[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // baselineSubtract.cc: Obtaining and subtracting spectral baselines. |
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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 <iostream> |
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| 29 | #include <iomanip> |
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[103] | 30 | #include <math.h> |
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[393] | 31 | #include <duchamp/param.hh> |
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| 32 | #include <duchamp/ATrous/filter.hh> |
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| 33 | #include <duchamp/ATrous/atrous.hh> |
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| 34 | #include <duchamp/Utils/utils.hh> |
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| 35 | #include <duchamp/Utils/feedback.hh> |
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[3] | 36 | |
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[378] | 37 | namespace duchamp |
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[3] | 38 | { |
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[232] | 39 | |
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[378] | 40 | void baselineSubtract(long numSpec, long specLength, float *originalCube, |
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| 41 | float *baselineValues, Param &par) |
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| 42 | { |
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[528] | 43 | /// A routine to find the baseline of each spectrum in a cube (the spectral |
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| 44 | /// direction is assumed to be the third dimension) and subtract it off |
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| 45 | /// the original. |
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| 46 | /// \param numSpec Number of spatial pixels in original cube. |
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| 47 | /// \param specLength Size of spectral dimension of original cube. |
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| 48 | /// \param originalCube The cube that is to have its baseline removed. |
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| 49 | /// \param baselineValues The cube of baseline values -- the same |
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| 50 | /// size as the original. |
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| 51 | /// \param par The Param set: information on BLANK values and on how |
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| 52 | /// the subtraction is done. |
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[3] | 53 | |
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[378] | 54 | float *spec = new float[specLength]; |
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| 55 | float *thisBaseline = new float[specLength]; |
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| 56 | int minscale = par.getMinScale(); |
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| 57 | par.setMinScale(par.filter().getNumScales(specLength)); |
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| 58 | float atrouscut = par.getAtrousCut(); |
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| 59 | par.setAtrousCut(1); |
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| 60 | bool flagVerb = par.isVerbose(); |
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| 61 | par.setVerbosity(false); |
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[3] | 62 | |
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[378] | 63 | ProgressBar bar; |
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| 64 | if(flagVerb) bar.init(numSpec); |
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| 65 | for(int pix=0; pix<numSpec; pix++){ // for each spatial pixel... |
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[3] | 66 | |
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[378] | 67 | if(flagVerb) bar.update(pix+1); |
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[3] | 68 | |
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[378] | 69 | for(int z=0; z<specLength; z++) |
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| 70 | spec[z] = originalCube[z*numSpec + pix]; |
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[3] | 71 | |
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[378] | 72 | atrous1DReconstruct(specLength,spec,thisBaseline,par); |
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[3] | 73 | |
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[378] | 74 | for(int z=0; z<specLength; z++) { |
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| 75 | baselineValues[z*numSpec+pix] = thisBaseline[z]; |
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| 76 | if(!par.isBlank(originalCube[z*numSpec+pix])) |
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| 77 | originalCube[z*numSpec+pix] = originalCube[z*numSpec+pix] - |
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| 78 | baselineValues[z*numSpec+pix]; |
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| 79 | } |
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[3] | 80 | |
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[378] | 81 | } |
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| 82 | if(flagVerb) bar.rewind(); |
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| 83 | |
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| 84 | par.setMinScale(minscale); |
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| 85 | par.setAtrousCut(atrouscut); |
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| 86 | par.setVerbosity(flagVerb); |
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[3] | 87 | |
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[378] | 88 | delete [] spec; |
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| 89 | delete [] thisBaseline; |
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[3] | 90 | |
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[378] | 91 | } |
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[3] | 92 | |
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[378] | 93 | void getBaseline(long size, float *input, float *baseline, Param &par) |
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| 94 | { |
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[528] | 95 | /// Uses the a trous reconstruction, keeping only the highest two scales, |
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| 96 | /// to reconstruct the baseline. |
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| 97 | /// To avoid contamination by very strong signals, the input spectrum is |
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| 98 | /// trimmed at 5*MADFM above the median before reconstruction. |
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| 99 | /// This reduces the strong dips created by the presence of very strong |
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| 100 | /// signals. |
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| 101 | /// \param size Length of the spectrum. |
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| 102 | /// \param input The input array : this is not affected. |
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| 103 | /// \param baseline The returned baseline array. This needs to be allocated |
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| 104 | /// before the function is called. |
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| 105 | /// \param par The Param set, needed for the atrous reconstruction. |
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[3] | 106 | |
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[378] | 107 | int minscale = par.getMinScale(); |
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| 108 | par.setMinScale(par.filter().getNumScales(size)); |
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| 109 | float atrouscut = par.getAtrousCut(); |
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| 110 | par.setAtrousCut(1); |
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| 111 | bool flagVerb = par.isVerbose(); |
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| 112 | par.setVerbosity(false); |
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[43] | 113 | |
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[378] | 114 | float *spec = new float[size]; |
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| 115 | float med,sig; |
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| 116 | findMedianStats(input,size,med,sig); |
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| 117 | float threshold = 5. * sig; |
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| 118 | for(int i=0;i<size;i++) { |
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| 119 | if(fabs(input[i]-med)>threshold){ |
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| 120 | if(input[i]>med) spec[i] = med + threshold; |
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| 121 | else spec[i] = med - threshold; |
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| 122 | } |
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| 123 | else spec[i] = input[i]; |
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[43] | 124 | } |
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| 125 | |
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[378] | 126 | // atrous1DReconstruct(size, input, baseline, par); |
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| 127 | atrous1DReconstruct(size, spec, baseline, par); |
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[43] | 128 | |
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[378] | 129 | par.setMinScale(minscale); |
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| 130 | par.setAtrousCut(atrouscut); |
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| 131 | par.setVerbosity(flagVerb); |
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[43] | 132 | |
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[378] | 133 | delete [] spec; |
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[43] | 134 | |
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[378] | 135 | } |
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[43] | 136 | |
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| 137 | |
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[378] | 138 | void getBaseline(long size, float *input, float *baseline) |
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| 139 | { |
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[528] | 140 | /// This version is designed for programs not using Param classes -- it |
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| 141 | /// keeps that side of things hidden from the user. |
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| 142 | /// Uses the a trous reconstruction, keeping only the highest two scales, |
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| 143 | /// to reconstruct the baseline. |
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| 144 | /// To avoid contamination by very strong signals, the input spectrum is |
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| 145 | /// trimmed at 8*MADFM above the median before reconstruction. This |
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| 146 | /// reduces the strong dips created by the presence of very strong |
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| 147 | /// signals. |
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| 148 | /// \param size Length of the spectrum. |
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| 149 | /// \param input The input array : this is not affected. |
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| 150 | /// \param baseline The returned baseline array. This needs to be allocated |
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| 151 | /// before the function is called. |
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[3] | 152 | |
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[378] | 153 | Param par; |
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| 154 | par.setMinScale(par.filter().getNumScales(size)); |
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| 155 | par.setAtrousCut(1); |
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| 156 | par.setVerbosity(false); |
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[43] | 157 | |
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[378] | 158 | float *spec = new float[size]; |
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| 159 | float med,sig; |
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| 160 | findMedianStats(input,size,med,sig); |
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| 161 | float threshold = 8. * sig; |
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| 162 | for(int i=0;i<size;i++) { |
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| 163 | if(fabs(input[i]-med)>threshold){ |
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| 164 | if(input[i]>med) spec[i] = med + threshold; |
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| 165 | else spec[i] = med - threshold; |
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| 166 | } |
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| 167 | else spec[i] = input[i]; |
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[43] | 168 | } |
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| 169 | |
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[378] | 170 | atrous1DReconstruct(size, spec, baseline, par); |
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[43] | 171 | |
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[378] | 172 | delete [] spec; |
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[43] | 173 | |
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[378] | 174 | } |
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| 175 | |
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[3] | 176 | } |
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