Mercurial > hg > orthanc-ohif
annotate Sources/Plugin.cpp @ 37:63a5b4277cfc
note
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 22 Mar 2024 09:44:47 +0100 |
| parents | 5f8d66f7fa06 |
| children | fae02fc69b46 |
| rev | line source |
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| 0 | 1 /** |
| 30 | 2 * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
| 0 | 3 * SPDX-License-Identifier: GPL-3.0-or-later |
| 4 */ | |
| 5 | |
| 6 /** | |
| 7 * OHIF plugin for Orthanc | |
| 30 | 8 * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
| 0 | 9 * |
| 10 * This program is free software: you can redistribute it and/or | |
| 11 * modify it under the terms of the GNU General Public License as | |
| 12 * published by the Free Software Foundation, either version 3 of the | |
| 13 * License, or (at your option) any later version. | |
| 14 * | |
| 15 * This program is distributed in the hope that it will be useful, but | |
| 16 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 18 * General Public License for more details. | |
| 19 * | |
| 20 * You should have received a copy of the GNU General Public License | |
| 21 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 22 **/ | |
| 23 | |
| 24 | |
| 25 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" | |
| 26 | |
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27 #include <Compression/GzipCompressor.h> |
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28 #include <DicomFormat/DicomInstanceHasher.h> |
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29 #include <DicomFormat/DicomMap.h> |
| 0 | 30 #include <Logging.h> |
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31 #include <MultiThreading/SharedMessageQueue.h> |
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32 #include <SerializationToolbox.h> |
| 0 | 33 #include <SystemToolbox.h> |
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34 #include <Toolbox.h> |
| 0 | 35 |
| 36 #include <EmbeddedResources.h> | |
| 37 | |
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38 #include <boost/thread.hpp> |
| 0 | 39 #include <boost/thread/shared_mutex.hpp> |
| 40 | |
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41 |
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42 static const std::string METADATA_OHIF = "4202"; |
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43 static const char* const KEY_VERSION = "Version"; |
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44 static const unsigned int MAX_INSTANCES_IN_QUEUE = 10000; |
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45 |
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46 |
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47 enum DataSource |
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48 { |
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49 DataSource_DicomWeb, |
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50 DataSource_DicomJson |
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51 }; |
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52 |
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53 |
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54 // Reference: https://v3-docs.ohif.org/configuration/dataSources/dicom-json |
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55 |
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56 enum DataType |
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57 { |
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58 DataType_String, |
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59 DataType_Integer, |
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60 DataType_Float, |
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61 DataType_ListOfFloats, |
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62 DataType_ListOfStrings, |
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63 DataType_None |
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64 }; |
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65 |
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66 class TagInformation |
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67 { |
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68 private: |
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69 DataType type_; |
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70 std::string name_; |
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71 |
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72 public: |
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73 TagInformation() : |
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74 type_(DataType_None) |
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75 { |
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76 } |
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77 |
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78 TagInformation(DataType type, |
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79 const std::string& name) : |
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80 type_(type), |
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81 name_(name) |
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82 { |
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83 } |
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84 |
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85 DataType GetType() const |
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86 { |
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87 return type_; |
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88 } |
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89 |
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90 const std::string& GetName() const |
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91 { |
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92 return name_; |
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93 } |
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94 |
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95 bool operator== (const TagInformation& other) const |
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96 { |
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97 return (type_ == other.type_ && |
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98 name_ == other.name_); |
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99 } |
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100 }; |
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101 |
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102 typedef std::map<Orthanc::DicomTag, TagInformation> TagsDictionary; |
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103 |
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104 static TagsDictionary ohifStudyTags_, ohifSeriesTags_, ohifInstanceTags_, allTags_; |
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105 |
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106 |
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107 static const Orthanc::DicomTag RADIOPHARMACEUTICAL_INFORMATION_SEQUENCE(0x0054, 0x0016); |
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108 |
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109 static void InitializeOhifTags() |
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110 { |
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111 /** |
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112 * Those are the tags that are found in the documentation of the |
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113 * "DICOM JSON" data source: |
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114 * https://docs.ohif.org/configuration/dataSources/dicom-json |
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115 **/ |
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116 ohifStudyTags_[Orthanc::DICOM_TAG_STUDY_INSTANCE_UID] = TagInformation(DataType_String, "StudyInstanceUID"); |
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117 ohifStudyTags_[Orthanc::DICOM_TAG_STUDY_DATE] = TagInformation(DataType_String, "StudyDate"); |
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118 ohifStudyTags_[Orthanc::DICOM_TAG_STUDY_TIME] = TagInformation(DataType_String, "StudyTime"); |
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119 ohifStudyTags_[Orthanc::DICOM_TAG_STUDY_DESCRIPTION] = TagInformation(DataType_String, "StudyDescription"); |
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120 ohifStudyTags_[Orthanc::DICOM_TAG_PATIENT_NAME] = TagInformation(DataType_String, "PatientName"); |
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121 ohifStudyTags_[Orthanc::DICOM_TAG_PATIENT_ID] = TagInformation(DataType_String, "PatientID"); |
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122 ohifStudyTags_[Orthanc::DICOM_TAG_ACCESSION_NUMBER] = TagInformation(DataType_String, "AccessionNumber"); |
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123 ohifStudyTags_[Orthanc::DicomTag(0x0010, 0x1010)] = TagInformation(DataType_String, "PatientAge"); |
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124 ohifStudyTags_[Orthanc::DICOM_TAG_PATIENT_SEX] = TagInformation(DataType_String, "PatientSex"); |
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125 |
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126 ohifSeriesTags_[Orthanc::DICOM_TAG_SERIES_INSTANCE_UID] = TagInformation(DataType_String, "SeriesInstanceUID"); |
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127 ohifSeriesTags_[Orthanc::DICOM_TAG_SERIES_NUMBER] = TagInformation(DataType_Integer, "SeriesNumber"); |
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128 ohifSeriesTags_[Orthanc::DICOM_TAG_SERIES_DESCRIPTION] = TagInformation(DataType_String, "SeriesDescription"); |
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129 ohifSeriesTags_[Orthanc::DICOM_TAG_MODALITY] = TagInformation(DataType_String, "Modality"); |
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130 ohifSeriesTags_[Orthanc::DICOM_TAG_SLICE_THICKNESS] = TagInformation(DataType_Float, "SliceThickness"); |
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131 |
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132 ohifInstanceTags_[Orthanc::DICOM_TAG_COLUMNS] = TagInformation(DataType_Integer, "Columns"); |
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133 ohifInstanceTags_[Orthanc::DICOM_TAG_ROWS] = TagInformation(DataType_Integer, "Rows"); |
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134 ohifInstanceTags_[Orthanc::DICOM_TAG_INSTANCE_NUMBER] = TagInformation(DataType_Integer, "InstanceNumber"); |
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135 ohifInstanceTags_[Orthanc::DICOM_TAG_SOP_CLASS_UID] = TagInformation(DataType_String, "SOPClassUID"); |
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136 ohifInstanceTags_[Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION] = TagInformation(DataType_String, "PhotometricInterpretation"); |
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137 ohifInstanceTags_[Orthanc::DICOM_TAG_BITS_ALLOCATED] = TagInformation(DataType_Integer, "BitsAllocated"); |
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138 ohifInstanceTags_[Orthanc::DICOM_TAG_BITS_STORED] = TagInformation(DataType_Integer, "BitsStored"); |
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139 ohifInstanceTags_[Orthanc::DICOM_TAG_PIXEL_REPRESENTATION] = TagInformation(DataType_Integer, "PixelRepresentation"); |
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140 ohifInstanceTags_[Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL] = TagInformation(DataType_Integer, "SamplesPerPixel"); |
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141 ohifInstanceTags_[Orthanc::DICOM_TAG_PIXEL_SPACING] = TagInformation(DataType_ListOfFloats, "PixelSpacing"); |
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142 ohifInstanceTags_[Orthanc::DICOM_TAG_HIGH_BIT] = TagInformation(DataType_Integer, "HighBit"); |
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143 ohifInstanceTags_[Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT] = TagInformation(DataType_ListOfFloats, "ImageOrientationPatient"); |
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144 ohifInstanceTags_[Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT] = TagInformation(DataType_ListOfFloats, "ImagePositionPatient"); |
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145 ohifInstanceTags_[Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID] = TagInformation(DataType_String, "FrameOfReferenceUID"); |
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146 ohifInstanceTags_[Orthanc::DicomTag(0x0008, 0x0008)] = TagInformation(DataType_ListOfStrings, "ImageType"); |
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147 ohifInstanceTags_[Orthanc::DICOM_TAG_MODALITY] = TagInformation(DataType_String, "Modality"); |
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148 ohifInstanceTags_[Orthanc::DICOM_TAG_SOP_INSTANCE_UID] = TagInformation(DataType_String, "SOPInstanceUID"); |
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149 ohifInstanceTags_[Orthanc::DICOM_TAG_SERIES_INSTANCE_UID] = TagInformation(DataType_String, "SeriesInstanceUID"); |
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150 ohifInstanceTags_[Orthanc::DICOM_TAG_STUDY_INSTANCE_UID] = TagInformation(DataType_String, "StudyInstanceUID"); |
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151 ohifInstanceTags_[Orthanc::DICOM_TAG_WINDOW_CENTER] = TagInformation(DataType_Float, "WindowCenter"); |
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152 ohifInstanceTags_[Orthanc::DICOM_TAG_WINDOW_WIDTH] = TagInformation(DataType_Float, "WindowWidth"); |
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153 ohifInstanceTags_[Orthanc::DICOM_TAG_SERIES_DATE] = TagInformation(DataType_String, "SeriesDate"); |
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154 |
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155 /** |
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156 * The items below are related to PET scans. Their list can be found |
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157 * by looking for "required metadata are missing" in |
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158 * "extensions/default/src/getPTImageIdInstanceMetadata.ts" |
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159 **/ |
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160 ohifInstanceTags_[Orthanc::DICOM_TAG_ACQUISITION_DATE] = TagInformation(DataType_String, "AcquisitionDate"); |
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161 ohifInstanceTags_[Orthanc::DICOM_TAG_ACQUISITION_TIME] = TagInformation(DataType_String, "AcquisitionTime"); |
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162 ohifInstanceTags_[Orthanc::DICOM_TAG_SERIES_TIME] = TagInformation(DataType_String, "SeriesTime"); |
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163 ohifInstanceTags_[Orthanc::DicomTag(0x0010, 0x1020)] = TagInformation(DataType_Float, "PatientSize"); |
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164 ohifInstanceTags_[Orthanc::DicomTag(0x0010, 0x1030)] = TagInformation(DataType_Float, "PatientWeight"); |
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165 ohifInstanceTags_[Orthanc::DicomTag(0x0018, 0x1242)] = TagInformation(DataType_Integer, "ActualFrameDuration"); |
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166 ohifInstanceTags_[Orthanc::DicomTag(0x0028, 0x0051)] = TagInformation(DataType_ListOfStrings, "CorrectedImage"); |
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167 ohifInstanceTags_[Orthanc::DicomTag(0x0054, 0x1001)] = TagInformation(DataType_String, "Units"); |
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168 ohifInstanceTags_[Orthanc::DicomTag(0x0054, 0x1102)] = TagInformation(DataType_String, "DecayCorrection"); |
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169 ohifInstanceTags_[Orthanc::DicomTag(0x0054, 0x1300)] = TagInformation(DataType_Float, "FrameReferenceTime"); |
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170 ohifInstanceTags_[RADIOPHARMACEUTICAL_INFORMATION_SEQUENCE] = TagInformation(DataType_None, "RadiopharmaceuticalInformationSequence"); |
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171 |
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172 // UNTESTED |
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173 ohifInstanceTags_[Orthanc::DicomTag(0x7053, 0x1000)] = TagInformation(DataType_Float, "70531000"); // Philips SUVScaleFactor |
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174 ohifInstanceTags_[Orthanc::DicomTag(0x7053, 0x1009)] = TagInformation(DataType_Float, "70531009"); // Philips ActivityConcentrationScaleFactor |
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175 ohifInstanceTags_[Orthanc::DicomTag(0x0009, 0x100d)] = TagInformation(DataType_String, "0009100d"); // GE PrivatePostInjectionDateTime |
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176 |
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177 for (TagsDictionary::const_iterator it = ohifStudyTags_.begin(); it != ohifStudyTags_.end(); ++it) |
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178 { |
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179 assert(allTags_.find(it->first) == allTags_.end() || |
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180 allTags_[it->first] == it->second); |
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181 allTags_[it->first] = it->second; |
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182 } |
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183 |
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184 for (TagsDictionary::const_iterator it = ohifSeriesTags_.begin(); it != ohifSeriesTags_.end(); ++it) |
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185 { |
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186 assert(allTags_.find(it->first) == allTags_.end() || |
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187 allTags_[it->first] == it->second); |
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188 allTags_[it->first] = it->second; |
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189 } |
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190 |
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191 for (TagsDictionary::const_iterator it = ohifInstanceTags_.begin(); it != ohifInstanceTags_.end(); ++it) |
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192 { |
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193 assert(allTags_.find(it->first) == allTags_.end() || |
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194 allTags_[it->first] == it->second); |
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195 allTags_[it->first] = it->second; |
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196 } |
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197 } |
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198 |
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199 |
| 0 | 200 // Forward declaration |
| 201 void ReadStaticAsset(std::string& target, | |
| 202 const std::string& path); | |
| 203 | |
| 204 | |
| 205 /** | |
| 206 * As the OHIF static assets are gzipped by the "EmbedStaticAssets.py" | |
| 207 * script, we use a cache to maintain the uncompressed assets in order | |
| 208 * to avoid multiple gzip decodings. | |
| 209 **/ | |
| 210 class ResourcesCache : public boost::noncopyable | |
| 211 { | |
| 212 private: | |
| 213 typedef std::map<std::string, std::string*> Content; | |
| 214 | |
| 215 boost::shared_mutex mutex_; | |
| 216 Content content_; | |
| 217 | |
| 218 public: | |
| 219 ~ResourcesCache() | |
| 220 { | |
| 221 for (Content::iterator it = content_.begin(); it != content_.end(); ++it) | |
| 222 { | |
| 223 assert(it->second != NULL); | |
| 224 delete it->second; | |
| 225 } | |
| 226 } | |
| 227 | |
| 228 void Answer(OrthancPluginContext* context, | |
| 229 OrthancPluginRestOutput* output, | |
| 230 const std::string& path) | |
| 231 { | |
| 232 const std::string mime = Orthanc::EnumerationToString(Orthanc::SystemToolbox::AutodetectMimeType(path)); | |
| 233 | |
| 234 { | |
| 235 // Check whether the cache already contains the resource | |
| 236 boost::shared_lock<boost::shared_mutex> lock(mutex_); | |
| 237 | |
| 238 Content::const_iterator found = content_.find(path); | |
| 239 | |
| 240 if (found != content_.end()) | |
| 241 { | |
| 242 assert(found->second != NULL); | |
| 243 OrthancPluginAnswerBuffer(context, output, found->second->c_str(), found->second->size(), mime.c_str()); | |
| 244 return; | |
| 245 } | |
| 246 } | |
| 247 | |
| 248 // This resource has not been cached yet | |
| 249 | |
| 250 std::unique_ptr<std::string> item(new std::string); | |
| 251 ReadStaticAsset(*item, path); | |
|
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252 |
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253 // patch OHIF for https://github.com/OHIF/Viewers/issues/3928 |
| 37 | 254 // TODO - Remove after official release OHIF 3.8.0 |
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255 if (Orthanc::Toolbox::StartsWith(path, "app.bundle.")) |
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256 { |
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257 boost::replace_all(*item, "window.location.origin + location.pathname + location.search", "window.location.origin + window.location.pathname + location.search"); |
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258 } |
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259 |
| 0 | 260 OrthancPluginAnswerBuffer(context, output, item->c_str(), item->size(), mime.c_str()); |
| 261 | |
| 262 { | |
| 263 // Store the resource into the cache | |
| 264 boost::unique_lock<boost::shared_mutex> lock(mutex_); | |
| 265 | |
| 266 if (content_.find(path) == content_.end()) | |
| 267 { | |
| 268 content_[path] = item.release(); | |
| 269 } | |
| 270 } | |
| 271 } | |
| 272 }; | |
| 273 | |
| 274 | |
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275 static bool ParseTagFromOrthanc(Json::Value& target, |
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276 const Orthanc::DicomTag& tag, |
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277 const std::string& name, |
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278 DataType type, |
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279 const Json::Value& source) |
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280 { |
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281 const std::string formattedTag = tag.Format(); |
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282 |
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283 if (source.isMember(formattedTag)) |
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284 { |
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285 const Json::Value& value = source[formattedTag]; |
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286 |
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287 /** |
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288 * The cases below derive from "Toolbox::SimplifyDicomAsJson()" |
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289 * with "DicomToJsonFormat_Short", which is invoked by the REST |
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290 * API call to "/instances/.../tags?short". |
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291 **/ |
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292 |
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293 switch (value.type()) |
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294 { |
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295 case Json::nullValue: |
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296 return false; |
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297 |
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298 case Json::arrayValue: |
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299 // This should never happen, as this would correspond to a sequence |
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300 return false; |
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301 |
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302 case Json::stringValue: |
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303 { |
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304 switch (type) |
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305 { |
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306 case DataType_String: |
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307 target[name] = value; |
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308 return true; |
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309 |
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310 case DataType_Integer: |
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311 { |
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312 int32_t v; |
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313 if (Orthanc::SerializationToolbox::ParseInteger32(v, value.asString())) |
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314 { |
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315 target[name] = v; |
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316 } |
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317 return true; |
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318 } |
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319 |
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320 case DataType_Float: |
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321 { |
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322 float v; |
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323 if (Orthanc::SerializationToolbox::ParseFloat(v, value.asString())) |
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324 { |
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325 target[name] = v; |
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326 } |
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327 return true; |
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328 } |
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329 |
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330 case DataType_ListOfStrings: |
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331 { |
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332 std::vector<std::string> tokens; |
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333 Orthanc::Toolbox::TokenizeString(tokens, value.asString(), '\\'); |
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334 target[name] = Json::arrayValue; |
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335 for (size_t i = 0; i < tokens.size(); i++) |
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336 { |
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337 target[name].append(tokens[i]); |
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338 } |
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339 return true; |
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340 } |
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341 |
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342 case DataType_ListOfFloats: |
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343 { |
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344 std::vector<std::string> tokens; |
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345 Orthanc::Toolbox::TokenizeString(tokens, value.asString(), '\\'); |
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346 target[name] = Json::arrayValue; |
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347 for (size_t i = 0; i < tokens.size(); i++) |
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348 { |
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349 float v; |
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350 if (Orthanc::SerializationToolbox::ParseFloat(v, tokens[i])) |
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351 { |
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352 target[name].append(v); |
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353 } |
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354 } |
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355 return true; |
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356 } |
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357 |
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358 default: |
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359 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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360 } |
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361 } |
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362 |
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363 default: |
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364 // This should never happen |
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365 return false; |
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366 } |
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367 } |
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368 else |
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369 { |
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370 return false; |
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371 } |
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372 } |
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373 |
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374 |
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375 static bool EncodeOhifInstance(Json::Value& target, |
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376 const std::string& instanceId) |
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377 { |
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378 Json::Value source; |
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379 if (!OrthancPlugins::RestApiGet(source, "/instances/" + instanceId + "/tags?short", false)) |
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380 { |
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381 return false; |
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382 } |
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383 else if (source.type() != Json::objectValue) |
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384 { |
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385 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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386 } |
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387 else |
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388 { |
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389 target[KEY_VERSION] = static_cast<int>(METADATA_VERSION); |
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390 |
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391 for (TagsDictionary::const_iterator it = allTags_.begin(); it != allTags_.end(); ++it) |
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392 { |
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393 ParseTagFromOrthanc(target, it->first, it->first.Format(), it->second.GetType(), source); |
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394 } |
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395 |
|
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396 /** |
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397 * This is a sequence for PET scans that is manually injected, to be |
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398 * used in function "getPTImageIdInstanceMetadata()" of |
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399 * "extensions/default/src/getPTImageIdInstanceMetadata.ts" |
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400 **/ |
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401 static const Orthanc::DicomTag RADIONUCLIDE_HALF_LIFE(0x0018, 0x1075); |
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402 static const Orthanc::DicomTag RADIONUCLIDE_TOTAL_DOSE(0x0018, 0x1074); |
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403 static const Orthanc::DicomTag RADIOPHARMACEUTICAL_START_DATETIME(0x0018, 0x1078); |
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404 static const Orthanc::DicomTag RADIOPHARMACEUTICAL_START_TIME(0x0018, 0x1072); |
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405 |
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406 if (source.isMember(RADIOPHARMACEUTICAL_INFORMATION_SEQUENCE.Format())) |
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407 { |
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408 const Json::Value& pharma = source[RADIOPHARMACEUTICAL_INFORMATION_SEQUENCE.Format()]; |
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409 if (pharma.type() == Json::arrayValue && |
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410 pharma.size() > 0 && |
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411 pharma[0].type() == Json::objectValue) |
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412 { |
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413 Json::Value info; |
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414 if (ParseTagFromOrthanc(info, RADIONUCLIDE_HALF_LIFE, "RadionuclideHalfLife", DataType_Float, pharma[0]) && |
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415 ParseTagFromOrthanc(info, RADIONUCLIDE_TOTAL_DOSE, "RadionuclideTotalDose", DataType_Float, pharma[0]) && |
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416 (ParseTagFromOrthanc(info, RADIOPHARMACEUTICAL_START_DATETIME, "RadiopharmaceuticalStartDateTime", DataType_String, pharma[0]) || |
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417 ParseTagFromOrthanc(info, RADIOPHARMACEUTICAL_START_TIME, "RadiopharmaceuticalStartTime", DataType_String, pharma[0]))) |
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418 { |
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419 Json::Value sequence = Json::arrayValue; |
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420 sequence.append(info); |
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421 |
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422 target[RADIOPHARMACEUTICAL_INFORMATION_SEQUENCE.Format()] = sequence; |
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423 } |
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424 } |
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425 } |
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426 |
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427 return true; |
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428 } |
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429 } |
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430 |
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431 |
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432 static std::string GetCacheUri(const std::string& instanceId) |
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433 { |
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434 return "/instances/" + instanceId + "/metadata/" + METADATA_OHIF; |
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435 } |
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436 |
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437 |
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438 static void CacheAsMetadata(const Json::Value& instanceTags, |
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439 const std::string& instanceId) |
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440 { |
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441 std::string uncompressed; |
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442 Orthanc::Toolbox::WriteFastJson(uncompressed, instanceTags); |
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443 |
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444 std::string compressed; |
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445 Orthanc::GzipCompressor compressor; |
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446 Orthanc::IBufferCompressor::Compress(compressed, compressor, uncompressed); |
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447 |
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448 std::string metadata; |
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449 Orthanc::Toolbox::EncodeBase64(metadata, compressed); |
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450 |
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451 Json::Value answer; |
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452 OrthancPlugins::RestApiPut(answer, GetCacheUri(instanceId), metadata.c_str(), metadata.size(), false); |
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453 } |
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454 |
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455 |
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456 static bool GetOhifInstance(Json::Value& target, |
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457 const std::string& instanceId) |
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458 { |
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459 const std::string uri = GetCacheUri(instanceId); |
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460 |
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461 std::string metadata; |
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462 |
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463 if (OrthancPlugins::RestApiGetString(metadata, uri, false)) |
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464 { |
|
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465 try |
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466 { |
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467 std::string compressed; |
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468 Orthanc::Toolbox::DecodeBase64(compressed, metadata); |
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469 |
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470 std::string uncompressed; |
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471 Orthanc::GzipCompressor compressor; |
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472 Orthanc::IBufferCompressor::Uncompress(uncompressed, compressor, compressed); |
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473 |
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474 if (Orthanc::Toolbox::ReadJson(target, uncompressed) && |
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475 target.isMember(KEY_VERSION) && |
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476 target[KEY_VERSION].type() == Json::intValue && |
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477 target[KEY_VERSION].asInt() == METADATA_VERSION) |
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478 { |
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479 // Success, we can reuse the cached value |
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480 return true; |
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481 } |
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482 } |
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483 catch (Orthanc::OrthancException&) |
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484 { |
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485 } |
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486 |
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487 // Remove corrupted or metadata with an earlier version |
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488 OrthancPlugins::RestApiDelete(uri, false); |
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489 } |
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490 |
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491 if (EncodeOhifInstance(target, instanceId)) |
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492 { |
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493 CacheAsMetadata(target, instanceId); |
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494 return true; |
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495 } |
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496 else |
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497 { |
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498 return false; |
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499 } |
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500 } |
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501 |
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502 |
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503 static ResourcesCache cache_; |
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504 static std::string userConfiguration_; |
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505 static std::string routerBasename_; |
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506 static DataSource dataSource_; |
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507 static bool preload_; |
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508 static boost::thread metadataThread_; |
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509 static Orthanc::SharedMessageQueue pendingInstances_; |
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510 static bool continueThread_; |
| 0 | 511 |
| 512 void ServeFile(OrthancPluginRestOutput* output, | |
| 513 const char* url, | |
| 514 const OrthancPluginHttpRequest* request) | |
| 515 { | |
| 516 OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); | |
| 517 | |
| 518 // The next 3 HTTP headers are required to enable SharedArrayBuffer | |
| 519 // (https://web.dev/coop-coep/) | |
| 520 OrthancPluginSetHttpHeader(context, output, "Cross-Origin-Embedder-Policy", "require-corp"); | |
| 521 OrthancPluginSetHttpHeader(context, output, "Cross-Origin-Opener-Policy", "same-origin"); | |
| 522 OrthancPluginSetHttpHeader(context, output, "Cross-Origin-Resource-Policy", "same-origin"); | |
| 523 | |
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524 std::string uri; |
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525 if (request->groupsCount > 0) |
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526 { |
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527 uri = request->groups[0]; |
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528 } |
| 0 | 529 |
| 530 if (uri == "app-config.js") | |
| 531 { | |
|
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532 std::string system; |
| 0 | 533 Orthanc::EmbeddedResources::GetFileResource(system, Orthanc::EmbeddedResources::APP_CONFIG_SYSTEM); |
|
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534 |
|
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535 std::map<std::string, std::string> dictionary; |
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536 dictionary["ROUTER_BASENAME"] = routerBasename_; |
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537 dictionary["USE_DICOM_WEB"] = (dataSource_ == DataSource_DicomWeb ? "true" : "false"); |
|
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538 |
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539 system = Orthanc::Toolbox::SubstituteVariables(system, dictionary); |
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540 |
|
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541 std::string s = (userConfiguration_ + "\n" + system); |
|
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Fixed wrong MIME type for app-config.js that prevents the OHIF viewer from loading with Orthanc 1.12.2
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542 OrthancPluginAnswerBuffer(context, output, s.c_str(), s.size(), "text/javascript"); |
| 0 | 543 } |
|
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diff
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|
544 else if (uri == "" || // Study list |
|
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diff
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|
545 uri == "tmtv" || // Total metabolic tumor volume |
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diff
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|
546 uri == "viewer" || // Default viewer (including MPR) |
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547 uri == "segmentation" || // Segmentation mode |
|
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Enabled support for segmentation and microscopy modes
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|
548 uri == "microscopy" // Microscopy mode |
|
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|
549 ) |
|
6
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550 { |
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551 // Those correspond to the different modes of the OHIF platform: |
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552 // https://v3-docs.ohif.org/platform/modes/ |
| 0 | 553 cache_.Answer(context, output, "index.html"); |
| 554 } | |
| 555 else | |
| 556 { | |
| 557 cache_.Answer(context, output, uri); | |
| 558 } | |
| 559 } | |
| 560 | |
| 561 | |
|
5
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562 static void GenerateOhifStudy(Json::Value& target, |
|
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563 const std::string& studyId) |
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564 { |
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565 // https://v3-docs.ohif.org/configuration/dataSources/dicom-json |
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566 static const char* const KEY_ID = "ID"; |
|
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567 const std::string KEY_PATIENT_ID = Orthanc::DICOM_TAG_PATIENT_ID.Format(); |
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568 const std::string KEY_STUDY_INSTANCE_UID = Orthanc::DICOM_TAG_STUDY_INSTANCE_UID.Format(); |
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569 const std::string KEY_SERIES_INSTANCE_UID = Orthanc::DICOM_TAG_SERIES_INSTANCE_UID.Format(); |
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570 const std::string KEY_SOP_INSTANCE_UID = Orthanc::DICOM_TAG_SOP_INSTANCE_UID.Format(); |
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571 |
|
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added the possibility to replace DICOMweb by DICOM JSON
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572 Json::Value instancesIds; |
|
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added the possibility to replace DICOMweb by DICOM JSON
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573 if (!OrthancPlugins::RestApiGet(instancesIds, "/studies/" + studyId + "/instances", false)) |
|
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574 { |
|
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575 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
|
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576 } |
|
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diff
changeset
|
577 |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
578 if (instancesIds.type() != Json::arrayValue) |
|
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|
579 { |
|
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|
580 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
|
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|
581 } |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
582 |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
583 std::vector<Json::Value> instancesTags; |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
584 instancesTags.reserve(instancesIds.size()); |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
585 |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
586 for (Json::ArrayIndex i = 0; i < instancesIds.size(); i++) |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
587 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
588 if (instancesIds[i].type() != Json::objectValue || |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
589 !instancesIds[i].isMember(KEY_ID) || |
|
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|
590 instancesIds[i][KEY_ID].type() != Json::stringValue) |
|
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added the possibility to replace DICOMweb by DICOM JSON
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diff
changeset
|
591 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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parents:
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|
592 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
593 } |
|
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added the possibility to replace DICOMweb by DICOM JSON
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4
diff
changeset
|
594 |
|
8c1fe0ca24f5
added the possibility to replace DICOMweb by DICOM JSON
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diff
changeset
|
595 Json::Value t; |
|
9
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caching OHIF dicom-json as metadata
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8
diff
changeset
|
596 if (GetOhifInstance(t, instancesIds[i][KEY_ID].asString())) |
|
5
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added the possibility to replace DICOMweb by DICOM JSON
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diff
changeset
|
597 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
598 instancesTags.push_back(t); |
|
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diff
changeset
|
599 } |
|
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added the possibility to replace DICOMweb by DICOM JSON
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parents:
4
diff
changeset
|
600 } |
|
8c1fe0ca24f5
added the possibility to replace DICOMweb by DICOM JSON
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diff
changeset
|
601 |
|
8c1fe0ca24f5
added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
602 typedef std::list<const Json::Value*> ListOfResources; |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
603 typedef std::map<std::string, ListOfResources> MapOfResources; |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
604 |
|
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added the possibility to replace DICOMweb by DICOM JSON
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diff
changeset
|
605 MapOfResources studies; |
|
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added the possibility to replace DICOMweb by DICOM JSON
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diff
changeset
|
606 for (Json::ArrayIndex i = 0; i < instancesTags.size(); i++) |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
607 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
608 if (instancesTags[i].isMember(KEY_STUDY_INSTANCE_UID)) |
|
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added the possibility to replace DICOMweb by DICOM JSON
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diff
changeset
|
609 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
610 if (instancesTags[i][KEY_STUDY_INSTANCE_UID].type() != Json::stringValue) |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
611 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
612 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
|
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|
613 } |
|
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added the possibility to replace DICOMweb by DICOM JSON
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|
614 else |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
615 { |
|
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616 const std::string& studyInstanceUid = instancesTags[i][KEY_STUDY_INSTANCE_UID].asString(); |
|
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617 studies[studyInstanceUid].push_back(&instancesTags[i]); |
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618 } |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
619 } |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
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620 } |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
621 |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
622 target["studies"] = Json::arrayValue; |
|
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changeset
|
623 |
|
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added the possibility to replace DICOMweb by DICOM JSON
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624 for (MapOfResources::const_iterator it = studies.begin(); it != studies.end(); ++it) |
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625 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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626 if (!it->second.empty()) |
|
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added the possibility to replace DICOMweb by DICOM JSON
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627 { |
|
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added the possibility to replace DICOMweb by DICOM JSON
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changeset
|
628 assert(it->second.front() != NULL); |
|
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|
629 const Json::Value& firstInstanceInStudy = *it->second.front(); |
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changeset
|
630 |
|
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changeset
|
631 Json::Value study = Json::objectValue; |
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632 for (TagsDictionary::const_iterator tag = ohifStudyTags_.begin(); tag != ohifStudyTags_.end(); ++tag) |
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633 { |
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changeset
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634 if (firstInstanceInStudy.isMember(tag->first.Format())) |
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changeset
|
635 { |
|
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changeset
|
636 study[tag->second.GetName()] = firstInstanceInStudy[tag->first.Format()]; |
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637 } |
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638 } |
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639 |
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640 MapOfResources seriesInStudy; |
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641 for (ListOfResources::const_iterator it2 = it->second.begin(); it2 != it->second.end(); ++it2) |
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642 { |
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643 assert(*it2 != NULL); |
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644 const Json::Value& instanceInStudy = **it2; |
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645 |
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646 if (instanceInStudy.isMember(KEY_SERIES_INSTANCE_UID)) |
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647 { |
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648 if (instanceInStudy[KEY_SERIES_INSTANCE_UID].type() != Json::stringValue) |
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649 { |
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650 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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651 } |
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652 else |
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653 { |
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654 const std::string& seriesInstanceUid = instanceInStudy[KEY_SERIES_INSTANCE_UID].asString(); |
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655 seriesInStudy[seriesInstanceUid].push_back(&instanceInStudy); |
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656 } |
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657 } |
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658 } |
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659 |
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660 study["series"] = Json::arrayValue; |
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661 |
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662 for (MapOfResources::const_iterator it3 = seriesInStudy.begin(); it3 != seriesInStudy.end(); ++it3) |
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663 { |
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664 if (!it3->second.empty()) |
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665 { |
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666 assert(it3->second.front() != NULL); |
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667 const Json::Value& firstInstanceInSeries = *it3->second.front(); |
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668 |
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669 Json::Value series = Json::objectValue; |
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670 for (TagsDictionary::const_iterator tag = ohifSeriesTags_.begin(); tag != ohifSeriesTags_.end(); ++tag) |
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671 { |
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672 if (firstInstanceInSeries.isMember(tag->first.Format())) |
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673 { |
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674 series[tag->second.GetName()] = firstInstanceInSeries[tag->first.Format()]; |
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675 } |
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676 } |
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677 |
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678 series["instances"] = Json::arrayValue; |
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679 |
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680 for (ListOfResources::const_iterator it4 = it3->second.begin(); it4 != it3->second.end(); ++it4) |
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681 { |
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682 assert(*it4 != NULL); |
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683 const Json::Value& instanceInSeries = **it4; |
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684 |
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685 Json::Value metadata; |
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686 for (TagsDictionary::const_iterator tag = ohifInstanceTags_.begin(); tag != ohifInstanceTags_.end(); ++tag) |
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687 { |
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688 if (instanceInSeries.isMember(tag->first.Format())) |
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689 { |
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690 metadata[tag->second.GetName()] = instanceInSeries[tag->first.Format()]; |
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691 } |
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692 } |
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693 |
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694 Orthanc::DicomInstanceHasher hasher(instanceInSeries[KEY_PATIENT_ID].asString(), |
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695 instanceInSeries[KEY_STUDY_INSTANCE_UID].asString(), |
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696 instanceInSeries[KEY_SERIES_INSTANCE_UID].asString(), |
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697 instanceInSeries[KEY_SOP_INSTANCE_UID].asString()); |
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698 |
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699 Json::Value instance = Json::objectValue; |
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700 instance["metadata"] = metadata; |
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701 instance["url"] = "dicomweb:../instances/" + hasher.HashInstance() + "/file"; |
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702 |
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703 series["instances"].append(instance); |
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704 } |
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705 |
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706 study["series"].append(series); |
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707 } |
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708 } |
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changeset
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709 |
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710 target["studies"].append(study); |
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711 } |
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712 } |
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713 } |
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changeset
|
714 |
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715 |
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716 void GetOhifStudy(OrthancPluginRestOutput* output, |
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717 const char* url, |
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718 const OrthancPluginHttpRequest* request) |
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719 { |
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720 OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); |
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721 |
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722 const std::string studyId = request->groups[0]; |
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723 |
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724 Json::Value v; |
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725 GenerateOhifStudy(v, studyId); |
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726 |
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727 std::string s; |
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728 Orthanc::Toolbox::WriteFastJson(s, v); |
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changeset
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729 |
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730 OrthancPluginAnswerBuffer(context, output, s.c_str(), s.size(), "application/json"); |
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731 } |
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changeset
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732 |
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733 |
|
10
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734 static void MetadataThread() |
|
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735 { |
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736 while (continueThread_) |
|
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737 { |
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|
738 std::unique_ptr<Orthanc::IDynamicObject> instance(pendingInstances_.Dequeue(100)); |
|
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739 if (instance.get() != NULL) |
|
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740 { |
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741 const std::string instanceId = dynamic_cast<Orthanc::SingleValueObject<std::string>&>(*instance).GetValue(); |
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742 const std::string uri = GetCacheUri(instanceId); |
|
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743 |
|
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744 Json::Value instanceTags; |
|
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745 std::string metadata; |
|
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746 if (!OrthancPlugins::RestApiGetString(metadata, uri, false) && |
|
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747 EncodeOhifInstance(instanceTags, instanceId)) |
|
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748 { |
|
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749 CacheAsMetadata(instanceTags, instanceId); |
|
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750 } |
|
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751 } |
|
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752 } |
|
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753 } |
|
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|
754 |
|
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diff
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|
755 |
| 0 | 756 OrthancPluginErrorCode OnChangeCallback(OrthancPluginChangeType changeType, |
| 757 OrthancPluginResourceType resourceType, | |
| 758 const char* resourceId) | |
| 759 { | |
| 760 try | |
| 761 { | |
|
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762 switch (changeType) |
| 0 | 763 { |
|
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764 case OrthancPluginChangeType_OrthancStarted: |
|
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changeset
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765 { |
|
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766 continueThread_ = true; |
|
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767 |
|
11
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changeset
|
768 switch (dataSource_) |
|
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769 { |
|
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|
770 case DataSource_DicomWeb: |
|
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|
771 { |
|
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|
772 Json::Value info; |
|
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773 if (!OrthancPlugins::RestApiGet(info, "/plugins/dicom-web", false)) |
|
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|
774 { |
|
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|
775 throw Orthanc::OrthancException( |
|
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|
776 Orthanc::ErrorCode_InternalError, |
|
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diff
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777 "The OHIF plugin requires the DICOMweb plugin to be installed"); |
|
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diff
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|
778 } |
|
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|
779 |
|
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|
780 if (info.type() != Json::objectValue || |
|
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781 !info.isMember("ID") || |
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782 !info.isMember("Version") || |
|
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|
783 info["ID"].type() != Json::stringValue || |
|
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|
784 info["Version"].type() != Json::stringValue || |
|
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changeset
|
785 info["ID"].asString() != "dicom-web") |
|
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|
786 { |
|
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|
787 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, |
|
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changeset
|
788 "The DICOMweb plugin is required by OHIF, but is not properly installed"); |
|
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|
789 } |
|
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changeset
|
790 |
|
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|
791 break; |
|
10
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|
792 } |
|
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changeset
|
793 |
|
11
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|
794 case DataSource_DicomJson: |
|
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795 { |
|
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|
796 if (preload_) |
|
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|
797 { |
|
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|
798 metadataThread_ = boost::thread(MetadataThread); |
|
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|
799 LOG(INFO) << "Started the OHIF preload thread"; |
|
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|
800 } |
|
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changeset
|
801 else |
|
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diff
changeset
|
802 { |
|
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|
803 LOG(INFO) << "The OHIF preload thread was not started, as indicated in the configuration file"; |
|
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|
804 } |
|
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changeset
|
805 break; |
|
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|
806 } |
|
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changeset
|
807 |
|
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diff
changeset
|
808 default: |
|
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|
809 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
|
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|
810 } |
|
11
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changeset
|
811 |
|
10
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|
812 break; |
|
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changeset
|
813 } |
|
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changeset
|
814 |
|
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changeset
|
815 case OrthancPluginChangeType_OrthancStopped: |
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|
816 { |
|
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|
817 continueThread_ = false; |
|
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|
818 |
|
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changeset
|
819 if (metadataThread_.joinable()) |
|
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|
820 { |
|
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|
821 LOG(INFO) << "Stopping the OHIF preload thread"; |
|
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|
822 metadataThread_.join(); |
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|
823 } |
|
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|
824 break; |
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|
825 } |
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|
826 |
|
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|
827 case OrthancPluginChangeType_NewInstance: |
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|
828 { |
|
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|
829 if (metadataThread_.joinable() && |
|
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830 pendingInstances_.GetSize() < MAX_INSTANCES_IN_QUEUE) /* avoid overwhelming Orthanc */ |
|
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|
831 { |
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|
832 pendingInstances_.Enqueue(new Orthanc::SingleValueObject<std::string>(resourceId)); |
|
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|
833 } |
|
4
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|
834 |
|
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|
835 break; |
| 0 | 836 } |
|
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|
837 |
|
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|
838 default: |
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|
839 break; |
| 0 | 840 } |
| 841 } | |
| 842 catch (Orthanc::OrthancException& e) | |
| 843 { | |
| 844 LOG(ERROR) << "Exception: " << e.What(); | |
| 845 return static_cast<OrthancPluginErrorCode>(e.GetErrorCode()); | |
| 846 } | |
| 847 | |
| 848 return OrthancPluginErrorCode_Success; | |
| 849 } | |
| 850 | |
| 851 | |
| 852 extern "C" | |
| 853 { | |
| 854 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) | |
| 855 { | |
| 856 OrthancPlugins::SetGlobalContext(context); | |
| 857 | |
| 858 /* Check the version of the Orthanc core */ | |
| 859 if (OrthancPluginCheckVersion(context) == 0) | |
| 860 { | |
| 861 char info[1024]; | |
| 862 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", | |
| 863 context->orthancVersion, | |
| 864 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, | |
| 865 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, | |
| 866 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); | |
| 867 OrthancPluginLogError(context, info); | |
| 868 return -1; | |
| 869 } | |
| 870 | |
| 871 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) | |
| 872 Orthanc::Logging::InitializePluginContext(context); | |
| 873 #else | |
| 874 Orthanc::Logging::Initialize(context); | |
| 875 #endif | |
| 876 | |
|
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|
877 try |
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|
878 { |
|
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|
879 InitializeOhifTags(); |
|
3
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|
880 |
|
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|
881 OrthancPlugins::OrthancConfiguration configuration; |
|
2
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changeset
|
882 |
|
11
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|
883 { |
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|
884 OrthancPlugins::OrthancConfiguration globalConfiguration; |
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|
885 globalConfiguration.GetSection(configuration, "OHIF"); |
|
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|
886 } |
|
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diff
changeset
|
887 |
|
12
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888 routerBasename_ = configuration.GetStringValue("RouterBasename", "/ohif/"); |
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889 std::string s = configuration.GetStringValue("DataSource", "dicom-json"); |
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890 std::string userConfigurationPath = configuration.GetStringValue("UserConfiguration", ""); |
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891 preload_ = configuration.GetBooleanValue("Preload", true); |
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892 |
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893 if (s == "dicom-web") |
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894 { |
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895 dataSource_ = DataSource_DicomWeb; |
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896 } |
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897 else if (s == "dicom-json") |
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898 { |
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899 dataSource_ = DataSource_DicomJson; |
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900 } |
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901 else |
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902 { |
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903 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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904 "Configuration option \"OHIF.DataSource\" must be either " |
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905 "\"dicomweb\" or \"dicom-json\", but found: " + s); |
|
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906 } |
|
6
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diff
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907 |
|
12
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908 if (userConfigurationPath.empty()) |
|
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909 { |
|
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910 Orthanc::EmbeddedResources::GetFileResource(userConfiguration_, Orthanc::EmbeddedResources::APP_CONFIG_USER); |
|
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911 } |
|
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912 else |
|
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|
913 { |
|
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|
914 Orthanc::SystemToolbox::ReadFile(userConfiguration_, userConfigurationPath); |
|
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915 } |
|
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|
916 |
|
11
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|
917 // Make sure that the router basename ends with a trailing slash |
|
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918 if (routerBasename_.empty() || |
|
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919 routerBasename_[routerBasename_.size() - 1] != '/') |
|
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920 { |
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921 routerBasename_ += "/"; |
|
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922 } |
|
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added configuration option "Preload"
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923 |
|
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924 OrthancPluginSetDescription(context, "OHIF plugin for Orthanc."); |
|
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925 |
|
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added configuration option "Preload"
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changeset
|
926 OrthancPlugins::RegisterRestCallback<ServeFile>("/ohif", true); |
|
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added configuration option "Preload"
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|
927 OrthancPlugins::RegisterRestCallback<ServeFile>("/ohif/(.*)", true); |
|
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added configuration option "Preload"
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928 OrthancPlugins::RegisterRestCallback<GetOhifStudy>("/studies/([0-9a-f-]+)/ohif-dicom-json", true); |
| 0 | 929 |
|
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930 OrthancPluginRegisterOnChangeCallback(context, OnChangeCallback); |
|
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|
931 |
|
16b9f1ff491d
added configuration option "Preload"
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changeset
|
932 { |
|
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added configuration option "Preload"
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diff
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|
933 // Extend the default Orthanc Explorer with custom JavaScript for OHIF |
|
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added configuration option "Preload"
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|
934 std::string explorer; |
|
16b9f1ff491d
added configuration option "Preload"
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|
935 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); |
| 0 | 936 |
|
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937 std::map<std::string, std::string> dictionary; |
|
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938 dictionary["USE_DICOM_WEB"] = (dataSource_ == DataSource_DicomWeb ? "true" : "false"); |
|
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939 explorer = Orthanc::Toolbox::SubstituteVariables(explorer, dictionary); |
|
16b9f1ff491d
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diff
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|
940 |
|
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added configuration option "Preload"
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diff
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|
941 OrthancPluginExtendOrthancExplorer(context, explorer.c_str()); |
|
16b9f1ff491d
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diff
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|
942 } |
|
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diff
changeset
|
943 } |
|
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diff
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|
944 catch (Orthanc::OrthancException& e) |
|
5
8c1fe0ca24f5
added the possibility to replace DICOMweb by DICOM JSON
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diff
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|
945 { |
|
11
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diff
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|
946 return -1; |
|
5
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added the possibility to replace DICOMweb by DICOM JSON
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|
947 } |
| 0 | 948 |
| 949 return 0; | |
| 950 } | |
| 951 | |
| 952 | |
| 953 ORTHANC_PLUGINS_API void OrthancPluginFinalize() | |
| 954 { | |
| 955 } | |
| 956 | |
| 957 | |
| 958 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() | |
| 959 { | |
| 960 return "ohif"; | |
| 961 } | |
| 962 | |
| 963 | |
| 964 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() | |
| 965 { | |
| 966 return ORTHANC_OHIF_VERSION; | |
| 967 } | |
| 968 } |