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 | |
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7 | using std::endl; |
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8 | using std::setw; |
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9 | |
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10 | void atrous3DReconstruct(long &xdim, long &ydim, long &zdim, float *&input,float *&output, Param &par) |
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11 | { |
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12 | extern Filter reconFilter; |
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13 | long size = xdim * ydim * zdim; |
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14 | long mindim = xdim; |
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15 | if (ydim<mindim) mindim = ydim; |
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16 | if (zdim<mindim) mindim = zdim; |
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17 | int numScales = reconFilter.getNumScales(mindim); |
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18 | /* |
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19 | if(numScales>maxNumScales3D){ |
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20 | std::cerr<<"Error in atrous3DReconstruct:: numScales ("<<numScales<<") > "<<maxNumScales3D<<"\n"; |
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21 | std::cerr<<"Don't have correction factors for this many scales...\n"; |
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22 | std::cerr<<"Exiting...\n"; |
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23 | exit(1); |
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24 | } |
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25 | */ |
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26 | double *sigmaFactors = new double[numScales+1]; |
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27 | // for(int i=0;i<=numScales;i++){ |
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28 | // if(i<=maxNumScales3D) sigmaFactors[i] = sigmaFactors3D[i]; |
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29 | // else sigmaFactors[i] = sigmaFactors[i-1] / sqrt(8.); |
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30 | // } |
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31 | for(int i=0;i<=numScales;i++){ |
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32 | if(i<=reconFilter.maxFactor(3)) sigmaFactors[i] = reconFilter.sigmaFactor(3,i); |
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33 | else sigmaFactors[i] = sigmaFactors[i-1] / sqrt(8.); |
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34 | } |
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35 | |
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36 | float mean,sigma,originalSigma,originalMean,oldsigma,newsigma; |
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37 | bool *isGood = new bool[size]; |
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38 | bool flagBlank = par.getFlagBlankPix(); |
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39 | float blankPixValue = par.getBlankPixVal(); |
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40 | for(int pos=0;pos<size;pos++) //isGood[pos] = (!flagBlank) || (input[pos]!=blankPixValue); |
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41 | isGood[pos] = !par.isBlank(input[pos]); |
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42 | |
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43 | float *array = new float[size]; |
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44 | int goodSize=0; |
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45 | for(int i=0;i<size;i++) if(isGood[i]) array[goodSize++] = input[i]; |
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46 | findMedianStats(array,goodSize,originalMean,originalSigma); |
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47 | originalSigma /= correctionFactor; // correct from MADFM to sigma estimator. |
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48 | delete [] array; |
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49 | |
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50 | float *coeffs = new float[size]; |
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51 | float *wavelet = new float[size]; |
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52 | |
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53 | for(int pos=0;pos<size;pos++) output[pos]=0.; |
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54 | |
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55 | /***********************************************************************/ |
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56 | ///// 3-DIMENSIONAL TRANSFORM |
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57 | |
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58 | // int filterHW = filterwidth/2; |
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59 | // int fsize = filterwidth*filterwidth*filterwidth; |
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60 | // double *filter = new double[fsize]; |
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61 | // for(int i=0;i<filterwidth;i++){ |
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62 | // for(int j=0;j<filterwidth;j++){ |
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63 | // for(int k=0;k<filterwidth;k++){ |
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64 | // filter[i +j*filterwidth + k*filterwidth*filterwidth] = |
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65 | // filter1D[i] * filter1D[j] * filter1D[k]; |
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66 | // } |
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67 | // } |
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68 | // } |
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69 | int filterwidth = reconFilter.width(); |
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70 | int filterHW = filterwidth/2; |
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71 | int fsize = filterwidth*filterwidth*filterwidth; |
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72 | double *filter = new double[fsize]; |
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73 | for(int i=0;i<filterwidth;i++){ |
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74 | for(int j=0;j<filterwidth;j++){ |
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75 | for(int k=0;k<filterwidth;k++){ |
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76 | filter[i +j*filterwidth + k*filterwidth*filterwidth] = |
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77 | reconFilter.coeff(i) * reconFilter.coeff(j) * reconFilter.coeff(k); |
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78 | } |
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79 | } |
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80 | } |
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81 | |
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82 | |
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83 | // locating the borders of the image -- ignoring BLANK pixels |
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84 | // HAVE NOT DONE THIS FOR Z --> ASSUMING NO TRIMMING IN SPECTRAL DIRECTION |
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85 | // int xLim1 = 0, yLim1 = 0, xLim2 = xdim-1, yLim2 = ydim-1; |
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86 | // for(int col=0;col<xdim;col++){ |
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87 | // while((yLim1<yLim2)&&(input[col+xdim*yLim1]==blankPixValue) ) yLim1++; |
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88 | // while((yLim2>yLim1)&&(input[col+xdim*yLim1]==blankPixValue) ) yLim2--; |
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89 | // } |
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90 | // for(int row=0;row<ydim;row++){ |
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91 | // while((xLim1<xLim2)&&(input[row*xdim+xLim1]==blankPixValue) ) xLim1++; |
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92 | // while((xLim2>xLim1)&&(input[row*xdim+xLim1]==blankPixValue) ) xLim2--; |
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93 | // } |
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94 | int *xLim1 = new int[ydim]; |
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95 | int *yLim1 = new int[xdim]; |
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96 | int *xLim2 = new int[ydim]; |
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97 | int *yLim2 = new int[xdim]; |
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98 | float avGapX = 0, avGapY = 0; |
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99 | for(int row=0;row<ydim;row++){ |
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100 | int ct1 = 0; |
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101 | int ct2 = xdim - 1; |
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102 | while((ct1<ct2)&&(input[row*xdim+ct1]==blankPixValue) ) ct1++; |
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103 | while((ct2>ct1)&&(input[row*xdim+ct2]==blankPixValue) ) ct2--; |
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104 | xLim1[row] = ct1; |
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105 | xLim2[row] = ct2; |
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106 | avGapX += ct2 - ct1; |
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107 | } |
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108 | avGapX /= float(ydim); |
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109 | |
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110 | for(int col=0;col<xdim;col++){ |
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111 | int ct1=0; |
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112 | int ct2=ydim-1; |
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113 | while((ct1<ct2)&&(input[col+xdim*ct1]==blankPixValue) ) ct1++; |
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114 | while((ct2>ct1)&&(input[col+xdim*ct2]==blankPixValue) ) ct2--; |
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115 | yLim1[col] = ct1; |
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116 | yLim2[col] = ct2; |
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117 | avGapY += ct2 - ct1; |
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118 | } |
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119 | avGapY /= float(ydim); |
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120 | |
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121 | mindim = int(avGapX); |
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122 | if(avGapY < avGapX) mindim = int(avGapY); |
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123 | numScales = reconFilter.getNumScales(mindim); |
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124 | |
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125 | float threshold; |
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126 | int iteration=0; |
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127 | newsigma = 1.e9; |
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128 | for(int i=0;i<size;i++) output[i] = 0; |
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129 | do{ |
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130 | if(par.isVerbose()) std::cout << "Iteration #"<<setw(2)<<++iteration<<": "; |
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131 | // first, get the value of oldsigma, set it to the previous newsigma value |
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132 | oldsigma = newsigma; |
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133 | // we are transforming the residual array (input array first time around) |
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134 | for(int i=0;i<size;i++) coeffs[i] = input[i] - output[i]; |
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135 | |
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136 | int spacing = 1; |
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137 | for(int scale = 1; scale<=numScales; scale++){ |
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138 | |
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139 | if(par.isVerbose()){ |
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140 | std::cout << "Scale "; |
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141 | std::cout << setw(2)<<scale<<" / "<<setw(2)<<numScales |
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142 | << "\b\b\b\b\b\b\b\b\b\b\b\b\b"<<std::flush; |
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143 | } |
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144 | |
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145 | for(int zpos = 0; zpos<zdim; zpos++){ |
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146 | // std::cout << setw(4)<<zpos<<"\b\b\b\b"; |
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147 | for(int ypos = 0; ypos<ydim; ypos++){ |
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148 | for(int xpos = 0; xpos<xdim; xpos++){ |
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149 | // loops over each pixel in the image |
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150 | int pos = zpos*xdim*ydim + ypos*xdim + xpos; |
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151 | |
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152 | wavelet[pos] = coeffs[pos]; |
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153 | |
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154 | if(!isGood[pos] ) wavelet[pos] = 0.; |
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155 | else{ |
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156 | |
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157 | for(int zoffset=-filterHW; zoffset<=filterHW; zoffset++){ |
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158 | int z = zpos + spacing*zoffset; |
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159 | if(z<0) z = -z; // boundary conditions are |
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160 | if(z>=zdim) z = 2*(zdim-1) - z; // reflection. |
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161 | |
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162 | for(int yoffset=-filterHW; yoffset<=filterHW; yoffset++){ |
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163 | int y = ypos + spacing*yoffset; |
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164 | //if(y<0) y = -y; // boundary conditions are |
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165 | //if(y>=ydim) y = 2*(ydim-1) - y; // reflection. |
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166 | // if(y<yLim1) y = 2*yLim1 - y; // boundary conditions are |
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167 | // if(y>yLim2) y = 2*yLim2 - y; // reflection. |
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168 | |
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169 | for(int xoffset=-filterHW; xoffset<=filterHW; xoffset++){ |
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170 | int x = xpos + spacing*xoffset; |
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171 | //if(x<0) x = -x; // boundary conditions are |
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172 | //if(x>=xdim) x = 2*(xdim-1) - x; // reflection. |
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173 | // if(x<xLim1) x = 2*xLim1 - x; // boundary conditions are |
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174 | // if(x>xLim2) x = 2*xLim2 - x; // reflection. |
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175 | |
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176 | // boundary conditions are reflection. |
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177 | // if(y<yLim1[xpos]) newy = 2*yLim1[xpos] - y; |
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178 | // else if(y>yLim2[xpos]) newy = 2*yLim2[xpos] - y; |
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179 | // else newy = y; |
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180 | |
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181 | if(yLim1[xpos]!=yLim2[xpos]){ |
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182 | // if these are equal we will get into an infinite loop here |
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183 | while((y<yLim1[xpos])||(y>yLim2[xpos])){ |
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184 | if(y<yLim1[xpos]) y = 2*yLim1[xpos] - y; |
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185 | else if(y>yLim2[xpos]) y = 2*yLim2[xpos] - y; |
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186 | } |
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187 | } |
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188 | |
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189 | // if(x<xLim1[ypos]) newx = 2*xLim1[ypos] - x; |
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190 | // else if(x>xLim2[ypos]) newx = 2*xLim2[ypos] - x; |
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191 | // else newx=x; |
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192 | |
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193 | if(xLim1[ypos]!=xLim2[ypos]){ |
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194 | // if these are equal we will get into an infinite loop here |
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195 | while((x<xLim1[ypos])||(x>xLim2[ypos])){ |
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196 | if(x<xLim1[ypos]) x = 2*xLim1[ypos] - x; |
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197 | else if(x>xLim2[ypos]) x = 2*xLim2[ypos] - x; |
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198 | } |
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199 | } |
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200 | |
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201 | // x = newx; |
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202 | // y = newy; |
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203 | |
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204 | int filterpos = (zoffset+filterHW)*filterwidth*filterwidth + |
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205 | (yoffset+filterHW)*filterwidth + (xoffset+filterHW); |
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206 | int oldpos = z*xdim*ydim + y*xdim + x; |
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207 | if(oldpos>=size) |
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208 | std::cerr<<"oldpos ("<<oldpos<<") exceeds array size("<<size<<")!\n" |
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209 | <<"x="<<x<<", y="<<y<<", z="<<z<<endl |
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210 | <<"xpos="<<xpos<<", ypos="<<ypos<<", zpos="<<zpos<<endl |
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211 | <<"cf. xdim="<<xdim<<", ydim="<<ydim<<", zdim="<<zdim<<endl; |
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212 | |
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213 | if(isGood[oldpos]) |
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214 | wavelet[pos] -= filter[filterpos]*coeffs[oldpos]; |
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215 | |
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216 | } //-> end of xoffset loop |
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217 | } //-> end of yoffset loop |
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218 | } //-> end of zoffset loop |
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219 | } //-> end of else{ ( from if(!isGood[pos]) ) |
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220 | |
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221 | } //-> end of xpos loop |
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222 | } //-> end of ypos loop |
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223 | } //-> end of zpos loop |
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224 | |
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225 | // Need to do this after we've done *all* the convolving |
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226 | for(int pos=0;pos<size;pos++) coeffs[pos] = coeffs[pos] - wavelet[pos]; |
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227 | |
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228 | // Have found wavelet coeffs for this scale -- now threshold |
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229 | if(scale>=par.getMinScale()){ |
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230 | array = new float[size]; |
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231 | goodSize=0; |
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232 | for(int pos=0;pos<size;pos++) if(isGood[pos]) array[goodSize++] = wavelet[pos]; |
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233 | findMedianStats(array,goodSize,mean,sigma); |
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234 | delete [] array; |
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235 | |
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236 | threshold = mean + par.getAtrousCut() * originalSigma * sigmaFactors[scale]; |
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237 | for(int pos=0;pos<size;pos++){ |
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238 | if(!isGood[pos]) output[pos] = blankPixValue; // preserve the Blank pixel values in the output. |
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239 | else if( fabs(wavelet[pos]) > threshold ) output[pos] += wavelet[pos]; |
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240 | } |
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241 | } |
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242 | |
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243 | spacing *= 2; |
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244 | |
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245 | } //-> end of scale loop |
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246 | |
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247 | for(int pos=0;pos<size;pos++) if(isGood[pos]) output[pos] += coeffs[pos]; |
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248 | |
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249 | array = new float[size]; |
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250 | goodSize=0; |
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251 | for(int i=0;i<size;i++) if(isGood[i]) array[goodSize++] = input[i] - output[i]; |
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252 | findNormalStats(array,goodSize,mean,newsigma); |
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253 | delete [] array; |
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254 | |
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255 | if(par.isVerbose()) std::cout << "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b"; |
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256 | |
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257 | } while( (iteration==1) || |
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258 | (fabsf(oldsigma-newsigma)/newsigma > reconTolerance) ); |
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259 | |
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260 | if(par.isVerbose()) std::cout << "Completed "<<iteration<<" iterations. "; |
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261 | |
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262 | delete [] coeffs; |
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263 | delete [] wavelet; |
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264 | delete [] isGood; |
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265 | delete [] filter; |
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266 | delete [] sigmaFactors; |
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267 | } |
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