1 | // ----------------------------------------------------------------------- |
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2 | // cubes.cc: Member functions for the DataArray, Cube and Image classes. |
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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 <unistd.h> |
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29 | #include <iostream> |
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30 | #include <iomanip> |
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31 | #include <vector> |
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32 | #include <algorithm> |
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33 | #include <string> |
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34 | #include <math.h> |
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35 | |
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36 | #include <wcslib/wcs.h> |
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37 | |
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38 | #include <duchamp/pgheader.hh> |
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39 | |
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40 | #include <duchamp/duchamp.hh> |
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41 | #include <duchamp/param.hh> |
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42 | #include <duchamp/fitsHeader.hh> |
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43 | #include <duchamp/Cubes/cubes.hh> |
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44 | #include <duchamp/PixelMap/Voxel.hh> |
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45 | #include <duchamp/PixelMap/Object3D.hh> |
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46 | #include <duchamp/Detection/detection.hh> |
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47 | #include <duchamp/Detection/columns.hh> |
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48 | #include <duchamp/Detection/finders.hh> |
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49 | #include <duchamp/Utils/utils.hh> |
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50 | #include <duchamp/Utils/feedback.hh> |
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51 | #include <duchamp/Utils/mycpgplot.hh> |
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52 | #include <duchamp/Utils/Statistics.hh> |
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53 | #include <duchamp/FitsIO/DuchampBeam.hh> |
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54 | |
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55 | using namespace mycpgplot; |
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56 | using namespace Statistics; |
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57 | using namespace PixelInfo; |
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58 | |
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59 | #ifdef TEST_DEBUG |
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60 | const bool TESTING=true; |
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61 | #else |
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62 | const bool TESTING=false; |
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63 | #endif |
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64 | |
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65 | namespace duchamp |
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66 | { |
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67 | |
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68 | using namespace Column; |
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69 | |
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70 | /****************************************************************/ |
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71 | /////////////////////////////////////////////////// |
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72 | //// Functions for DataArray class: |
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73 | /////////////////////////////////////////////////// |
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74 | |
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75 | DataArray::DataArray(){ |
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76 | /// Fundamental constructor for DataArray. |
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77 | /// Number of dimensions and pixels are set to 0. Nothing else allocated. |
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78 | |
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79 | this->numDim=0; |
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80 | this->numPixels=0; |
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81 | this->objectList = new std::vector<Detection>; |
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82 | this->axisDimAllocated = false; |
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83 | this->arrayAllocated = false; |
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84 | } |
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85 | //-------------------------------------------------------------------- |
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86 | |
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87 | DataArray::DataArray(const DataArray &d){ |
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88 | operator=(d); |
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89 | } |
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90 | |
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91 | DataArray& DataArray::operator=(const DataArray &d){ |
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92 | if(this==&d) return *this; |
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93 | this->numDim = d.numDim; |
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94 | if(this->axisDimAllocated) delete [] this->axisDim; |
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95 | this->axisDimAllocated = d.axisDimAllocated; |
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96 | if(this->axisDimAllocated){ |
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97 | this->axisDim = new size_t[this->numDim]; |
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98 | for(size_t i=0;i<size_t(this->numDim);i++) this->axisDim[i] = d.axisDim[i]; |
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99 | } |
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100 | this->numPixels = d.numPixels; |
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101 | if(this->arrayAllocated) delete [] this->array; |
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102 | this->arrayAllocated = d.arrayAllocated; |
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103 | if(this->arrayAllocated) { |
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104 | this->array = new float[this->numPixels]; |
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105 | for(size_t i=0;i<size_t(this->numPixels);i++) this->array[i] = d.array[i]; |
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106 | } |
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107 | this->objectList = d.objectList; |
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108 | this->par = d.par; |
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109 | this->Stats = d.Stats; |
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110 | return *this; |
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111 | } |
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112 | |
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113 | |
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114 | DataArray::DataArray(short int nDim){ |
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115 | /// @details |
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116 | /// N-dimensional constructor for DataArray. |
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117 | /// Number of dimensions defined, and dimension array allocated. |
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118 | /// Number of pixels are set to 0. |
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119 | /// \param nDim Number of dimensions. |
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120 | |
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121 | this->axisDimAllocated = false; |
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122 | this->arrayAllocated = false; |
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123 | if(nDim>0){ |
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124 | this->axisDim = new size_t[nDim]; |
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125 | this->axisDimAllocated = true; |
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126 | } |
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127 | this->numDim=nDim; |
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128 | this->numPixels=0; |
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129 | this->objectList = new std::vector<Detection>; |
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130 | } |
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131 | //-------------------------------------------------------------------- |
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132 | |
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133 | DataArray::DataArray(short int nDim, size_t size){ |
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134 | /// @details |
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135 | /// N-dimensional constructor for DataArray. |
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136 | /// Number of dimensions and number of pixels defined. |
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137 | /// Arrays allocated based on these values. |
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138 | /// \param nDim Number of dimensions. |
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139 | /// \param size Number of pixels. |
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140 | /// |
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141 | /// Note that we can assign values to the dimension array. |
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142 | |
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143 | this->axisDimAllocated = false; |
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144 | this->arrayAllocated = false; |
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145 | if(size<0){ |
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146 | DUCHAMPERROR("DataArray(nDim,size)", "Negative size -- could not define DataArray"); |
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147 | } |
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148 | else if(nDim<0){ |
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149 | DUCHAMPERROR("DataArray(nDim,size)", "Negative number of dimensions: could not define DataArray"); |
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150 | } |
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151 | else { |
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152 | if(size>0){ |
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153 | this->array = new float[size]; |
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154 | this->arrayAllocated = true; |
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155 | } |
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156 | this->numPixels = size; |
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157 | if(nDim>0){ |
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158 | this->axisDim = new size_t[nDim]; |
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159 | this->axisDimAllocated = true; |
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160 | } |
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161 | this->numDim = nDim; |
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162 | } |
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163 | this->objectList = new std::vector<Detection>; |
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164 | } |
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165 | //-------------------------------------------------------------------- |
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166 | |
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167 | DataArray::DataArray(short int nDim, size_t *dimensions) |
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168 | { |
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169 | /// @details |
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170 | /// Most robust constructor for DataArray. |
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171 | /// Number and sizes of dimensions are defined, and hence the number of |
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172 | /// pixels. Arrays allocated based on these values. |
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173 | /// \param nDim Number of dimensions. |
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174 | /// \param dimensions Array giving sizes of dimensions. |
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175 | |
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176 | this->axisDimAllocated = false; |
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177 | this->arrayAllocated = false; |
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178 | if(nDim<0){ |
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179 | DUCHAMPERROR("DataArray(nDim,dimArray)", "Negative number of dimensions: could not define DataArray"); |
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180 | } |
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181 | else { |
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182 | int size = dimensions[0]; |
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183 | for(int i=1;i<nDim;i++) size *= dimensions[i]; |
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184 | if(size<0){ |
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185 | DUCHAMPERROR("DataArray(nDim,dimArray)", "Negative size: could not define DataArray"); |
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186 | } |
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187 | else{ |
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188 | this->numPixels = size; |
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189 | if(size>0){ |
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190 | this->array = new float[size]; |
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191 | this->arrayAllocated = true; |
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192 | } |
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193 | this->numDim=nDim; |
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194 | if(nDim>0){ |
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195 | this->axisDim = new size_t[nDim]; |
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196 | this->axisDimAllocated = true; |
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197 | } |
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198 | for(int i=0;i<nDim;i++) this->axisDim[i] = dimensions[i]; |
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199 | } |
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200 | } |
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201 | } |
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202 | //-------------------------------------------------------------------- |
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203 | |
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204 | DataArray::~DataArray() |
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205 | { |
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206 | /// @details |
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207 | /// Destructor -- arrays deleted if they have been allocated, and the |
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208 | /// object list is deleted. |
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209 | |
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210 | if(this->numPixels>0 && this->arrayAllocated){ |
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211 | delete [] this->array; |
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212 | this->arrayAllocated = false; |
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213 | } |
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214 | if(this->numDim>0 && this->axisDimAllocated){ |
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215 | delete [] this->axisDim; |
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216 | this->axisDimAllocated = false; |
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217 | } |
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218 | delete this->objectList; |
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219 | } |
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220 | //-------------------------------------------------------------------- |
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221 | //-------------------------------------------------------------------- |
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222 | |
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223 | void DataArray::getDim(size_t &x, size_t &y, size_t &z) |
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224 | { |
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225 | /// @details |
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226 | /// The sizes of the first three dimensions (if they exist) are returned. |
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227 | /// \param x The first dimension. Defaults to 0 if numDim \f$\le\f$ 0. |
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228 | /// \param y The second dimension. Defaults to 1 if numDim \f$\le\f$ 1. |
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229 | /// \param z The third dimension. Defaults to 1 if numDim \f$\le\f$ 2. |
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230 | |
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231 | if(this->numDim>0) x=this->axisDim[0]; |
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232 | else x=0; |
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233 | if(this->numDim>1) y=this->axisDim[1]; |
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234 | else y=1; |
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235 | if(this->numDim>2) z=this->axisDim[2]; |
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236 | else z=1; |
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237 | } |
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238 | //-------------------------------------------------------------------- |
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239 | |
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240 | void DataArray::getDimArray(size_t *output) |
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241 | { |
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242 | /// @details |
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243 | /// The axisDim array is written to output. This needs to be defined |
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244 | /// beforehand: no checking is done on the memory. |
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245 | /// \param output The array that is written to. |
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246 | |
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247 | for(int i=0;i<this->numDim;i++) output[i] = this->axisDim[i]; |
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248 | } |
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249 | //-------------------------------------------------------------------- |
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250 | |
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251 | void DataArray::getArray(float *output) |
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252 | { |
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253 | /// @details |
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254 | /// The pixel value array is written to output. This needs to be defined |
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255 | /// beforehand: no checking is done on the memory. |
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256 | /// \param output The array that is written to. |
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257 | |
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258 | for(size_t i=0;i<this->numPixels;i++) output[i] = this->array[i]; |
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259 | } |
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260 | //-------------------------------------------------------------------- |
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261 | |
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262 | void DataArray::saveArray(float *input, size_t size) |
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263 | { |
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264 | /// @details |
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265 | /// Saves the array in input to the pixel array DataArray::array. |
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266 | /// The size of the array given must be the same as the current number of |
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267 | /// pixels, else an error message is returned and nothing is done. |
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268 | /// \param input The array of values to be saved. |
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269 | /// \param size The size of input. |
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270 | |
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271 | if(size != this->numPixels){ |
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272 | DUCHAMPERROR("DataArray::saveArray", "Input array different size to existing array. Cannot save."); |
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273 | } |
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274 | else { |
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275 | if(this->numPixels>0 && this->arrayAllocated) delete [] this->array; |
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276 | this->numPixels = size; |
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277 | this->array = new float[size]; |
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278 | this->arrayAllocated = true; |
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279 | for(size_t i=0;i<size;i++) this->array[i] = input[i]; |
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280 | } |
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281 | } |
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282 | //-------------------------------------------------------------------- |
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283 | |
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284 | void DataArray::addObject(Detection object) |
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285 | { |
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286 | /// \param object The object to be added to the object list. |
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287 | |
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288 | // objectList is a vector, so just use push_back() |
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289 | this->objectList->push_back(object); |
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290 | } |
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291 | //-------------------------------------------------------------------- |
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292 | |
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293 | void DataArray::addObjectList(std::vector <Detection> newlist) |
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294 | { |
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295 | /// \param newlist The list of objects to be added to the object list. |
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296 | |
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297 | std::vector<Detection>::iterator obj; |
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298 | for(obj=newlist.begin();obj<newlist.end();obj++) this->objectList->push_back(*obj); |
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299 | } |
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300 | //-------------------------------------------------------------------- |
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301 | |
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302 | bool DataArray::isDetection(float value) |
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303 | { |
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304 | /// @details |
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305 | /// Is a given value a detection, based on the statistics in the |
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306 | /// DataArray's StatsContainer? |
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307 | /// \param value The pixel value to test. |
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308 | |
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309 | if(par.isBlank(value)) return false; |
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310 | else return Stats.isDetection(value); |
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311 | } |
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312 | //-------------------------------------------------------------------- |
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313 | |
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314 | bool DataArray::isDetection(size_t voxel) |
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315 | { |
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316 | /// @details |
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317 | /// Is a given pixel a detection, based on the statistics in the |
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318 | /// DataArray's StatsContainer? |
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319 | /// If the pixel lies outside the valid range for the data array, return false. |
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320 | /// \param voxel Location of the DataArray's pixel to be tested. |
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321 | |
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322 | if((voxel<0)||(voxel>this->numPixels)) return false; |
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323 | else if(par.isBlank(this->array[voxel])) return false; |
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324 | else return Stats.isDetection(this->array[voxel]); |
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325 | } |
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326 | //-------------------------------------------------------------------- |
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327 | |
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328 | std::ostream& operator<< ( std::ostream& theStream, DataArray &array) |
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329 | { |
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330 | /// @details |
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331 | /// A way to print out the pixel coordinates & flux values of the |
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332 | /// list of detected objects belonging to the DataArray. |
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333 | /// These are formatted nicely according to the << operator for Detection, |
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334 | /// with a line indicating the number of detections at the start. |
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335 | /// \param theStream The ostream object to which the output should be sent. |
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336 | /// \param array The DataArray containing the list of objects. |
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337 | |
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338 | for(int i=0;i<array.numDim;i++){ |
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339 | if(i>0) theStream<<"x"; |
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340 | theStream<<array.axisDim[i]; |
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341 | } |
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342 | theStream<<std::endl; |
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343 | |
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344 | theStream<<"Threshold\tmiddle\tspread\trobust\n" << array.stats().getThreshold() << "\t"; |
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345 | if(array.pars().getFlagUserThreshold()) |
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346 | theStream << "0.0000\t" << array.stats().getThreshold() << "\t"; |
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347 | else |
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348 | theStream << array.stats().getMiddle() << " " << array.stats().getSpread() << "\t"; |
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349 | theStream << array.stats().getRobust()<<"\n"; |
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350 | |
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351 | theStream<<array.objectList->size()<<" detections:\n--------------\n"; |
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352 | std::vector<Detection>::iterator obj; |
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353 | for(obj=array.objectList->begin();obj<array.objectList->end();obj++){ |
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354 | theStream << "Detection #" << obj->getID()<<std::endl; |
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355 | Detection *newobj = new Detection; |
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356 | *newobj = *obj; |
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357 | newobj->addOffsets(); |
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358 | theStream<<*newobj; |
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359 | delete newobj; |
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360 | } |
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361 | theStream<<"--------------\n"; |
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362 | return theStream; |
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363 | } |
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364 | |
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365 | /****************************************************************/ |
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366 | ///////////////////////////////////////////////////////////// |
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367 | //// Functions for Cube class |
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368 | ///////////////////////////////////////////////////////////// |
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369 | |
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370 | Cube::Cube() |
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371 | { |
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372 | /// @details |
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373 | /// Basic Constructor for Cube class. |
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374 | /// numDim set to 3, but numPixels to 0 and all bool flags to false. |
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375 | /// No allocation done. |
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376 | |
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377 | numPixels=0; numDim=3; |
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378 | reconExists = false; reconAllocated = false; baselineAllocated = false; |
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379 | } |
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380 | //-------------------------------------------------------------------- |
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381 | |
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382 | Cube::Cube(size_t size) |
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383 | { |
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384 | /// @details |
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385 | /// Alternative Cube constructor, where size is given but not individual |
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386 | /// dimensions. Arrays are allocated as appropriate (according to the |
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387 | /// relevant flags in Param set), but the Cube::axisDim array is not. |
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388 | |
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389 | this->reconAllocated = false; |
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390 | this->baselineAllocated = false; |
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391 | this->axisDimAllocated = false; |
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392 | this->arrayAllocated = false; |
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393 | this->numPixels = this->numDim = 0; |
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394 | if(size<0){ |
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395 | DUCHAMPERROR("Cube(size)","Negative size -- could not define Cube"); |
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396 | } |
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397 | else{ |
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398 | if(size>0){ |
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399 | this->array = new float[size]; |
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400 | this->arrayAllocated = true; |
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401 | if(this->par.getFlagATrous()||this->par.getFlagSmooth()){ |
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402 | this->recon = new float[size]; |
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403 | this->reconAllocated = true; |
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404 | } |
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405 | if(this->par.getFlagBaseline()){ |
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406 | this->baseline = new float[size]; |
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407 | this->baselineAllocated = true; |
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408 | } |
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409 | } |
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410 | this->numPixels = size; |
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411 | this->axisDim = new size_t[3]; |
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412 | this->axisDimAllocated = true; |
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413 | this->numDim = 3; |
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414 | this->reconExists = false; |
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415 | } |
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416 | } |
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417 | //-------------------------------------------------------------------- |
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418 | |
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419 | Cube::Cube(size_t *dimensions) |
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420 | { |
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421 | /// Alternative Cube constructor, where sizes of dimensions are given. |
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422 | /// Arrays are allocated as appropriate (according to the |
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423 | /// relevant flags in Param set), as is the Cube::axisDim array. |
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424 | |
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425 | int size = dimensions[0] * dimensions[1] * dimensions[2]; |
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426 | int imsize = dimensions[0] * dimensions[1]; |
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427 | this->reconAllocated = false; |
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428 | this->baselineAllocated = false; |
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429 | this->axisDimAllocated = false; |
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430 | this->arrayAllocated = false; |
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431 | this->numPixels = this->numDim = 0; |
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432 | if((size<0) || (imsize<0) ){ |
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433 | DUCHAMPERROR("Cube(dimArray)","Negative size -- could not define Cube"); |
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434 | } |
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435 | else{ |
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436 | this->numPixels = size; |
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437 | if(size>0){ |
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438 | this->array = new float[size]; |
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439 | this->arrayAllocated = true; |
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440 | this->detectMap = new short[imsize]; |
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441 | if(this->par.getFlagATrous()||this->par.getFlagSmooth()){ |
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442 | this->recon = new float[size]; |
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443 | this->reconAllocated = true; |
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444 | } |
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445 | if(this->par.getFlagBaseline()){ |
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446 | this->baseline = new float[size]; |
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447 | this->baselineAllocated = true; |
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448 | } |
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449 | } |
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450 | this->numDim = 3; |
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451 | this->axisDim = new size_t[3]; |
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452 | this->axisDimAllocated = true; |
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453 | for(int i=0;i<3 ;i++) this->axisDim[i] = dimensions[i]; |
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454 | for(int i=0;i<imsize;i++) this->detectMap[i] = 0; |
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455 | this->reconExists = false; |
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456 | } |
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457 | } |
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458 | //-------------------------------------------------------------------- |
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459 | |
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460 | Cube::~Cube() |
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461 | { |
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462 | /// @details |
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463 | /// The destructor deletes the memory allocated for Cube::detectMap, and, |
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464 | /// if these have been allocated, Cube::recon and Cube::baseline. |
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465 | |
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466 | if(this->numPixels>0 && this->arrayAllocated) delete [] this->detectMap; |
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467 | if(this->reconAllocated) delete [] this->recon; |
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468 | if(this->baselineAllocated) delete [] this->baseline; |
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469 | } |
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470 | //-------------------------------------------------------------------- |
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471 | |
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472 | Cube::Cube(const Cube &c): |
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473 | DataArray(c) |
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474 | { |
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475 | this->operator=(c); |
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476 | } |
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477 | //-------------------------------------------------------------------- |
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478 | |
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479 | Cube& Cube::operator=(const Cube &c) |
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480 | { |
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481 | if(this==&c) return *this; |
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482 | if(this->arrayAllocated) delete [] this->detectMap; |
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483 | ((DataArray &) *this) = c; |
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484 | this->reconExists = c.reconExists; |
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485 | if(this->reconAllocated) delete [] this->recon; |
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486 | this->reconAllocated = c.reconAllocated; |
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487 | if(this->reconAllocated) { |
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488 | this->recon = new float[this->numPixels]; |
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489 | for(size_t i=0;i<size_t(this->numPixels);i++) this->recon[i] = c.recon[i]; |
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490 | } |
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491 | if(this->arrayAllocated){ |
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492 | this->detectMap = new short[this->axisDim[0]*this->axisDim[1]]; |
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493 | for(size_t i=0;i<size_t(this->axisDim[0]*this->axisDim[1]);i++) this->detectMap[i] = c.detectMap[i]; |
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494 | } |
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495 | if(this->baselineAllocated) delete [] this->baseline; |
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496 | this->baselineAllocated = c.baselineAllocated; |
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497 | if(this->baselineAllocated){ |
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498 | this->baseline = new float[this->numPixels]; |
---|
499 | for(size_t i=0;i<size_t(this->numPixels);i++) this->baseline[i] = c.baseline[i]; |
---|
500 | } |
---|
501 | this->head = c.head; |
---|
502 | this->fullCols = c.fullCols; |
---|
503 | this->logCols = c.logCols; |
---|
504 | return *this; |
---|
505 | } |
---|
506 | //-------------------------------------------------------------------- |
---|
507 | |
---|
508 | Cube* Cube::slice(Section subsection) |
---|
509 | { |
---|
510 | Cube *output = new Cube; |
---|
511 | Section thisSection; |
---|
512 | std::string nullsec=nullSection(this->numDim); |
---|
513 | if(this->par.section().isParsed()) thisSection=this->par.section(); |
---|
514 | else{ |
---|
515 | thisSection = Section(nullsec); |
---|
516 | thisSection.parse(this->axisDim, this->numDim); |
---|
517 | } |
---|
518 | |
---|
519 | subsection.parse(this->axisDim, this->numDim); |
---|
520 | if(subsection.isValid()){ |
---|
521 | output->par = this->par; |
---|
522 | output->par.section() = thisSection * subsection; |
---|
523 | output->par.setXOffset(output->par.getXOffset()+subsection.getStart(0)); |
---|
524 | output->par.setYOffset(output->par.getYOffset()+subsection.getStart(1)); |
---|
525 | output->par.setZOffset(output->par.getZOffset()+subsection.getStart(2)); |
---|
526 | output->head = this->head; |
---|
527 | // correct the reference pixel in the WCS |
---|
528 | output->head.WCS().crpix[output->head.WCS().lng] -= subsection.getStart(output->head.WCS().lng); |
---|
529 | output->head.WCS().crpix[output->head.WCS().lat] -= subsection.getStart(output->head.WCS().lat); |
---|
530 | if(output->head.WCS().spec>0) |
---|
531 | output->head.WCS().crpix[output->head.WCS().spec] -= subsection.getStart(output->head.WCS().spec); |
---|
532 | output->Stats = this->Stats; |
---|
533 | output->fullCols = this->fullCols; |
---|
534 | output->logCols = this->logCols; |
---|
535 | size_t *dims = new size_t[3]; |
---|
536 | for(size_t i=0;i<3;i++){ |
---|
537 | dims[i] = subsection.getDimList()[i]; |
---|
538 | std::cout << "Dim " << i+1 << " = " << dims[i] << "\n"; |
---|
539 | } |
---|
540 | |
---|
541 | output->initialiseCube(dims,true); |
---|
542 | for(size_t z=0;z<output->axisDim[2];z++){ |
---|
543 | for(size_t y=0;y<output->axisDim[1];y++){ |
---|
544 | for(size_t x=0;x<output->axisDim[0];x++){ |
---|
545 | size_t impos=x+y*output->axisDim[0]; |
---|
546 | size_t pos=impos+z*output->axisDim[0]*output->axisDim[1]; |
---|
547 | if(pos>=output->numPixels) DUCHAMPERROR("cube slicer","Out of bounds in new Cube"); |
---|
548 | size_t imposIn=(x+subsection.getStart(0)) + (y+subsection.getStart(1))*this->axisDim[0]; |
---|
549 | size_t posIn=imposIn + (z+subsection.getStart(2))*this->axisDim[0]*this->axisDim[1]; |
---|
550 | if(posIn>=this->numPixels) DUCHAMPERROR("cube slicer","Out of bounds in new Cube"); |
---|
551 | output->array[pos] = this->array[posIn]; |
---|
552 | output->detectMap[impos] = this->detectMap[imposIn]; |
---|
553 | if(this->reconAllocated) output->recon[pos] = this->recon[posIn]; |
---|
554 | if(this->baselineAllocated) output->baseline[pos] = this->baseline[posIn]; |
---|
555 | } |
---|
556 | } |
---|
557 | } |
---|
558 | std::cout << this->par << "\n"<<output->par <<"\n"; |
---|
559 | } |
---|
560 | else{ |
---|
561 | DUCHAMPERROR("cube slicer","Subsection does not parse"); |
---|
562 | } |
---|
563 | |
---|
564 | return output; |
---|
565 | |
---|
566 | } |
---|
567 | //-------------------------------------------------------------------- |
---|
568 | |
---|
569 | OUTCOME Cube::initialiseCube(long *dimensions, bool allocateArrays) |
---|
570 | { |
---|
571 | int numAxes = this->head.getNumAxes(); |
---|
572 | if(numAxes<=0) numAxes=3; |
---|
573 | size_t *dim = new size_t[numAxes]; |
---|
574 | for(int i=0;i<numAxes;i++) dim[i]=dimensions[i]; |
---|
575 | OUTCOME outcome=this->initialiseCube(dim,allocateArrays); |
---|
576 | delete [] dim; |
---|
577 | return outcome; |
---|
578 | } |
---|
579 | |
---|
580 | |
---|
581 | OUTCOME Cube::initialiseCube(size_t *dimensions, bool allocateArrays) |
---|
582 | { |
---|
583 | /// @details |
---|
584 | /// This function will set the sizes of all arrays that will be used by Cube. |
---|
585 | /// It will also define the values of the axis dimensions: this will be done |
---|
586 | /// using the WCS in the FitsHeader class, so the WCS needs to be good and |
---|
587 | /// have three axes. If this is not the case, the axes are assumed to be |
---|
588 | /// ordered in the sense of lng,lat,spc. |
---|
589 | /// |
---|
590 | /// \param dimensions An array of values giving the dimensions (sizes) for |
---|
591 | /// all axes. |
---|
592 | /// \param allocateArrays A flag indicating whether to allocate |
---|
593 | /// the memory for the data arrays: the default is true. The |
---|
594 | /// dimension arrays will be allocated and filled. |
---|
595 | |
---|
596 | int lng,lat,spc; |
---|
597 | size_t size,imsize; |
---|
598 | |
---|
599 | int numAxes = this->head.getNumAxes(); |
---|
600 | if(numAxes<=0) numAxes=3; |
---|
601 | |
---|
602 | if(this->head.isWCS() && (numAxes>=3) && (this->head.WCS().spec>=0)){ |
---|
603 | // if there is a WCS and there is at least 3 axes |
---|
604 | lng = this->head.WCS().lng; |
---|
605 | lat = this->head.WCS().lat; |
---|
606 | spc = this->head.WCS().spec; |
---|
607 | } |
---|
608 | else{ |
---|
609 | // just take dimensions[] at face value |
---|
610 | lng = 0; |
---|
611 | lat = 1; |
---|
612 | spc = 2; |
---|
613 | } |
---|
614 | |
---|
615 | size = dimensions[lng]; |
---|
616 | if(numAxes>1) size *= dimensions[lat]; |
---|
617 | if(this->head.canUseThirdAxis() && numAxes>spc) size *= dimensions[spc]; |
---|
618 | |
---|
619 | imsize = dimensions[lng]; |
---|
620 | if(numAxes>1) imsize *= dimensions[lat]; |
---|
621 | |
---|
622 | this->reconAllocated = false; |
---|
623 | this->baselineAllocated = false; |
---|
624 | |
---|
625 | if(this->axisDimAllocated){ |
---|
626 | delete [] this->axisDim; |
---|
627 | this->axisDimAllocated = false; |
---|
628 | } |
---|
629 | |
---|
630 | if(this->arrayAllocated){ |
---|
631 | delete [] this->array; |
---|
632 | delete [] this->detectMap; |
---|
633 | this->arrayAllocated = false; |
---|
634 | } |
---|
635 | if(this->reconAllocated){ |
---|
636 | delete [] this->recon; |
---|
637 | this->reconAllocated = false; |
---|
638 | } |
---|
639 | if(this->baselineAllocated){ |
---|
640 | delete [] this->baseline; |
---|
641 | this->baselineAllocated = false; |
---|
642 | } |
---|
643 | |
---|
644 | if((size<0) || (imsize<0) ) { |
---|
645 | DUCHAMPERROR("Cube::initialiseCube(dimArray)", "Negative size -- could not define Cube."); |
---|
646 | return FAILURE; |
---|
647 | } |
---|
648 | else{ |
---|
649 | this->numPixels = size; |
---|
650 | this->numDim = 3; |
---|
651 | |
---|
652 | this->axisDim = new size_t[this->numDim]; |
---|
653 | this->axisDimAllocated = true; |
---|
654 | this->axisDim[0] = dimensions[lng]; |
---|
655 | if(numAxes>1) this->axisDim[1] = dimensions[lat]; |
---|
656 | else this->axisDim[1] = 1; |
---|
657 | if(this->head.canUseThirdAxis() && numAxes>spc) this->axisDim[2] = dimensions[spc]; |
---|
658 | else this->axisDim[2] = 1; |
---|
659 | |
---|
660 | this->numNondegDim=0; |
---|
661 | for(int i=0;i<3;i++) if(this->axisDim[i]>1) this->numNondegDim++; |
---|
662 | |
---|
663 | if(this->numNondegDim == 1){ |
---|
664 | if(!head.isWCS()) std::swap(this->axisDim[0],this->axisDim[2]); |
---|
665 | imsize=this->axisDim[2]; |
---|
666 | } |
---|
667 | |
---|
668 | bool haveChanged=false; |
---|
669 | int change=0; |
---|
670 | if(this->par.getMinPix() > this->axisDim[0]*this->axisDim[1]){ |
---|
671 | DUCHAMPWARN("Cube::initialiseCube", "The value of minPix ("<<this->par.getMinPix()<<") is greater than the image size. Setting to "<<this->axisDim[0]*this->axisDim[1]); |
---|
672 | change=this->par.getMinPix() - this->axisDim[0]*this->axisDim[1]; |
---|
673 | haveChanged=true; |
---|
674 | this->par.setMinPix(this->axisDim[0]*this->axisDim[1]); |
---|
675 | } |
---|
676 | if(this->par.getMinChannels() > this->axisDim[2]){ |
---|
677 | DUCHAMPWARN("Cube::initialiseCube", "The value of minChannels ("<<this->par.getMinChannels()<<") is greater than the spectral size. Setting to "<<this->axisDim[2]); |
---|
678 | change=this->par.getMinChannels() - this->axisDim[2]; |
---|
679 | haveChanged=true; |
---|
680 | this->par.setMinChannels(this->axisDim[2]); |
---|
681 | } |
---|
682 | if(haveChanged){ |
---|
683 | DUCHAMPWARN("Cube::initialiseCube","Reducing minVoxels to "<<this->par.getMinVoxels() - change<<" to accomodate these changes" ); |
---|
684 | this->par.setMinVoxels(this->par.getMinVoxels() - change); |
---|
685 | } |
---|
686 | |
---|
687 | if(this->par.getFlagSmooth()){ |
---|
688 | if(this->par.getSmoothType()=="spectral" && this->numNondegDim==2){ |
---|
689 | DUCHAMPWARN("Cube::initialiseCube", "Spectral smooth requested, but have a 2D image. Setting flagSmooth=false"); |
---|
690 | this->par.setFlagSmooth(false); |
---|
691 | } |
---|
692 | if(this->par.getSmoothType()=="spatial" && this->numNondegDim==1){ |
---|
693 | DUCHAMPWARN("Cube::initialiseCube", "Spatial smooth requested, but have a 1D image. Setting flagSmooth=false"); |
---|
694 | this->par.setFlagSmooth(false); |
---|
695 | } |
---|
696 | } |
---|
697 | if(this->par.getFlagATrous()){ |
---|
698 | for(int d=3; d>=1; d--){ |
---|
699 | if(this->par.getReconDim()==d && this->numNondegDim==(d-1)){ |
---|
700 | DUCHAMPWARN("Cube::initialiseCube", d << "D reconstruction requested, but image is " << d-1 <<"D. Setting flagAtrous=false"); |
---|
701 | this->par.setFlagATrous(false); |
---|
702 | } |
---|
703 | } |
---|
704 | } |
---|
705 | |
---|
706 | if(allocateArrays && this->par.isVerbose()) this->reportMemorySize(std::cout,allocateArrays); |
---|
707 | |
---|
708 | this->reconExists = false; |
---|
709 | if(size>0 && allocateArrays){ |
---|
710 | this->array = new float[size]; |
---|
711 | this->arrayAllocated = true; |
---|
712 | this->detectMap = new short[imsize]; |
---|
713 | for(size_t i=0;i<imsize;i++) this->detectMap[i] = 0; |
---|
714 | if(this->par.getFlagATrous() || this->par.getFlagSmooth()){ |
---|
715 | this->recon = new float[size]; |
---|
716 | this->reconAllocated = true; |
---|
717 | for(size_t i=0;i<size;i++) this->recon[i] = 0.; |
---|
718 | } |
---|
719 | if(this->par.getFlagBaseline()){ |
---|
720 | this->baseline = new float[size]; |
---|
721 | this->baselineAllocated = true; |
---|
722 | for(size_t i=0;i<size;i++) this->baseline[i] = 0.; |
---|
723 | } |
---|
724 | } |
---|
725 | } |
---|
726 | return SUCCESS; |
---|
727 | } |
---|
728 | //-------------------------------------------------------------------- |
---|
729 | |
---|
730 | void Cube::reportMemorySize(std::ostream &theStream, bool allocateArrays) |
---|
731 | { |
---|
732 | std::string unitlist[4]={"kB","MB","GB","TB"}; |
---|
733 | size_t size=axisDim[0]*axisDim[1]*axisDim[2]; |
---|
734 | size_t imsize=axisDim[0]*axisDim[1]; |
---|
735 | |
---|
736 | // Calculate and report the total size of memory to be allocated. |
---|
737 | float allocSize=3*sizeof(size_t); // axisDim |
---|
738 | float arrAllocSize=0.; |
---|
739 | if(size>0 && allocateArrays){ |
---|
740 | allocSize += size * sizeof(float); // array |
---|
741 | arrAllocSize = size*sizeof(float); |
---|
742 | allocSize += imsize * sizeof(short); // detectMap |
---|
743 | if(this->par.getFlagATrous() || this->par.getFlagSmooth()) |
---|
744 | allocSize += size * sizeof(float); // recon |
---|
745 | if(this->par.getFlagBaseline()) |
---|
746 | allocSize += size * sizeof(float); // baseline |
---|
747 | } |
---|
748 | std::string units="bytes"; |
---|
749 | for(int i=0;i<4 && allocSize>1024.;i++){ |
---|
750 | allocSize/=1024.; |
---|
751 | arrAllocSize /= 1024.; |
---|
752 | units=unitlist[i]; |
---|
753 | } |
---|
754 | |
---|
755 | theStream << "\n About to allocate " << allocSize << units; |
---|
756 | if(arrAllocSize > 0.) theStream << " of which " << arrAllocSize << units << " is for the image\n"; |
---|
757 | else theStream << "\n"; |
---|
758 | } |
---|
759 | |
---|
760 | |
---|
761 | bool Cube::is2D() |
---|
762 | { |
---|
763 | /// @details |
---|
764 | /// Check whether the image is 2-dimensional, by counting |
---|
765 | /// the number of dimensions that are greater than 1 |
---|
766 | |
---|
767 | if(this->head.WCS().naxis==2) return true; |
---|
768 | else{ |
---|
769 | int numDim=0; |
---|
770 | for(int i=0;i<this->numDim;i++) if(axisDim[i]>1) numDim++; |
---|
771 | return numDim<=2; |
---|
772 | } |
---|
773 | |
---|
774 | } |
---|
775 | //-------------------------------------------------------------------- |
---|
776 | |
---|
777 | OUTCOME Cube::getCube() |
---|
778 | { |
---|
779 | /// @details |
---|
780 | /// A front-end to the Cube::getCube() function, that does |
---|
781 | /// subsection checks. |
---|
782 | /// Assumes the Param is set up properly. |
---|
783 | |
---|
784 | std::string fname = par.getImageFile(); |
---|
785 | if(par.getFlagSubsection()) fname+=par.getSubsection(); |
---|
786 | return getCube(fname); |
---|
787 | } |
---|
788 | //-------------------------------------------------------------------- |
---|
789 | |
---|
790 | void Cube::saveArray(float *input, size_t size) |
---|
791 | { |
---|
792 | if(size != this->numPixels){ |
---|
793 | DUCHAMPERROR("Cube::saveArray","Input array different size to existing array (" << size << " cf. " << this->numPixels << "). Cannot save."); |
---|
794 | } |
---|
795 | else { |
---|
796 | if(this->numPixels>0 && this->arrayAllocated) delete [] array; |
---|
797 | this->numPixels = size; |
---|
798 | this->array = new float[size]; |
---|
799 | this->arrayAllocated = true; |
---|
800 | for(size_t i=0;i<size;i++) this->array[i] = input[i]; |
---|
801 | } |
---|
802 | } |
---|
803 | //-------------------------------------------------------------------- |
---|
804 | |
---|
805 | void Cube::saveArray(std::vector<float> &input) |
---|
806 | { |
---|
807 | /// @details |
---|
808 | /// Saves the array in input to the pixel array Cube::array. |
---|
809 | /// The size of the array given must be the same as the current number of |
---|
810 | /// pixels, else an error message is returned and nothing is done. |
---|
811 | /// \param input The array of values to be saved. |
---|
812 | |
---|
813 | if(input.size() != this->numPixels){ |
---|
814 | DUCHAMPERROR("Cube::saveArray","Input array different size to existing array (" << input.size() << " cf. " << this->numPixels << "). Cannot save."); |
---|
815 | } |
---|
816 | else { |
---|
817 | if(this->numPixels>0 && this->arrayAllocated) delete [] this->array; |
---|
818 | this->numPixels = input.size(); |
---|
819 | this->array = new float[input.size()]; |
---|
820 | this->arrayAllocated = true; |
---|
821 | for(size_t i=0;i<input.size();i++) this->array[i] = input[i]; |
---|
822 | } |
---|
823 | } |
---|
824 | //-------------------------------------------------------------------- |
---|
825 | |
---|
826 | void Cube::saveRecon(float *input, size_t size) |
---|
827 | { |
---|
828 | /// @details |
---|
829 | /// Saves the array in input to the reconstructed array Cube::recon |
---|
830 | /// The size of the array given must be the same as the current number of |
---|
831 | /// pixels, else an error message is returned and nothing is done. |
---|
832 | /// If the recon array has already been allocated, it is deleted first, and |
---|
833 | /// then the space is allocated. |
---|
834 | /// Afterwards, the appropriate flags are set. |
---|
835 | /// \param input The array of values to be saved. |
---|
836 | /// \param size The size of input. |
---|
837 | |
---|
838 | if(size != this->numPixels){ |
---|
839 | DUCHAMPERROR("Cube::saveRecon","Input array different size to existing array (" << size << " cf. " << this->numPixels << "). Cannot save."); |
---|
840 | } |
---|
841 | else { |
---|
842 | if(this->numPixels>0){ |
---|
843 | if(this->reconAllocated) delete [] this->recon; |
---|
844 | this->numPixels = size; |
---|
845 | this->recon = new float[size]; |
---|
846 | this->reconAllocated = true; |
---|
847 | for(size_t i=0;i<size;i++) this->recon[i] = input[i]; |
---|
848 | this->reconExists = true; |
---|
849 | } |
---|
850 | } |
---|
851 | } |
---|
852 | //-------------------------------------------------------------------- |
---|
853 | |
---|
854 | void Cube::getRecon(float *output) |
---|
855 | { |
---|
856 | /// @details |
---|
857 | /// The reconstructed array is written to output. The output array needs to |
---|
858 | /// be defined beforehand: no checking is done on the memory. |
---|
859 | /// \param output The array that is written to. |
---|
860 | |
---|
861 | // Need check for change in number of pixels! |
---|
862 | for(size_t i=0;i<this->numPixels;i++){ |
---|
863 | if(this->reconExists) output[i] = this->recon[i]; |
---|
864 | else output[i] = 0.; |
---|
865 | } |
---|
866 | } |
---|
867 | //-------------------------------------------------------------------- |
---|
868 | |
---|
869 | void Cube::removeMW() |
---|
870 | { |
---|
871 | /// @details |
---|
872 | /// The channels corresponding to the Milky Way range (as given by the Param |
---|
873 | /// set) are all set to 0 in the pixel array. |
---|
874 | /// Only done if the appropriate flag is set, and the pixels are not BLANK. |
---|
875 | /// \deprecated |
---|
876 | |
---|
877 | if(this->par.getFlagMW()){ |
---|
878 | for(size_t pix=0;pix<this->axisDim[0]*this->axisDim[1];pix++){ |
---|
879 | for(size_t z=0;z<this->axisDim[2];z++){ |
---|
880 | size_t pos = z*this->axisDim[0]*this->axisDim[1] + pix; |
---|
881 | if(!this->isBlank(pos) && this->par.isInMW(z)) this->array[pos]=0.; |
---|
882 | } |
---|
883 | } |
---|
884 | } |
---|
885 | } |
---|
886 | //-------------------------------------------------------------------- |
---|
887 | |
---|
888 | void Cube::setCubeStats() |
---|
889 | { |
---|
890 | /// @details |
---|
891 | /// Calculates the full statistics for the cube: |
---|
892 | /// mean, rms, median, madfm |
---|
893 | /// Only do this if the threshold has not been defined (ie. is still 0., |
---|
894 | /// its default). |
---|
895 | /// Also work out the threshold and store it in the par set. |
---|
896 | /// |
---|
897 | /// Different from Cube::setCubeStatsOld() as it doesn't use the |
---|
898 | /// getStats functions but has own versions of them hardcoded to |
---|
899 | /// ignore BLANKs and MW channels. This saves on memory usage -- necessary |
---|
900 | /// for dealing with very big files. |
---|
901 | /// |
---|
902 | /// Three cases exist: |
---|
903 | /// <ul><li>Simple case, with no reconstruction/smoothing: all stats |
---|
904 | /// calculated from the original array. |
---|
905 | /// <li>Wavelet reconstruction: mean & median calculated from the |
---|
906 | /// original array, and stddev & madfm from the residual. |
---|
907 | /// <li>Smoothing: all four stats calculated from the recon array |
---|
908 | /// (which holds the smoothed data). |
---|
909 | /// </ul> |
---|
910 | |
---|
911 | if(this->par.getFlagUserThreshold() ){ |
---|
912 | // if the user has defined a threshold, set this in the StatsContainer |
---|
913 | this->Stats.setThreshold( this->par.getThreshold() ); |
---|
914 | } |
---|
915 | else{ |
---|
916 | // only work out the stats if we need to. |
---|
917 | // the only reason we don't is if the user has specified a threshold. |
---|
918 | |
---|
919 | this->Stats.setRobust(this->par.getFlagRobustStats()); |
---|
920 | |
---|
921 | if(this->par.isVerbose()) |
---|
922 | std::cout << "Calculating the cube statistics... " << std::flush; |
---|
923 | |
---|
924 | // size_t xysize = this->axisDim[0]*this->axisDim[1]; |
---|
925 | |
---|
926 | bool *mask = new bool[this->numPixels]; |
---|
927 | size_t vox=0,goodSize = 0; |
---|
928 | for(size_t z=0;z<this->axisDim[2];z++){ |
---|
929 | for(size_t y=0;y<this->axisDim[1];y++){ |
---|
930 | for(size_t x=0;x<this->axisDim[0];x++){ |
---|
931 | // vox = z * xysize + y*this->axisDim[0] + x; |
---|
932 | bool isBlank=this->isBlank(vox); |
---|
933 | bool isMW = this->par.isInMW(z); |
---|
934 | bool statOK = this->par.isStatOK(x,y,z); |
---|
935 | mask[vox] = (!isBlank && !isMW && statOK ); |
---|
936 | if(mask[vox]) goodSize++; |
---|
937 | vox++; |
---|
938 | } |
---|
939 | } |
---|
940 | } |
---|
941 | |
---|
942 | // float mean,median,stddev,madfm; |
---|
943 | if( this->par.getFlagATrous() ){ |
---|
944 | // Case #2 -- wavelet reconstruction |
---|
945 | // just get mean & median from orig array, and rms & madfm from |
---|
946 | // residual recompute array values to be residuals & then find |
---|
947 | // stddev & madfm |
---|
948 | if(!this->reconExists){ |
---|
949 | DUCHAMPERROR("setCubeStats", "Reconstruction not yet done! Cannot calculate stats!"); |
---|
950 | } |
---|
951 | else{ |
---|
952 | float *tempArray = new float[goodSize]; |
---|
953 | |
---|
954 | goodSize=0; |
---|
955 | vox=0; |
---|
956 | for(size_t z=0;z<this->axisDim[2];z++){ |
---|
957 | for(size_t y=0;y<this->axisDim[1];y++){ |
---|
958 | for(size_t x=0;x<this->axisDim[0];x++){ |
---|
959 | // vox = z * xysize + y*this->axisDim[0] + x; |
---|
960 | if(mask[vox]) tempArray[goodSize++] = this->array[vox]; |
---|
961 | vox++; |
---|
962 | } |
---|
963 | } |
---|
964 | } |
---|
965 | |
---|
966 | // First, find the mean of the original array. Store it. |
---|
967 | this->Stats.setMean( findMean<float>(tempArray, goodSize) ); |
---|
968 | |
---|
969 | // Now sort it and find the median. Store it. |
---|
970 | this->Stats.setMedian( findMedian<float>(tempArray, goodSize, true) ); |
---|
971 | |
---|
972 | // Now calculate the residuals and find the mean & median of |
---|
973 | // them. We don't store these, but they are necessary to find |
---|
974 | // the sttdev & madfm. |
---|
975 | goodSize = 0; |
---|
976 | // for(int p=0;p<xysize;p++){ |
---|
977 | vox=0; |
---|
978 | for(size_t z=0;z<this->axisDim[2];z++){ |
---|
979 | for(size_t y=0;y<this->axisDim[1];y++){ |
---|
980 | for(size_t x=0;x<this->axisDim[0];x++){ |
---|
981 | // vox = z * xysize + p; |
---|
982 | if(mask[vox]) |
---|
983 | tempArray[goodSize++] = this->array[vox] - this->recon[vox]; |
---|
984 | vox++; |
---|
985 | } |
---|
986 | } |
---|
987 | } |
---|
988 | |
---|
989 | this->Stats.setStddev( findStddev<float>(tempArray, goodSize) ); |
---|
990 | |
---|
991 | // Now find the madfm of the residuals. Store it. |
---|
992 | this->Stats.setMadfm( findMADFM(tempArray, goodSize, true) ); |
---|
993 | |
---|
994 | delete [] tempArray; |
---|
995 | } |
---|
996 | } |
---|
997 | else if(this->par.getFlagSmooth()) { |
---|
998 | // Case #3 -- smoothing |
---|
999 | // get all four stats from the recon array, which holds the |
---|
1000 | // smoothed data. This can just be done with the |
---|
1001 | // StatsContainer::calculate function, using the mask generated |
---|
1002 | // earlier. |
---|
1003 | if(!this->reconExists){ |
---|
1004 | DUCHAMPERROR("setCubeStats","Smoothing not yet done! Cannot calculate stats!"); |
---|
1005 | } |
---|
1006 | else this->Stats.calculate(this->recon,this->numPixels,mask); |
---|
1007 | } |
---|
1008 | else{ |
---|
1009 | // Case #1 -- default case, with no smoothing or reconstruction. |
---|
1010 | // get all four stats from the original array. This can just be |
---|
1011 | // done with the StatsContainer::calculate function, using the |
---|
1012 | // mask generated earlier. |
---|
1013 | this->Stats.calculate(this->array,this->numPixels,mask); |
---|
1014 | } |
---|
1015 | |
---|
1016 | this->Stats.setUseFDR( this->par.getFlagFDR() ); |
---|
1017 | // If the FDR method has been requested, define the P-value |
---|
1018 | // threshold |
---|
1019 | if(this->par.getFlagFDR()) this->setupFDR(); |
---|
1020 | else{ |
---|
1021 | // otherwise, calculate threshold based on the requested SNR cut |
---|
1022 | // level, and then set the threshold parameter in the Par set. |
---|
1023 | this->Stats.setThresholdSNR( this->par.getCut() ); |
---|
1024 | this->par.setThreshold( this->Stats.getThreshold() ); |
---|
1025 | } |
---|
1026 | |
---|
1027 | delete [] mask; |
---|
1028 | |
---|
1029 | } |
---|
1030 | |
---|
1031 | if(this->par.isVerbose()){ |
---|
1032 | std::cout << "Using "; |
---|
1033 | if(this->par.getFlagFDR()) std::cout << "effective "; |
---|
1034 | std::cout << "flux threshold of: "; |
---|
1035 | float thresh = this->Stats.getThreshold(); |
---|
1036 | if(this->par.getFlagNegative()) thresh *= -1.; |
---|
1037 | std::cout << thresh; |
---|
1038 | if(this->par.getFlagGrowth()){ |
---|
1039 | std::cout << " and growing to threshold of: "; |
---|
1040 | if(this->par.getFlagUserGrowthThreshold()) thresh= this->par.getGrowthThreshold(); |
---|
1041 | else thresh= this->Stats.snrToValue(this->par.getGrowthCut()); |
---|
1042 | if(this->par.getFlagNegative()) thresh *= -1.; |
---|
1043 | std::cout << thresh; |
---|
1044 | } |
---|
1045 | std::cout << std::endl; |
---|
1046 | } |
---|
1047 | |
---|
1048 | } |
---|
1049 | //-------------------------------------------------------------------- |
---|
1050 | |
---|
1051 | void Cube::setupFDR() |
---|
1052 | { |
---|
1053 | /// @details |
---|
1054 | /// Call the setupFDR(float *) function on the pixel array of the |
---|
1055 | /// cube. This is the usual way of running it. |
---|
1056 | /// |
---|
1057 | /// However, if we are in smoothing mode, we calculate the FDR |
---|
1058 | /// parameters using the recon array, which holds the smoothed |
---|
1059 | /// data. Gives an error message if the reconExists flag is not set. |
---|
1060 | |
---|
1061 | if(this->par.getFlagSmooth()) |
---|
1062 | if(this->reconExists) this->setupFDR(this->recon); |
---|
1063 | else{ |
---|
1064 | DUCHAMPERROR("setupFDR", "Smoothing not done properly! Using original array for defining threshold."); |
---|
1065 | this->setupFDR(this->array); |
---|
1066 | } |
---|
1067 | else if( this->par.getFlagATrous() ){ |
---|
1068 | if(this->reconExists) this->setupFDR(this->recon); |
---|
1069 | else{ |
---|
1070 | DUCHAMPERROR("setupFDR", "Reconstruction not done properly! Using original array for defining threshold."); |
---|
1071 | this->setupFDR(this->array); |
---|
1072 | } |
---|
1073 | } |
---|
1074 | else{ |
---|
1075 | this->setupFDR(this->array); |
---|
1076 | } |
---|
1077 | } |
---|
1078 | //-------------------------------------------------------------------- |
---|
1079 | |
---|
1080 | void Cube::setupFDR(float *input) |
---|
1081 | { |
---|
1082 | /// @details |
---|
1083 | /// Determines the critical Probability value for the False |
---|
1084 | /// Discovery Rate detection routine. All pixels in the given arry |
---|
1085 | /// with Prob less than this value will be considered detections. |
---|
1086 | /// |
---|
1087 | /// Note that the Stats of the cube need to be calculated first. |
---|
1088 | /// |
---|
1089 | /// The Prob here is the probability, assuming a Normal |
---|
1090 | /// distribution, of obtaining a value as high or higher than the |
---|
1091 | /// pixel value (ie. only the positive tail of the PDF). |
---|
1092 | /// |
---|
1093 | /// The probabilities are calculated using the |
---|
1094 | /// StatsContainer::getPValue(), which calculates the z-statistic, |
---|
1095 | /// and then the probability via |
---|
1096 | /// \f$0.5\operatorname{erfc}(z/\sqrt{2})\f$ -- giving the positive |
---|
1097 | /// tail probability. |
---|
1098 | |
---|
1099 | // first calculate p-value for each pixel -- assume Gaussian for now. |
---|
1100 | |
---|
1101 | float *orderedP = new float[this->numPixels]; |
---|
1102 | size_t count = 0; |
---|
1103 | for(size_t x=0;x<this->axisDim[0];x++){ |
---|
1104 | for(size_t y=0;y<this->axisDim[1];y++){ |
---|
1105 | for(size_t z=0;z<this->axisDim[2];z++){ |
---|
1106 | size_t pix = z * this->axisDim[0]*this->axisDim[1] + |
---|
1107 | y*this->axisDim[0] + x; |
---|
1108 | |
---|
1109 | if(!(this->par.isBlank(this->array[pix])) && !this->par.isInMW(z)){ |
---|
1110 | // only look at non-blank, valid pixels |
---|
1111 | // orderedP[count++] = this->Stats.getPValue(this->array[pix]); |
---|
1112 | orderedP[count++] = this->Stats.getPValue(input[pix]); |
---|
1113 | } |
---|
1114 | } |
---|
1115 | } |
---|
1116 | } |
---|
1117 | |
---|
1118 | // now order them |
---|
1119 | std::stable_sort(orderedP,orderedP+count); |
---|
1120 | |
---|
1121 | // now find the maximum P value. |
---|
1122 | size_t max = 0; |
---|
1123 | double cN = 0.; |
---|
1124 | // Calculate number of correlated pixels. Assume all spatial |
---|
1125 | // pixels within the beam are correlated, and multiply this by the |
---|
1126 | // number of correlated pixels as determined by the beam |
---|
1127 | int numVox; |
---|
1128 | if(this->head.beam().isDefined()) numVox = int(ceil(this->head.beam().area())); |
---|
1129 | else numVox = 1; |
---|
1130 | if(this->head.canUseThirdAxis()) numVox *= this->par.getFDRnumCorChan(); |
---|
1131 | for(int psfCtr=1;psfCtr<=numVox;psfCtr++) cN += 1./float(psfCtr); |
---|
1132 | |
---|
1133 | double slope = this->par.getAlpha()/cN; |
---|
1134 | for(size_t loopCtr=0;loopCtr<count;loopCtr++) { |
---|
1135 | if( orderedP[loopCtr] < (slope * double(loopCtr+1)/ double(count)) ){ |
---|
1136 | max = loopCtr; |
---|
1137 | } |
---|
1138 | } |
---|
1139 | |
---|
1140 | this->Stats.setPThreshold( orderedP[max] ); |
---|
1141 | |
---|
1142 | |
---|
1143 | // Find real value of the P threshold by finding the inverse of the |
---|
1144 | // error function -- root finding with brute force technique |
---|
1145 | // (relatively slow, but we only do it once). |
---|
1146 | double zStat = 0.; |
---|
1147 | double deltaZ = 0.1; |
---|
1148 | double tolerance = 1.e-6; |
---|
1149 | double initial = 0.5 * erfc(zStat/M_SQRT2) - this->Stats.getPThreshold(); |
---|
1150 | do{ |
---|
1151 | zStat+=deltaZ; |
---|
1152 | double current = 0.5 * erfc(zStat/M_SQRT2) - this->Stats.getPThreshold(); |
---|
1153 | if((initial*current)<0.){ |
---|
1154 | zStat-=deltaZ; |
---|
1155 | deltaZ/=2.; |
---|
1156 | } |
---|
1157 | }while(deltaZ>tolerance); |
---|
1158 | this->Stats.setThreshold( zStat*this->Stats.getSpread() + |
---|
1159 | this->Stats.getMiddle() ); |
---|
1160 | |
---|
1161 | /////////////////////////// |
---|
1162 | // if(TESTING){ |
---|
1163 | // std::stringstream ss; |
---|
1164 | // float *xplot = new float[2*max]; |
---|
1165 | // for(int i=0;i<2*max;i++) xplot[i]=float(i)/float(count); |
---|
1166 | // cpgopen("latestFDR.ps/vcps"); |
---|
1167 | // cpgpap(8.,1.); |
---|
1168 | // cpgslw(3); |
---|
1169 | // cpgenv(0,float(2*max)/float(count),0,orderedP[2*max],0,0); |
---|
1170 | // cpglab("i/N (index)", "p-value",""); |
---|
1171 | // cpgpt(2*max,xplot,orderedP,DOT); |
---|
1172 | |
---|
1173 | // ss.str(""); |
---|
1174 | // ss << "\\gm = " << this->Stats.getMiddle(); |
---|
1175 | // cpgtext(max/(4.*count),0.9*orderedP[2*max],ss.str().c_str()); |
---|
1176 | // ss.str(""); |
---|
1177 | // ss << "\\gs = " << this->Stats.getSpread(); |
---|
1178 | // cpgtext(max/(4.*count),0.85*orderedP[2*max],ss.str().c_str()); |
---|
1179 | // ss.str(""); |
---|
1180 | // ss << "Slope = " << slope; |
---|
1181 | // cpgtext(max/(4.*count),0.8*orderedP[2*max],ss.str().c_str()); |
---|
1182 | // ss.str(""); |
---|
1183 | // ss << "Alpha = " << this->par.getAlpha(); |
---|
1184 | // cpgtext(max/(4.*count),0.75*orderedP[2*max],ss.str().c_str()); |
---|
1185 | // ss.str(""); |
---|
1186 | // ss << "c\\dN\\u = " << cN; |
---|
1187 | // cpgtext(max/(4.*count),0.7*orderedP[2*max],ss.str().c_str()); |
---|
1188 | // ss.str(""); |
---|
1189 | // ss << "max = "<<max << " (out of " << count << ")"; |
---|
1190 | // cpgtext(max/(4.*count),0.65*orderedP[2*max],ss.str().c_str()); |
---|
1191 | // ss.str(""); |
---|
1192 | // ss << "Threshold = "<<zStat*this->Stats.getSpread()+this->Stats.getMiddle(); |
---|
1193 | // cpgtext(max/(4.*count),0.6*orderedP[2*max],ss.str().c_str()); |
---|
1194 | |
---|
1195 | // cpgslw(1); |
---|
1196 | // cpgsci(RED); |
---|
1197 | // cpgmove(0,0); |
---|
1198 | // cpgdraw(1,slope); |
---|
1199 | // cpgsci(BLUE); |
---|
1200 | // cpgsls(DOTTED); |
---|
1201 | // cpgmove(0,orderedP[max]); |
---|
1202 | // cpgdraw(2*max/float(count),orderedP[max]); |
---|
1203 | // cpgmove(max/float(count),0); |
---|
1204 | // cpgdraw(max/float(count),orderedP[2*max]); |
---|
1205 | // cpgsci(GREEN); |
---|
1206 | // cpgsls(SOLID); |
---|
1207 | // for(int i=1;i<=10;i++) { |
---|
1208 | // ss.str(""); |
---|
1209 | // ss << float(i)/2. << "\\gs"; |
---|
1210 | // float prob = 0.5*erfc((float(i)/2.)/M_SQRT2); |
---|
1211 | // cpgtick(0, 0, 0, orderedP[2*max], |
---|
1212 | // prob/orderedP[2*max], |
---|
1213 | // 0, 1, 1.5, 90., ss.str().c_str()); |
---|
1214 | // } |
---|
1215 | // cpgend(); |
---|
1216 | // delete [] xplot; |
---|
1217 | // } |
---|
1218 | delete [] orderedP; |
---|
1219 | |
---|
1220 | } |
---|
1221 | //-------------------------------------------------------------------- |
---|
1222 | |
---|
1223 | void Cube::Search() |
---|
1224 | { |
---|
1225 | /// @details |
---|
1226 | /// This acts as a switching function to select the correct searching function based on the user's parameters. |
---|
1227 | /// @param verboseFlag If true, text is written to stdout describing the search function being used. |
---|
1228 | if(this->par.getFlagATrous()){ |
---|
1229 | if(this->par.isVerbose()) std::cout<<"Commencing search in reconstructed cube..."<<std::endl; |
---|
1230 | this->ReconSearch(); |
---|
1231 | } |
---|
1232 | else if(this->par.getFlagSmooth()){ |
---|
1233 | if(this->par.isVerbose()) std::cout<<"Commencing search in smoothed cube..."<<std::endl; |
---|
1234 | this->SmoothSearch(); |
---|
1235 | } |
---|
1236 | else{ |
---|
1237 | if(this->par.isVerbose()) std::cout<<"Commencing search in cube..."<<std::endl; |
---|
1238 | this->CubicSearch(); |
---|
1239 | } |
---|
1240 | |
---|
1241 | } |
---|
1242 | |
---|
1243 | bool Cube::isDetection(size_t x, size_t y, size_t z) |
---|
1244 | { |
---|
1245 | /// @details |
---|
1246 | /// Is a given voxel at position (x,y,z) a detection, based on the statistics |
---|
1247 | /// in the Cube's StatsContainer? |
---|
1248 | /// If the pixel lies outside the valid range for the data array, |
---|
1249 | /// return false. |
---|
1250 | /// \param x X-value of the Cube's voxel to be tested. |
---|
1251 | /// \param y Y-value of the Cube's voxel to be tested. |
---|
1252 | /// \param z Z-value of the Cube's voxel to be tested. |
---|
1253 | |
---|
1254 | size_t voxel = z*axisDim[0]*axisDim[1] + y*axisDim[0] + x; |
---|
1255 | return DataArray::isDetection(array[voxel]); |
---|
1256 | } |
---|
1257 | //-------------------------------------------------------------------- |
---|
1258 | |
---|
1259 | void Cube::calcObjectFluxes() |
---|
1260 | { |
---|
1261 | /// @details |
---|
1262 | /// A function to calculate the fluxes and centroids for each |
---|
1263 | /// object in the Cube's list of detections. Uses |
---|
1264 | /// Detection::calcFluxes() for each object. |
---|
1265 | |
---|
1266 | std::vector<Detection>::iterator obj; |
---|
1267 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1268 | obj->calcFluxes(this->array, this->axisDim); |
---|
1269 | if(this->par.getFlagUserThreshold()) |
---|
1270 | obj->setPeakSNR( obj->getPeakFlux() / this->Stats.getThreshold() ); |
---|
1271 | else |
---|
1272 | obj->setPeakSNR( (obj->getPeakFlux() - this->Stats.getMiddle()) / this->Stats.getSpread() ); |
---|
1273 | } |
---|
1274 | } |
---|
1275 | //-------------------------------------------------------------------- |
---|
1276 | |
---|
1277 | void Cube::calcObjectWCSparams() |
---|
1278 | { |
---|
1279 | /// @details |
---|
1280 | /// A function that calculates the WCS parameters for each object in the |
---|
1281 | /// Cube's list of detections. |
---|
1282 | /// Each object gets an ID number assigned to it (which is simply its order |
---|
1283 | /// in the list), and if the WCS is good, the WCS paramters are calculated. |
---|
1284 | |
---|
1285 | std::vector<Detection>::iterator obj; |
---|
1286 | int ct=0; |
---|
1287 | ProgressBar bar; |
---|
1288 | if(this->par.isVerbose()) bar.init(this->objectList->size()); |
---|
1289 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1290 | // std::cerr << ct << ' ' << this->array << '\n'; |
---|
1291 | if(this->par.isVerbose()) bar.update(ct); |
---|
1292 | obj->setID(ct++); |
---|
1293 | if(!obj->hasParams()){ |
---|
1294 | obj->setCentreType(this->par.getPixelCentre()); |
---|
1295 | obj->calcFluxes(this->array,this->axisDim); |
---|
1296 | // obj->calcWCSparams(this->array,this->axisDim,this->head); |
---|
1297 | obj->calcWCSparams(this->head); |
---|
1298 | obj->calcIntegFlux(this->array,this->axisDim,this->head); |
---|
1299 | |
---|
1300 | if(this->par.getFlagUserThreshold()) |
---|
1301 | obj->setPeakSNR( obj->getPeakFlux() / this->Stats.getThreshold() ); |
---|
1302 | else |
---|
1303 | obj->setPeakSNR( (obj->getPeakFlux() - this->Stats.getMiddle()) / this->Stats.getSpread() ); |
---|
1304 | } |
---|
1305 | } |
---|
1306 | if(this->par.isVerbose()) bar.remove(); |
---|
1307 | |
---|
1308 | if(!this->head.isWCS()){ |
---|
1309 | // if the WCS is bad, set the object names to Obj01 etc |
---|
1310 | int numspaces = int(log10(this->objectList->size())) + 1; |
---|
1311 | std::stringstream ss; |
---|
1312 | for(size_t i=0;i<this->objectList->size();i++){ |
---|
1313 | ss.str(""); |
---|
1314 | ss << "Obj" << std::setfill('0') << std::setw(numspaces) << i+1; |
---|
1315 | this->objectList->at(i).setName(ss.str()); |
---|
1316 | } |
---|
1317 | } |
---|
1318 | |
---|
1319 | } |
---|
1320 | //-------------------------------------------------------------------- |
---|
1321 | |
---|
1322 | void Cube::calcObjectWCSparams(std::vector< std::vector<PixelInfo::Voxel> > bigVoxList) |
---|
1323 | { |
---|
1324 | /// @details |
---|
1325 | /// A function that calculates the WCS parameters for each object in the |
---|
1326 | /// Cube's list of detections. |
---|
1327 | /// Each object gets an ID number assigned to it (which is simply its order |
---|
1328 | /// in the list), and if the WCS is good, the WCS paramters are calculated. |
---|
1329 | /// |
---|
1330 | /// This version uses vectors of Voxels to define the fluxes. |
---|
1331 | /// |
---|
1332 | /// \param bigVoxList A vector of vectors of Voxels, with the same |
---|
1333 | /// number of elements as this->objectList, where each element is a |
---|
1334 | /// vector of Voxels corresponding to the same voxels in each |
---|
1335 | /// detection and indicating the flux of each voxel. |
---|
1336 | |
---|
1337 | std::vector<Detection>::iterator obj; |
---|
1338 | int ct=0; |
---|
1339 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1340 | obj->setID(ct+1); |
---|
1341 | if(!obj->hasParams()){ |
---|
1342 | obj->setCentreType(this->par.getPixelCentre()); |
---|
1343 | obj->calcFluxes(bigVoxList[ct]); |
---|
1344 | obj->calcWCSparams(this->head); |
---|
1345 | obj->calcIntegFlux(this->axisDim[2],bigVoxList[ct],this->head); |
---|
1346 | |
---|
1347 | if(this->par.getFlagUserThreshold()) |
---|
1348 | obj->setPeakSNR( obj->getPeakFlux() / this->Stats.getThreshold() ); |
---|
1349 | else |
---|
1350 | obj->setPeakSNR( (obj->getPeakFlux() - this->Stats.getMiddle()) / this->Stats.getSpread() ); |
---|
1351 | } |
---|
1352 | ct++; |
---|
1353 | } |
---|
1354 | |
---|
1355 | if(!this->head.isWCS()){ |
---|
1356 | // if the WCS is bad, set the object names to Obj01 etc |
---|
1357 | int numspaces = int(log10(this->objectList->size())) + 1; |
---|
1358 | std::stringstream ss; |
---|
1359 | for(size_t i=0;i<this->objectList->size();i++){ |
---|
1360 | ss.str(""); |
---|
1361 | ss << "Obj" << std::setfill('0') << std::setw(numspaces) << i+1; |
---|
1362 | this->objectList->at(i).setName(ss.str()); |
---|
1363 | } |
---|
1364 | } |
---|
1365 | |
---|
1366 | } |
---|
1367 | //-------------------------------------------------------------------- |
---|
1368 | |
---|
1369 | void Cube::calcObjectWCSparams(std::map<PixelInfo::Voxel,float> &voxelMap) |
---|
1370 | { |
---|
1371 | /// @details |
---|
1372 | /// A function that calculates the WCS parameters for each object in the |
---|
1373 | /// Cube's list of detections. |
---|
1374 | /// Each object gets an ID number assigned to it (which is simply its order |
---|
1375 | /// in the list), and if the WCS is good, the WCS paramters are calculated. |
---|
1376 | /// |
---|
1377 | /// This version uses vectors of Voxels to define the fluxes. |
---|
1378 | /// |
---|
1379 | /// \param bigVoxList A vector of vectors of Voxels, with the same |
---|
1380 | /// number of elements as this->objectList, where each element is a |
---|
1381 | /// vector of Voxels corresponding to the same voxels in each |
---|
1382 | /// detection and indicating the flux of each voxel. |
---|
1383 | |
---|
1384 | std::vector<Detection>::iterator obj; |
---|
1385 | int ct=0; |
---|
1386 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1387 | obj->setID(ct+1); |
---|
1388 | if(!obj->hasParams()){ |
---|
1389 | obj->setCentreType(this->par.getPixelCentre()); |
---|
1390 | obj->calcFluxes(voxelMap); |
---|
1391 | obj->calcWCSparams(this->head); |
---|
1392 | obj->calcIntegFlux(this->axisDim[2],voxelMap,this->head); |
---|
1393 | |
---|
1394 | if(this->par.getFlagUserThreshold()) |
---|
1395 | obj->setPeakSNR( obj->getPeakFlux() / this->Stats.getThreshold() ); |
---|
1396 | else |
---|
1397 | obj->setPeakSNR( (obj->getPeakFlux() - this->Stats.getMiddle()) / this->Stats.getSpread() ); |
---|
1398 | } |
---|
1399 | ct++; |
---|
1400 | } |
---|
1401 | |
---|
1402 | if(!this->head.isWCS()){ |
---|
1403 | // if the WCS is bad, set the object names to Obj01 etc |
---|
1404 | int numspaces = int(log10(this->objectList->size())) + 1; |
---|
1405 | std::stringstream ss; |
---|
1406 | for(size_t i=0;i<this->objectList->size();i++){ |
---|
1407 | ss.str(""); |
---|
1408 | ss << "Obj" << std::setfill('0') << std::setw(numspaces) << i+1; |
---|
1409 | this->objectList->at(i).setName(ss.str()); |
---|
1410 | } |
---|
1411 | } |
---|
1412 | |
---|
1413 | } |
---|
1414 | //-------------------------------------------------------------------- |
---|
1415 | |
---|
1416 | void Cube::updateDetectMap() |
---|
1417 | { |
---|
1418 | /// @details A function that, for each detected object in the |
---|
1419 | /// cube's list, increments the cube's detection map by the |
---|
1420 | /// required amount at each pixel. Uses |
---|
1421 | /// updateDetectMap(Detection). |
---|
1422 | |
---|
1423 | std::vector<Detection>::iterator obj; |
---|
1424 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1425 | this->updateDetectMap(*obj); |
---|
1426 | } |
---|
1427 | |
---|
1428 | } |
---|
1429 | //-------------------------------------------------------------------- |
---|
1430 | |
---|
1431 | void Cube::updateDetectMap(Detection obj) |
---|
1432 | { |
---|
1433 | /// @details |
---|
1434 | /// A function that, for the given object, increments the cube's |
---|
1435 | /// detection map by the required amount at each pixel. |
---|
1436 | /// |
---|
1437 | /// \param obj A Detection object that is being incorporated into the map. |
---|
1438 | |
---|
1439 | std::vector<Voxel> vlist = obj.getPixelSet(); |
---|
1440 | for(std::vector<Voxel>::iterator vox=vlist.begin();vox<vlist.end();vox++) { |
---|
1441 | if(this->numNondegDim==1) |
---|
1442 | this->detectMap[vox->getZ()]++; |
---|
1443 | else |
---|
1444 | this->detectMap[vox->getX()+vox->getY()*this->axisDim[0]]++; |
---|
1445 | } |
---|
1446 | } |
---|
1447 | //-------------------------------------------------------------------- |
---|
1448 | |
---|
1449 | float Cube::enclosedFlux(Detection obj) |
---|
1450 | { |
---|
1451 | /// @details |
---|
1452 | /// A function to calculate the flux enclosed by the range |
---|
1453 | /// of pixels detected in the object obj (not necessarily all |
---|
1454 | /// pixels will have been detected). |
---|
1455 | /// |
---|
1456 | /// \param obj The Detection under consideration. |
---|
1457 | |
---|
1458 | obj.calcFluxes(this->array, this->axisDim); |
---|
1459 | int xsize = obj.getXmax()-obj.getXmin()+1; |
---|
1460 | int ysize = obj.getYmax()-obj.getYmin()+1; |
---|
1461 | int zsize = obj.getZmax()-obj.getZmin()+1; |
---|
1462 | std::vector <float> fluxArray(xsize*ysize*zsize,0.); |
---|
1463 | for(int x=0;x<xsize;x++){ |
---|
1464 | for(int y=0;y<ysize;y++){ |
---|
1465 | for(int z=0;z<zsize;z++){ |
---|
1466 | fluxArray[x+y*xsize+z*ysize*xsize] = |
---|
1467 | this->getPixValue(x+obj.getXmin(), |
---|
1468 | y+obj.getYmin(), |
---|
1469 | z+obj.getZmin()); |
---|
1470 | if(this->par.getFlagNegative()) |
---|
1471 | fluxArray[x+y*xsize+z*ysize*xsize] *= -1.; |
---|
1472 | } |
---|
1473 | } |
---|
1474 | } |
---|
1475 | float sum = 0.; |
---|
1476 | for(size_t i=0;i<fluxArray.size();i++) |
---|
1477 | if(!this->par.isBlank(fluxArray[i])) sum+=fluxArray[i]; |
---|
1478 | return sum; |
---|
1479 | } |
---|
1480 | //-------------------------------------------------------------------- |
---|
1481 | |
---|
1482 | void Cube::setupColumns() |
---|
1483 | { |
---|
1484 | /// @details |
---|
1485 | /// A front-end to the two setup routines in columns.cc. |
---|
1486 | /// |
---|
1487 | /// This first gets the starting precisions, which may be from |
---|
1488 | /// the input parameters. It then sets up the columns (calculates |
---|
1489 | /// their widths and precisions and so on based on the values |
---|
1490 | /// within). The precisions are also stored in each Detection |
---|
1491 | /// object. |
---|
1492 | /// |
---|
1493 | /// Need to have called calcObjectWCSparams() somewhere |
---|
1494 | /// beforehand. |
---|
1495 | |
---|
1496 | std::vector<Detection>::iterator obj; |
---|
1497 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1498 | obj->setVelPrec( this->par.getPrecVel() ); |
---|
1499 | obj->setFpeakPrec( this->par.getPrecFlux() ); |
---|
1500 | obj->setXYZPrec( Column::prXYZ ); |
---|
1501 | obj->setPosPrec( Column::prWPOS ); |
---|
1502 | obj->setFintPrec( this->par.getPrecFlux() ); |
---|
1503 | obj->setSNRPrec( this->par.getPrecSNR() ); |
---|
1504 | } |
---|
1505 | |
---|
1506 | this->fullCols.clear(); |
---|
1507 | this->fullCols = getFullColSet(*(this->objectList), this->head); |
---|
1508 | |
---|
1509 | this->logCols.clear(); |
---|
1510 | this->logCols = getLogColSet(*(this->objectList), this->head); |
---|
1511 | |
---|
1512 | int vel,fpeak,fint,pos,xyz,snr; |
---|
1513 | vel = fullCols[VEL].getPrecision(); |
---|
1514 | fpeak = fullCols[FPEAK].getPrecision(); |
---|
1515 | snr = fullCols[SNRPEAK].getPrecision(); |
---|
1516 | xyz = fullCols[X].getPrecision(); |
---|
1517 | xyz = std::max(xyz, fullCols[Y].getPrecision()); |
---|
1518 | xyz = std::max(xyz, fullCols[Z].getPrecision()); |
---|
1519 | if(this->head.isWCS()) fint = fullCols[FINT].getPrecision(); |
---|
1520 | else fint = fullCols[FTOT].getPrecision(); |
---|
1521 | pos = fullCols[WRA].getPrecision(); |
---|
1522 | pos = std::max(pos, fullCols[WDEC].getPrecision()); |
---|
1523 | |
---|
1524 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1525 | obj->setVelPrec(vel); |
---|
1526 | obj->setFpeakPrec(fpeak); |
---|
1527 | obj->setXYZPrec(xyz); |
---|
1528 | obj->setPosPrec(pos); |
---|
1529 | obj->setFintPrec(fint); |
---|
1530 | obj->setSNRPrec(snr); |
---|
1531 | } |
---|
1532 | |
---|
1533 | } |
---|
1534 | //-------------------------------------------------------------------- |
---|
1535 | |
---|
1536 | bool Cube::objAtSpatialEdge(Detection obj) |
---|
1537 | { |
---|
1538 | /// @details |
---|
1539 | /// A function to test whether the object obj |
---|
1540 | /// lies at the edge of the cube's spatial field -- |
---|
1541 | /// either at the boundary, or next to BLANKs. |
---|
1542 | /// |
---|
1543 | /// \param obj The Detection under consideration. |
---|
1544 | |
---|
1545 | bool atEdge = false; |
---|
1546 | |
---|
1547 | size_t pix = 0; |
---|
1548 | std::vector<Voxel> voxlist = obj.getPixelSet(); |
---|
1549 | while(!atEdge && pix<voxlist.size()){ |
---|
1550 | // loop over each pixel in the object, until we find an edge pixel. |
---|
1551 | for(int dx=-1;dx<=1;dx+=2){ |
---|
1552 | if( ((voxlist[pix].getX()+dx)<0) || |
---|
1553 | ((voxlist[pix].getX()+dx)>=int(this->axisDim[0])) ) |
---|
1554 | atEdge = true; |
---|
1555 | else if(this->isBlank(voxlist[pix].getX()+dx, |
---|
1556 | voxlist[pix].getY(), |
---|
1557 | voxlist[pix].getZ())) |
---|
1558 | atEdge = true; |
---|
1559 | } |
---|
1560 | for(int dy=-1;dy<=1;dy+=2){ |
---|
1561 | if( ((voxlist[pix].getY()+dy)<0) || |
---|
1562 | ((voxlist[pix].getY()+dy)>=int(this->axisDim[1])) ) |
---|
1563 | atEdge = true; |
---|
1564 | else if(this->isBlank(voxlist[pix].getX(), |
---|
1565 | voxlist[pix].getY()+dy, |
---|
1566 | voxlist[pix].getZ())) |
---|
1567 | atEdge = true; |
---|
1568 | } |
---|
1569 | pix++; |
---|
1570 | } |
---|
1571 | |
---|
1572 | return atEdge; |
---|
1573 | } |
---|
1574 | //-------------------------------------------------------------------- |
---|
1575 | |
---|
1576 | bool Cube::objAtSpectralEdge(Detection obj) |
---|
1577 | { |
---|
1578 | /// @details |
---|
1579 | /// A function to test whether the object obj |
---|
1580 | /// lies at the edge of the cube's spectral extent -- |
---|
1581 | /// either at the boundary, or next to BLANKs. |
---|
1582 | /// |
---|
1583 | /// \param obj The Detection under consideration. |
---|
1584 | |
---|
1585 | bool atEdge = false; |
---|
1586 | |
---|
1587 | size_t pix = 0; |
---|
1588 | std::vector<Voxel> voxlist = obj.getPixelSet(); |
---|
1589 | while(!atEdge && pix<voxlist.size()){ |
---|
1590 | // loop over each pixel in the object, until we find an edge pixel. |
---|
1591 | for(int dz=-1;dz<=1;dz+=2){ |
---|
1592 | if( ((voxlist[pix].getZ()+dz)<0) || |
---|
1593 | ((voxlist[pix].getZ()+dz)>=int(this->axisDim[2])) ) |
---|
1594 | atEdge = true; |
---|
1595 | else if(this->isBlank(voxlist[pix].getX(), |
---|
1596 | voxlist[pix].getY(), |
---|
1597 | voxlist[pix].getZ()+dz)) |
---|
1598 | atEdge = true; |
---|
1599 | } |
---|
1600 | pix++; |
---|
1601 | } |
---|
1602 | |
---|
1603 | return atEdge; |
---|
1604 | } |
---|
1605 | //-------------------------------------------------------------------- |
---|
1606 | |
---|
1607 | bool Cube::objNextToMW(Detection obj) |
---|
1608 | { |
---|
1609 | /// @details A function to test whether the object obj lies |
---|
1610 | /// adjacent to the MW range or straddles it (conceivably, you |
---|
1611 | /// could have disconnected channels in your object that don't |
---|
1612 | /// touch the MW range, but lie either side - in this case we |
---|
1613 | /// want the flag). If flagMW=false we will always return false. |
---|
1614 | /// |
---|
1615 | /// \param obj The Detection under consideration. |
---|
1616 | |
---|
1617 | bool isNext = this->par.getFlagMW() && |
---|
1618 | ((obj.getZmin() <= this->par.getMaxMW()+1) && (obj.getZmax() >= this->par.getMinMW()-1)); |
---|
1619 | |
---|
1620 | return isNext; |
---|
1621 | |
---|
1622 | } |
---|
1623 | //-------------------------------------------------------------------- |
---|
1624 | |
---|
1625 | void Cube::setObjectFlags() |
---|
1626 | { |
---|
1627 | /// @details |
---|
1628 | /// A function to set any warning flags for all the detected objects |
---|
1629 | /// associated with the cube. |
---|
1630 | /// Flags to be looked for: |
---|
1631 | /// <ul><li> Negative enclosed flux (N) |
---|
1632 | /// <li> Detection at edge of field (spatially) (E) |
---|
1633 | /// <li> Detection at edge of spectral region (S) |
---|
1634 | /// </ul> |
---|
1635 | |
---|
1636 | std::vector<Detection>::iterator obj; |
---|
1637 | for(obj=this->objectList->begin();obj<this->objectList->end();obj++){ |
---|
1638 | |
---|
1639 | if( this->enclosedFlux(*obj) < 0. ) |
---|
1640 | obj->addToFlagText("N"); |
---|
1641 | |
---|
1642 | if( this->objAtSpatialEdge(*obj) ) |
---|
1643 | obj->addToFlagText("E"); |
---|
1644 | |
---|
1645 | if( this->objAtSpectralEdge(*obj) && (this->axisDim[2] > 2)) |
---|
1646 | obj->addToFlagText("S"); |
---|
1647 | |
---|
1648 | if( this->objNextToMW(*obj) ) |
---|
1649 | obj->addToFlagText("M"); |
---|
1650 | |
---|
1651 | if(obj->getFlagText()=="") obj->addToFlagText("-"); |
---|
1652 | |
---|
1653 | } |
---|
1654 | |
---|
1655 | } |
---|
1656 | //-------------------------------------------------------------------- |
---|
1657 | |
---|
1658 | /****************************************************************/ |
---|
1659 | ///////////////////////////////////////////////////////////// |
---|
1660 | //// Functions for Image class |
---|
1661 | ///////////////////////////////////////////////////////////// |
---|
1662 | |
---|
1663 | Image::Image(size_t size) |
---|
1664 | { |
---|
1665 | // need error handling in case size<0 !!! |
---|
1666 | this->numPixels = this->numDim = 0; |
---|
1667 | this->minSize = 2; |
---|
1668 | if(size<0){ |
---|
1669 | DUCHAMPERROR("Image(size)","Negative size -- could not define Image"); |
---|
1670 | } |
---|
1671 | else{ |
---|
1672 | if(size>0 && !this->arrayAllocated){ |
---|
1673 | this->array = new float[size]; |
---|
1674 | this->arrayAllocated = true; |
---|
1675 | } |
---|
1676 | this->numPixels = size; |
---|
1677 | this->axisDim = new size_t[2]; |
---|
1678 | this->axisDimAllocated = true; |
---|
1679 | this->numDim = 2; |
---|
1680 | } |
---|
1681 | } |
---|
1682 | //-------------------------------------------------------------------- |
---|
1683 | |
---|
1684 | Image::Image(size_t *dimensions) |
---|
1685 | { |
---|
1686 | this->numPixels = this->numDim = 0; |
---|
1687 | this->minSize = 2; |
---|
1688 | int size = dimensions[0] * dimensions[1]; |
---|
1689 | if(size<0){ |
---|
1690 | DUCHAMPERROR("Image(dimArray)","Negative size -- could not define Image"); |
---|
1691 | } |
---|
1692 | else{ |
---|
1693 | this->numPixels = size; |
---|
1694 | if(size>0){ |
---|
1695 | this->array = new float[size]; |
---|
1696 | this->arrayAllocated = true; |
---|
1697 | } |
---|
1698 | this->numDim=2; |
---|
1699 | this->axisDim = new size_t[2]; |
---|
1700 | this->axisDimAllocated = true; |
---|
1701 | for(int i=0;i<2;i++) this->axisDim[i] = dimensions[i]; |
---|
1702 | } |
---|
1703 | } |
---|
1704 | //-------------------------------------------------------------------- |
---|
1705 | Image::Image(const Image &i): |
---|
1706 | DataArray(i) |
---|
1707 | { |
---|
1708 | this->operator=(i); |
---|
1709 | } |
---|
1710 | |
---|
1711 | Image& Image::operator=(const Image &i) |
---|
1712 | { |
---|
1713 | if(this==&i) return *this; |
---|
1714 | ((DataArray &) *this) = i; |
---|
1715 | this->minSize = i.minSize; |
---|
1716 | return *this; |
---|
1717 | } |
---|
1718 | |
---|
1719 | //-------------------------------------------------------------------- |
---|
1720 | |
---|
1721 | void Image::saveArray(float *input, size_t size) |
---|
1722 | { |
---|
1723 | /// @details |
---|
1724 | /// Saves the array in input to the pixel array Image::array. |
---|
1725 | /// The size of the array given must be the same as the current number of |
---|
1726 | /// pixels, else an error message is returned and nothing is done. |
---|
1727 | /// \param input The array of values to be saved. |
---|
1728 | /// \param size The size of input. |
---|
1729 | |
---|
1730 | if(size != this->numPixels){ |
---|
1731 | DUCHAMPERROR("Image::saveArray", "Input array different size to existing array. Cannot save."); |
---|
1732 | } |
---|
1733 | else { |
---|
1734 | if(this->numPixels>0 && this->arrayAllocated) delete [] array; |
---|
1735 | this->numPixels = size; |
---|
1736 | if(this->numPixels>0){ |
---|
1737 | this->array = new float[size]; |
---|
1738 | this->arrayAllocated = true; |
---|
1739 | for(size_t i=0;i<size;i++) this->array[i] = input[i]; |
---|
1740 | } |
---|
1741 | } |
---|
1742 | } |
---|
1743 | //-------------------------------------------------------------------- |
---|
1744 | |
---|
1745 | void Image::extractSpectrum(float *Array, size_t *dim, size_t pixel) |
---|
1746 | { |
---|
1747 | /// @details |
---|
1748 | /// A function to extract a 1-D spectrum from a 3-D array. |
---|
1749 | /// The array is assumed to be 3-D with the third dimension the spectral one. |
---|
1750 | /// The spectrum extracted is the one lying in the spatial pixel referenced |
---|
1751 | /// by the third argument. |
---|
1752 | /// The extracted spectrum is stored in the pixel array Image::array. |
---|
1753 | /// \param Array The array containing the pixel values, from which |
---|
1754 | /// the spectrum is extracted. |
---|
1755 | /// \param dim The array of dimension values. |
---|
1756 | /// \param pixel The spatial pixel that contains the desired spectrum. |
---|
1757 | |
---|
1758 | if((pixel<0)||(pixel>=dim[0]*dim[1])){ |
---|
1759 | DUCHAMPERROR("Image::extractSpectrum", "Requested spatial pixel outside allowed range. Cannot save."); |
---|
1760 | } |
---|
1761 | else if(dim[2] != this->numPixels){ |
---|
1762 | DUCHAMPERROR("Image::extractSpectrum", "Input array different size to existing array. Cannot save."); |
---|
1763 | } |
---|
1764 | else { |
---|
1765 | if(this->numPixels>0 && this->arrayAllocated) delete [] array; |
---|
1766 | this->numPixels = dim[2]; |
---|
1767 | if(this->numPixels>0){ |
---|
1768 | this->array = new float[dim[2]]; |
---|
1769 | this->arrayAllocated = true; |
---|
1770 | for(size_t z=0;z<dim[2];z++) this->array[z] = Array[z*dim[0]*dim[1] + pixel]; |
---|
1771 | } |
---|
1772 | } |
---|
1773 | } |
---|
1774 | //-------------------------------------------------------------------- |
---|
1775 | |
---|
1776 | void Image::extractSpectrum(Cube &cube, size_t pixel) |
---|
1777 | { |
---|
1778 | /// @details |
---|
1779 | /// A function to extract a 1-D spectrum from a Cube class |
---|
1780 | /// The spectrum extracted is the one lying in the spatial pixel referenced |
---|
1781 | /// by the second argument. |
---|
1782 | /// The extracted spectrum is stored in the pixel array Image::array. |
---|
1783 | /// \param cube The Cube containing the pixel values, from which the spectrum is extracted. |
---|
1784 | /// \param pixel The spatial pixel that contains the desired spectrum. |
---|
1785 | |
---|
1786 | size_t zdim = cube.getDimZ(); |
---|
1787 | size_t spatSize = cube.getDimX()*cube.getDimY(); |
---|
1788 | if((pixel<0)||(pixel>=spatSize)){ |
---|
1789 | DUCHAMPERROR("Image::extractSpectrum", "Requested spatial pixel outside allowed range. Cannot save."); |
---|
1790 | } |
---|
1791 | else if(zdim != this->numPixels){ |
---|
1792 | DUCHAMPERROR("Image::extractSpectrum", "Input array different size to existing array. Cannot save."); |
---|
1793 | } |
---|
1794 | else { |
---|
1795 | if(this->numPixels>0 && this->arrayAllocated) delete [] array; |
---|
1796 | this->numPixels = zdim; |
---|
1797 | if(this->numPixels>0){ |
---|
1798 | this->array = new float[zdim]; |
---|
1799 | this->arrayAllocated = true; |
---|
1800 | for(size_t z=0;z<zdim;z++) |
---|
1801 | this->array[z] = cube.getPixValue(z*spatSize + pixel); |
---|
1802 | } |
---|
1803 | } |
---|
1804 | } |
---|
1805 | //-------------------------------------------------------------------- |
---|
1806 | |
---|
1807 | void Image::extractImage(float *Array, size_t *dim, size_t channel) |
---|
1808 | { |
---|
1809 | /// @details |
---|
1810 | /// A function to extract a 2-D image from a 3-D array. |
---|
1811 | /// The array is assumed to be 3-D with the third dimension the spectral one. |
---|
1812 | /// The dimensions of the array are in the dim[] array. |
---|
1813 | /// The image extracted is the one lying in the channel referenced |
---|
1814 | /// by the third argument. |
---|
1815 | /// The extracted image is stored in the pixel array Image::array. |
---|
1816 | /// \param Array The array containing the pixel values, from which the image is extracted. |
---|
1817 | /// \param dim The array of dimension values. |
---|
1818 | /// \param channel The spectral channel that contains the desired image. |
---|
1819 | |
---|
1820 | size_t spatSize = dim[0]*dim[1]; |
---|
1821 | if((channel<0)||(channel>=dim[2])){ |
---|
1822 | DUCHAMPERROR("Image::extractImage", "Requested channel outside allowed range. Cannot save."); |
---|
1823 | } |
---|
1824 | else if(spatSize != this->numPixels){ |
---|
1825 | DUCHAMPERROR("Image::extractImage", "Input array different size to existing array. Cannot save."); |
---|
1826 | } |
---|
1827 | else { |
---|
1828 | if(this->numPixels>0 && this->arrayAllocated) delete [] array; |
---|
1829 | this->numPixels = spatSize; |
---|
1830 | if(this->numPixels>0){ |
---|
1831 | this->array = new float[spatSize]; |
---|
1832 | this->arrayAllocated = true; |
---|
1833 | for(size_t npix=0; npix<spatSize; npix++) |
---|
1834 | this->array[npix] = Array[channel*spatSize + npix]; |
---|
1835 | } |
---|
1836 | } |
---|
1837 | } |
---|
1838 | //-------------------------------------------------------------------- |
---|
1839 | |
---|
1840 | void Image::extractImage(Cube &cube, size_t channel) |
---|
1841 | { |
---|
1842 | /// @details |
---|
1843 | /// A function to extract a 2-D image from Cube class. |
---|
1844 | /// The image extracted is the one lying in the channel referenced |
---|
1845 | /// by the second argument. |
---|
1846 | /// The extracted image is stored in the pixel array Image::array. |
---|
1847 | /// \param cube The Cube containing the pixel values, from which the image is extracted. |
---|
1848 | /// \param channel The spectral channel that contains the desired image. |
---|
1849 | |
---|
1850 | size_t spatSize = cube.getDimX()*cube.getDimY(); |
---|
1851 | if((channel<0)||(channel>=cube.getDimZ())){ |
---|
1852 | DUCHAMPERROR("Image::extractImage", "Requested channel outside allowed range. Cannot save."); |
---|
1853 | } |
---|
1854 | else if(spatSize != this->numPixels){ |
---|
1855 | DUCHAMPERROR("Image::extractImage", "Input array different size to existing array. Cannot save."); |
---|
1856 | } |
---|
1857 | else { |
---|
1858 | if(this->numPixels>0 && this->arrayAllocated) delete [] array; |
---|
1859 | this->numPixels = spatSize; |
---|
1860 | if(this->numPixels>0){ |
---|
1861 | this->array = new float[spatSize]; |
---|
1862 | this->arrayAllocated = true; |
---|
1863 | for(size_t npix=0; npix<spatSize; npix++) |
---|
1864 | this->array[npix] = cube.getPixValue(channel*spatSize + npix); |
---|
1865 | } |
---|
1866 | } |
---|
1867 | } |
---|
1868 | //-------------------------------------------------------------------- |
---|
1869 | |
---|
1870 | void Image::removeMW() |
---|
1871 | { |
---|
1872 | /// @details |
---|
1873 | /// A function to remove the Milky Way range of channels from a 1-D spectrum. |
---|
1874 | /// The array in this Image is assumed to be 1-D, with only the first axisDim |
---|
1875 | /// equal to 1. |
---|
1876 | /// The values of the MW channels are set to 0, unless they are BLANK. |
---|
1877 | |
---|
1878 | if(this->par.getFlagMW() && (this->axisDim[1]==1) ){ |
---|
1879 | for(size_t z=0;z<this->axisDim[0];z++){ |
---|
1880 | if(!this->isBlank(z) && this->par.isInMW(z)) this->array[z]=0.; |
---|
1881 | } |
---|
1882 | } |
---|
1883 | } |
---|
1884 | //-------------------------------------------------------------------- |
---|
1885 | |
---|
1886 | std::vector<Object2D> Image::findSources2D() |
---|
1887 | { |
---|
1888 | std::vector<bool> thresholdedArray(this->axisDim[0]*this->axisDim[1]); |
---|
1889 | for(size_t posY=0;posY<this->axisDim[1];posY++){ |
---|
1890 | for(size_t posX=0;posX<this->axisDim[0];posX++){ |
---|
1891 | size_t loc = posX + this->axisDim[0]*posY; |
---|
1892 | thresholdedArray[loc] = this->isDetection(posX,posY); |
---|
1893 | } |
---|
1894 | } |
---|
1895 | return lutz_detect(thresholdedArray, this->axisDim[0], this->axisDim[1], this->minSize); |
---|
1896 | } |
---|
1897 | |
---|
1898 | std::vector<Scan> Image::findSources1D() |
---|
1899 | { |
---|
1900 | std::vector<bool> thresholdedArray(this->axisDim[0]); |
---|
1901 | for(size_t posX=0;posX<this->axisDim[0];posX++){ |
---|
1902 | thresholdedArray[posX] = this->isDetection(posX,0); |
---|
1903 | } |
---|
1904 | return spectrumDetect(thresholdedArray, this->axisDim[0], this->minSize); |
---|
1905 | } |
---|
1906 | |
---|
1907 | |
---|
1908 | std::vector< std::vector<PixelInfo::Voxel> > Cube::getObjVoxList() |
---|
1909 | { |
---|
1910 | |
---|
1911 | std::vector< std::vector<PixelInfo::Voxel> > biglist; |
---|
1912 | |
---|
1913 | std::vector<Detection>::iterator obj; |
---|
1914 | for(obj=this->objectList->begin(); obj<this->objectList->end(); obj++) { |
---|
1915 | |
---|
1916 | Cube *subcube = new Cube; |
---|
1917 | subcube->pars() = this->par; |
---|
1918 | subcube->pars().setVerbosity(false); |
---|
1919 | subcube->pars().setFlagSubsection(true); |
---|
1920 | duchamp::Section sec = obj->getBoundingSection(); |
---|
1921 | subcube->pars().setSubsection( sec.getSection() ); |
---|
1922 | if(subcube->pars().verifySubsection() == FAILURE) |
---|
1923 | DUCHAMPERROR("get object voxel list","Unable to verify the subsection - something's wrong!"); |
---|
1924 | if(subcube->getCube() == FAILURE) |
---|
1925 | DUCHAMPERROR("get object voxel list","Unable to read the FITS file - something's wrong!"); |
---|
1926 | std::vector<PixelInfo::Voxel> voxlist = obj->getPixelSet(); |
---|
1927 | std::vector<PixelInfo::Voxel>::iterator vox; |
---|
1928 | for(vox=voxlist.begin(); vox<voxlist.end(); vox++){ |
---|
1929 | size_t pix = (vox->getX()-subcube->pars().getXOffset()) + |
---|
1930 | subcube->getDimX()*(vox->getY()-subcube->pars().getYOffset()) + |
---|
1931 | subcube->getDimX()*subcube->getDimY()*(vox->getZ()-subcube->pars().getZOffset()); |
---|
1932 | vox->setF( subcube->getPixValue(pix) ); |
---|
1933 | } |
---|
1934 | biglist.push_back(voxlist); |
---|
1935 | delete subcube; |
---|
1936 | |
---|
1937 | } |
---|
1938 | |
---|
1939 | return biglist; |
---|
1940 | |
---|
1941 | } |
---|
1942 | |
---|
1943 | } |
---|