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0
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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 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU Affero General Public License
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8 * as published by the Free Software Foundation, either version 3 of
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9 * the License, or (at your option) any later version.
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10 *
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11 * This program is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty of
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13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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14 * Affero General Public License for more details.
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15 *
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16 * You should have received a copy of the GNU Affero General Public License
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17 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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18 **/
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19
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20
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21 #include "HierarchicalTiffWriter.h"
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22
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23 #include "../Orthanc/Core/Logging.h"
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24 #include "../Orthanc/Core/OrthancException.h"
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25 #include "../Orthanc/Core/Uuid.h"
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26
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27 namespace OrthancWSI
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28 {
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29 class HierarchicalTiffWriter::PendingTile
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30 {
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31 private:
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32 HierarchicalTiffWriter& that_;
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33 unsigned int level_;
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34 unsigned int tileX_;
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35 unsigned int tileY_;
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36 Orthanc::Toolbox::TemporaryFile file_;
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37
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38 public:
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39 PendingTile(HierarchicalTiffWriter& that,
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40 unsigned int level,
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41 unsigned int tileX,
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42 unsigned int tileY,
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43 const std::string& tile) :
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44 that_(that),
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45 level_(level),
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46 tileX_(tileX),
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47 tileY_(tileY)
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48 {
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49 file_.Write(tile);
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50 }
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51
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52 unsigned int GetLevel() const
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53 {
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54 return level_;
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55 }
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56
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57 unsigned int GetTileX() const
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58 {
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59 return tileX_;
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60 }
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61
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62 unsigned int GetTileY() const
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63 {
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64 return tileY_;
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65 }
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66
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67 void Store(TIFF* tiff)
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68 {
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69 std::string tile;
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70 file_.Read(tile);
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71 that_.StoreTile(tile, tileX_, tileY_);
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72 }
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73 };
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74
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75
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76 struct HierarchicalTiffWriter::Comparator
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77 {
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78 inline bool operator() (PendingTile* const& a,
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79 PendingTile* const& b)
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80 {
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81 if (a->GetLevel() < b->GetLevel())
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82 {
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83 return true;
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84 }
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85
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86 if (a->GetLevel() > b->GetLevel())
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87 {
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88 return false;
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89 }
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90
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91 if (a->GetTileY() < b->GetTileY())
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92 {
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93 return true;
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94 }
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95
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96 if (a->GetTileY() > b->GetTileY())
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97 {
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98 return false;
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99 }
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100
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101 return a->GetTileX() < b->GetTileX();
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102 }
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103 };
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104
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105
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106 static uint8_t GetUint8(const std::string& tile,
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107 size_t index)
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108 {
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109 if (index >= tile.size())
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110 {
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111 return 0;
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112 }
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113 else
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114 {
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115 return static_cast<uint8_t>(tile[index]);
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116 }
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117 }
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118
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119
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120 #if 0
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121 static uint16_t GetUint16(const std::string& tile,
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122 size_t index)
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123 {
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124 if (index + 1 >= tile.size())
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125 {
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126 return 0;
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127 }
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128 else
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129 {
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130 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]);
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131 }
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132 }
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133 #endif
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134
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135
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136 static void CheckJpegTile(const std::string& tile,
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137 Orthanc::PixelFormat pixelFormat)
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138 {
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139 // Check the sampling by accessing the "Start of Frame" header of JPEG
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140
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141 if (tile.size() < 3 ||
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142 static_cast<uint8_t>(tile[0]) != 0xff ||
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143 static_cast<uint8_t>(tile[1]) != 0xd8 ||
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144 static_cast<uint8_t>(tile[2]) != 0xff)
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145 {
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146 LOG(WARNING) << "The source image does not contain JPEG tiles";
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147 return;
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148 }
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149
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150 // Look for the "Start of Frame" header (FF C0)
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151 for (size_t i = 2; i + 1 < tile.size(); i++)
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152 {
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153 if (static_cast<uint8_t>(tile[i]) == 0xff &&
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154 static_cast<uint8_t>(tile[i + 1]) == 0xc0)
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155 {
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156 uint8_t numberOfComponents = GetUint8(tile, i + 9);
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157
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158 switch (pixelFormat)
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159 {
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160 case Orthanc::PixelFormat_Grayscale8:
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161 if (numberOfComponents != 3)
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162 {
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163 LOG(WARNING) << "The source image does not contain a grayscale image as expected";
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164 }
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165 break;
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166
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167 case Orthanc::PixelFormat_RGB24:
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168 {
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169 if (numberOfComponents != 3)
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170 {
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171 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected";
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172 }
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173
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174 // Read the header corresponding to the first component
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175 const size_t component = 0;
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176 const size_t offset = i + 10 + component * 3;
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177 const uint8_t sampling = GetUint8(tile, offset + 1);
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178 const int samplingH = sampling / 16;
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179 const int samplingV = sampling % 16;
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180
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181 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV;
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182
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183 if (samplingH != 2 ||
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184 samplingV != 2)
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185 {
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186 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, "
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187 << "you should consider using option \"--reencode\"";
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188 }
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189
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190 break;
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191 }
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192
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193 default:
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194 break;
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195 }
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196 }
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197 }
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198 }
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199
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200
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201
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202 void HierarchicalTiffWriter::StoreTile(const std::string& tile,
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203 unsigned int tileX,
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204 unsigned int tileY)
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205 {
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206 // Get the index of the tile
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207 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/);
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208
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209 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) !=
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210 static_cast<tsize_t>(tile.size()))
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211 {
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212 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile);
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213 }
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214
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215 if (isFirst_ &&
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216 GetImageCompression() == ImageCompression_Jpeg)
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217 {
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218 CheckJpegTile(tile, GetPixelFormat());
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219 }
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220
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221 isFirst_ = false;
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222 }
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223
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224
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225 void HierarchicalTiffWriter::ConfigureLevel(const Level& level,
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226 bool createLevel)
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227 {
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228 if (createLevel && TIFFWriteDirectory(tiff_) != 1)
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229 {
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230 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile);
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231 }
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232
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233 if (TIFFFlush(tiff_) != 1)
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234 {
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235 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile);
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236 }
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237
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238 currentLevel_ = level.z_;
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239 nextX_ = 0;
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240 nextY_ = 0;
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241
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242 switch (GetImageCompression())
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243 {
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244 case ImageCompression_Jpeg:
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245 {
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246 uint16_t c = COMPRESSION_JPEG;
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247
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248 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1)
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249 {
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250 Close();
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251 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile);
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252 }
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253
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254 break;
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255 }
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256
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257 default:
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258 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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259 }
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260
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261
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262 switch (GetPixelFormat())
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263 {
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264 case Orthanc::PixelFormat_RGB24:
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265 {
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266 uint16_t samplesPerPixel = 3;
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267 uint16_t photometric = PHOTOMETRIC_YCBCR;
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268 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB
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269 uint16_t bpp = 8;
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270 uint16_t subsampleHorizontal = 2;
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271 uint16_t subsampleVertical = 2;
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272
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273 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 ||
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274 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 ||
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275 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 ||
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276 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 ||
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277 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1)
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278 {
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279 Close();
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280 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile);
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281 }
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282
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283 break;
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284 }
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285
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286 default:
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287 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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288 }
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289
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290 uint32_t w = level.width_;
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291 uint32_t h = level.height_;
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292 uint32_t tw = GetTileWidth();
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293 uint32_t th = GetTileHeight();
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294
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295 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 ||
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296 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 ||
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297 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 ||
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298 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1)
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299 {
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300 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile);
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301 }
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302 }
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303
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304
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305 void HierarchicalTiffWriter::AdvanceToNextTile()
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306 {
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307 assert(currentLevel_ < levels_.size());
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308
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309 nextX_ += 1;
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310 if (nextX_ >= levels_[currentLevel_].countTilesX_)
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311 {
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312 nextX_ = 0;
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313 nextY_ += 1;
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314
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315 if (nextY_ >= levels_[currentLevel_].countTilesY_)
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316 {
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317 currentLevel_ += 1;
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318
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319 if (currentLevel_ < levels_.size())
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320 {
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321 ConfigureLevel(levels_[currentLevel_], true);
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322 }
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323 }
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324 }
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325 }
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326
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327
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328 void HierarchicalTiffWriter::ScanPending()
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329 {
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330 std::sort(pending_.begin(), pending_.end(), Comparator());
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331
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332 while (currentLevel_ < levels_.size() &&
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333 !pending_.empty() &&
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334 pending_.front()->GetLevel() == currentLevel_ &&
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335 pending_.front()->GetTileX() == nextX_ &&
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336 pending_.front()->GetTileY() == nextY_)
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337 {
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338 pending_.front()->Store(tiff_);
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339 delete pending_.front();
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340 pending_.pop_front();
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341 AdvanceToNextTile();
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342 }
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343 }
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344
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345
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346 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile,
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347 const Level& level,
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348 unsigned int tileX,
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349 unsigned int tileY)
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350 {
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351 boost::mutex::scoped_lock lock(mutex_);
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352
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353 if (level.z_ == currentLevel_ &&
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354 tileX == nextX_ &&
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355 tileY == nextY_)
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356 {
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357 StoreTile(tile, tileX, tileY);
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358 AdvanceToNextTile();
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359 ScanPending();
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360 }
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361 else
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362 {
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363 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile));
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364 }
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365 }
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366
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367
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368 void HierarchicalTiffWriter::AddLevelInternal(const Level& level)
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369 {
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370 if (level.z_ == 0)
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371 {
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372 // Configure the finest level on initialization
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373 ConfigureLevel(level, false);
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374 }
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375
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376 levels_.push_back(level);
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377 }
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378
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379
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380 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path,
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381 Orthanc::PixelFormat pixelFormat,
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382 ImageCompression compression,
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383 unsigned int tileWidth,
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384 unsigned int tileHeight) :
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385 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight),
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386 currentLevel_(0),
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387 isFirst_(true)
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388 {
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389 tiff_ = TIFFOpen(path.c_str(), "w");
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390 if (tiff_ == NULL)
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391 {
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392 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile);
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393 }
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394 }
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395
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396
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397 HierarchicalTiffWriter::~HierarchicalTiffWriter()
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398 {
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399 if (pending_.size())
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400 {
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401 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file";
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402 }
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403
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404 for (size_t i = 0; i < pending_.size(); i++)
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405 {
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406 if (pending_[i])
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407 {
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408 delete pending_[i];
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409 }
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410 }
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411
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412 Close();
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413 }
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414
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415
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416 void HierarchicalTiffWriter::Flush()
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417 {
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418 boost::mutex::scoped_lock lock(mutex_);
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419 ScanPending();
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420 }
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421 }
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