Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 61:147bd6dc28db
refactoring using new items in the plugin toolbox of Orthanc
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 25 Nov 2016 17:15:55 +0100 |
| parents | 7a3853d51c45 |
| children | f45cec2c32e2 |
| rev | line source |
|---|---|
| 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 | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU Affero General Public License | |
| 8 * as published by the Free Software Foundation, either version 3 of | |
| 9 * the License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * Affero General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU Affero General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
|
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21 #include "../PrecompiledHeadersWSI.h" |
| 0 | 22 #include "DicomPyramidInstance.h" |
| 23 | |
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24 #include "../../Resources/Orthanc/Core/Logging.h" |
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25 #include "../../Resources/Orthanc/Core/OrthancException.h" |
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26 #include "../../Resources/Orthanc/Core/Toolbox.h" |
| 0 | 27 #include "../DicomToolbox.h" |
| 28 | |
| 29 #include <cassert> | |
| 30 | |
| 31 namespace OrthancWSI | |
| 32 { | |
| 33 static ImageCompression DetectImageCompression(const Json::Value& header) | |
| 34 { | |
| 35 std::string s = Orthanc::Toolbox::StripSpaces | |
| 36 (DicomToolbox::GetMandatoryStringTag(header, "TransferSyntaxUID")); | |
| 37 | |
| 38 if (s == "1.2.840.10008.1.2" || | |
| 39 s == "1.2.840.10008.1.2.1") | |
| 40 { | |
| 41 return ImageCompression_None; | |
| 42 } | |
| 43 else if (s == "1.2.840.10008.1.2.4.50") | |
| 44 { | |
| 45 return ImageCompression_Jpeg; | |
| 46 } | |
| 47 else if (s == "1.2.840.10008.1.2.4.90" || | |
| 48 s == "1.2.840.10008.1.2.4.91") | |
| 49 { | |
| 50 return ImageCompression_Jpeg2000; | |
| 51 } | |
| 52 else | |
| 53 { | |
| 54 LOG(ERROR) << "Unsupported transfer syntax: " << s; | |
| 55 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 56 } | |
| 57 } | |
| 58 | |
| 59 | |
| 60 static Orthanc::PixelFormat DetectPixelFormat(const Json::Value& dicom) | |
| 61 { | |
| 62 std::string photometric = Orthanc::Toolbox::StripSpaces | |
| 63 (DicomToolbox::GetMandatoryStringTag(dicom, "PhotometricInterpretation")); | |
| 64 | |
| 65 if (photometric == "PALETTE") | |
| 66 { | |
| 67 LOG(ERROR) << "Unsupported photometric interpretation: " << photometric; | |
| 68 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 69 } | |
| 70 | |
| 71 unsigned int bitsStored = DicomToolbox::GetUnsignedIntegerTag(dicom, "BitsStored"); | |
| 72 unsigned int samplesPerPixel = DicomToolbox::GetUnsignedIntegerTag(dicom, "SamplesPerPixel"); | |
| 73 bool isSigned = (DicomToolbox::GetUnsignedIntegerTag(dicom, "PixelRepresentation") != 0); | |
| 74 | |
| 75 if (bitsStored == 8 && | |
| 76 samplesPerPixel == 1 && | |
| 77 !isSigned) | |
| 78 { | |
| 79 return Orthanc::PixelFormat_Grayscale8; | |
| 80 } | |
| 81 else if (bitsStored == 8 && | |
| 82 samplesPerPixel == 3 && | |
| 83 !isSigned) | |
| 84 { | |
| 85 return Orthanc::PixelFormat_RGB24; | |
| 86 } | |
| 87 else | |
| 88 { | |
| 89 LOG(ERROR) << "Unsupported pixel format"; | |
| 90 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 91 } | |
| 92 } | |
| 93 | |
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94 |
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95 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancPlugins::IOrthancConnection& orthanc) |
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96 { |
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97 /** |
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98 * Lazy detection of the image compression using the transfer |
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99 * syntax stored inside the DICOM header. Given the fact that |
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100 * reading the header is a time-consuming operation (it implies |
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101 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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102 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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103 * "/header" REST call is delayed until it is really required. |
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104 **/ |
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105 |
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106 if (!hasCompression_) |
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107 { |
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108 Json::Value header; |
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109 OrthancPlugins::IOrthancConnection::RestApiGet |
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110 (header, orthanc, "/instances/" + instanceId_ + "/header?simplify"); |
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111 |
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112 hasCompression_ = true; |
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113 compression_ = DetectImageCompression(header); |
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114 } |
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115 |
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116 return compression_; |
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117 } |
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118 |
| 0 | 119 |
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120 DicomPyramidInstance::DicomPyramidInstance(OrthancPlugins::IOrthancConnection& orthanc, |
| 0 | 121 const std::string& instanceId) : |
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122 instanceId_(instanceId), |
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123 hasCompression_(false) |
| 0 | 124 { |
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125 Json::Value dicom; |
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126 OrthancPlugins::IOrthancConnection::RestApiGet |
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127 (dicom, orthanc, "/instances/" + instanceId + "/tags?simplify"); |
| 0 | 128 |
| 129 if (DicomToolbox::GetMandatoryStringTag(dicom, "SOPClassUID") != "1.2.840.10008.5.1.4.1.1.77.1.6" || | |
| 130 DicomToolbox::GetMandatoryStringTag(dicom, "Modality") != "SM") | |
| 131 { | |
| 132 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 133 } | |
| 134 | |
| 135 format_ = DetectPixelFormat(dicom); | |
| 136 tileWidth_ = DicomToolbox::GetUnsignedIntegerTag(dicom, "Columns"); | |
| 137 tileHeight_ = DicomToolbox::GetUnsignedIntegerTag(dicom, "Rows"); | |
| 138 totalWidth_ = DicomToolbox::GetUnsignedIntegerTag(dicom, "TotalPixelMatrixColumns"); | |
| 139 totalHeight_ = DicomToolbox::GetUnsignedIntegerTag(dicom, "TotalPixelMatrixRows"); | |
| 140 | |
| 141 const Json::Value& frames = DicomToolbox::GetSequenceTag(dicom, "PerFrameFunctionalGroupsSequence"); | |
| 142 | |
| 143 if (frames.size() != DicomToolbox::GetUnsignedIntegerTag(dicom, "NumberOfFrames")) | |
| 144 { | |
| 145 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; | |
| 146 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 147 } | |
| 148 | |
| 149 frames_.resize(frames.size()); | |
| 150 | |
| 151 for (Json::Value::ArrayIndex i = 0; i < frames.size(); i++) | |
| 152 { | |
| 153 const Json::Value& frame = DicomToolbox::GetSequenceTag(frames[i], "PlanePositionSlideSequence"); | |
| 154 if (frame.size() != 1) | |
| 155 { | |
| 156 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 157 } | |
| 158 | |
| 159 // "-1", because coordinates are shifted by 1 in DICOM | |
| 160 int xx = DicomToolbox::GetIntegerTag(frame[0], "ColumnPositionInTotalImagePixelMatrix") - 1; | |
| 161 int yy = DicomToolbox::GetIntegerTag(frame[0], "RowPositionInTotalImagePixelMatrix") - 1; | |
| 162 | |
| 163 unsigned int x = static_cast<unsigned int>(xx); | |
| 164 unsigned int y = static_cast<unsigned int>(yy); | |
| 165 | |
| 166 if (xx < 0 || | |
| 167 yy < 0 || | |
| 168 x % tileWidth_ != 0 || | |
| 169 y % tileHeight_ != 0 || | |
| 170 x >= totalWidth_ || | |
| 171 y >= totalHeight_) | |
| 172 { | |
| 173 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" | |
| 174 << x << "," << y << ") in instance: " << instanceId; | |
| 175 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 176 } | |
| 177 | |
| 178 frames_[i].first = x / tileWidth_; | |
| 179 frames_[i].second = y / tileHeight_; | |
| 180 } | |
| 181 } | |
| 182 | |
| 183 | |
| 184 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const | |
| 185 { | |
| 186 assert(frame < frames_.size()); | |
| 187 return frames_[frame].first; | |
| 188 } | |
| 189 | |
| 190 | |
| 191 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
| 192 { | |
| 193 assert(frame < frames_.size()); | |
| 194 return frames_[frame].second; | |
| 195 } | |
| 196 } |