Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 192:f299c191cd76
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 11 Jun 2020 07:41:22 +0200 |
parents | e3cbf890b588 |
children | e57e6ca5303d |
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 | |
192 | 25 #include <Logging.h> |
26 #include <OrthancException.h> | |
27 #include <Toolbox.h> | |
28 | |
29 #include <DicomDatasetReader.h> | |
30 #include <FullOrthancDataset.h> | |
31 | |
0 | 32 #include "../DicomToolbox.h" |
33 | |
34 #include <cassert> | |
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35 #include <json/writer.h> |
0 | 36 |
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37 #define SERIALIZED_METADATA "4200" |
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38 |
0 | 39 namespace OrthancWSI |
40 { | |
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41 static ImageCompression DetectImageCompression(OrthancPlugins::IOrthancConnection& orthanc, |
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42 const std::string& instanceId) |
0 | 43 { |
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44 using namespace OrthancPlugins; |
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45 |
87 | 46 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header"); |
47 DicomDatasetReader header(dataset); | |
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48 |
0 | 49 std::string s = Orthanc::Toolbox::StripSpaces |
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50 (header.GetMandatoryStringValue(DICOM_TAG_TRANSFER_SYNTAX_UID)); |
0 | 51 |
52 if (s == "1.2.840.10008.1.2" || | |
53 s == "1.2.840.10008.1.2.1") | |
54 { | |
55 return ImageCompression_None; | |
56 } | |
57 else if (s == "1.2.840.10008.1.2.4.50") | |
58 { | |
59 return ImageCompression_Jpeg; | |
60 } | |
61 else if (s == "1.2.840.10008.1.2.4.90" || | |
62 s == "1.2.840.10008.1.2.4.91") | |
63 { | |
64 return ImageCompression_Jpeg2000; | |
65 } | |
66 else | |
67 { | |
68 LOG(ERROR) << "Unsupported transfer syntax: " << s; | |
69 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
70 } | |
71 } | |
72 | |
73 | |
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74 static void DetectPixelFormat(Orthanc::PixelFormat& format, |
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75 Orthanc::PhotometricInterpretation& photometric, |
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76 OrthancPlugins::DicomDatasetReader& reader) |
0 | 77 { |
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78 using namespace OrthancPlugins; |
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79 |
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80 std::string p = Orthanc::Toolbox::StripSpaces |
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81 (reader.GetMandatoryStringValue(DICOM_TAG_PHOTOMETRIC_INTERPRETATION)); |
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82 |
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83 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
0 | 84 |
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85 if (photometric == Orthanc::PhotometricInterpretation_Palette) |
0 | 86 { |
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87 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
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88 "Unsupported photometric interpretation: " + p); |
0 | 89 } |
90 | |
89 | 91 unsigned int bitsStored, samplesPerPixel, tmp; |
92 | |
93 if (!reader.GetUnsignedIntegerValue(bitsStored, DICOM_TAG_BITS_STORED) || | |
94 !reader.GetUnsignedIntegerValue(samplesPerPixel, DICOM_TAG_SAMPLES_PER_PIXEL) || | |
95 !reader.GetUnsignedIntegerValue(tmp, DICOM_TAG_PIXEL_REPRESENTATION)) | |
96 { | |
97 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
98 } | |
99 | |
100 bool isSigned = (tmp != 0); | |
0 | 101 |
102 if (bitsStored == 8 && | |
103 samplesPerPixel == 1 && | |
104 !isSigned) | |
105 { | |
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106 format = Orthanc::PixelFormat_Grayscale8; |
0 | 107 } |
108 else if (bitsStored == 8 && | |
109 samplesPerPixel == 3 && | |
110 !isSigned) | |
111 { | |
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112 format = Orthanc::PixelFormat_RGB24; |
0 | 113 } |
114 else | |
115 { | |
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116 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format"); |
0 | 117 } |
118 } | |
119 | |
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120 |
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121 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancPlugins::IOrthancConnection& orthanc) |
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122 { |
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123 /** |
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124 * Lazy detection of the image compression using the transfer |
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125 * syntax stored inside the DICOM header. Given the fact that |
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126 * reading the header is a time-consuming operation (it implies |
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127 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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128 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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129 * "/header" REST call is delayed until it is really required. |
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130 **/ |
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131 |
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132 if (!hasCompression_) |
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133 { |
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134 compression_ = DetectImageCompression(orthanc, instanceId_); |
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135 hasCompression_ = true; |
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136 } |
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137 |
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138 return compression_; |
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139 } |
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140 |
0 | 141 |
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142 void DicomPyramidInstance::Load(OrthancPlugins::IOrthancConnection& orthanc, |
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143 const std::string& instanceId) |
0 | 144 { |
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145 using namespace OrthancPlugins; |
0 | 146 |
87 | 147 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags"); |
148 DicomDatasetReader reader(dataset); | |
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149 |
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150 if (reader.GetMandatoryStringValue(DICOM_TAG_SOP_CLASS_UID) != "1.2.840.10008.5.1.4.1.1.77.1.6" || |
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151 reader.GetMandatoryStringValue(DICOM_TAG_MODALITY) != "SM") |
0 | 152 { |
153 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
154 } | |
155 | |
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156 hasCompression_ = false; |
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157 DetectPixelFormat(format_, photometric_, reader); |
89 | 158 |
159 unsigned int tmp; | |
160 if (!reader.GetUnsignedIntegerValue(tileWidth_, DICOM_TAG_COLUMNS) || | |
161 !reader.GetUnsignedIntegerValue(tileHeight_, DICOM_TAG_ROWS) || | |
162 !reader.GetUnsignedIntegerValue(totalWidth_, DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS) || | |
163 !reader.GetUnsignedIntegerValue(totalHeight_, DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS) || | |
164 !reader.GetUnsignedIntegerValue(tmp, DICOM_TAG_NUMBER_OF_FRAMES)) | |
165 { | |
166 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
167 } | |
0 | 168 |
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169 size_t countFrames; |
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170 if (!reader.GetDataset().GetSequenceSize(countFrames, DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE)) |
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171 { |
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172 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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173 } |
0 | 174 |
89 | 175 if (countFrames != tmp) |
0 | 176 { |
177 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; | |
178 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
179 } | |
180 | |
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181 frames_.resize(countFrames); |
0 | 182 |
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183 for (size_t i = 0; i < countFrames; i++) |
0 | 184 { |
89 | 185 DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
186 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
187 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
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188 |
89 | 189 DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
190 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
191 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
192 | |
193 int xx, yy; | |
194 if (!reader.GetIntegerValue(xx, pathX) || | |
195 !reader.GetIntegerValue(yy, pathY)) | |
196 { | |
197 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
198 } | |
0 | 199 |
200 // "-1", because coordinates are shifted by 1 in DICOM | |
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201 xx -= 1; |
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202 yy -= 1; |
0 | 203 |
204 unsigned int x = static_cast<unsigned int>(xx); | |
205 unsigned int y = static_cast<unsigned int>(yy); | |
206 | |
207 if (xx < 0 || | |
208 yy < 0 || | |
209 x % tileWidth_ != 0 || | |
210 y % tileHeight_ != 0 || | |
211 x >= totalWidth_ || | |
212 y >= totalHeight_) | |
213 { | |
214 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" | |
215 << x << "," << y << ") in instance: " << instanceId; | |
216 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
217 } | |
218 | |
219 frames_[i].first = x / tileWidth_; | |
220 frames_[i].second = y / tileHeight_; | |
221 } | |
222 } | |
223 | |
224 | |
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225 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc, |
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226 const std::string& instanceId, |
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227 bool useCache) : |
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228 instanceId_(instanceId), |
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229 hasCompression_(false) |
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230 { |
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231 if (useCache) |
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232 { |
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233 try |
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234 { |
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235 // Try and deserialized the cached information about this instance |
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236 std::string serialized; |
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237 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA); |
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238 Deserialize(serialized); |
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239 return; // Success |
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240 } |
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241 catch (Orthanc::OrthancException&) |
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242 { |
70 | 243 // No cached information yet |
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244 } |
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245 } |
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246 |
70 | 247 // Compute information about this instance from scratch |
68
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248 Load(orthanc, instanceId); |
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249 |
70 | 250 if (useCache) |
251 { | |
252 // Serialize the computed information and cache it as a metadata | |
253 std::string serialized, tmp; | |
254 Serialize(serialized); | |
255 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized); | |
256 } | |
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257 } |
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258 |
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259 |
0 | 260 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const |
261 { | |
262 assert(frame < frames_.size()); | |
263 return frames_[frame].first; | |
264 } | |
265 | |
266 | |
267 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
268 { | |
269 assert(frame < frames_.size()); | |
270 return frames_[frame].second; | |
271 } | |
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272 |
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273 |
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274 void DicomPyramidInstance::Serialize(std::string& result) const |
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275 { |
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276 Json::Value frames = Json::arrayValue; |
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277 for (size_t i = 0; i < frames_.size(); i++) |
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278 { |
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279 Json::Value frame = Json::arrayValue; |
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280 frame.append(frames_[i].first); |
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281 frame.append(frames_[i].second); |
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282 |
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283 frames.append(frame); |
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284 } |
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285 |
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286 Json::Value content; |
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287 content["Frames"] = frames; |
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288 content["TileHeight"] = tileHeight_; |
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289 content["TileWidth"] = tileWidth_; |
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290 content["TotalHeight"] = totalHeight_; |
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291 content["TotalWidth"] = totalWidth_; |
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292 |
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293 switch (format_) |
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294 { |
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295 case Orthanc::PixelFormat_RGB24: |
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296 content["PixelFormat"] = 0; |
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297 break; |
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298 |
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299 case Orthanc::PixelFormat_Grayscale8: |
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300 content["PixelFormat"] = 1; |
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301 break; |
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302 |
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303 default: |
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304 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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305 } |
64
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306 |
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307 Json::FastWriter writer; |
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308 result = writer.write(content); |
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309 } |
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310 |
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311 |
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312 void DicomPyramidInstance::Deserialize(const std::string& s) |
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313 { |
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314 hasCompression_ = false; |
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315 |
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316 Json::Value content; |
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317 OrthancPlugins::IOrthancConnection::ParseJson(content, s); |
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318 |
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319 if (content.type() != Json::objectValue || |
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320 !content.isMember("Frames") || |
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321 !content.isMember("PixelFormat") || |
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322 !content.isMember("TileHeight") || |
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323 !content.isMember("TileWidth") || |
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324 !content.isMember("TotalHeight") || |
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325 !content.isMember("TotalWidth") || |
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326 content["Frames"].type() != Json::arrayValue || |
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327 content["PixelFormat"].type() != Json::intValue || |
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328 content["TileHeight"].type() != Json::intValue || |
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329 content["TileWidth"].type() != Json::intValue || |
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330 content["TotalHeight"].type() != Json::intValue || |
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331 content["TotalWidth"].type() != Json::intValue || |
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332 content["TileHeight"].asInt() < 0 || |
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333 content["TileWidth"].asInt() < 0 || |
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334 content["TotalHeight"].asInt() < 0 || |
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335 content["TotalWidth"].asInt() < 0) |
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336 { |
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337 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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338 } |
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339 |
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340 switch (content["PixelFormat"].asInt()) |
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341 { |
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342 case 0: |
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343 format_ = Orthanc::PixelFormat_RGB24; |
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344 break; |
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345 |
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346 case 1: |
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347 format_ = Orthanc::PixelFormat_Grayscale8; |
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348 break; |
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349 |
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350 default: |
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351 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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352 } |
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353 |
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354 hasCompression_ = false; |
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355 tileHeight_ = static_cast<unsigned int>(content["TileHeight"].asInt()); |
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356 tileWidth_ = static_cast<unsigned int>(content["TileWidth"].asInt()); |
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357 totalHeight_ = static_cast<unsigned int>(content["TotalHeight"].asInt()); |
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358 totalWidth_ = static_cast<unsigned int>(content["TotalWidth"].asInt()); |
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359 |
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360 const Json::Value f = content["Frames"]; |
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361 frames_.resize(f.size()); |
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362 |
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363 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++) |
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364 { |
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365 if (f[i].type() != Json::arrayValue || |
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366 f[i].size() != 2 || |
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367 f[i][0].type() != Json::intValue || |
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368 f[i][1].type() != Json::intValue || |
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DicomPyramidInstance::Deserialize
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369 f[i][0].asInt() < 0 || |
c619c8bd72ed
DicomPyramidInstance::Deserialize
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370 f[i][1].asInt() < 0) |
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DicomPyramidInstance::Deserialize
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371 { |
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DicomPyramidInstance::Deserialize
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372 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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DicomPyramidInstance::Deserialize
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373 } |
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DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
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374 |
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DicomPyramidInstance::Deserialize
Sebastien Jodogne <s.jodogne@gmail.com>
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375 frames_[i].first = f[i][0].asInt(); |
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DicomPyramidInstance::Deserialize
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376 frames_[i].second = f[i][1].asInt(); |
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DicomPyramidInstance::Deserialize
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377 } |
64
63d0a5c74460
DicomPyramidInstance::Serialize
Sebastien Jodogne <s.jodogne@gmail.com>
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378 } |
0 | 379 } |