Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 112:999a17ecf9b6
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sat, 26 Aug 2017 12:23:09 +0200 |
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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 Osimis, 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 "../../Resources/Orthanc/Core/Logging.h" |
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26 #include "../../Resources/Orthanc/Core/OrthancException.h" |
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27 #include "../../Resources/Orthanc/Core/Toolbox.h" |
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28 #include "../../Resources/Orthanc/Plugins/Samples/Common/DicomDatasetReader.h" |
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29 #include "../../Resources/Orthanc/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 Orthanc::PixelFormat DetectPixelFormat(OrthancPlugins::DicomDatasetReader& reader) |
0 | 73 { |
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74 using namespace OrthancPlugins; |
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75 |
0 | 76 std::string photometric = Orthanc::Toolbox::StripSpaces |
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77 (reader.GetMandatoryStringValue(DICOM_TAG_PHOTOMETRIC_INTERPRETATION)); |
0 | 78 |
79 if (photometric == "PALETTE") | |
80 { | |
81 LOG(ERROR) << "Unsupported photometric interpretation: " << photometric; | |
82 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
83 } | |
84 | |
89 | 85 unsigned int bitsStored, samplesPerPixel, tmp; |
86 | |
87 if (!reader.GetUnsignedIntegerValue(bitsStored, DICOM_TAG_BITS_STORED) || | |
88 !reader.GetUnsignedIntegerValue(samplesPerPixel, DICOM_TAG_SAMPLES_PER_PIXEL) || | |
89 !reader.GetUnsignedIntegerValue(tmp, DICOM_TAG_PIXEL_REPRESENTATION)) | |
90 { | |
91 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
92 } | |
93 | |
94 bool isSigned = (tmp != 0); | |
0 | 95 |
96 if (bitsStored == 8 && | |
97 samplesPerPixel == 1 && | |
98 !isSigned) | |
99 { | |
100 return Orthanc::PixelFormat_Grayscale8; | |
101 } | |
102 else if (bitsStored == 8 && | |
103 samplesPerPixel == 3 && | |
104 !isSigned) | |
105 { | |
106 return Orthanc::PixelFormat_RGB24; | |
107 } | |
108 else | |
109 { | |
110 LOG(ERROR) << "Unsupported pixel format"; | |
111 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
112 } | |
113 } | |
114 | |
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115 |
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116 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancPlugins::IOrthancConnection& orthanc) |
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117 { |
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118 /** |
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119 * Lazy detection of the image compression using the transfer |
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120 * syntax stored inside the DICOM header. Given the fact that |
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121 * reading the header is a time-consuming operation (it implies |
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122 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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123 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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124 * "/header" REST call is delayed until it is really required. |
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125 **/ |
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126 |
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127 if (!hasCompression_) |
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128 { |
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129 compression_ = DetectImageCompression(orthanc, instanceId_); |
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130 hasCompression_ = true; |
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131 } |
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132 |
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133 return compression_; |
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134 } |
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135 |
0 | 136 |
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137 void DicomPyramidInstance::Load(OrthancPlugins::IOrthancConnection& orthanc, |
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138 const std::string& instanceId) |
0 | 139 { |
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140 using namespace OrthancPlugins; |
0 | 141 |
87 | 142 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags"); |
143 DicomDatasetReader reader(dataset); | |
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144 |
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145 if (reader.GetMandatoryStringValue(DICOM_TAG_SOP_CLASS_UID) != "1.2.840.10008.5.1.4.1.1.77.1.6" || |
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146 reader.GetMandatoryStringValue(DICOM_TAG_MODALITY) != "SM") |
0 | 147 { |
148 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
149 } | |
150 | |
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151 hasCompression_ = false; |
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152 format_ = DetectPixelFormat(reader); |
89 | 153 |
154 unsigned int tmp; | |
155 if (!reader.GetUnsignedIntegerValue(tileWidth_, DICOM_TAG_COLUMNS) || | |
156 !reader.GetUnsignedIntegerValue(tileHeight_, DICOM_TAG_ROWS) || | |
157 !reader.GetUnsignedIntegerValue(totalWidth_, DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS) || | |
158 !reader.GetUnsignedIntegerValue(totalHeight_, DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS) || | |
159 !reader.GetUnsignedIntegerValue(tmp, DICOM_TAG_NUMBER_OF_FRAMES)) | |
160 { | |
161 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
162 } | |
0 | 163 |
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164 size_t countFrames; |
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165 if (!reader.GetDataset().GetSequenceSize(countFrames, DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE)) |
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166 { |
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167 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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168 } |
0 | 169 |
89 | 170 if (countFrames != tmp) |
0 | 171 { |
172 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; | |
173 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
174 } | |
175 | |
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176 frames_.resize(countFrames); |
0 | 177 |
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178 for (size_t i = 0; i < countFrames; i++) |
0 | 179 { |
89 | 180 DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
181 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
182 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
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183 |
89 | 184 DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
185 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
186 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
187 | |
188 int xx, yy; | |
189 if (!reader.GetIntegerValue(xx, pathX) || | |
190 !reader.GetIntegerValue(yy, pathY)) | |
191 { | |
192 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
193 } | |
0 | 194 |
195 // "-1", because coordinates are shifted by 1 in DICOM | |
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196 xx -= 1; |
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197 yy -= 1; |
0 | 198 |
199 unsigned int x = static_cast<unsigned int>(xx); | |
200 unsigned int y = static_cast<unsigned int>(yy); | |
201 | |
202 if (xx < 0 || | |
203 yy < 0 || | |
204 x % tileWidth_ != 0 || | |
205 y % tileHeight_ != 0 || | |
206 x >= totalWidth_ || | |
207 y >= totalHeight_) | |
208 { | |
209 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" | |
210 << x << "," << y << ") in instance: " << instanceId; | |
211 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
212 } | |
213 | |
214 frames_[i].first = x / tileWidth_; | |
215 frames_[i].second = y / tileHeight_; | |
216 } | |
217 } | |
218 | |
219 | |
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220 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc, |
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221 const std::string& instanceId, |
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222 bool useCache) : |
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223 instanceId_(instanceId), |
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224 hasCompression_(false) |
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225 { |
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226 if (useCache) |
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227 { |
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228 try |
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229 { |
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230 // Try and deserialized the cached information about this instance |
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231 std::string serialized; |
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232 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA); |
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233 Deserialize(serialized); |
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234 return; // Success |
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235 } |
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236 catch (Orthanc::OrthancException&) |
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237 { |
70 | 238 // No cached information yet |
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239 } |
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240 } |
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241 |
70 | 242 // Compute information about this instance from scratch |
68
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243 Load(orthanc, instanceId); |
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244 |
70 | 245 if (useCache) |
246 { | |
247 // Serialize the computed information and cache it as a metadata | |
248 std::string serialized, tmp; | |
249 Serialize(serialized); | |
250 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized); | |
251 } | |
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252 } |
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253 |
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254 |
0 | 255 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const |
256 { | |
257 assert(frame < frames_.size()); | |
258 return frames_[frame].first; | |
259 } | |
260 | |
261 | |
262 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
263 { | |
264 assert(frame < frames_.size()); | |
265 return frames_[frame].second; | |
266 } | |
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267 |
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268 |
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269 void DicomPyramidInstance::Serialize(std::string& result) const |
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270 { |
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271 Json::Value frames = Json::arrayValue; |
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272 for (size_t i = 0; i < frames_.size(); i++) |
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273 { |
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274 Json::Value frame = Json::arrayValue; |
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275 frame.append(frames_[i].first); |
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276 frame.append(frames_[i].second); |
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277 |
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278 frames.append(frame); |
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279 } |
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280 |
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281 Json::Value content; |
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282 content["Frames"] = frames; |
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283 content["TileHeight"] = tileHeight_; |
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284 content["TileWidth"] = tileWidth_; |
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285 content["TotalHeight"] = totalHeight_; |
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286 content["TotalWidth"] = totalWidth_; |
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287 |
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288 switch (format_) |
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289 { |
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290 case Orthanc::PixelFormat_RGB24: |
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291 content["PixelFormat"] = 0; |
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292 break; |
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293 |
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294 case Orthanc::PixelFormat_Grayscale8: |
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295 content["PixelFormat"] = 1; |
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296 break; |
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297 |
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298 default: |
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299 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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300 } |
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301 |
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302 Json::FastWriter writer; |
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303 result = writer.write(content); |
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304 } |
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305 |
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306 |
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307 void DicomPyramidInstance::Deserialize(const std::string& s) |
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308 { |
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309 hasCompression_ = false; |
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310 |
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311 Json::Value content; |
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312 OrthancPlugins::IOrthancConnection::ParseJson(content, s); |
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313 |
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314 if (content.type() != Json::objectValue || |
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315 !content.isMember("Frames") || |
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316 !content.isMember("PixelFormat") || |
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317 !content.isMember("TileHeight") || |
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318 !content.isMember("TileWidth") || |
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319 !content.isMember("TotalHeight") || |
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320 !content.isMember("TotalWidth") || |
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321 content["Frames"].type() != Json::arrayValue || |
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322 content["PixelFormat"].type() != Json::intValue || |
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323 content["TileHeight"].type() != Json::intValue || |
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324 content["TileWidth"].type() != Json::intValue || |
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325 content["TotalHeight"].type() != Json::intValue || |
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326 content["TotalWidth"].type() != Json::intValue || |
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327 content["TileHeight"].asInt() < 0 || |
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328 content["TileWidth"].asInt() < 0 || |
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329 content["TotalHeight"].asInt() < 0 || |
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330 content["TotalWidth"].asInt() < 0) |
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331 { |
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332 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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333 } |
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334 |
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335 switch (content["PixelFormat"].asInt()) |
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336 { |
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337 case 0: |
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338 format_ = Orthanc::PixelFormat_RGB24; |
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339 break; |
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340 |
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341 case 1: |
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342 format_ = Orthanc::PixelFormat_Grayscale8; |
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343 break; |
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344 |
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345 default: |
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346 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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347 } |
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348 |
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349 hasCompression_ = false; |
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350 tileHeight_ = static_cast<unsigned int>(content["TileHeight"].asInt()); |
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351 tileWidth_ = static_cast<unsigned int>(content["TileWidth"].asInt()); |
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352 totalHeight_ = static_cast<unsigned int>(content["TotalHeight"].asInt()); |
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353 totalWidth_ = static_cast<unsigned int>(content["TotalWidth"].asInt()); |
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354 |
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355 const Json::Value f = content["Frames"]; |
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356 frames_.resize(f.size()); |
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357 |
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358 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++) |
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359 { |
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360 if (f[i].type() != Json::arrayValue || |
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361 f[i].size() != 2 || |
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362 f[i][0].type() != Json::intValue || |
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363 f[i][1].type() != Json::intValue || |
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364 f[i][0].asInt() < 0 || |
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365 f[i][1].asInt() < 0) |
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366 { |
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367 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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368 } |
c619c8bd72ed
DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
64
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369 |
c619c8bd72ed
DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
64
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370 frames_[i].first = f[i][0].asInt(); |
c619c8bd72ed
DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
64
diff
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371 frames_[i].second = f[i][1].asInt(); |
c619c8bd72ed
DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
64
diff
changeset
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372 } |
64
63d0a5c74460
DicomPyramidInstance::Serialize
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
62
diff
changeset
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373 } |
0 | 374 } |