Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 175:e3cbf890b588
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 31 Jan 2020 17:44:03 +0100 |
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children | f299c191cd76 |
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 | |
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
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22 #include "../PrecompiledHeadersWSI.h" |
0 | 23 #include "DicomPyramidInstance.h" |
24 | |
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25 #include <Core/Logging.h> |
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26 #include <Core/OrthancException.h> |
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27 #include <Core/Toolbox.h> |
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28 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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29 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
0 | 30 #include "../DicomToolbox.h" |
31 | |
32 #include <cassert> | |
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33 #include <json/writer.h> |
0 | 34 |
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35 #define SERIALIZED_METADATA "4200" |
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36 |
0 | 37 namespace OrthancWSI |
38 { | |
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39 static ImageCompression DetectImageCompression(OrthancPlugins::IOrthancConnection& orthanc, |
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40 const std::string& instanceId) |
0 | 41 { |
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42 using namespace OrthancPlugins; |
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43 |
87 | 44 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header"); |
45 DicomDatasetReader header(dataset); | |
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46 |
0 | 47 std::string s = Orthanc::Toolbox::StripSpaces |
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48 (header.GetMandatoryStringValue(DICOM_TAG_TRANSFER_SYNTAX_UID)); |
0 | 49 |
50 if (s == "1.2.840.10008.1.2" || | |
51 s == "1.2.840.10008.1.2.1") | |
52 { | |
53 return ImageCompression_None; | |
54 } | |
55 else if (s == "1.2.840.10008.1.2.4.50") | |
56 { | |
57 return ImageCompression_Jpeg; | |
58 } | |
59 else if (s == "1.2.840.10008.1.2.4.90" || | |
60 s == "1.2.840.10008.1.2.4.91") | |
61 { | |
62 return ImageCompression_Jpeg2000; | |
63 } | |
64 else | |
65 { | |
66 LOG(ERROR) << "Unsupported transfer syntax: " << s; | |
67 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
68 } | |
69 } | |
70 | |
71 | |
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72 static void DetectPixelFormat(Orthanc::PixelFormat& format, |
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73 Orthanc::PhotometricInterpretation& photometric, |
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74 OrthancPlugins::DicomDatasetReader& reader) |
0 | 75 { |
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76 using namespace OrthancPlugins; |
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77 |
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78 std::string p = Orthanc::Toolbox::StripSpaces |
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79 (reader.GetMandatoryStringValue(DICOM_TAG_PHOTOMETRIC_INTERPRETATION)); |
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80 |
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81 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
0 | 82 |
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83 if (photometric == Orthanc::PhotometricInterpretation_Palette) |
0 | 84 { |
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85 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
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86 "Unsupported photometric interpretation: " + p); |
0 | 87 } |
88 | |
89 | 89 unsigned int bitsStored, samplesPerPixel, tmp; |
90 | |
91 if (!reader.GetUnsignedIntegerValue(bitsStored, DICOM_TAG_BITS_STORED) || | |
92 !reader.GetUnsignedIntegerValue(samplesPerPixel, DICOM_TAG_SAMPLES_PER_PIXEL) || | |
93 !reader.GetUnsignedIntegerValue(tmp, DICOM_TAG_PIXEL_REPRESENTATION)) | |
94 { | |
95 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
96 } | |
97 | |
98 bool isSigned = (tmp != 0); | |
0 | 99 |
100 if (bitsStored == 8 && | |
101 samplesPerPixel == 1 && | |
102 !isSigned) | |
103 { | |
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104 format = Orthanc::PixelFormat_Grayscale8; |
0 | 105 } |
106 else if (bitsStored == 8 && | |
107 samplesPerPixel == 3 && | |
108 !isSigned) | |
109 { | |
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110 format = Orthanc::PixelFormat_RGB24; |
0 | 111 } |
112 else | |
113 { | |
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114 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format"); |
0 | 115 } |
116 } | |
117 | |
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118 |
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119 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancPlugins::IOrthancConnection& orthanc) |
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120 { |
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121 /** |
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122 * Lazy detection of the image compression using the transfer |
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123 * syntax stored inside the DICOM header. Given the fact that |
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124 * reading the header is a time-consuming operation (it implies |
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125 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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126 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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127 * "/header" REST call is delayed until it is really required. |
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128 **/ |
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129 |
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130 if (!hasCompression_) |
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131 { |
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132 compression_ = DetectImageCompression(orthanc, instanceId_); |
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133 hasCompression_ = true; |
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134 } |
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135 |
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136 return compression_; |
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137 } |
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138 |
0 | 139 |
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140 void DicomPyramidInstance::Load(OrthancPlugins::IOrthancConnection& orthanc, |
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141 const std::string& instanceId) |
0 | 142 { |
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143 using namespace OrthancPlugins; |
0 | 144 |
87 | 145 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags"); |
146 DicomDatasetReader reader(dataset); | |
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147 |
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148 if (reader.GetMandatoryStringValue(DICOM_TAG_SOP_CLASS_UID) != "1.2.840.10008.5.1.4.1.1.77.1.6" || |
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149 reader.GetMandatoryStringValue(DICOM_TAG_MODALITY) != "SM") |
0 | 150 { |
151 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
152 } | |
153 | |
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154 hasCompression_ = false; |
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155 DetectPixelFormat(format_, photometric_, reader); |
89 | 156 |
157 unsigned int tmp; | |
158 if (!reader.GetUnsignedIntegerValue(tileWidth_, DICOM_TAG_COLUMNS) || | |
159 !reader.GetUnsignedIntegerValue(tileHeight_, DICOM_TAG_ROWS) || | |
160 !reader.GetUnsignedIntegerValue(totalWidth_, DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS) || | |
161 !reader.GetUnsignedIntegerValue(totalHeight_, DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS) || | |
162 !reader.GetUnsignedIntegerValue(tmp, DICOM_TAG_NUMBER_OF_FRAMES)) | |
163 { | |
164 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
165 } | |
0 | 166 |
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167 size_t countFrames; |
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168 if (!reader.GetDataset().GetSequenceSize(countFrames, DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE)) |
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169 { |
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170 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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171 } |
0 | 172 |
89 | 173 if (countFrames != tmp) |
0 | 174 { |
175 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; | |
176 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
177 } | |
178 | |
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179 frames_.resize(countFrames); |
0 | 180 |
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181 for (size_t i = 0; i < countFrames; i++) |
0 | 182 { |
89 | 183 DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
184 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
185 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
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186 |
89 | 187 DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
188 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
189 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
190 | |
191 int xx, yy; | |
192 if (!reader.GetIntegerValue(xx, pathX) || | |
193 !reader.GetIntegerValue(yy, pathY)) | |
194 { | |
195 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
196 } | |
0 | 197 |
198 // "-1", because coordinates are shifted by 1 in DICOM | |
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199 xx -= 1; |
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200 yy -= 1; |
0 | 201 |
202 unsigned int x = static_cast<unsigned int>(xx); | |
203 unsigned int y = static_cast<unsigned int>(yy); | |
204 | |
205 if (xx < 0 || | |
206 yy < 0 || | |
207 x % tileWidth_ != 0 || | |
208 y % tileHeight_ != 0 || | |
209 x >= totalWidth_ || | |
210 y >= totalHeight_) | |
211 { | |
212 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" | |
213 << x << "," << y << ") in instance: " << instanceId; | |
214 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
215 } | |
216 | |
217 frames_[i].first = x / tileWidth_; | |
218 frames_[i].second = y / tileHeight_; | |
219 } | |
220 } | |
221 | |
222 | |
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223 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc, |
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224 const std::string& instanceId, |
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225 bool useCache) : |
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226 instanceId_(instanceId), |
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227 hasCompression_(false) |
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228 { |
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229 if (useCache) |
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230 { |
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231 try |
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232 { |
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233 // Try and deserialized the cached information about this instance |
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234 std::string serialized; |
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235 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA); |
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236 Deserialize(serialized); |
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237 return; // Success |
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238 } |
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239 catch (Orthanc::OrthancException&) |
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240 { |
70 | 241 // No cached information yet |
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242 } |
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243 } |
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244 |
70 | 245 // Compute information about this instance from scratch |
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246 Load(orthanc, instanceId); |
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247 |
70 | 248 if (useCache) |
249 { | |
250 // Serialize the computed information and cache it as a metadata | |
251 std::string serialized, tmp; | |
252 Serialize(serialized); | |
253 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized); | |
254 } | |
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255 } |
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256 |
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257 |
0 | 258 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const |
259 { | |
260 assert(frame < frames_.size()); | |
261 return frames_[frame].first; | |
262 } | |
263 | |
264 | |
265 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
266 { | |
267 assert(frame < frames_.size()); | |
268 return frames_[frame].second; | |
269 } | |
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270 |
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271 |
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272 void DicomPyramidInstance::Serialize(std::string& result) const |
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273 { |
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274 Json::Value frames = Json::arrayValue; |
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275 for (size_t i = 0; i < frames_.size(); i++) |
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276 { |
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277 Json::Value frame = Json::arrayValue; |
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278 frame.append(frames_[i].first); |
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279 frame.append(frames_[i].second); |
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280 |
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281 frames.append(frame); |
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282 } |
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283 |
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284 Json::Value content; |
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285 content["Frames"] = frames; |
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286 content["TileHeight"] = tileHeight_; |
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287 content["TileWidth"] = tileWidth_; |
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288 content["TotalHeight"] = totalHeight_; |
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289 content["TotalWidth"] = totalWidth_; |
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290 |
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291 switch (format_) |
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292 { |
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293 case Orthanc::PixelFormat_RGB24: |
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294 content["PixelFormat"] = 0; |
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295 break; |
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296 |
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297 case Orthanc::PixelFormat_Grayscale8: |
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298 content["PixelFormat"] = 1; |
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299 break; |
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300 |
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301 default: |
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302 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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303 } |
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304 |
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305 Json::FastWriter writer; |
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306 result = writer.write(content); |
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307 } |
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308 |
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309 |
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310 void DicomPyramidInstance::Deserialize(const std::string& s) |
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311 { |
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312 hasCompression_ = false; |
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313 |
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314 Json::Value content; |
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315 OrthancPlugins::IOrthancConnection::ParseJson(content, s); |
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316 |
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317 if (content.type() != Json::objectValue || |
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318 !content.isMember("Frames") || |
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319 !content.isMember("PixelFormat") || |
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320 !content.isMember("TileHeight") || |
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321 !content.isMember("TileWidth") || |
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322 !content.isMember("TotalHeight") || |
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323 !content.isMember("TotalWidth") || |
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324 content["Frames"].type() != Json::arrayValue || |
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325 content["PixelFormat"].type() != Json::intValue || |
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326 content["TileHeight"].type() != Json::intValue || |
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327 content["TileWidth"].type() != Json::intValue || |
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328 content["TotalHeight"].type() != Json::intValue || |
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329 content["TotalWidth"].type() != Json::intValue || |
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330 content["TileHeight"].asInt() < 0 || |
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331 content["TileWidth"].asInt() < 0 || |
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332 content["TotalHeight"].asInt() < 0 || |
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333 content["TotalWidth"].asInt() < 0) |
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334 { |
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335 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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336 } |
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337 |
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338 switch (content["PixelFormat"].asInt()) |
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339 { |
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340 case 0: |
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341 format_ = Orthanc::PixelFormat_RGB24; |
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342 break; |
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343 |
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344 case 1: |
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345 format_ = Orthanc::PixelFormat_Grayscale8; |
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346 break; |
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347 |
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348 default: |
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349 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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350 } |
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351 |
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352 hasCompression_ = false; |
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353 tileHeight_ = static_cast<unsigned int>(content["TileHeight"].asInt()); |
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354 tileWidth_ = static_cast<unsigned int>(content["TileWidth"].asInt()); |
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355 totalHeight_ = static_cast<unsigned int>(content["TotalHeight"].asInt()); |
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356 totalWidth_ = static_cast<unsigned int>(content["TotalWidth"].asInt()); |
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357 |
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358 const Json::Value f = content["Frames"]; |
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359 frames_.resize(f.size()); |
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360 |
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361 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++) |
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362 { |
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363 if (f[i].type() != Json::arrayValue || |
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364 f[i].size() != 2 || |
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365 f[i][0].type() != Json::intValue || |
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366 f[i][1].type() != Json::intValue || |
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367 f[i][0].asInt() < 0 || |
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368 f[i][1].asInt() < 0) |
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369 { |
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370 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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371 } |
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372 |
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373 frames_[i].first = f[i][0].asInt(); |
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374 frames_[i].second = f[i][1].asInt(); |
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375 } |
64
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376 } |
0 | 377 } |