Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 269:30fb01ce97a3 iiif
integration mainline->iiif
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 10 Jul 2023 16:23:46 +0200 |
parents | dab414e5b520 a6e4834ac141 |
children | 7020852a8fa9 |
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 | |
254 | 5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium | |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
9 * modify it under the terms of the GNU Affero General Public License | |
10 * as published by the Free Software Foundation, either version 3 of | |
11 * the License, or (at your option) any later version. | |
12 * | |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
16 * Affero General Public License for more details. | |
17 * | |
18 * You should have received a copy of the GNU Affero General Public License | |
19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
20 **/ | |
21 | |
22 | |
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23 #include "../PrecompiledHeadersWSI.h" |
0 | 24 #include "DicomPyramidInstance.h" |
25 | |
194 | 26 #include "../DicomToolbox.h" |
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27 #include "../../Resources/Orthanc/Stone/DicomDatasetReader.h" |
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28 #include "../../Resources/Orthanc/Stone/FullOrthancDataset.h" |
194 | 29 |
192 | 30 #include <Logging.h> |
31 #include <OrthancException.h> | |
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32 #include <SerializationToolbox.h> |
192 | 33 #include <Toolbox.h> |
34 | |
0 | 35 #include <cassert> |
36 | |
226 | 37 #if !ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
38 # include <json/writer.h> | |
39 #endif | |
40 | |
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41 #define SERIALIZED_METADATA "4201" // Was "4200" if versions <= 0.7 of this plugin |
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42 |
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43 |
0 | 44 namespace OrthancWSI |
45 { | |
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46 static const Orthanc::DicomTag DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021e); |
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47 static const Orthanc::DicomTag DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE(0x5200, 0x9230); |
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48 static const Orthanc::DicomTag DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE(0x0048, 0x021a); |
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49 static const Orthanc::DicomTag DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021f); |
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50 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS(0x0048, 0x0006); |
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51 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS(0x0048, 0x0007); |
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52 static const Orthanc::DicomTag DICOM_TAG_IMAGE_TYPE(0x0008, 0x0008); |
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53 |
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54 static ImageCompression DetectImageCompression(OrthancStone::IOrthancConnection& orthanc, |
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55 const std::string& instanceId) |
0 | 56 { |
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57 using namespace OrthancStone; |
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58 |
87 | 59 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header"); |
60 DicomDatasetReader header(dataset); | |
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61 |
0 | 62 std::string s = Orthanc::Toolbox::StripSpaces |
239 | 63 (header.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_TRANSFER_SYNTAX_UID))); |
0 | 64 |
65 if (s == "1.2.840.10008.1.2" || | |
66 s == "1.2.840.10008.1.2.1") | |
67 { | |
68 return ImageCompression_None; | |
69 } | |
70 else if (s == "1.2.840.10008.1.2.4.50") | |
71 { | |
72 return ImageCompression_Jpeg; | |
73 } | |
74 else if (s == "1.2.840.10008.1.2.4.90" || | |
75 s == "1.2.840.10008.1.2.4.91") | |
76 { | |
77 return ImageCompression_Jpeg2000; | |
78 } | |
79 else | |
80 { | |
81 LOG(ERROR) << "Unsupported transfer syntax: " << s; | |
82 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
83 } | |
84 } | |
85 | |
86 | |
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87 static void DetectPixelFormat(Orthanc::PixelFormat& format, |
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88 Orthanc::PhotometricInterpretation& photometric, |
216 | 89 const OrthancStone::DicomDatasetReader& reader) |
0 | 90 { |
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91 using namespace OrthancStone; |
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92 |
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93 std::string p = Orthanc::Toolbox::StripSpaces |
239 | 94 (reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION))); |
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95 |
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96 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
0 | 97 |
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98 if (photometric == Orthanc::PhotometricInterpretation_Palette) |
0 | 99 { |
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100 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
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101 "Unsupported photometric interpretation: " + p); |
0 | 102 } |
103 | |
89 | 104 unsigned int bitsStored, samplesPerPixel, tmp; |
105 | |
239 | 106 if (!reader.GetUnsignedIntegerValue(bitsStored, Orthanc::DicomPath(Orthanc::DICOM_TAG_BITS_STORED)) || |
107 !reader.GetUnsignedIntegerValue(samplesPerPixel, Orthanc::DicomPath(Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL)) || | |
108 !reader.GetUnsignedIntegerValue(tmp, Orthanc::DicomPath(Orthanc::DICOM_TAG_PIXEL_REPRESENTATION))) | |
89 | 109 { |
110 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
111 } | |
112 | |
113 bool isSigned = (tmp != 0); | |
0 | 114 |
115 if (bitsStored == 8 && | |
116 samplesPerPixel == 1 && | |
117 !isSigned) | |
118 { | |
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119 format = Orthanc::PixelFormat_Grayscale8; |
0 | 120 } |
121 else if (bitsStored == 8 && | |
122 samplesPerPixel == 3 && | |
123 !isSigned) | |
124 { | |
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125 format = Orthanc::PixelFormat_RGB24; |
0 | 126 } |
127 else | |
128 { | |
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129 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format"); |
0 | 130 } |
131 } | |
132 | |
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133 |
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134 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancStone::IOrthancConnection& orthanc) |
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135 { |
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136 /** |
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137 * Lazy detection of the image compression using the transfer |
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138 * syntax stored inside the DICOM header. Given the fact that |
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139 * reading the header is a time-consuming operation (it implies |
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140 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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141 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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142 * "/header" REST call is delayed until it is really required. |
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143 **/ |
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144 |
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145 if (!hasCompression_) |
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146 { |
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147 compression_ = DetectImageCompression(orthanc, instanceId_); |
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148 hasCompression_ = true; |
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149 } |
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150 |
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151 return compression_; |
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152 } |
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153 |
0 | 154 |
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155 void DicomPyramidInstance::Load(OrthancStone::IOrthancConnection& orthanc, |
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156 const std::string& instanceId) |
0 | 157 { |
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158 using namespace OrthancStone; |
0 | 159 |
87 | 160 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags"); |
161 DicomDatasetReader reader(dataset); | |
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162 |
265 | 163 if (reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_SOP_CLASS_UID)) != VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD || |
239 | 164 reader.GetMandatoryStringValue(Orthanc::DicomPath(Orthanc::DICOM_TAG_MODALITY)) != "SM") |
0 | 165 { |
166 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
167 } | |
168 | |
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169 hasCompression_ = false; |
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170 DetectPixelFormat(format_, photometric_, reader); |
89 | 171 |
172 unsigned int tmp; | |
239 | 173 if (!reader.GetUnsignedIntegerValue(tileWidth_, Orthanc::DicomPath(Orthanc::DICOM_TAG_COLUMNS)) || |
174 !reader.GetUnsignedIntegerValue(tileHeight_, Orthanc::DicomPath(Orthanc::DICOM_TAG_ROWS)) || | |
175 !reader.GetUnsignedIntegerValue(totalWidth_, Orthanc::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS)) || | |
176 !reader.GetUnsignedIntegerValue(totalHeight_, Orthanc::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS)) || | |
177 !reader.GetUnsignedIntegerValue(tmp, Orthanc::DicomPath(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))) | |
89 | 178 { |
179 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
180 } | |
0 | 181 |
239 | 182 imageType_ = reader.GetStringValue(Orthanc::DicomPath(DICOM_TAG_IMAGE_TYPE), ""); |
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183 |
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184 size_t countFrames; |
239 | 185 if (reader.GetDataset().GetSequenceSize(countFrames, Orthanc::DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE))) |
0 | 186 { |
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187 if (countFrames != tmp) |
89 | 188 { |
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189 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; |
0 | 190 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
191 } | |
192 | |
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193 frames_.reserve(countFrames); |
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194 |
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195 for (size_t i = 0; i < countFrames; i++) |
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196 { |
239 | 197 Orthanc::DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
198 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
199 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
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200 |
239 | 201 Orthanc::DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
202 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, | |
203 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); | |
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204 |
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205 int xx, yy; |
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206 if (!reader.GetIntegerValue(xx, pathX) || |
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207 !reader.GetIntegerValue(yy, pathY)) |
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208 { |
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209 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); |
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210 } |
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211 |
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212 // "-1", because coordinates are shifted by 1 in DICOM |
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213 xx -= 1; |
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214 yy -= 1; |
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215 |
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216 unsigned int x = static_cast<unsigned int>(xx); |
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217 unsigned int y = static_cast<unsigned int>(yy); |
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218 |
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219 if (xx < 0 || |
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220 yy < 0 || |
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221 x % tileWidth_ != 0 || |
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222 y % tileHeight_ != 0 || |
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223 x >= totalWidth_ || |
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224 y >= totalHeight_) |
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225 { |
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226 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" |
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227 << x << "," << y << ") in instance: " << instanceId; |
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228 } |
268
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229 else |
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230 { |
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231 frames_.push_back(std::make_pair(x / tileWidth_, y / tileHeight_)); |
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232 } |
215
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233 } |
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234 } |
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235 else |
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236 { |
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237 // No "Per frame functional groups sequence" tag. Assume regular grid. |
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238 frames_.resize(tmp); |
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239 |
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240 // Compute "ceiling(totalWidth_ / tileWidth_) |
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241 unsigned int w = totalWidth_ / tileWidth_; |
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242 if (totalWidth_ % tileWidth_ != 0) |
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243 { |
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244 w += 1; |
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245 } |
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246 |
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247 unsigned int h = totalHeight_ / tileHeight_; |
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248 if (totalHeight_ % tileHeight_ != 0) |
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249 { |
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250 h += 1; |
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251 } |
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252 |
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253 if (w * h != tmp) |
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254 { |
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255 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; |
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256 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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257 } |
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258 |
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259 for (size_t i = 0; i < frames_.size(); i++) |
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260 { |
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261 frames_[i].first = i % w; |
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262 frames_[i].second = i / w; |
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263 } |
0 | 264 } |
265 } | |
266 | |
267 | |
196
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268 DicomPyramidInstance::DicomPyramidInstance(OrthancStone::IOrthancConnection& orthanc, |
69
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269 const std::string& instanceId, |
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270 bool useCache) : |
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271 instanceId_(instanceId), |
217
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272 hasCompression_(false), |
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273 compression_(ImageCompression_None) // Dummy initialization for serialization |
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274 { |
69
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275 if (useCache) |
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276 { |
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277 try |
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278 { |
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279 // Try and deserialized the cached information about this instance |
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280 std::string serialized; |
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281 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA); |
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282 Deserialize(serialized); |
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283 return; // Success |
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284 } |
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285 catch (Orthanc::OrthancException&) |
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286 { |
70 | 287 // No cached information yet |
69
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288 } |
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289 } |
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290 |
70 | 291 // Compute information about this instance from scratch |
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292 Load(orthanc, instanceId); |
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293 |
70 | 294 if (useCache) |
295 { | |
296 // Serialize the computed information and cache it as a metadata | |
297 std::string serialized, tmp; | |
298 Serialize(serialized); | |
299 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized); | |
300 } | |
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301 } |
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302 |
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303 |
0 | 304 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const |
305 { | |
306 assert(frame < frames_.size()); | |
307 return frames_[frame].first; | |
308 } | |
309 | |
310 | |
311 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
312 { | |
313 assert(frame < frames_.size()); | |
314 return frames_[frame].second; | |
315 } | |
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316 |
217
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317 |
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318 |
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319 static const char* const HAS_COMPRESSION = "HasCompression"; |
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320 static const char* const IMAGE_COMPRESSION = "ImageCompression"; |
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321 static const char* const PIXEL_FORMAT = "PixelFormat"; |
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322 static const char* const FRAMES = "Frames"; |
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323 static const char* const TILE_WIDTH = "TileWidth"; |
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324 static const char* const TILE_HEIGHT = "TileHeight"; |
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325 static const char* const TOTAL_WIDTH = "TotalWidth"; |
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326 static const char* const TOTAL_HEIGHT = "TotalHeight"; |
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327 static const char* const PHOTOMETRIC_INTERPRETATION = "PhotometricInterpretation"; |
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328 static const char* const IMAGE_TYPE = "ImageType"; |
217
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329 |
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330 |
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331 void DicomPyramidInstance::Serialize(std::string& result) const |
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332 { |
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333 Json::Value frames = Json::arrayValue; |
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334 for (size_t i = 0; i < frames_.size(); i++) |
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335 { |
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336 Json::Value frame = Json::arrayValue; |
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337 frame.append(frames_[i].first); |
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338 frame.append(frames_[i].second); |
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339 frames.append(frame); |
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340 } |
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341 |
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342 Json::Value content = Json::objectValue; |
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343 content[FRAMES] = frames; |
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344 |
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345 // "instanceId_" is set by the constructor |
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346 |
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347 content[HAS_COMPRESSION] = hasCompression_; |
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348 content[IMAGE_COMPRESSION] = static_cast<int>(compression_); |
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349 content[PIXEL_FORMAT] = static_cast<int>(format_); |
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350 content[TILE_WIDTH] = tileWidth_; |
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351 content[TILE_HEIGHT] = tileHeight_; |
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352 content[TOTAL_WIDTH] = totalWidth_; |
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353 content[TOTAL_HEIGHT] = totalHeight_; |
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354 content[PHOTOMETRIC_INTERPRETATION] = Orthanc::EnumerationToString(photometric_); |
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355 content[IMAGE_TYPE] = imageType_; |
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356 |
226 | 357 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
358 Orthanc::Toolbox::WriteFastJson(result, content); | |
359 #else | |
360 Json::FastWriter writer; | |
361 result = writer.write(content); | |
362 #endif | |
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363 } |
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364 |
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365 |
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366 void DicomPyramidInstance::Deserialize(const std::string& s) |
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367 { |
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368 Json::Value content; |
226 | 369 OrthancStone::IOrthancConnection::ParseJson(content, s); |
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370 |
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371 if (content.type() != Json::objectValue || |
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372 !content.isMember(FRAMES) || |
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373 content[FRAMES].type() != Json::arrayValue) |
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374 { |
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375 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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376 } |
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377 |
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378 hasCompression_ = Orthanc::SerializationToolbox::ReadBoolean(content, HAS_COMPRESSION); |
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379 compression_ = static_cast<ImageCompression>(Orthanc::SerializationToolbox::ReadInteger(content, IMAGE_COMPRESSION)); |
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380 format_ = static_cast<Orthanc::PixelFormat>(Orthanc::SerializationToolbox::ReadInteger(content, PIXEL_FORMAT)); |
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381 tileWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_WIDTH); |
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382 tileHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_HEIGHT); |
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383 totalWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_WIDTH); |
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384 totalHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_HEIGHT); |
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385 |
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386 std::string p = Orthanc::SerializationToolbox::ReadString(content, PHOTOMETRIC_INTERPRETATION); |
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387 photometric_ = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
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388 |
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389 imageType_ = Orthanc::SerializationToolbox::ReadString(content, IMAGE_TYPE); |
217
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390 |
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391 const Json::Value f = content[FRAMES]; |
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392 frames_.resize(f.size()); |
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393 |
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394 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++) |
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395 { |
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396 if (f[i].type() != Json::arrayValue || |
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397 f[i].size() != 2 || |
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398 f[i][0].type() != Json::intValue || |
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399 f[i][1].type() != Json::intValue || |
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400 f[i][0].asInt() < 0 || |
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401 f[i][1].asInt() < 0) |
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402 { |
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403 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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404 } |
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405 |
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406 frames_[i].first = f[i][0].asInt(); |
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407 frames_[i].second = f[i][1].asInt(); |
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408 } |
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409 } |
0 | 410 } |