1 | // ----------------------------------------------------------------------- |
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2 | // smoothCube: Smooth a Cube's array, and search for objects. |
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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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28 | #include <vector> |
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29 | #include <duchamp/duchamp.hh> |
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30 | #include <duchamp/Cubes/cubes.hh> |
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31 | #include <duchamp/Detection/detection.hh> |
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32 | #include <duchamp/PixelMap/Object2D.hh> |
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33 | #include <duchamp/Utils/feedback.hh> |
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34 | #include <duchamp/Utils/Hanning.hh> |
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35 | #include <duchamp/Utils/GaussSmooth2D.hh> |
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36 | #include <duchamp/Utils/Statistics.hh> |
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37 | #include <duchamp/Utils/utils.hh> |
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38 | |
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39 | namespace duchamp |
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40 | { |
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41 | |
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42 | void Cube::SmoothSearch() |
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43 | { |
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44 | /// @details |
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45 | /// The Cube is first smoothed, using Cube::SmoothCube(). |
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46 | /// It is then searched, using search3DArray() |
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47 | /// The resulting object list is stored in the Cube, and outputted |
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48 | /// to the log file if the user so requests. |
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49 | |
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50 | if(!this->par.getFlagSmooth()){ |
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51 | DUCHAMPWARN("SmoothSearch","FlagSmooth not set! Using basic CubicSearch."); |
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52 | this->CubicSearch(); |
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53 | } |
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54 | else{ |
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55 | |
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56 | this->SmoothCube(); |
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57 | |
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58 | if(this->par.isVerbose()) std::cout << " "; |
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59 | |
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60 | this->setCubeStats(); |
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61 | |
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62 | if(this->par.isVerbose()) std::cout << " Searching... " << std::flush; |
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63 | |
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64 | *(this->objectList) = search3DArray(this->axisDim,this->recon, |
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65 | this->par,this->Stats); |
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66 | |
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67 | if(this->par.isVerbose()) std::cout << " Updating detection map... " |
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68 | << std::flush; |
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69 | this->updateDetectMap(); |
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70 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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71 | |
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72 | if(this->par.getFlagLog()){ |
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73 | if(this->par.isVerbose()) |
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74 | std::cout << " Logging intermediate detections... " << std::flush; |
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75 | this->logDetectionList(); |
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76 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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77 | } |
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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 | |
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84 | void Cube::SmoothCube() |
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85 | { |
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86 | /// @details |
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87 | /// Switching function that chooses the appropriate function with |
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88 | /// which to smooth the cube, based on the Param::smoothType |
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89 | /// parameter. |
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90 | |
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91 | if(this->par.getSmoothType()=="spectral"){ |
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92 | |
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93 | this->SpectralSmooth(); |
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94 | |
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95 | } |
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96 | else if(this->par.getSmoothType()=="spatial"){ |
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97 | |
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98 | this->SpatialSmooth(); |
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99 | |
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100 | } |
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101 | } |
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102 | //----------------------------------------------------------- |
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103 | |
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104 | void Cube::SpectralSmooth() |
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105 | { |
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106 | /// @details |
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107 | /// A function that smoothes each spectrum in the cube using the |
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108 | /// Hanning smoothing function. The degree of smoothing is given |
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109 | /// by the parameter Param::hanningWidth. |
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110 | |
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111 | size_t xySize = this->axisDim[0]*this->axisDim[1]; |
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112 | size_t zdim = this->axisDim[2]; |
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113 | ProgressBar bar; |
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114 | |
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115 | if(!this->reconExists && this->par.getSmoothType()=="spectral"){ |
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116 | // if(!this->head.isSpecOK()) |
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117 | if(!this->head.canUseThirdAxis()){ |
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118 | DUCHAMPWARN("SpectralSmooth","There is no spectral axis, so cannot do the spectral smoothing."); |
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119 | } |
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120 | else{ |
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121 | |
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122 | Hanning hann(this->par.getHanningWidth()); |
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123 | |
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124 | float *spectrum = new float[this->axisDim[2]]; |
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125 | |
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126 | if(this->par.isVerbose()) { |
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127 | std::cout<<" Smoothing spectrally... "; |
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128 | bar.init(xySize); |
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129 | } |
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130 | |
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131 | for(size_t pix=0;pix<xySize;pix++){ |
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132 | |
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133 | if( this->par.isVerbose() ) bar.update(pix+1); |
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134 | |
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135 | for(size_t z=0;z<zdim;z++){ |
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136 | if(this->isBlank(z*xySize+pix)) spectrum[z]=0.; |
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137 | else spectrum[z] = this->array[z*xySize+pix]; |
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138 | } |
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139 | |
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140 | float *smoothed = hann.smooth(spectrum,zdim); |
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141 | |
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142 | for(size_t z=0;z<zdim;z++){ |
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143 | if(this->isBlank(z*xySize+pix)) |
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144 | this->recon[z*xySize+pix] = this->array[z*xySize+pix]; |
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145 | else |
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146 | this->recon[z*xySize+pix] = smoothed[z]; |
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147 | } |
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148 | delete [] smoothed; |
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149 | } |
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150 | this->reconExists = true; |
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151 | if(this->par.isVerbose()) bar.fillSpace("All Done.\n"); |
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152 | |
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153 | delete [] spectrum; |
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154 | |
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155 | } |
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156 | } |
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157 | } |
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158 | //----------------------------------------------------------- |
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159 | |
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160 | void Cube::SpatialSmooth() |
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161 | { |
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162 | |
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163 | if(!this->reconExists && this->par.getSmoothType()=="spatial"){ |
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164 | |
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165 | if( this->head.getNumAxes() < 2 ){ |
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166 | DUCHAMPWARN("SpatialSmooth","There are not enough axes to do the spatial smoothing."); |
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167 | } |
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168 | else{ |
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169 | |
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170 | size_t xySize = this->axisDim[0]*this->axisDim[1]; |
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171 | size_t xdim = this->axisDim[0]; |
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172 | size_t ydim = this->axisDim[1]; |
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173 | size_t zdim = this->axisDim[2]; |
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174 | |
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175 | ProgressBar bar; |
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176 | bool useBar = this->par.isVerbose() && (zdim > 1); |
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177 | |
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178 | // if kernMin is negative (not defined), make it equal to kernMaj |
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179 | if(this->par.getKernMin() < 0) |
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180 | this->par.setKernMin(this->par.getKernMaj()); |
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181 | |
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182 | std::cout << " "; |
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183 | GaussSmooth2D<float> gauss(this->par.getKernMaj(), |
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184 | this->par.getKernMin(), |
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185 | this->par.getKernPA(), |
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186 | this->par.getSpatialSmoothCutoff()); |
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187 | |
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188 | if(this->par.isVerbose()) { |
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189 | std::cout<<" Smoothing spatially... " << std::flush; |
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190 | if(useBar) bar.init(zdim); |
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191 | } |
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192 | |
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193 | // pointer used to point to start of a given channel's image |
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194 | // Can do this because the spatial axes vary the quickest. |
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195 | float *image=0; |
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196 | |
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197 | EDGES edgeTreatment=EQUALTOEDGE; |
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198 | if(this->par.getSmoothEdgeMethod()=="equal") edgeTreatment=EQUALTOEDGE; |
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199 | else if(this->par.getSmoothEdgeMethod()=="truncate") edgeTreatment=TRUNCATE; |
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200 | else if(this->par.getSmoothEdgeMethod()=="scale") edgeTreatment=SCALEBYCOVERAGE; |
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201 | |
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202 | |
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203 | for(size_t z=0;z<zdim;z++){ |
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204 | |
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205 | if(useBar) bar.update(z+1); |
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206 | |
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207 | // update pointer to point to current channel |
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208 | image = this->array + z*xySize; |
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209 | |
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210 | std::vector<bool> mask = this->par.makeBlankMask(image,xySize); |
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211 | |
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212 | float *smoothed = gauss.smooth(image,xdim,ydim,mask,edgeTreatment); |
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213 | |
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214 | for(size_t pix=0;pix<xySize;pix++) |
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215 | this->recon[z*xySize+pix] = smoothed[pix]; |
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216 | |
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217 | if(gauss.isAllocated()) delete [] smoothed; |
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218 | } |
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219 | |
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220 | this->reconExists = true; |
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221 | |
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222 | if(par.isVerbose()){ |
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223 | if(useBar) bar.fillSpace("All Done."); |
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224 | std::cout << "\n"; |
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225 | } |
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226 | |
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227 | } |
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228 | } |
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229 | } |
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230 | //----------------------------------------------------------- |
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231 | |
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232 | void Cube::SpatialSmoothNSearch() |
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233 | { |
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234 | |
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235 | size_t xySize = this->axisDim[0]*this->axisDim[1]; |
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236 | size_t xdim = this->axisDim[0]; |
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237 | size_t ydim = this->axisDim[1]; |
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238 | size_t zdim = this->axisDim[2]; |
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239 | int numFound=0; |
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240 | ProgressBar bar; |
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241 | |
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242 | GaussSmooth2D<float> gauss(this->par.getKernMaj(), |
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243 | this->par.getKernMin(), |
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244 | this->par.getKernPA()); |
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245 | |
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246 | this->Stats.scaleNoise(1./gauss.getStddevScale()); |
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247 | if(this->par.getFlagFDR()) this->setupFDR(); |
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248 | |
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249 | if(this->par.isVerbose()) { |
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250 | std::cout<<" Smoothing spatially & searching... " << std::flush; |
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251 | bar.init(zdim); |
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252 | } |
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253 | |
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254 | std::vector <Detection> outputList; |
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255 | size_t *imdim = new size_t[2]; |
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256 | imdim[0] = xdim; imdim[1] = ydim; |
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257 | Image *channelImage = new Image(imdim); |
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258 | delete [] imdim; |
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259 | channelImage->saveParam(this->par); |
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260 | channelImage->saveStats(this->Stats); |
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261 | channelImage->setMinSize(1); |
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262 | |
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263 | float *image = new float[xySize]; |
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264 | float *smoothed=0; |
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265 | float median,madfm;//,threshold; |
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266 | for(size_t z=0;z<zdim;z++){ |
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267 | |
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268 | if( this->par.isVerbose() ) bar.update(z+1); |
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269 | |
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270 | if(!this->par.isFlaggedChannel(z)){ |
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271 | |
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272 | for(size_t pix=0;pix<xySize;pix++) image[pix] = this->array[z*xySize+pix]; |
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273 | |
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274 | std::vector<bool> mask = this->par.makeBlankMask(image+z*xySize,xySize); |
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275 | |
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276 | smoothed = gauss.smooth(image,xdim,ydim,mask); |
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277 | |
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278 | findMedianStats(smoothed,xySize,mask,median,madfm); |
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279 | |
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280 | channelImage->saveArray(smoothed,xySize); |
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281 | |
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282 | std::vector<PixelInfo::Object2D> objlist = channelImage->findSources2D(); |
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283 | std::vector<PixelInfo::Object2D>::iterator obj; |
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284 | numFound += objlist.size(); |
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285 | for(obj=objlist.begin();obj<objlist.end();obj++){ |
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286 | Detection newObject; |
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287 | newObject.addChannel(z,*obj); |
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288 | newObject.setOffsets(this->par); |
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289 | mergeIntoList(newObject,outputList,this->par); |
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290 | } |
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291 | |
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292 | } |
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293 | |
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294 | } |
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295 | |
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296 | delete [] smoothed; |
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297 | delete [] image; |
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298 | delete channelImage; |
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299 | |
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300 | // this->reconExists = true; |
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301 | if(par.isVerbose()){ |
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302 | bar.fillSpace("Found "); |
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303 | std::cout << numFound << ".\n"; |
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304 | } |
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305 | |
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306 | *this->objectList = outputList; |
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307 | |
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308 | } |
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309 | |
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310 | } |
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