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annotate Framework/Inputs/OpenSlidePyramid.cpp @ 318:8ad12abde290

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sparse re-encoding with OpenSlide (notably for MIRAX format)
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 11 Sep 2024 16:11:16 +0200
parents f611fb47d0e8
children 0c34b6625c67
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
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7020852a8fa9 updated year to 2024
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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8 *
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9 * This program is free software: you can redistribute it and/or
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10 * modify it under the terms of the GNU Affero General Public License
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11 * as published by the Free Software Foundation, either version 3 of
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12 * the License, or (at your option) any later version.
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13 *
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14 * This program is distributed in the hope that it will be useful, but
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 * Affero General Public License for more details.
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18 *
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19 * You should have received a copy of the GNU Affero General Public License
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20 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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21 **/
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22
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23
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24 #include "../PrecompiledHeadersWSI.h"
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25 #include "OpenSlidePyramid.h"
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26
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27 #include <Compatibility.h> // For std::unique_ptr
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28 #include <Images/ImageProcessing.h>
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29 #include <OrthancException.h>
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30 #include <SerializationToolbox.h>
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31 #include <Logging.h>
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32
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33 #include <boost/math/special_functions/round.hpp>
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34 #include <memory>
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35
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36 namespace OrthancWSI
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37 {
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38 void OpenSlidePyramid::ReadRegion(Orthanc::ImageAccessor& target,
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39 bool& isEmpty,
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40 unsigned int level,
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41 unsigned int x,
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42 unsigned int y)
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43 {
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44 std::unique_ptr<Orthanc::ImageAccessor> source(image_.ReadRegion(level, x, y, target.GetWidth(), target.GetHeight()));
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45
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46 if (target.GetWidth() != source->GetWidth() ||
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47 target.GetHeight() != source->GetHeight())
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48 {
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49 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize);
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50 }
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51
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52 const unsigned int width = source->GetWidth();
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53 const unsigned int height = source->GetHeight();
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54
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55 if (source->GetFormat() == Orthanc::PixelFormat_BGRA32)
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56 {
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57 isEmpty = true;
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58
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59 for (unsigned int y = 0; y < height && isEmpty; y++)
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60 {
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61 const uint8_t* p = reinterpret_cast<const uint8_t*>(source->GetConstRow(y));
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62 for (unsigned int x = 0; x < width && isEmpty; x++)
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63 {
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64 if (p[3] != 0)
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65 {
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66 isEmpty = false;
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67 }
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68
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69 p += 4;
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70 }
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71 }
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72 }
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73 else
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74 {
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75 isEmpty = false;
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76 }
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77
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78 if (target.GetFormat() == Orthanc::PixelFormat_RGB24 &&
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79 source->GetFormat() == Orthanc::PixelFormat_BGRA32)
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80 {
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81 // Implements alpha blending: https://en.wikipedia.org/wiki/Alpha_compositing#Alpha_blending
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82
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83 uint8_t backgroundRed, backgroundGreen, backgroundBlue;
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84 GetBackgroundColor(backgroundRed, backgroundGreen, backgroundBlue);
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85
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86 for (unsigned int y = 0; y < height; y++)
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87 {
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88 const uint8_t* p = reinterpret_cast<const uint8_t*>(source->GetConstRow(y));
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89 uint8_t* q = reinterpret_cast<uint8_t*>(target.GetRow(y));
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90 for (unsigned int x = 0; x < width; x++)
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91 {
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92 /**
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93 Alpha blending using integer arithmetics only (16 bits avoids overflows)
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94
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95 p = (1 - alpha) * background + alpha * value
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96 <=> p = (1 - p[3] / 255) * background + p[3] / 255 * value
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97 <=> p = ((255 - p[3]) * background + p[3] * value) / 255
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98
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99 **/
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100
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101 uint16_t alpha = p[3];
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102 q[0] = static_cast<uint8_t>(((255 - alpha) * backgroundRed + alpha * p[2]) / 255);
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103 q[1] = static_cast<uint8_t>(((255 - alpha) * backgroundGreen + alpha * p[1]) / 255);
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104 q[2] = static_cast<uint8_t>(((255 - alpha) * backgroundBlue + alpha * p[0]) / 255);
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105
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106 p += 4;
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107 q += 3;
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108 }
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109 }
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110 }
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111 else
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112 {
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113 Orthanc::ImageProcessing::Convert(target, *source);
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114 }
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115 }
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116
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117
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118 OpenSlidePyramid::OpenSlidePyramid(const std::string& path,
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119 unsigned int tileWidth,
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120 unsigned int tileHeight) :
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121 image_(path),
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122 tileWidth_(tileWidth),
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123 tileHeight_(tileHeight)
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124 {
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125 }
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126
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127
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128 bool OpenSlidePyramid::LookupImagedVolumeSize(float& width,
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129 float& height) const
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130 {
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131 std::string s;
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132 double mppx;
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133 double mppy;
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134
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135 if (image_.LookupProperty(s, "openslide.mpp-x") &&
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136 Orthanc::SerializationToolbox::ParseDouble(mppx, s) &&
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137 image_.LookupProperty(s, "openslide.mpp-y") &&
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138 Orthanc::SerializationToolbox::ParseDouble(mppy, s))
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139 {
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140 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates!
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141 width = mppy / 1000.0 * static_cast<double>(image_.GetLevelHeight(0));
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142 height = mppx / 1000.0 * static_cast<double>(image_.GetLevelWidth(0));
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143 return true;
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144 }
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145 else
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146 {
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147 return false;
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148 }
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149 }
0
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150 }