[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // baseline.cc: Removing and replacing the spectral baseline of a 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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[74] | 28 | #include <iostream> |
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| 29 | #include <iomanip> |
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[393] | 30 | #include <duchamp/param.hh> |
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| 31 | #include <duchamp/ATrous/atrous.hh> |
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| 32 | #include <duchamp/Cubes/cubes.hh> |
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| 33 | #include <duchamp/Utils/feedback.hh> |
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[74] | 34 | |
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[378] | 35 | namespace duchamp |
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[74] | 36 | { |
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| 37 | |
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[378] | 38 | void Cube::removeBaseline() |
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| 39 | { |
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[528] | 40 | /// @details |
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[1259] | 41 | /// A front-end to the findAtrousBaseline routine, specialised for the |
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| 42 | /// Cube data structure. Calls findAtrousBaseline on each spectrum individually. |
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[528] | 43 | /// Upon exit, the original array minus its spectral baseline is stored |
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| 44 | /// in this->array and the baseline is in this->baseline. |
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| 45 | /// If the reconstructed array exists, the baseline is subtracted from |
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| 46 | /// it as well. |
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[74] | 47 | |
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[378] | 48 | float *spec = new float[this->axisDim[2]]; |
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| 49 | float *thisBaseline = new float[this->axisDim[2]]; |
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[995] | 50 | size_t numSpec = this->axisDim[0]*this->axisDim[1]; |
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[74] | 51 | |
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[378] | 52 | ProgressBar bar; |
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| 53 | if(this->par.isVerbose()) bar.init(numSpec); |
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[995] | 54 | for(size_t pix=0; pix<numSpec; pix++){ // for each spatial pixel... |
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[74] | 55 | |
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[378] | 56 | if(this->par.isVerbose() ) bar.update(pix+1); |
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[74] | 57 | |
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[894] | 58 | for(size_t z=0; z<this->axisDim[2]; z++) |
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[378] | 59 | spec[z] = this->array[z*numSpec + pix]; |
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[74] | 60 | |
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[1259] | 61 | if(this->par.getBaselineType()=="atrous") |
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| 62 | findAtrousBaseline(this->axisDim[2], spec, thisBaseline, this->par); |
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| 63 | else |
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| 64 | findMedianBaseline(this->axisDim[2], spec, this->par.getBaselineBoxWidth(), thisBaseline); |
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[74] | 65 | |
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[894] | 66 | for(size_t z=0; z<this->axisDim[2]; z++) { |
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[378] | 67 | this->baseline[z*numSpec+pix] = thisBaseline[z]; |
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| 68 | if(!par.isBlank(this->array[z*numSpec+pix])){ |
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| 69 | this->array[z*numSpec+pix] -= thisBaseline[z]; |
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| 70 | if(this->reconExists) this->recon[z*numSpec+pix] -= thisBaseline[z]; |
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| 71 | } |
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| 72 | } |
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[86] | 73 | |
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[378] | 74 | } |
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| 75 | |
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| 76 | delete [] spec; |
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| 77 | delete [] thisBaseline; |
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[74] | 78 | |
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[378] | 79 | if(this->par.isVerbose()) bar.remove(); |
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| 80 | } |
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[74] | 81 | |
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[86] | 82 | |
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| 83 | |
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[1361] | 84 | void Cube::replaceBaseline(bool fixObjects) |
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[378] | 85 | { |
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[528] | 86 | /// @details |
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| 87 | /// A routine to replace the baseline flux on the reconstructed array |
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| 88 | /// (if it exists) and the fluxes of each of the detected objects (if any). |
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[74] | 89 | |
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[378] | 90 | if(this->par.getFlagBaseline()){ |
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[74] | 91 | |
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[894] | 92 | for(size_t i=0;i<this->numPixels;i++){ |
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[74] | 93 | if(!(this->par.isBlank(this->array[i]))) |
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[378] | 94 | this->array[i] += this->baseline[i]; |
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[74] | 95 | } |
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[378] | 96 | |
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| 97 | if(this->reconExists){ |
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| 98 | // if we made a reconstruction, we need to add the baseline back in |
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| 99 | // for plotting purposes |
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[894] | 100 | for(size_t i=0;i<this->numPixels;i++){ |
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[378] | 101 | if(!(this->par.isBlank(this->array[i]))) |
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| 102 | this->recon[i] += this->baseline[i]; |
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| 103 | } |
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| 104 | } |
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[74] | 105 | |
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[1361] | 106 | if (fixObjects) { |
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| 107 | std::vector<Detection>::iterator obj; |
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| 108 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
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| 109 | // for each detection, correct the flux calculations. |
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| 110 | obj->calcFluxes(this->array, this->axisDim); |
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| 111 | } |
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[378] | 112 | } |
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| 113 | |
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[74] | 114 | } |
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[378] | 115 | |
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[74] | 116 | } |
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| 117 | |
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| 118 | } |
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