Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 68:c619c8bd72ed
DicomPyramidInstance::Deserialize
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 25 Nov 2016 21:18:46 +0100 |
parents | 63d0a5c74460 |
children | d529d9ce3c7e |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU Affero General Public License | |
8 * as published by the Free Software Foundation, either version 3 of | |
9 * the License, or (at your option) any later version. | |
10 * | |
11 * This program is distributed in the hope that it will be useful, but | |
12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
14 * Affero General Public License for more details. | |
15 * | |
16 * You should have received a copy of the GNU Affero General Public License | |
17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
18 **/ | |
19 | |
20 | |
16
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21 #include "../PrecompiledHeadersWSI.h" |
0 | 22 #include "DicomPyramidInstance.h" |
23 | |
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24 #include "../../Resources/Orthanc/Core/Logging.h" |
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25 #include "../../Resources/Orthanc/Core/OrthancException.h" |
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26 #include "../../Resources/Orthanc/Core/Toolbox.h" |
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27 #include "../../Resources/Orthanc/Plugins/Samples/Common/DicomDatasetReader.h" |
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28 #include "../../Resources/Orthanc/Plugins/Samples/Common/FullOrthancDataset.h" |
0 | 29 #include "../DicomToolbox.h" |
30 | |
31 #include <cassert> | |
64
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32 #include <json/writer.h> |
0 | 33 |
34 namespace OrthancWSI | |
35 { | |
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36 static ImageCompression DetectImageCompression(OrthancPlugins::IOrthancConnection& orthanc, |
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37 const std::string& instanceId) |
0 | 38 { |
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39 using namespace OrthancPlugins; |
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40 |
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41 DicomDatasetReader header(new FullOrthancDataset |
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42 (orthanc, "/instances/" + instanceId + "/header")); |
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43 |
0 | 44 std::string s = Orthanc::Toolbox::StripSpaces |
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45 (header.GetMandatoryStringValue(DICOM_TAG_TRANSFER_SYNTAX_UID)); |
0 | 46 |
47 if (s == "1.2.840.10008.1.2" || | |
48 s == "1.2.840.10008.1.2.1") | |
49 { | |
50 return ImageCompression_None; | |
51 } | |
52 else if (s == "1.2.840.10008.1.2.4.50") | |
53 { | |
54 return ImageCompression_Jpeg; | |
55 } | |
56 else if (s == "1.2.840.10008.1.2.4.90" || | |
57 s == "1.2.840.10008.1.2.4.91") | |
58 { | |
59 return ImageCompression_Jpeg2000; | |
60 } | |
61 else | |
62 { | |
63 LOG(ERROR) << "Unsupported transfer syntax: " << s; | |
64 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
65 } | |
66 } | |
67 | |
68 | |
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69 static Orthanc::PixelFormat DetectPixelFormat(OrthancPlugins::DicomDatasetReader& reader) |
0 | 70 { |
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71 using namespace OrthancPlugins; |
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72 |
0 | 73 std::string photometric = Orthanc::Toolbox::StripSpaces |
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74 (reader.GetMandatoryStringValue(DICOM_TAG_PHOTOMETRIC_INTERPRETATION)); |
0 | 75 |
76 if (photometric == "PALETTE") | |
77 { | |
78 LOG(ERROR) << "Unsupported photometric interpretation: " << photometric; | |
79 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
80 } | |
81 | |
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82 unsigned int bitsStored = reader.GetUnsignedIntegerValue(DICOM_TAG_BITS_STORED); |
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83 unsigned int samplesPerPixel = reader.GetUnsignedIntegerValue(DICOM_TAG_SAMPLES_PER_PIXEL); |
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84 bool isSigned = (reader.GetUnsignedIntegerValue(DICOM_TAG_PIXEL_REPRESENTATION) != 0); |
0 | 85 |
86 if (bitsStored == 8 && | |
87 samplesPerPixel == 1 && | |
88 !isSigned) | |
89 { | |
90 return Orthanc::PixelFormat_Grayscale8; | |
91 } | |
92 else if (bitsStored == 8 && | |
93 samplesPerPixel == 3 && | |
94 !isSigned) | |
95 { | |
96 return Orthanc::PixelFormat_RGB24; | |
97 } | |
98 else | |
99 { | |
100 LOG(ERROR) << "Unsupported pixel format"; | |
101 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
102 } | |
103 } | |
104 | |
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105 |
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106 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancPlugins::IOrthancConnection& orthanc) |
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107 { |
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108 /** |
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109 * Lazy detection of the image compression using the transfer |
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110 * syntax stored inside the DICOM header. Given the fact that |
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111 * reading the header is a time-consuming operation (it implies |
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112 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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113 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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114 * "/header" REST call is delayed until it is really required. |
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115 **/ |
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116 |
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117 if (!hasCompression_) |
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118 { |
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119 compression_ = DetectImageCompression(orthanc, instanceId_); |
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120 hasCompression_ = true; |
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121 } |
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122 |
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123 return compression_; |
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124 } |
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125 |
0 | 126 |
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127 void DicomPyramidInstance::Load(OrthancPlugins::IOrthancConnection& orthanc, |
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128 const std::string& instanceId) |
0 | 129 { |
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130 using namespace OrthancPlugins; |
0 | 131 |
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132 DicomDatasetReader reader(new FullOrthancDataset(orthanc, "/instances/" + instanceId + "/tags")); |
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133 |
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134 if (reader.GetMandatoryStringValue(DICOM_TAG_SOP_CLASS_UID) != "1.2.840.10008.5.1.4.1.1.77.1.6" || |
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135 reader.GetMandatoryStringValue(DICOM_TAG_MODALITY) != "SM") |
0 | 136 { |
137 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
138 } | |
139 | |
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140 format_ = DetectPixelFormat(reader); |
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141 tileWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_COLUMNS); |
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142 tileHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_ROWS); |
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143 totalWidth_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS); |
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144 totalHeight_ = reader.GetUnsignedIntegerValue(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS); |
0 | 145 |
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146 size_t countFrames; |
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147 if (!reader.GetDataset().GetSequenceSize(countFrames, DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE)) |
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148 { |
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149 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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150 } |
0 | 151 |
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152 if (countFrames != reader.GetUnsignedIntegerValue(DICOM_TAG_NUMBER_OF_FRAMES)) |
0 | 153 { |
154 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; | |
155 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
156 } | |
157 | |
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158 frames_.resize(countFrames); |
0 | 159 |
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160 for (size_t i = 0; i < countFrames; i++) |
0 | 161 { |
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162 int xx = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
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163 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, |
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164 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX)); |
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165 |
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166 int yy = reader.GetIntegerValue(DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
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167 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, |
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168 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX)); |
0 | 169 |
170 // "-1", because coordinates are shifted by 1 in DICOM | |
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171 xx -= 1; |
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172 yy -= 1; |
0 | 173 |
174 unsigned int x = static_cast<unsigned int>(xx); | |
175 unsigned int y = static_cast<unsigned int>(yy); | |
176 | |
177 if (xx < 0 || | |
178 yy < 0 || | |
179 x % tileWidth_ != 0 || | |
180 y % tileHeight_ != 0 || | |
181 x >= totalWidth_ || | |
182 y >= totalHeight_) | |
183 { | |
184 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" | |
185 << x << "," << y << ") in instance: " << instanceId; | |
186 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
187 } | |
188 | |
189 frames_[i].first = x / tileWidth_; | |
190 frames_[i].second = y / tileHeight_; | |
191 } | |
192 } | |
193 | |
194 | |
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195 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc, |
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196 const std::string& instanceId) : |
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197 instanceId_(instanceId), |
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198 hasCompression_(false) |
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199 { |
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200 Load(orthanc, instanceId); |
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201 } |
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202 |
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203 |
0 | 204 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const |
205 { | |
206 assert(frame < frames_.size()); | |
207 return frames_[frame].first; | |
208 } | |
209 | |
210 | |
211 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
212 { | |
213 assert(frame < frames_.size()); | |
214 return frames_[frame].second; | |
215 } | |
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216 |
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217 |
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218 void DicomPyramidInstance::Serialize(std::string& result) const |
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219 { |
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220 Json::Value frames = Json::arrayValue; |
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221 for (size_t i = 0; i < frames_.size(); i++) |
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222 { |
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223 Json::Value frame = Json::arrayValue; |
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224 frame.append(frames_[i].first); |
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225 frame.append(frames_[i].second); |
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226 |
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227 frames.append(frame); |
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228 } |
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229 |
68
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230 Json::Value content; |
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231 content["Frames"] = frames; |
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232 content["TileHeight"] = tileHeight_; |
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233 content["TileWidth"] = tileWidth_; |
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234 content["TotalHeight"] = totalHeight_; |
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235 content["TotalWidth"] = totalWidth_; |
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236 |
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237 switch (format_) |
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238 { |
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239 case Orthanc::PixelFormat_RGB24: |
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240 content["PixelFormat"] = 0; |
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241 break; |
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242 |
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243 case Orthanc::PixelFormat_Grayscale8: |
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244 content["PixelFormat"] = 1; |
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245 break; |
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246 |
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247 default: |
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248 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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249 } |
64
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250 |
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251 Json::FastWriter writer; |
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252 result = writer.write(content); |
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253 } |
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254 |
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255 |
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256 void DicomPyramidInstance::Deserialize(const std::string& s) |
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257 { |
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258 hasCompression_ = false; |
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259 |
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260 Json::Value content; |
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261 OrthancPlugins::IOrthancConnection::ParseJson(content, s); |
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262 |
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263 if (content.type() != Json::objectValue || |
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264 !content.isMember("Frames") || |
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265 !content.isMember("PixelFormat") || |
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266 !content.isMember("TileHeight") || |
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267 !content.isMember("TileWidth") || |
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268 !content.isMember("TotalHeight") || |
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269 !content.isMember("TotalWidth") || |
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270 content["Frames"].type() != Json::arrayValue || |
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271 content["PixelFormat"].type() != Json::intValue || |
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272 content["TileHeight"].type() != Json::intValue || |
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273 content["TileWidth"].type() != Json::intValue || |
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274 content["TotalHeight"].type() != Json::intValue || |
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275 content["TotalWidth"].type() != Json::intValue || |
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276 content["TileHeight"].asInt() < 0 || |
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277 content["TileWidth"].asInt() < 0 || |
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278 content["TotalHeight"].asInt() < 0 || |
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279 content["TotalWidth"].asInt() < 0) |
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280 { |
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281 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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282 } |
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283 |
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284 switch (content["Frames"].asInt()) |
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285 { |
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286 case 0: |
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287 format_ = Orthanc::PixelFormat_RGB24; |
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288 break; |
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289 |
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290 case 1: |
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291 format_ = Orthanc::PixelFormat_Grayscale8; |
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292 break; |
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293 |
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294 default: |
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295 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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296 } |
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297 |
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298 tileHeight_ = static_cast<unsigned int>(content["TileHeight"].asInt()); |
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299 tileWidth_ = static_cast<unsigned int>(content["TileWidth"].asInt()); |
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300 totalHeight_ = static_cast<unsigned int>(content["TotalHeight"].asInt()); |
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301 totalWidth_ = static_cast<unsigned int>(content["TotalWidth"].asInt()); |
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302 |
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303 const Json::Value f = content["Frames"]; |
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304 frames_.resize(f.size()); |
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305 |
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306 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++) |
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307 { |
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308 if (f[i].type() != Json::arrayValue || |
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309 f[i].size() != 2 || |
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310 f[i][0].type() != Json::intValue || |
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311 f[i][1].type() != Json::intValue || |
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312 f[i][0].asInt() < 0 || |
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313 f[i][1].asInt() < 0) |
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314 { |
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315 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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316 } |
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317 |
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318 frames_[i].first = f[i][0].asInt(); |
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319 frames_[i].second = f[i][1].asInt(); |
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320 } |
64
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321 } |
0 | 322 } |