[299] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // smoothCube: Smooth a Cube's array, and search for objects. |
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| 3 | // ----------------------------------------------------------------------- |
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| 4 | // Copyright (C) 2006, Matthew Whiting, ATNF |
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| 5 | // |
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| 6 | // This program is free software; you can redistribute it and/or modify it |
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| 7 | // under the terms of the GNU General Public License as published by the |
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| 8 | // Free Software Foundation; either version 2 of the License, or (at your |
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| 9 | // option) any later version. |
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| 10 | // |
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| 11 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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| 12 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 13 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 14 | // for more details. |
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| 15 | // |
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| 16 | // You should have received a copy of the GNU General Public License |
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| 17 | // along with Duchamp; if not, write to the Free Software Foundation, |
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| 18 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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| 19 | // |
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| 20 | // Correspondence concerning Duchamp may be directed to: |
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| 21 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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| 22 | // Postal address: Dr. Matthew Whiting |
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| 23 | // Australia Telescope National Facility, CSIRO |
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| 24 | // PO Box 76 |
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| 25 | // Epping NSW 1710 |
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| 26 | // AUSTRALIA |
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| 27 | // ----------------------------------------------------------------------- |
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[275] | 28 | #include <vector> |
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[393] | 29 | #include <duchamp/duchamp.hh> |
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| 30 | #include <duchamp/Cubes/cubes.hh> |
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| 31 | #include <duchamp/Detection/detection.hh> |
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| 32 | #include <duchamp/PixelMap/Object2D.hh> |
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| 33 | #include <duchamp/Utils/feedback.hh> |
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| 34 | #include <duchamp/Utils/Hanning.hh> |
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[638] | 35 | #include <duchamp/Utils/GaussSmooth2D.hh> |
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[393] | 36 | #include <duchamp/Utils/Statistics.hh> |
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| 37 | #include <duchamp/Utils/utils.hh> |
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[201] | 38 | |
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[378] | 39 | namespace duchamp |
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| 40 | { |
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| 41 | |
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[258] | 42 | void Cube::SmoothSearch() |
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| 43 | { |
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[528] | 44 | /// @details |
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| 45 | /// The Cube is first smoothed, using Cube::SmoothCube(). |
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| 46 | /// It is then searched, using search3DArray() |
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| 47 | /// The resulting object list is stored in the Cube, and outputted |
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| 48 | /// to the log file if the user so requests. |
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[275] | 49 | |
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| 50 | if(!this->par.getFlagSmooth()){ |
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[913] | 51 | DUCHAMPWARN("SmoothSearch","FlagSmooth not set! Using basic CubicSearch."); |
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[275] | 52 | this->CubicSearch(); |
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| 53 | } |
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| 54 | else{ |
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[258] | 55 | |
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[290] | 56 | this->SmoothCube(); |
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[258] | 57 | |
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[275] | 58 | if(this->par.isVerbose()) std::cout << " "; |
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| 59 | |
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| 60 | this->setCubeStats(); |
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| 61 | |
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| 62 | if(this->par.isVerbose()) std::cout << " Searching... " << std::flush; |
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| 63 | |
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[686] | 64 | *(this->objectList) = search3DArray(this->axisDim,this->recon, |
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| 65 | this->par,this->Stats); |
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[275] | 66 | |
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| 67 | if(this->par.isVerbose()) std::cout << " Updating detection map... " |
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| 68 | << std::flush; |
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| 69 | this->updateDetectMap(); |
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[258] | 70 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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[275] | 71 | |
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| 72 | if(this->par.getFlagLog()){ |
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| 73 | if(this->par.isVerbose()) |
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| 74 | std::cout << " Logging intermediate detections... " << std::flush; |
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| 75 | this->logDetectionList(); |
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| 76 | if(this->par.isVerbose()) std::cout << "Done.\n"; |
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| 77 | } |
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| 78 | |
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[258] | 79 | } |
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| 80 | |
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| 81 | } |
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[275] | 82 | //----------------------------------------------------------- |
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[258] | 83 | |
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[290] | 84 | void Cube::SmoothCube() |
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| 85 | { |
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[528] | 86 | /// @details |
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| 87 | /// Switching function that chooses the appropriate function with |
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| 88 | /// which to smooth the cube, based on the Param::smoothType |
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| 89 | /// parameter. |
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| 90 | |
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[290] | 91 | if(this->par.getSmoothType()=="spectral"){ |
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| 92 | |
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| 93 | this->SpectralSmooth(); |
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[377] | 94 | |
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| 95 | } |
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| 96 | else if(this->par.getSmoothType()=="spatial"){ |
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| 97 | |
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| 98 | this->SpatialSmooth(); |
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| 99 | |
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| 100 | } |
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[290] | 101 | } |
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| 102 | //----------------------------------------------------------- |
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| 103 | |
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[275] | 104 | void Cube::SpectralSmooth() |
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[201] | 105 | { |
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[528] | 106 | /// @details |
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| 107 | /// A function that smoothes each spectrum in the cube using the |
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| 108 | /// Hanning smoothing function. The degree of smoothing is given |
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| 109 | /// by the parameter Param::hanningWidth. |
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[201] | 110 | |
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[884] | 111 | size_t xySize = this->axisDim[0]*this->axisDim[1]; |
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| 112 | size_t zdim = this->axisDim[2]; |
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[275] | 113 | ProgressBar bar; |
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| 114 | |
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[277] | 115 | if(!this->reconExists && this->par.getSmoothType()=="spectral"){ |
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[365] | 116 | // if(!this->head.isSpecOK()) |
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[913] | 117 | if(!this->head.canUseThirdAxis()){ |
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| 118 | DUCHAMPWARN("SpectralSmooth","There is no spectral axis, so cannot do the spectral smoothing."); |
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| 119 | } |
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[277] | 120 | else{ |
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| 121 | |
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| 122 | Hanning hann(this->par.getHanningWidth()); |
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[201] | 123 | |
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[277] | 124 | float *spectrum = new float[this->axisDim[2]]; |
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[275] | 125 | |
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[277] | 126 | if(this->par.isVerbose()) { |
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| 127 | std::cout<<" Smoothing spectrally... "; |
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| 128 | bar.init(xySize); |
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| 129 | } |
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[275] | 130 | |
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[894] | 131 | for(size_t pix=0;pix<xySize;pix++){ |
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[275] | 132 | |
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[277] | 133 | if( this->par.isVerbose() ) bar.update(pix+1); |
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[275] | 134 | |
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[894] | 135 | for(size_t z=0;z<zdim;z++){ |
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[277] | 136 | if(this->isBlank(z*xySize+pix)) spectrum[z]=0.; |
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| 137 | else spectrum[z] = this->array[z*xySize+pix]; |
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| 138 | } |
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[275] | 139 | |
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[277] | 140 | float *smoothed = hann.smooth(spectrum,zdim); |
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[275] | 141 | |
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[894] | 142 | for(size_t z=0;z<zdim;z++){ |
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[277] | 143 | if(this->isBlank(z*xySize+pix)) |
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[285] | 144 | this->recon[z*xySize+pix] = this->array[z*xySize+pix]; |
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[277] | 145 | else |
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| 146 | this->recon[z*xySize+pix] = smoothed[z]; |
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| 147 | } |
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| 148 | delete [] smoothed; |
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[275] | 149 | } |
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[277] | 150 | this->reconExists = true; |
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| 151 | if(this->par.isVerbose()) bar.fillSpace("All Done.\n"); |
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[275] | 152 | |
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[277] | 153 | delete [] spectrum; |
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[275] | 154 | |
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[277] | 155 | } |
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[275] | 156 | } |
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| 157 | } |
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| 158 | //----------------------------------------------------------- |
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| 159 | |
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| 160 | void Cube::SpatialSmooth() |
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| 161 | { |
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| 162 | |
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[277] | 163 | if(!this->reconExists && this->par.getSmoothType()=="spatial"){ |
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[201] | 164 | |
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[913] | 165 | if( this->head.getNumAxes() < 2 ){ |
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| 166 | DUCHAMPWARN("SpatialSmooth","There are not enough axes to do the spatial smoothing."); |
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| 167 | } |
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[277] | 168 | else{ |
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[201] | 169 | |
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[884] | 170 | size_t xySize = this->axisDim[0]*this->axisDim[1]; |
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| 171 | size_t xdim = this->axisDim[0]; |
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| 172 | size_t ydim = this->axisDim[1]; |
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| 173 | size_t zdim = this->axisDim[2]; |
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[275] | 174 | |
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[277] | 175 | ProgressBar bar; |
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[1195] | 176 | bool useBar = this->par.isVerbose() && (zdim > 1); |
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[372] | 177 | |
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[285] | 178 | // if kernMin is negative (not defined), make it equal to kernMaj |
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| 179 | if(this->par.getKernMin() < 0) |
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| 180 | this->par.setKernMin(this->par.getKernMaj()); |
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| 181 | |
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[1279] | 182 | std::cout << " "; |
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[638] | 183 | GaussSmooth2D<float> gauss(this->par.getKernMaj(), |
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[1279] | 184 | this->par.getKernMin(), |
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| 185 | this->par.getKernPA(), |
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[1281] | 186 | this->par.getSpatialSmoothCutoff()); |
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[1279] | 187 | |
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[277] | 188 | if(this->par.isVerbose()) { |
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| 189 | std::cout<<" Smoothing spatially... " << std::flush; |
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[372] | 190 | if(useBar) bar.init(zdim); |
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[277] | 191 | } |
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| 192 | |
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[1194] | 193 | // pointer used to point to start of a given channel's image |
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| 194 | // Can do this because the spatial axes vary the quickest. |
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[1187] | 195 | float *image=0; |
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[291] | 196 | |
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[1279] | 197 | EDGES edgeTreatment=EQUALTOEDGE; |
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| 198 | if(this->par.getSmoothEdgeMethod()=="equal") edgeTreatment=EQUALTOEDGE; |
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| 199 | else if(this->par.getSmoothEdgeMethod()=="truncate") edgeTreatment=TRUNCATE; |
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| 200 | else if(this->par.getSmoothEdgeMethod()=="scale") edgeTreatment=SCALEBYCOVERAGE; |
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| 201 | |
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| 202 | |
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[894] | 203 | for(size_t z=0;z<zdim;z++){ |
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[277] | 204 | |
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[1194] | 205 | if(useBar) bar.update(z+1); |
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[275] | 206 | |
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[1194] | 207 | // update pointer to point to current channel |
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[1187] | 208 | image = this->array + z*xySize; |
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[201] | 209 | |
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[1393] | 210 | std::vector<bool> mask = this->par.makeBlankMask(image,xySize); |
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[275] | 211 | |
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[1279] | 212 | float *smoothed = gauss.smooth(image,xdim,ydim,mask,edgeTreatment); |
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[275] | 213 | |
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[1187] | 214 | for(size_t pix=0;pix<xySize;pix++) |
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[285] | 215 | this->recon[z*xySize+pix] = smoothed[pix]; |
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[201] | 216 | |
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[1187] | 217 | if(gauss.isAllocated()) delete [] smoothed; |
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[277] | 218 | } |
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[201] | 219 | |
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[277] | 220 | this->reconExists = true; |
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[275] | 221 | |
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[372] | 222 | if(par.isVerbose()){ |
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| 223 | if(useBar) bar.fillSpace("All Done."); |
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| 224 | std::cout << "\n"; |
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| 225 | } |
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| 226 | |
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| 227 | } |
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[277] | 228 | } |
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[275] | 229 | } |
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| 230 | //----------------------------------------------------------- |
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| 231 | |
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| 232 | void Cube::SpatialSmoothNSearch() |
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| 233 | { |
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| 234 | |
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[884] | 235 | size_t xySize = this->axisDim[0]*this->axisDim[1]; |
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| 236 | size_t xdim = this->axisDim[0]; |
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| 237 | size_t ydim = this->axisDim[1]; |
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| 238 | size_t zdim = this->axisDim[2]; |
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[275] | 239 | int numFound=0; |
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| 240 | ProgressBar bar; |
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| 241 | |
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[638] | 242 | GaussSmooth2D<float> gauss(this->par.getKernMaj(), |
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[516] | 243 | this->par.getKernMin(), |
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| 244 | this->par.getKernPA()); |
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[275] | 245 | |
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| 246 | this->Stats.scaleNoise(1./gauss.getStddevScale()); |
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| 247 | if(this->par.getFlagFDR()) this->setupFDR(); |
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| 248 | |
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| 249 | if(this->par.isVerbose()) { |
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| 250 | std::cout<<" Smoothing spatially & searching... " << std::flush; |
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| 251 | bar.init(zdim); |
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| 252 | } |
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| 253 | |
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| 254 | std::vector <Detection> outputList; |
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[884] | 255 | size_t *imdim = new size_t[2]; |
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[275] | 256 | imdim[0] = xdim; imdim[1] = ydim; |
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| 257 | Image *channelImage = new Image(imdim); |
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| 258 | delete [] imdim; |
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| 259 | channelImage->saveParam(this->par); |
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| 260 | channelImage->saveStats(this->Stats); |
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| 261 | channelImage->setMinSize(1); |
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| 262 | |
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| 263 | float *image = new float[xySize]; |
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[634] | 264 | float *smoothed=0; |
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[275] | 265 | float median,madfm;//,threshold; |
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[894] | 266 | for(size_t z=0;z<zdim;z++){ |
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[275] | 267 | |
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| 268 | if( this->par.isVerbose() ) bar.update(z+1); |
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| 269 | |
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[1242] | 270 | if(!this->par.isFlaggedChannel(z)){ |
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[275] | 271 | |
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[894] | 272 | for(size_t pix=0;pix<xySize;pix++) image[pix] = this->array[z*xySize+pix]; |
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[275] | 273 | |
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[1393] | 274 | std::vector<bool> mask = this->par.makeBlankMask(image+z*xySize,xySize); |
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[275] | 275 | |
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| 276 | smoothed = gauss.smooth(image,xdim,ydim,mask); |
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| 277 | |
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| 278 | findMedianStats(smoothed,xySize,mask,median,madfm); |
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| 279 | |
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| 280 | channelImage->saveArray(smoothed,xySize); |
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| 281 | |
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[582] | 282 | std::vector<PixelInfo::Object2D> objlist = channelImage->findSources2D(); |
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[623] | 283 | std::vector<PixelInfo::Object2D>::iterator obj; |
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[275] | 284 | numFound += objlist.size(); |
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[623] | 285 | for(obj=objlist.begin();obj<objlist.end();obj++){ |
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[275] | 286 | Detection newObject; |
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[623] | 287 | newObject.addChannel(z,*obj); |
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[275] | 288 | newObject.setOffsets(this->par); |
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[1430] | 289 | mergeIntoList(newObject,outputList,this->par); |
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[275] | 290 | } |
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| 291 | |
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[201] | 292 | } |
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[275] | 293 | |
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[201] | 294 | } |
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| 295 | |
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[275] | 296 | delete [] smoothed; |
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| 297 | delete [] image; |
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| 298 | delete channelImage; |
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| 299 | |
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[277] | 300 | // this->reconExists = true; |
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[275] | 301 | if(par.isVerbose()){ |
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| 302 | bar.fillSpace("Found "); |
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| 303 | std::cout << numFound << ".\n"; |
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| 304 | } |
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| 305 | |
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[291] | 306 | *this->objectList = outputList; |
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[201] | 307 | |
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| 308 | } |
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[378] | 309 | |
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| 310 | } |
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