1 | #include <iostream> |
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2 | #include <iomanip> |
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3 | #include <math.h> |
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4 | #include <ATrous/atrous.hh> |
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5 | #include <Utils/utils.hh> |
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6 | #include <param.hh> |
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7 | |
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8 | void baselineSubtract(long numSpec, long specLength, float *originalCube, |
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9 | float *baselineValues, Param &par) |
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10 | { |
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11 | /** |
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12 | * baselineSubtract(long numSpec, long specLength, float *originalCube, |
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13 | * float *baselineValues, Param &par) |
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14 | * |
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15 | * A routine to find the baseline of spectra in a cube (spectral direction |
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16 | * assumed to be the third dimension) and subtract it off the original. |
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17 | * The original cube has numSpec spatial pixels, each containing a spectrum |
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18 | * of length specLength. |
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19 | * The original cube is read in, and returned with the baseline removed. |
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20 | * This baseline is stored in the array baselineValues. |
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21 | * The Param variable par is needed to test for blank pixels -- these are kept as blank. |
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22 | */ |
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23 | extern Filter reconFilter; |
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24 | float *spec = new float[specLength]; |
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25 | float *thisBaseline = new float[specLength]; |
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26 | int minscale = par.getMinScale(); |
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27 | par.setMinScale(reconFilter.getNumScales(specLength)); |
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28 | float atrouscut = par.getAtrousCut(); |
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29 | par.setAtrousCut(1); |
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30 | bool flagVerb = par.isVerbose(); |
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31 | par.setVerbosity(false); |
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32 | |
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33 | std::cout << "| |" << std::flush; |
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34 | for(int pix=0; pix<numSpec; pix++){ // for each spatial pixel... |
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35 | |
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36 | if(flagVerb && ((100*(pix+1)/numSpec)%5 == 0) ){ |
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37 | std::cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b|"; |
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38 | for(int i=0;i<(100*(pix+1)/numSpec)/5;i++) std::cout << "#"; |
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39 | for(int i=(100*(pix+1)/numSpec)/5;i<20;i++) std::cout << " "; |
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40 | std::cout << "|" << std::flush; |
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41 | } |
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42 | |
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43 | for(int z=0; z<specLength; z++) |
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44 | spec[z] = originalCube[z*numSpec + pix]; |
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45 | |
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46 | atrous1DReconstruct(specLength,spec,thisBaseline,par); |
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47 | |
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48 | for(int z=0; z<specLength; z++) { |
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49 | baselineValues[z*numSpec+pix] = thisBaseline[z]; |
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50 | if(!par.isBlank(originalCube[z*numSpec+pix])) |
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51 | originalCube[z*numSpec+pix] = originalCube[z*numSpec+pix] - baselineValues[z*numSpec+pix]; |
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52 | } |
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53 | |
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54 | } |
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55 | if(flagVerb) std::cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b"; |
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56 | |
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57 | par.setMinScale(minscale); |
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58 | par.setAtrousCut(atrouscut); |
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59 | par.setVerbosity(flagVerb); |
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60 | |
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61 | delete [] spec; |
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62 | delete [] thisBaseline; |
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63 | |
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64 | } |
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65 | |
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66 | void getBaseline(long size, float *input, float *baseline, Param &par) |
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67 | { |
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68 | /** |
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69 | * getBaseline(long size, float *input, float *baseline, Param &par) |
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70 | * A function to find the baseline of an input (1-D) spectrum. |
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71 | * Uses the a trous reconstruction, keeping only the highest two scales, to |
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72 | * reconstruct the baseline. |
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73 | * To avoid contamination by very strong signals, the input spectrum is trimmed |
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74 | * at 8*MADFM above the median before reconstruction. This reduces the strong |
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75 | * dips created by the presence of very strong signals. |
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76 | * The baseline array is returned -- no change is made to the input array. |
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77 | */ |
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78 | |
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79 | extern Filter reconFilter; |
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80 | int minscale = par.getMinScale(); |
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81 | par.setMinScale(reconFilter.getNumScales(size)); |
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82 | float atrouscut = par.getAtrousCut(); |
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83 | par.setAtrousCut(1); |
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84 | bool flagVerb = par.isVerbose(); |
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85 | par.setVerbosity(false); |
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86 | |
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87 | float *spec = new float[size]; |
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88 | float med,sig; |
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89 | findMedianStats(input,size,med,sig); |
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90 | float threshold = 8. * sig; |
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91 | for(int i=0;i<size;i++) { |
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92 | if(fabs(input[i]-med)>threshold){ |
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93 | if(input[i]>med) spec[i] = med + threshold; |
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94 | else spec[i] = med - threshold; |
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95 | } |
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96 | else spec[i] = input[i]; |
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97 | } |
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98 | |
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99 | // atrous1DReconstruct(size, input, baseline, par); |
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100 | atrous1DReconstruct(size, spec, baseline, par); |
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101 | |
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102 | par.setMinScale(minscale); |
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103 | par.setAtrousCut(atrouscut); |
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104 | par.setVerbosity(flagVerb); |
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105 | |
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106 | delete [] spec; |
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107 | |
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108 | } |
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109 | |
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110 | |
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111 | void getBaseline(long size, float *input, float *baseline) |
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112 | { |
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113 | /** |
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114 | * getBaseline(long size, float *input, float *baseline) |
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115 | * A function to find the baseline of an input (1-D) spectrum. |
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116 | * This version is designed for programs not using Param classes -- it keeps |
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117 | * that side of things hidden from the user. |
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118 | * Uses the a trous reconstruction, keeping only the highest two scales, to |
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119 | * reconstruct the baseline. |
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120 | * To avoid contamination by very strong signals, the input spectrum is trimmed |
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121 | * at 8*MADFM above the median before reconstruction. This reduces the strong |
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122 | * dips created by the presence of very strong signals. |
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123 | * The baseline array is returned -- no change is made to the input array. |
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124 | */ |
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125 | |
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126 | extern Filter reconFilter; |
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127 | Param par; |
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128 | par.setMinScale(reconFilter.getNumScales(size)); |
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129 | par.setAtrousCut(1); |
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130 | par.setVerbosity(false); |
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131 | |
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132 | float *spec = new float[size]; |
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133 | float med,sig; |
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134 | findMedianStats(input,size,med,sig); |
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135 | float threshold = 8. * sig; |
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136 | for(int i=0;i<size;i++) { |
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137 | if(fabs(input[i]-med)>threshold){ |
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138 | if(input[i]>med) spec[i] = med + threshold; |
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139 | else spec[i] = med - threshold; |
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140 | } |
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141 | else spec[i] = input[i]; |
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142 | } |
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143 | |
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144 | atrous1DReconstruct(size, spec, baseline, par); |
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145 | |
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146 | delete [] spec; |
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147 | |
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148 | } |
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149 | |
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