Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 312:0683312e21ba
updated copyright, as Orthanc Team now replaces Osimis
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 30 May 2024 22:11:10 +0200 |
parents | 7020852a8fa9 |
children | c42083d50ddf |
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 | |
312
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 8 * |
9 * This program is free software: you can redistribute it and/or | |
10 * modify it under the terms of the GNU Affero General Public License | |
11 * as published by the Free Software Foundation, either version 3 of | |
12 * the License, or (at your option) any later version. | |
13 * | |
14 * This program is distributed in the hope that it will be useful, but | |
15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
17 * Affero General Public License for more details. | |
18 * | |
19 * You should have received a copy of the GNU Affero General Public License | |
20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
21 **/ | |
22 | |
23 | |
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24 #include "../PrecompiledHeadersWSI.h" |
0 | 25 #include "DicomPyramidInstance.h" |
26 | |
194 | 27 #include "../DicomToolbox.h" |
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28 #include "../../Resources/Orthanc/Stone/DicomDatasetReader.h" |
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29 #include "../../Resources/Orthanc/Stone/FullOrthancDataset.h" |
194 | 30 |
192 | 31 #include <Logging.h> |
32 #include <OrthancException.h> | |
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33 #include <SerializationToolbox.h> |
192 | 34 #include <Toolbox.h> |
35 | |
0 | 36 #include <cassert> |
37 | |
226 | 38 #if !ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
39 # include <json/writer.h> | |
40 #endif | |
41 | |
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42 #define SERIALIZED_METADATA "4201" // Was "4200" if versions <= 0.7 of this plugin |
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43 |
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44 |
0 | 45 namespace OrthancWSI |
46 { | |
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47 static const Orthanc::DicomTag DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021e); |
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48 static const Orthanc::DicomTag DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE(0x5200, 0x9230); |
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49 static const Orthanc::DicomTag DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE(0x0048, 0x021a); |
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50 static const Orthanc::DicomTag DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021f); |
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51 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS(0x0048, 0x0006); |
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52 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS(0x0048, 0x0007); |
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53 static const Orthanc::DicomTag DICOM_TAG_IMAGE_TYPE(0x0008, 0x0008); |
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54 |
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55 static ImageCompression DetectImageCompression(OrthancStone::IOrthancConnection& orthanc, |
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56 const std::string& instanceId) |
0 | 57 { |
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58 using namespace OrthancStone; |
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59 |
87 | 60 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header"); |
61 DicomDatasetReader header(dataset); | |
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62 |
0 | 63 std::string s = Orthanc::Toolbox::StripSpaces |
239 | 64 (header.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_TRANSFER_SYNTAX_UID))); |
0 | 65 |
66 if (s == "1.2.840.10008.1.2" || | |
67 s == "1.2.840.10008.1.2.1") | |
68 { | |
69 return ImageCompression_None; | |
70 } | |
71 else if (s == "1.2.840.10008.1.2.4.50") | |
72 { | |
73 return ImageCompression_Jpeg; | |
74 } | |
75 else if (s == "1.2.840.10008.1.2.4.90" || | |
76 s == "1.2.840.10008.1.2.4.91") | |
77 { | |
78 return ImageCompression_Jpeg2000; | |
79 } | |
80 else | |
81 { | |
82 LOG(ERROR) << "Unsupported transfer syntax: " << s; | |
83 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
84 } | |
85 } | |
86 | |
87 | |
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88 static void DetectPixelFormat(Orthanc::PixelFormat& format, |
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89 Orthanc::PhotometricInterpretation& photometric, |
216 | 90 const OrthancStone::DicomDatasetReader& reader) |
0 | 91 { |
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92 using namespace OrthancStone; |
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93 |
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94 std::string p = Orthanc::Toolbox::StripSpaces |
239 | 95 (reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION))); |
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96 |
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97 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
0 | 98 |
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99 if (photometric == Orthanc::PhotometricInterpretation_Palette) |
0 | 100 { |
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101 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
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102 "Unsupported photometric interpretation: " + p); |
0 | 103 } |
104 | |
89 | 105 unsigned int bitsStored, samplesPerPixel, tmp; |
106 | |
239 | 107 if (!reader.GetUnsignedIntegerValue(bitsStored, Orthanc::DicomPath(Orthanc::DICOM_TAG_BITS_STORED)) || |
108 !reader.GetUnsignedIntegerValue(samplesPerPixel, Orthanc::DicomPath(Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL)) || | |
109 !reader.GetUnsignedIntegerValue(tmp, Orthanc::DicomPath(Orthanc::DICOM_TAG_PIXEL_REPRESENTATION))) | |
89 | 110 { |
111 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
112 } | |
113 | |
114 bool isSigned = (tmp != 0); | |
0 | 115 |
116 if (bitsStored == 8 && | |
117 samplesPerPixel == 1 && | |
118 !isSigned) | |
119 { | |
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120 format = Orthanc::PixelFormat_Grayscale8; |
0 | 121 } |
122 else if (bitsStored == 8 && | |
123 samplesPerPixel == 3 && | |
124 !isSigned) | |
125 { | |
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126 format = Orthanc::PixelFormat_RGB24; |
0 | 127 } |
128 else | |
129 { | |
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130 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format"); |
0 | 131 } |
132 } | |
133 | |
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134 |
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135 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancStone::IOrthancConnection& orthanc) |
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136 { |
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137 /** |
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138 * Lazy detection of the image compression using the transfer |
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139 * syntax stored inside the DICOM header. Given the fact that |
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140 * reading the header is a time-consuming operation (it implies |
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141 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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142 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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143 * "/header" REST call is delayed until it is really required. |
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144 **/ |
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145 |
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146 if (!hasCompression_) |
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147 { |
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148 compression_ = DetectImageCompression(orthanc, instanceId_); |
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149 hasCompression_ = true; |
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150 } |
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151 |
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152 return compression_; |
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153 } |
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154 |
0 | 155 |
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156 void DicomPyramidInstance::Load(OrthancStone::IOrthancConnection& orthanc, |
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157 const std::string& instanceId) |
0 | 158 { |
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159 using namespace OrthancStone; |
0 | 160 |
87 | 161 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags"); |
162 DicomDatasetReader reader(dataset); | |
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163 |
265 | 164 if (reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_SOP_CLASS_UID)) != VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD || |
239 | 165 reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_MODALITY)) != "SM") |
0 | 166 { |
167 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
168 } | |
169 | |
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170 hasCompression_ = false; |
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171 DetectPixelFormat(format_, photometric_, reader); |
89 | 172 |
173 unsigned int tmp; | |
239 | 174 if (!reader.GetUnsignedIntegerValue(tileWidth_, Orthanc::DicomPath(Orthanc::DICOM_TAG_COLUMNS)) || |
175 !reader.GetUnsignedIntegerValue(tileHeight_, Orthanc::DicomPath(Orthanc::DICOM_TAG_ROWS)) || | |
176 !reader.GetUnsignedIntegerValue(totalWidth_, Orthanc::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS)) || | |
177 !reader.GetUnsignedIntegerValue(totalHeight_, Orthanc::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS)) || | |
178 !reader.GetUnsignedIntegerValue(tmp, Orthanc::DicomPath(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))) | |
89 | 179 { |
180 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
181 } | |
0 | 182 |
239 | 183 imageType_ = reader.GetStringValue(Orthanc::DicomPath(DICOM_TAG_IMAGE_TYPE), ""); |
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184 |
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185 size_t countFrames; |
239 | 186 if (reader.GetDataset().GetSequenceSize(countFrames, Orthanc::DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE))) |
0 | 187 { |
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188 if (countFrames != tmp) |
89 | 189 { |
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190 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; |
0 | 191 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
192 } | |
193 | |
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194 frames_.reserve(countFrames); |
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195 |
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196 for (size_t i = 0; i < countFrames; i++) |
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197 { |
239 | 198 Orthanc::DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
199 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
200 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
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201 |
239 | 202 Orthanc::DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
203 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
204 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
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205 |
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206 int xx, yy; |
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207 if (!reader.GetIntegerValue(xx, pathX) || |
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208 !reader.GetIntegerValue(yy, pathY)) |
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209 { |
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210 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); |
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211 } |
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212 |
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213 // "-1", because coordinates are shifted by 1 in DICOM |
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214 xx -= 1; |
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215 yy -= 1; |
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216 |
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217 unsigned int x = static_cast<unsigned int>(xx); |
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218 unsigned int y = static_cast<unsigned int>(yy); |
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219 |
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220 if (xx < 0 || |
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221 yy < 0 || |
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222 x % tileWidth_ != 0 || |
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223 y % tileHeight_ != 0 || |
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224 x >= totalWidth_ || |
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225 y >= totalHeight_) |
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226 { |
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227 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" |
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228 << x << "," << y << ") in instance: " << instanceId; |
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229 } |
268
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230 else |
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231 { |
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232 frames_.push_back(std::make_pair(x / tileWidth_, y / tileHeight_)); |
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233 } |
215
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234 } |
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235 } |
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236 else |
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237 { |
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238 // No "Per frame functional groups sequence" tag. Assume regular grid. |
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239 frames_.resize(tmp); |
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240 |
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241 // Compute "ceiling(totalWidth_ / tileWidth_) |
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242 unsigned int w = totalWidth_ / tileWidth_; |
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243 if (totalWidth_ % tileWidth_ != 0) |
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244 { |
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245 w += 1; |
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246 } |
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247 |
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248 unsigned int h = totalHeight_ / tileHeight_; |
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249 if (totalHeight_ % tileHeight_ != 0) |
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250 { |
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251 h += 1; |
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252 } |
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253 |
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254 if (w * h != tmp) |
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255 { |
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256 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; |
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257 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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258 } |
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259 |
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260 for (size_t i = 0; i < frames_.size(); i++) |
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261 { |
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262 frames_[i].first = i % w; |
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263 frames_[i].second = i / w; |
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264 } |
0 | 265 } |
266 } | |
267 | |
268 | |
196
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269 DicomPyramidInstance::DicomPyramidInstance(OrthancStone::IOrthancConnection& orthanc, |
69
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270 const std::string& instanceId, |
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271 bool useCache) : |
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272 instanceId_(instanceId), |
217
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273 hasCompression_(false), |
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274 compression_(ImageCompression_None) // Dummy initialization for serialization |
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275 { |
69
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276 if (useCache) |
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277 { |
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278 try |
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279 { |
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280 // Try and deserialized the cached information about this instance |
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281 std::string serialized; |
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282 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA); |
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283 Deserialize(serialized); |
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284 return; // Success |
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285 } |
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286 catch (Orthanc::OrthancException&) |
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287 { |
70 | 288 // No cached information yet |
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289 } |
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290 } |
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291 |
70 | 292 // Compute information about this instance from scratch |
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293 Load(orthanc, instanceId); |
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294 |
70 | 295 if (useCache) |
296 { | |
297 // Serialize the computed information and cache it as a metadata | |
298 std::string serialized, tmp; | |
299 Serialize(serialized); | |
300 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized); | |
301 } | |
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302 } |
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303 |
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304 |
0 | 305 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const |
306 { | |
307 assert(frame < frames_.size()); | |
308 return frames_[frame].first; | |
309 } | |
310 | |
311 | |
312 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
313 { | |
314 assert(frame < frames_.size()); | |
315 return frames_[frame].second; | |
316 } | |
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317 |
217
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318 |
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319 |
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320 static const char* const HAS_COMPRESSION = "HasCompression"; |
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321 static const char* const IMAGE_COMPRESSION = "ImageCompression"; |
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322 static const char* const PIXEL_FORMAT = "PixelFormat"; |
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323 static const char* const FRAMES = "Frames"; |
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324 static const char* const TILE_WIDTH = "TileWidth"; |
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325 static const char* const TILE_HEIGHT = "TileHeight"; |
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326 static const char* const TOTAL_WIDTH = "TotalWidth"; |
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327 static const char* const TOTAL_HEIGHT = "TotalHeight"; |
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328 static const char* const PHOTOMETRIC_INTERPRETATION = "PhotometricInterpretation"; |
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329 static const char* const IMAGE_TYPE = "ImageType"; |
217
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330 |
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331 |
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332 void DicomPyramidInstance::Serialize(std::string& result) const |
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333 { |
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334 Json::Value frames = Json::arrayValue; |
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335 for (size_t i = 0; i < frames_.size(); i++) |
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336 { |
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337 Json::Value frame = Json::arrayValue; |
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338 frame.append(frames_[i].first); |
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339 frame.append(frames_[i].second); |
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340 frames.append(frame); |
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341 } |
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342 |
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343 Json::Value content = Json::objectValue; |
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344 content[FRAMES] = frames; |
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345 |
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346 // "instanceId_" is set by the constructor |
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347 |
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348 content[HAS_COMPRESSION] = hasCompression_; |
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349 content[IMAGE_COMPRESSION] = static_cast<int>(compression_); |
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350 content[PIXEL_FORMAT] = static_cast<int>(format_); |
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351 content[TILE_WIDTH] = tileWidth_; |
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352 content[TILE_HEIGHT] = tileHeight_; |
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353 content[TOTAL_WIDTH] = totalWidth_; |
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354 content[TOTAL_HEIGHT] = totalHeight_; |
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355 content[PHOTOMETRIC_INTERPRETATION] = Orthanc::EnumerationToString(photometric_); |
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356 content[IMAGE_TYPE] = imageType_; |
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357 |
226 | 358 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
359 Orthanc::Toolbox::WriteFastJson(result, content); | |
360 #else | |
361 Json::FastWriter writer; | |
362 result = writer.write(content); | |
363 #endif | |
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364 } |
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365 |
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366 |
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367 void DicomPyramidInstance::Deserialize(const std::string& s) |
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368 { |
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369 Json::Value content; |
226 | 370 OrthancStone::IOrthancConnection::ParseJson(content, s); |
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371 |
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372 if (content.type() != Json::objectValue || |
217
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373 !content.isMember(FRAMES) || |
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374 content[FRAMES].type() != Json::arrayValue) |
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375 { |
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376 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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377 } |
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378 |
217
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379 hasCompression_ = Orthanc::SerializationToolbox::ReadBoolean(content, HAS_COMPRESSION); |
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380 compression_ = static_cast<ImageCompression>(Orthanc::SerializationToolbox::ReadInteger(content, IMAGE_COMPRESSION)); |
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381 format_ = static_cast<Orthanc::PixelFormat>(Orthanc::SerializationToolbox::ReadInteger(content, PIXEL_FORMAT)); |
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382 tileWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_WIDTH); |
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383 tileHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_HEIGHT); |
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384 totalWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_WIDTH); |
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385 totalHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_HEIGHT); |
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386 |
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387 std::string p = Orthanc::SerializationToolbox::ReadString(content, PHOTOMETRIC_INTERPRETATION); |
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388 photometric_ = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
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389 |
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390 imageType_ = Orthanc::SerializationToolbox::ReadString(content, IMAGE_TYPE); |
217
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391 |
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392 const Json::Value f = content[FRAMES]; |
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393 frames_.resize(f.size()); |
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394 |
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395 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++) |
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396 { |
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397 if (f[i].type() != Json::arrayValue || |
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398 f[i].size() != 2 || |
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399 f[i][0].type() != Json::intValue || |
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400 f[i][1].type() != Json::intValue || |
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401 f[i][0].asInt() < 0 || |
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402 f[i][1].asInt() < 0) |
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403 { |
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404 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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405 } |
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406 |
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407 frames_[i].first = f[i][0].asInt(); |
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408 frames_[i].second = f[i][1].asInt(); |
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409 } |
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410 } |
0 | 411 } |