Mercurial > hg > orthanc
annotate OrthancFramework/Sources/DicomFormat/DicomImageInformation.cpp @ 5036:877bc3b96476
Handle Dicom sequences in ExtraMainDicomTags and save them in the 'MainDicomSequences' metadata
author | Alain Mazy <am@osimis.io> |
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date | Fri, 24 Jun 2022 15:47:10 +0200 |
parents | df86d2505df8 |
children | 255b02c68908 |
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) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
853 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
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10 * as published by the Free Software Foundation, either version 3 of |
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11 * the License, or (at your option) any later version. |
3007 | 12 * |
853 | 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 | |
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16 * Lesser General Public License for more details. |
853 | 17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
853 | 21 **/ |
22 | |
23 | |
24 #include "../PrecompiledHeaders.h" | |
25 | |
26 #ifndef NOMINMAX | |
27 #define NOMINMAX | |
28 #endif | |
29 | |
30 #include "DicomImageInformation.h" | |
31 | |
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32 #include "../Compatibility.h" |
4882 | 33 #include "../Logging.h" |
853 | 34 #include "../OrthancException.h" |
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35 #include "../Toolbox.h" |
4882 | 36 |
853 | 37 #include <boost/lexical_cast.hpp> |
38 #include <limits> | |
39 #include <cassert> | |
40 #include <stdio.h> | |
2870 | 41 #include <memory> |
853 | 42 |
43 namespace Orthanc | |
44 { | |
45 DicomImageInformation::DicomImageInformation(const DicomMap& values) | |
46 { | |
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47 std::string sopClassUid; |
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48 if (values.LookupStringValue(sopClassUid, DICOM_TAG_SOP_CLASS_UID, false)) |
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49 { |
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50 sopClassUid = Toolbox::StripSpaces(sopClassUid); |
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51 if (sopClassUid == "1.2.840.10008.5.1.4.1.1.481.3" /* RT-STRUCT */) |
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52 { |
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53 LOG(WARNING) << "Orthanc::DicomImageInformation() should not be applied to SOP Class UID: " << sopClassUid; |
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54 } |
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55 } |
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56 |
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57 uint32_t pixelRepresentation = 0; |
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58 uint32_t planarConfiguration = 0; |
853 | 59 |
60 try | |
61 { | |
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62 std::string p = values.GetValue(DICOM_TAG_PHOTOMETRIC_INTERPRETATION).GetContent(); |
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63 Toolbox::ToUpperCase(p); |
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64 |
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65 if (p == "RGB") |
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66 { |
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67 photometric_ = PhotometricInterpretation_RGB; |
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68 } |
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69 else if (p == "MONOCHROME1") |
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70 { |
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71 photometric_ = PhotometricInterpretation_Monochrome1; |
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72 } |
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73 else if (p == "MONOCHROME2") |
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74 { |
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75 photometric_ = PhotometricInterpretation_Monochrome2; |
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76 } |
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77 else if (p == "PALETTE COLOR") |
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78 { |
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79 photometric_ = PhotometricInterpretation_Palette; |
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80 } |
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81 else if (p == "HSV") |
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82 { |
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83 photometric_ = PhotometricInterpretation_HSV; |
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84 } |
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85 else if (p == "ARGB") |
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86 { |
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87 photometric_ = PhotometricInterpretation_ARGB; |
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88 } |
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89 else if (p == "CMYK") |
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90 { |
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91 photometric_ = PhotometricInterpretation_CMYK; |
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92 } |
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93 else if (p == "YBR_FULL") |
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94 { |
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95 photometric_ = PhotometricInterpretation_YBRFull; |
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96 } |
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97 else if (p == "YBR_FULL_422") |
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98 { |
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99 photometric_ = PhotometricInterpretation_YBRFull422; |
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100 } |
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101 else if (p == "YBR_PARTIAL_420") |
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102 { |
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103 photometric_ = PhotometricInterpretation_YBRPartial420; |
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104 } |
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105 else if (p == "YBR_PARTIAL_422") |
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106 { |
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107 photometric_ = PhotometricInterpretation_YBRPartial422; |
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108 } |
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109 else if (p == "YBR_ICT") |
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110 { |
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111 photometric_ = PhotometricInterpretation_YBR_ICT; |
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112 } |
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113 else if (p == "YBR_RCT") |
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114 { |
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115 photometric_ = PhotometricInterpretation_YBR_RCT; |
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116 } |
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117 else |
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118 { |
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119 photometric_ = PhotometricInterpretation_Unknown; |
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120 } |
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121 |
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122 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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123 values.GetValue(DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_); |
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124 |
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125 if (!values.ParseUnsignedInteger32(bitsAllocated_, DICOM_TAG_BITS_ALLOCATED)) |
853 | 126 { |
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127 throw OrthancException(ErrorCode_BadFileFormat); |
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128 } |
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129 |
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130 if (!values.ParseUnsignedInteger32(samplesPerPixel_, DICOM_TAG_SAMPLES_PER_PIXEL)) |
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131 { |
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132 samplesPerPixel_ = 1; // Assume 1 color channel |
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133 } |
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134 |
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135 if (!values.ParseUnsignedInteger32(bitsStored_, DICOM_TAG_BITS_STORED)) |
853 | 136 { |
137 bitsStored_ = bitsAllocated_; | |
138 } | |
139 | |
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140 if (bitsStored_ > bitsAllocated_) |
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141 { |
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142 throw OrthancException(ErrorCode_BadFileFormat); |
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143 } |
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144 |
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145 if (!values.ParseUnsignedInteger32(highBit_, DICOM_TAG_HIGH_BIT)) |
853 | 146 { |
147 highBit_ = bitsStored_ - 1; | |
148 } | |
149 | |
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150 if (!values.ParseUnsignedInteger32(pixelRepresentation, DICOM_TAG_PIXEL_REPRESENTATION)) |
853 | 151 { |
152 pixelRepresentation = 0; // Assume unsigned pixels | |
153 } | |
154 | |
155 if (samplesPerPixel_ > 1) | |
156 { | |
157 // The "Planar Configuration" is only set when "Samples per Pixels" is greater than 1 | |
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158 // http://dicom.nema.org/medical/dicom/current/output/html/part03.html#sect_C.7.6.3.1.3 |
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159 |
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160 if (!values.ParseUnsignedInteger32(planarConfiguration, DICOM_TAG_PLANAR_CONFIGURATION)) |
853 | 161 { |
162 planarConfiguration = 0; // Assume interleaved color channels | |
163 } | |
164 } | |
165 } | |
166 catch (boost::bad_lexical_cast&) | |
167 { | |
168 throw OrthancException(ErrorCode_NotImplemented); | |
169 } | |
170 catch (OrthancException&) | |
171 { | |
172 throw OrthancException(ErrorCode_NotImplemented); | |
173 } | |
174 | |
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175 |
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176 if (values.HasTag(DICOM_TAG_NUMBER_OF_FRAMES)) |
853 | 177 { |
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178 if (!values.ParseUnsignedInteger32(numberOfFrames_, DICOM_TAG_NUMBER_OF_FRAMES)) |
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179 { |
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180 throw OrthancException(ErrorCode_NotImplemented); |
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181 } |
853 | 182 } |
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183 else |
853 | 184 { |
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185 numberOfFrames_ = 1; |
853 | 186 } |
187 | |
3007 | 188 if (bitsAllocated_ != 8 && bitsAllocated_ != 16 && |
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189 bitsAllocated_ != 24 && bitsAllocated_ != 32 && |
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190 bitsAllocated_ != 1 /* new in Orthanc 1.10.0 */) |
853 | 191 { |
3007 | 192 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported: " + boost::lexical_cast<std::string>(bitsAllocated_) + " bits allocated"); |
193 } | |
194 else if (numberOfFrames_ == 0) | |
195 { | |
196 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported (no frames)"); | |
197 } | |
198 else if (planarConfiguration != 0 && planarConfiguration != 1) | |
199 { | |
200 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported: planar configuration is " + boost::lexical_cast<std::string>(planarConfiguration)); | |
853 | 201 } |
202 | |
203 if (samplesPerPixel_ == 0) | |
204 { | |
3007 | 205 throw OrthancException(ErrorCode_IncompatibleImageFormat, "Image not supported: samples per pixel is 0"); |
853 | 206 } |
207 | |
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208 if (bitsStored_ == 1) |
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209 { |
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210 // This is the case of DICOM SEG, new in Orthanc 1.10.0 |
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211 if (bitsAllocated_ != 1) |
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212 { |
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213 throw OrthancException(ErrorCode_BadFileFormat); |
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214 } |
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215 else if (width_ % 8 != 0) |
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216 { |
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217 throw OrthancException(ErrorCode_BadFileFormat, "Bad number of columns for a black-and-white image"); |
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218 } |
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219 else |
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220 { |
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221 bytesPerValue_ = 0; // Arbitrary initialization |
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222 } |
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223 } |
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224 else |
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225 { |
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226 bytesPerValue_ = bitsAllocated_ / 8; |
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227 } |
853 | 228 |
229 isPlanar_ = (planarConfiguration != 0 ? true : false); | |
230 isSigned_ = (pixelRepresentation != 0 ? true : false); | |
231 } | |
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232 |
2870 | 233 DicomImageInformation* DicomImageInformation::Clone() const |
234 { | |
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235 std::unique_ptr<DicomImageInformation> target(new DicomImageInformation); |
2870 | 236 target->width_ = width_; |
237 target->height_ = height_; | |
238 target->samplesPerPixel_ = samplesPerPixel_; | |
239 target->numberOfFrames_ = numberOfFrames_; | |
240 target->isPlanar_ = isPlanar_; | |
241 target->isSigned_ = isSigned_; | |
242 target->bytesPerValue_ = bytesPerValue_; | |
243 target->bitsAllocated_ = bitsAllocated_; | |
244 target->bitsStored_ = bitsStored_; | |
245 target->highBit_ = highBit_; | |
246 target->photometric_ = photometric_; | |
247 | |
248 return target.release(); | |
249 } | |
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250 |
4297 | 251 unsigned int DicomImageInformation::GetWidth() const |
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252 { |
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253 return width_; |
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254 } |
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255 |
4297 | 256 unsigned int DicomImageInformation::GetHeight() const |
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257 { |
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258 return height_; |
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259 } |
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260 |
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261 unsigned int DicomImageInformation::GetNumberOfFrames() const |
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262 { |
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263 return numberOfFrames_; |
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264 } |
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265 |
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266 unsigned int DicomImageInformation::GetChannelCount() const |
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267 { |
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268 return samplesPerPixel_; |
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269 } |
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270 |
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271 unsigned int DicomImageInformation::GetBitsStored() const |
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272 { |
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273 return bitsStored_; |
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274 } |
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275 |
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276 size_t DicomImageInformation::GetBytesPerValue() const |
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277 { |
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278 if (bitsStored_ == 1) |
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279 { |
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280 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
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281 "This call is incompatible with black-and-white images"); |
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282 } |
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283 else |
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284 { |
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285 assert(bitsAllocated_ >= 8); |
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286 return bytesPerValue_; |
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287 } |
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288 } |
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289 |
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290 bool DicomImageInformation::IsSigned() const |
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291 { |
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292 return isSigned_; |
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293 } |
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294 |
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295 unsigned int DicomImageInformation::GetBitsAllocated() const |
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296 { |
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297 return bitsAllocated_; |
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298 } |
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299 |
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300 unsigned int DicomImageInformation::GetHighBit() const |
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301 { |
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302 return highBit_; |
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303 } |
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304 |
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305 bool DicomImageInformation::IsPlanar() const |
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306 { |
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307 return isPlanar_; |
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308 } |
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309 |
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310 unsigned int DicomImageInformation::GetShift() const |
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311 { |
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312 return highBit_ + 1 - bitsStored_; |
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313 } |
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314 |
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315 PhotometricInterpretation DicomImageInformation::GetPhotometricInterpretation() const |
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316 { |
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317 return photometric_; |
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318 } |
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319 |
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320 bool DicomImageInformation::ExtractPixelFormat(PixelFormat& format, |
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321 bool ignorePhotometricInterpretation) const |
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322 { |
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323 if (photometric_ == PhotometricInterpretation_Palette) |
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324 { |
2423
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325 if (GetBitsStored() == 8 && GetChannelCount() == 1 && !IsSigned()) |
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326 { |
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327 format = PixelFormat_RGB24; |
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328 return true; |
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329 } |
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330 |
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331 if (GetBitsStored() == 16 && GetChannelCount() == 1 && !IsSigned()) |
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332 { |
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333 format = PixelFormat_RGB48; |
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334 return true; |
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335 } |
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336 } |
2423
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337 |
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338 if (ignorePhotometricInterpretation || |
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339 photometric_ == PhotometricInterpretation_Monochrome1 || |
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340 photometric_ == PhotometricInterpretation_Monochrome2) |
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341 { |
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342 if (GetBitsStored() == 8 && GetChannelCount() == 1 && !IsSigned()) |
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343 { |
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344 format = PixelFormat_Grayscale8; |
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345 return true; |
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346 } |
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347 |
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348 if (GetBitsAllocated() == 16 && GetChannelCount() == 1 && !IsSigned()) |
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349 { |
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350 format = PixelFormat_Grayscale16; |
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351 return true; |
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352 } |
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353 |
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354 if (GetBitsAllocated() == 16 && GetChannelCount() == 1 && IsSigned()) |
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355 { |
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356 format = PixelFormat_SignedGrayscale16; |
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357 return true; |
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358 } |
2838
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359 |
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360 if (GetBitsAllocated() == 32 && GetChannelCount() == 1 && !IsSigned()) |
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361 { |
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362 format = PixelFormat_Grayscale32; |
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363 return true; |
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364 } |
4827
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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365 |
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366 if (GetBitsStored() == 1 && GetChannelCount() == 1 && !IsSigned()) |
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367 { |
4902
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Orthanc 1.9.8 is now known as Orthanc 1.10.0
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diff
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368 // This is the case of DICOM SEG, new in Orthanc 1.10.0 |
4827
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369 format = PixelFormat_Grayscale8; |
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370 return true; |
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371 } |
854
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372 } |
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373 |
3007 | 374 if (GetBitsStored() == 8 && |
375 GetChannelCount() == 3 && | |
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376 !IsSigned() && |
1905
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Huge speedup if decoding the family of JPEG transfer syntaxes
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377 (ignorePhotometricInterpretation || photometric_ == PhotometricInterpretation_RGB)) |
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378 { |
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379 format = PixelFormat_RGB24; |
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380 return true; |
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381 } |
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|
382 |
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diff
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383 return false; |
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fast version of image copy
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|
384 } |
1924
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
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|
385 |
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
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|
386 |
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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387 size_t DicomImageInformation::GetFrameSize() const |
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
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388 { |
4827
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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389 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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390 { |
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
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391 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
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392 |
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
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393 if (GetChannelCount() == 1) |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
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394 { |
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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395 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
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396 } |
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Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
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397 else |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
398 { |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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diff
changeset
|
399 throw OrthancException(ErrorCode_IncompatibleImageFormat, |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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parents:
4437
diff
changeset
|
400 "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
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4437
diff
changeset
|
401 } |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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parents:
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diff
changeset
|
402 } |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
403 else |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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parents:
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diff
changeset
|
404 { |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
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4437
diff
changeset
|
405 return (GetHeight() * |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
406 GetWidth() * |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
407 GetBytesPerValue() * |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
408 GetChannelCount()); |
4cfd96732076
Support decoding of black-and-white images (with 1 bit per pixel), notably DICOM SEG
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
409 } |
1924
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
410 } |
4312
6d49e3b6ff77
fix abi of DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4297
diff
changeset
|
411 |
6d49e3b6ff77
fix abi of DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4297
diff
changeset
|
412 |
6d49e3b6ff77
fix abi of DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4297
diff
changeset
|
413 unsigned int DicomImageInformation::GetUsefulTagLength() |
6d49e3b6ff77
fix abi of DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
414 { |
6d49e3b6ff77
fix abi of DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4297
diff
changeset
|
415 return 256; |
6d49e3b6ff77
fix abi of DicomImageInformation
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
4297
diff
changeset
|
416 } |
853 | 417 } |