
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| 279 | if(par.isVerbose()){ |
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| 280 | std::cout << "1D: "; |
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| 281 | bar.init(xySize); |
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[258] | 282 | } |
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[3] | 283 | |
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[378] | 284 | bool *doPixel = new bool[xySize]; |
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| 285 | // doPixel is a bool array to say whether to look in a given spectrum |
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| 286 | for(int npix=0; npix<xySize; npix++){ |
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| 287 | doPixel[npix] = false; |
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| 288 | for(int z=0;z<zdim;z++) { |
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| 289 | doPixel[npix] = doPixel[npix] || |
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| 290 | (!par.isBlank(originalArray[npix]) && !par.isInMW(z)); |
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| 291 | } |
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| 292 | // doPixel[i] is false only when there are no good pixels in spectrum |
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| 293 | // of pixel #i. |
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| 294 | } |
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[3] | 295 | |
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[378] | 296 | long *specdim = new long[2]; |
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| 297 | specdim[0] = zdim; specdim[1]=1; |
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| 298 | Image *spectrum = new Image(specdim); |
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| 299 | delete [] specdim; |
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| 300 | spectrum->saveParam(par); |
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| 301 | spectrum->saveStats(stats); |
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| 302 | spectrum->setMinSize(par.getMinChannels()); |
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| 303 | spectrum->pars().setBeamSize(2.); |
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| 304 | // beam size: for spectrum, only neighbouring channels correlated |
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[192] | 305 | |
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[378] | 306 | for(int y=0; y<dim[1]; y++){ |
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| 307 | for(int x=0; x<dim[0]; x++){ |
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[258] | 308 | |
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[378] | 309 | int npix = y*dim[0] + x; |
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| 310 | if( par.isVerbose() ) bar.update(npix+1); |
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[258] | 311 | |
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[378] | 312 | if(doPixel[npix]){ |
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| 313 | |
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| 314 | spectrum->extractSpectrum(reconArray,dim,npix); |
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| 315 | spectrum->removeMW(); // only works if flagMW is true |
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| 316 | std::vector<Scan> objlist = spectrum->spectrumDetect(); |
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| 317 | num += objlist.size(); |
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| 318 | for(int obj=0;obj<objlist.size();obj++){ |
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| 319 | Detection newObject; |
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| 320 | // Fix up coordinates of each pixel to match original array |
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| 321 | for(int z=objlist[obj].getX();z<=objlist[obj].getXmax();z++) { |
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| 322 | newObject.pixels().addPixel(x,y,z); |
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| 323 | } |
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| 324 | newObject.setOffsets(par); |
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| 325 | mergeIntoList(newObject,outputList,par); |
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[258] | 326 | } |
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[103] | 327 | } |
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[378] | 328 | |
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[3] | 329 | } |
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[378] | 330 | } |
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[258] | 331 | |
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[378] | 332 | delete spectrum; |
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| 333 | delete [] doPixel; |
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| 334 | |
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| 335 | if(par.isVerbose()) { |
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| 336 | bar.fillSpace("Found "); |
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| 337 | std::cout << num <<";" << std::flush; |
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[3] | 338 | } |
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| 339 | } |
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| 340 | |
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[378] | 341 | // Second search -- in each channel |
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| 342 | if(par.isVerbose()){ |
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| 343 | std::cout << " 2D: "; |
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| 344 | bar.init(zdim); |
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[175] | 345 | } |
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[3] | 346 | |
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[378] | 347 | num = 0; |
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[71] | 348 | |
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[378] | 349 | long *imdim = new long[2]; |
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| 350 | imdim[0] = dim[0]; imdim[1] = dim[1]; |
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| 351 | Image *channelImage = new Image(imdim); |
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| 352 | delete [] imdim; |
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| 353 | channelImage->saveParam(par); |
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| 354 | channelImage->saveStats(stats); |
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| 355 | channelImage->setMinSize(par.getMinPix()); |
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[146] | 356 | |
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[378] | 357 | for(int z=0; z<zdim; z++){ // loop over all channels |
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[258] | 358 | |
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[378] | 359 | if( par.isVerbose() ) bar.update(z+1); |
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[3] | 360 | |
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[378] | 361 | if(!par.isInMW(z)){ |
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| 362 | // purpose of this is to ignore the Milky Way channels |
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| 363 | // if we are flagging them |
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[3] | 364 | |
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[378] | 365 | channelImage->extractImage(reconArray,dim,z); |
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| 366 | std::vector<Object2D> objlist = channelImage->lutz_detect(); |
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| 367 | num += objlist.size(); |
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| 368 | for(int obj=0;obj<objlist.size();obj++){ |
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| 369 | Detection newObject; |
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| 370 | newObject.pixels().addChannel(z,objlist[obj]); |
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| 371 | newObject.setOffsets(par); |
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| 372 | mergeIntoList(newObject,outputList,par); |
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| 373 | } |
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[3] | 374 | } |
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[378] | 375 | |
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[258] | 376 | } |
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[3] | 377 | |
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[378] | 378 | delete channelImage; |
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[258] | 379 | |
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[378] | 380 | if(par.isVerbose()){ |
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| 381 | bar.fillSpace("Found "); |
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| 382 | std::cout << num << ".\n"; |
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| 383 | } |
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[86] | 384 | |
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[3] | 385 | |
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[378] | 386 | return outputList; |
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| 387 | } |
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[263] | 388 | |
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[378] | 389 | ///////////////////////////////////////////////////////////////////////////// |
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| 390 | std::vector <Detection> |
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| 391 | searchReconArraySimple(long *dim, float *originalArray, |
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| 392 | float *reconArray, Param &par, |
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| 393 | StatsContainer<float> &stats) |
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| 394 | { |
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| 395 | /** |
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| 396 | * This searches for objects in a cube that has been reconstructed. |
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| 397 | * |
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| 398 | * The search is conducted only in each channel image (zdim 2D |
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| 399 | * searches) -- no searches in 1D are done. |
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| 400 | * |
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| 401 | * The searches are done on the reconstructed array, although the detected |
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| 402 | * objects have fluxes drawn from the corresponding pixels of the original |
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| 403 | * array. |
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| 404 | * |
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| 405 | * \param dim Array of dimension sizes |
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| 406 | * \param originalArray Original, un-reconstructed image array. |
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| 407 | * \param reconArray Reconstructed image array |
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| 408 | * \param par The Param set. |
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| 409 | * \param stats The StatsContainer that defines what a detection is. |
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| 410 | * |
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| 411 | * \return A vector of Detections resulting from the search. |
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| 412 | */ |
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| 413 | std::vector <Detection> outputList; |
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| 414 | long zdim = dim[2]; |
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| 415 | int num=0; |
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| 416 | ProgressBar bar; |
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| 417 | bool useBar = (zdim>1); |
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| 418 | if(useBar&&par.isVerbose()) bar.init(zdim); |
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[263] | 419 | |
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[378] | 420 | long *imdim = new long[2]; |
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| 421 | imdim[0] = dim[0]; imdim[1] = dim[1]; |
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| 422 | Image *channelImage = new Image(imdim); |
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| 423 | delete [] imdim; |
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| 424 | channelImage->saveParam(par); |
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| 425 | channelImage->saveStats(stats); |
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| 426 | channelImage->setMinSize(1); |
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[263] | 427 | |
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[378] | 428 | for(int z=0; z<zdim; z++){ // loop over all channels |
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[263] | 429 | |
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[378] | 430 | if( par.isVerbose() && useBar ) bar.update(z+1); |
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[263] | 431 | |
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[378] | 432 | if(!par.isInMW(z)){ |
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| 433 | // purpose of this is to ignore the Milky Way channels |
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| 434 | // if we are flagging them |
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[263] | 435 | |
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[378] | 436 | channelImage->extractImage(reconArray,dim,z); |
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| 437 | std::vector<Object2D> objlist = channelImage->lutz_detect(); |
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| 438 | num += objlist.size(); |
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| 439 | for(int obj=0;obj<objlist.size();obj++){ |
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| 440 | Detection newObject; |
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| 441 | newObject.pixels().addChannel(z,objlist[obj]); |
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| 442 | newObject.setOffsets(par); |
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| 443 | mergeIntoList(newObject,outputList,par); |
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| 444 | } |
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[263] | 445 | } |
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[378] | 446 | |
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[263] | 447 | } |
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| 448 | |
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[378] | 449 | delete channelImage; |
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[263] | 450 | |
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[378] | 451 | if(par.isVerbose()){ |
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| 452 | if(useBar) bar.remove(); |
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| 453 | std::cout << "Found " << num << ".\n"; |
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| 454 | } |
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| 455 | |
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| 456 | |
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| 457 | return outputList; |
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[263] | 458 | } |
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| 459 | |
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| 460 | } |
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