Mercurial > hg > orthanc
annotate OrthancFramework/Sources/DicomFormat/DicomImageInformation.cpp @ 5841:57ab63fe9108 find-refactoring tip
tools/find: Limit and Since are now forbidden when filtering on DICOM tags that are not stored in DB
author | Alain Mazy <am@orthanc.team> |
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date | Thu, 24 Oct 2024 15:08:43 +0200 |
parents | f7adfb22e20e |
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rev | line source |
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853 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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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 |
853 | 8 * |
9 * This program is free software: you can redistribute it and/or | |
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10 * modify it under the terms of the GNU Lesser General Public License |
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11 * as published by the Free Software Foundation, either version 3 of |
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12 * the License, or (at your option) any later version. |
3007 | 13 * |
853 | 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 | |
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17 * Lesser General Public License for more details. |
853 | 18 * |
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19 * You should have received a copy of the GNU Lesser General Public |
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20 * License along with this program. If not, see |
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21 * <http://www.gnu.org/licenses/>. |
853 | 22 **/ |
23 | |
24 | |
25 #include "../PrecompiledHeaders.h" | |
26 | |
27 #ifndef NOMINMAX | |
28 #define NOMINMAX | |
29 #endif | |
30 | |
31 #include "DicomImageInformation.h" | |
32 | |
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33 #include "../Compatibility.h" |
4882 | 34 #include "../Logging.h" |
853 | 35 #include "../OrthancException.h" |
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36 #include "../Toolbox.h" |
4882 | 37 |
853 | 38 #include <boost/lexical_cast.hpp> |
39 #include <limits> | |
40 #include <cassert> | |
41 #include <stdio.h> | |
2870 | 42 #include <memory> |
853 | 43 |
44 namespace Orthanc | |
45 { | |
46 DicomImageInformation::DicomImageInformation(const DicomMap& values) | |
47 { | |
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48 std::string sopClassUid; |
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49 if (values.LookupStringValue(sopClassUid, DICOM_TAG_SOP_CLASS_UID, false)) |
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50 { |
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51 sopClassUid = Toolbox::StripSpaces(sopClassUid); |
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52 if (sopClassUid == "1.2.840.10008.5.1.4.1.1.481.3" /* RT-STRUCT */) |
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53 { |
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54 LOG(WARNING) << "Orthanc::DicomImageInformation() should not be applied to SOP Class UID: " << sopClassUid; |
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55 } |
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56 } |
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57 |
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58 uint32_t pixelRepresentation = 0; |
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59 uint32_t planarConfiguration = 0; |
853 | 60 |
61 try | |
62 { | |
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63 std::string p; |
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64 if (values.LookupStringValue(p, DICOM_TAG_PHOTOMETRIC_INTERPRETATION, false)) { |
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65 Toolbox::ToUpperCase(p); |
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66 |
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67 if (p == "RGB") |
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68 { |
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69 photometric_ = PhotometricInterpretation_RGB; |
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70 } |
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71 else if (p == "MONOCHROME1") |
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72 { |
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73 photometric_ = PhotometricInterpretation_Monochrome1; |
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74 } |
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75 else if (p == "MONOCHROME2") |
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76 { |
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77 photometric_ = PhotometricInterpretation_Monochrome2; |
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78 } |
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79 else if (p == "PALETTE COLOR") |
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80 { |
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81 photometric_ = PhotometricInterpretation_Palette; |
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82 } |
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83 else if (p == "HSV") |
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84 { |
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85 photometric_ = PhotometricInterpretation_HSV; |
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86 } |
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87 else if (p == "ARGB") |
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88 { |
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89 photometric_ = PhotometricInterpretation_ARGB; |
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90 } |
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91 else if (p == "CMYK") |
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92 { |
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93 photometric_ = PhotometricInterpretation_CMYK; |
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94 } |
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95 else if (p == "YBR_FULL") |
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96 { |
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97 photometric_ = PhotometricInterpretation_YBRFull; |
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98 } |
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99 else if (p == "YBR_FULL_422") |
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100 { |
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101 photometric_ = PhotometricInterpretation_YBRFull422; |
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102 } |
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103 else if (p == "YBR_PARTIAL_420") |
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104 { |
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105 photometric_ = PhotometricInterpretation_YBRPartial420; |
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106 } |
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107 else if (p == "YBR_PARTIAL_422") |
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108 { |
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109 photometric_ = PhotometricInterpretation_YBRPartial422; |
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110 } |
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111 else if (p == "YBR_ICT") |
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112 { |
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113 photometric_ = PhotometricInterpretation_YBR_ICT; |
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114 } |
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115 else if (p == "YBR_RCT") |
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116 { |
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117 photometric_ = PhotometricInterpretation_YBR_RCT; |
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118 } |
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119 else |
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120 { |
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121 photometric_ = PhotometricInterpretation_Unknown; |
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122 } |
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123 } |
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124 else |
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125 { |
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126 photometric_ = PhotometricInterpretation_Unknown; |
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127 } |
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128 |
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129 values.GetValue(DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_); // in some US images, we've seen tag values of "800\0"; that's why we parse the 'first' value |
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130 values.GetValue(DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_); |
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131 |
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132 if (!values.ParseUnsignedInteger32(bitsAllocated_, DICOM_TAG_BITS_ALLOCATED)) |
853 | 133 { |
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134 throw OrthancException(ErrorCode_BadFileFormat); |
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135 } |
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136 |
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137 if (!values.ParseUnsignedInteger32(samplesPerPixel_, DICOM_TAG_SAMPLES_PER_PIXEL)) |
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138 { |
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139 samplesPerPixel_ = 1; // Assume 1 color channel |
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140 } |
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141 |
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142 if (!values.ParseUnsignedInteger32(bitsStored_, DICOM_TAG_BITS_STORED)) |
853 | 143 { |
144 bitsStored_ = bitsAllocated_; | |
145 } | |
146 | |
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147 if (bitsStored_ > bitsAllocated_) |
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148 { |
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149 throw OrthancException(ErrorCode_BadFileFormat); |
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150 } |
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151 |
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152 if (!values.ParseUnsignedInteger32(highBit_, DICOM_TAG_HIGH_BIT)) |
853 | 153 { |
154 highBit_ = bitsStored_ - 1; | |
155 } | |
156 | |
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157 if (!values.ParseUnsignedInteger32(pixelRepresentation, DICOM_TAG_PIXEL_REPRESENTATION)) |
853 | 158 { |
159 pixelRepresentation = 0; // Assume unsigned pixels | |
160 } | |
161 | |
162 if (samplesPerPixel_ > 1) | |
163 { | |
164 // The "Planar Configuration" is only set when "Samples per Pixels" is greater than 1 | |
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165 // http://dicom.nema.org/medical/dicom/current/output/html/part03.html#sect_C.7.6.3.1.3 |
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166 |
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167 if (!values.ParseUnsignedInteger32(planarConfiguration, DICOM_TAG_PLANAR_CONFIGURATION)) |
853 | 168 { |
169 planarConfiguration = 0; // Assume interleaved color channels | |
170 } | |
171 } | |
172 } | |
173 catch (boost::bad_lexical_cast&) | |
174 { | |
175 throw OrthancException(ErrorCode_NotImplemented); | |
176 } | |
177 catch (OrthancException&) | |
178 { | |
179 throw OrthancException(ErrorCode_NotImplemented); | |
180 } | |
181 | |
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182 |
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183 if (values.HasTag(DICOM_TAG_NUMBER_OF_FRAMES)) |
853 | 184 { |
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185 if (!values.ParseUnsignedInteger32(numberOfFrames_, DICOM_TAG_NUMBER_OF_FRAMES)) |
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186 { |
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187 throw OrthancException(ErrorCode_NotImplemented); |
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188 } |
853 | 189 } |
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190 else |
853 | 191 { |
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192 numberOfFrames_ = 1; |
853 | 193 } |
194 | |
3007 | 195 if (bitsAllocated_ != 8 && bitsAllocated_ != 16 && |
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196 bitsAllocated_ != 24 && bitsAllocated_ != 32 && |
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197 bitsAllocated_ != 1 /* new in Orthanc 1.10.0 */) |
853 | 198 { |
3007 | 199 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported: " + boost::lexical_cast<std::string>(bitsAllocated_) + " bits allocated"); |
200 } | |
201 else if (numberOfFrames_ == 0) | |
202 { | |
203 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported (no frames)"); | |
204 } | |
205 else if (planarConfiguration != 0 && planarConfiguration != 1) | |
206 { | |
207 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported: planar configuration is " + boost::lexical_cast<std::string>(planarConfiguration)); | |
853 | 208 } |
209 | |
210 if (samplesPerPixel_ == 0) | |
211 { | |
3007 | 212 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported: samples per pixel is 0"); |
853 | 213 } |
214 | |
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215 if (bitsStored_ == 1) |
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216 { |
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217 // This is the case of DICOM SEG, new in Orthanc 1.10.0 |
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218 if (bitsAllocated_ != 1) |
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219 { |
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220 throw OrthancException(ErrorCode_BadFileFormat); |
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221 } |
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222 else if (width_ % 8 != 0) |
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223 { |
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224 throw OrthancException(ErrorCode_BadFileFormat, "Bad number of columns for a black-and-white image"); |
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225 } |
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226 else |
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227 { |
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228 bytesPerValue_ = 0; // Arbitrary initialization |
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229 } |
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230 } |
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231 else |
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232 { |
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233 bytesPerValue_ = bitsAllocated_ / 8; |
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234 } |
853 | 235 |
236 isPlanar_ = (planarConfiguration != 0 ? true : false); | |
237 isSigned_ = (pixelRepresentation != 0 ? true : false); | |
238 } | |
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239 |
2870 | 240 DicomImageInformation* DicomImageInformation::Clone() const |
241 { | |
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242 std::unique_ptr<DicomImageInformation> target(new DicomImageInformation); |
2870 | 243 target->width_ = width_; |
244 target->height_ = height_; | |
245 target->samplesPerPixel_ = samplesPerPixel_; | |
246 target->numberOfFrames_ = numberOfFrames_; | |
247 target->isPlanar_ = isPlanar_; | |
248 target->isSigned_ = isSigned_; | |
249 target->bytesPerValue_ = bytesPerValue_; | |
250 target->bitsAllocated_ = bitsAllocated_; | |
251 target->bitsStored_ = bitsStored_; | |
252 target->highBit_ = highBit_; | |
253 target->photometric_ = photometric_; | |
254 | |
255 return target.release(); | |
256 } | |
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257 |
4297 | 258 unsigned int DicomImageInformation::GetWidth() const |
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259 { |
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260 return width_; |
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261 } |
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262 |
4297 | 263 unsigned int DicomImageInformation::GetHeight() const |
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264 { |
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265 return height_; |
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266 } |
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267 |
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268 unsigned int DicomImageInformation::GetNumberOfFrames() const |
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269 { |
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270 return numberOfFrames_; |
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271 } |
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272 |
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273 unsigned int DicomImageInformation::GetChannelCount() const |
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274 { |
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275 return samplesPerPixel_; |
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276 } |
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277 |
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278 unsigned int DicomImageInformation::GetBitsStored() const |
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279 { |
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280 return bitsStored_; |
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281 } |
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282 |
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283 size_t DicomImageInformation::GetBytesPerValue() const |
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284 { |
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285 if (bitsStored_ == 1) |
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286 { |
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287 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
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288 "This call is incompatible with black-and-white images"); |
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289 } |
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290 else |
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291 { |
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292 assert(bitsAllocated_ >= 8); |
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293 return bytesPerValue_; |
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294 } |
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295 } |
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296 |
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297 bool DicomImageInformation::IsSigned() const |
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298 { |
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299 return isSigned_; |
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300 } |
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301 |
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302 unsigned int DicomImageInformation::GetBitsAllocated() const |
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303 { |
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304 return bitsAllocated_; |
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305 } |
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306 |
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307 unsigned int DicomImageInformation::GetHighBit() const |
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308 { |
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309 return highBit_; |
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310 } |
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311 |
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312 bool DicomImageInformation::IsPlanar() const |
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313 { |
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314 return isPlanar_; |
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315 } |
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316 |
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317 unsigned int DicomImageInformation::GetShift() const |
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318 { |
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319 return highBit_ + 1 - bitsStored_; |
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320 } |
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321 |
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322 PhotometricInterpretation DicomImageInformation::GetPhotometricInterpretation() const |
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323 { |
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324 return photometric_; |
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325 } |
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326 |
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327 bool DicomImageInformation::ExtractPixelFormat(PixelFormat& format, |
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328 bool ignorePhotometricInterpretation) const |
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329 { |
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330 if (photometric_ == PhotometricInterpretation_Palette) |
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331 { |
2423
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332 if (GetBitsStored() == 8 && GetChannelCount() == 1 && !IsSigned()) |
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333 { |
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334 format = PixelFormat_RGB24; |
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335 return true; |
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336 } |
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337 |
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338 if (GetBitsStored() == 16 && GetChannelCount() == 1 && !IsSigned()) |
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339 { |
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340 format = PixelFormat_RGB48; |
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341 return true; |
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342 } |
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343 } |
2423
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344 |
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345 if (ignorePhotometricInterpretation || |
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346 photometric_ == PhotometricInterpretation_Monochrome1 || |
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347 photometric_ == PhotometricInterpretation_Monochrome2) |
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348 { |
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349 if (GetBitsStored() == 8 && GetChannelCount() == 1 && !IsSigned()) |
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350 { |
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351 format = PixelFormat_Grayscale8; |
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352 return true; |
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353 } |
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354 |
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355 if (GetBitsAllocated() == 16 && GetChannelCount() == 1 && !IsSigned()) |
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356 { |
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357 format = PixelFormat_Grayscale16; |
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358 return true; |
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359 } |
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360 |
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361 if (GetBitsAllocated() == 16 && GetChannelCount() == 1 && IsSigned()) |
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362 { |
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363 format = PixelFormat_SignedGrayscale16; |
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364 return true; |
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365 } |
2838
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366 |
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367 if (GetBitsAllocated() == 32 && GetChannelCount() == 1 && !IsSigned()) |
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368 { |
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369 format = PixelFormat_Grayscale32; |
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370 return true; |
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371 } |
4827
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372 |
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373 if (GetBitsStored() == 1 && GetChannelCount() == 1 && !IsSigned()) |
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374 { |
4902
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Orthanc 1.9.8 is now known as Orthanc 1.10.0
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4882
diff
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375 // This is the case of DICOM SEG, new in Orthanc 1.10.0 |
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376 format = PixelFormat_Grayscale8; |
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377 return true; |
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378 } |
854
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379 } |
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380 |
3007 | 381 if (GetBitsStored() == 8 && |
382 GetChannelCount() == 3 && | |
1206
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|
383 !IsSigned() && |
1905
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Huge speedup if decoding the family of JPEG transfer syntaxes
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384 (ignorePhotometricInterpretation || photometric_ == PhotometricInterpretation_RGB)) |
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385 { |
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386 format = PixelFormat_RGB24; |
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387 return true; |
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388 } |
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389 |
5054
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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390 if (GetBitsStored() == 16 && |
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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diff
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391 GetChannelCount() == 3 && |
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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392 !IsSigned() && |
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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393 (ignorePhotometricInterpretation || photometric_ == PhotometricInterpretation_RGB)) |
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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394 { |
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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395 format = PixelFormat_RGB48; |
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396 return true; |
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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397 } |
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Added support for RGBA64 images in tools/create-dicom and /preview (Contribution from James Manners - Pliny)
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diff
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398 |
854
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399 return false; |
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|
400 } |
1924
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
401 |
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
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402 |
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
403 size_t DicomImageInformation::GetFrameSize() const |
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
404 { |
4827
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
405 if (bitsStored_ == 1) |
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
406 { |
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
407 assert(GetWidth() % 8 == 0); |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
408 |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
409 if (GetChannelCount() == 1) |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
410 { |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
411 return GetHeight() * GetWidth() / 8; |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
412 } |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
413 else |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
414 { |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
415 throw OrthancException(ErrorCode_IncompatibleImageFormat, |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
416 "Image not supported (multi-channel black-and-image image)"); |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
417 } |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
418 } |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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419 else |
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420 { |
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421 return (GetHeight() * |
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422 GetWidth() * |
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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423 GetBytesPerValue() * |
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424 GetChannelCount()); |
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425 } |
1924
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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426 } |
4312
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427 |
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428 |
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429 unsigned int DicomImageInformation::GetUsefulTagLength() |
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430 { |
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431 return 256; |
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432 } |
5323
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added DicomMap::GuessPixelDataValueRepresentation()
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433 |
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434 |
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435 ValueRepresentation DicomImageInformation::GuessPixelDataValueRepresentation(const DicomTransferSyntax& transferSyntax, |
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436 unsigned int bitsAllocated) |
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437 { |
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438 /** |
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439 * This approach is validated in "Tests/GuessPixelDataVR.py": |
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440 * https://orthanc.uclouvain.be/hg/orthanc-tests/file/default/Tests/GuessPixelDataVR.py |
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441 **/ |
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442 |
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443 if (transferSyntax == DicomTransferSyntax_LittleEndianExplicit || |
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444 transferSyntax == DicomTransferSyntax_BigEndianExplicit) |
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445 { |
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446 /** |
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447 * Same rules apply to Little Endian Explicit and Big Endian |
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448 * Explicit (now retired). The VR of the pixel data directly |
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449 * depends upon the "Bits Allocated (0028,0100)" tag: |
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450 * https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_A.2.html |
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451 * https://dicom.nema.org/medical/dicom/2016b/output/chtml/part05/sect_A.3.html |
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added DicomMap::GuessPixelDataValueRepresentation()
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452 **/ |
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453 if (bitsAllocated > 8) |
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454 { |
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455 return ValueRepresentation_OtherWord; |
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456 } |
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457 else |
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458 { |
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459 return ValueRepresentation_OtherByte; |
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460 } |
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461 } |
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462 else if (transferSyntax == DicomTransferSyntax_LittleEndianImplicit) |
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463 { |
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464 // Assume "OW" for DICOM Implicit VR Little Endian Transfer Syntax |
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added DicomMap::GuessPixelDataValueRepresentation()
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465 // https://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_A.html#sect_A.1 |
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466 return ValueRepresentation_OtherWord; |
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added DicomMap::GuessPixelDataValueRepresentation()
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467 } |
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468 else |
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added DicomMap::GuessPixelDataValueRepresentation()
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469 { |
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added DicomMap::GuessPixelDataValueRepresentation()
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470 // Assume "OB" for all the compressed transfer syntaxes |
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added DicomMap::GuessPixelDataValueRepresentation()
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471 // https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_A.4.html |
138e9d0c08c1
added DicomMap::GuessPixelDataValueRepresentation()
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472 return ValueRepresentation_OtherByte; |
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added DicomMap::GuessPixelDataValueRepresentation()
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473 } |
138e9d0c08c1
added DicomMap::GuessPixelDataValueRepresentation()
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474 } |
853 | 475 } |