Mercurial > hg > orthanc-java

annotate Samples/FHIR/src/main/java/OrthancResource.java @ 11:8d876a4f541b

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added sample FHIR server
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 21 Oct 2023 09:53:25 +0200
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children 0dc05fe76bd5
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1 /**
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2 * SPDX-FileCopyrightText: 2023 Sebastien Jodogne, UCLouvain, Belgium
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3 * SPDX-License-Identifier: GPL-3.0-or-later
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4 */
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5
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6 /**
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7 * Java plugin for Orthanc
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8 * Copyright (C) 2023 Sebastien Jodogne, UCLouvain, Belgium
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9 *
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10 * This program is free software: you can redistribute it and/or
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11 * modify it under the terms of the GNU General Public License as
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12 * published by the Free Software Foundation, either version 3 of the
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13 * License, or (at your option) any later version.
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14 *
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15 * This program is distributed in the hope that it will be useful, but
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16 * WITHOUT ANY WARRANTY; without even the implied warranty of
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17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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18 * General Public License for more details.
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19 *
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20 * You should have received a copy of the GNU General Public License
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21 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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22 **/
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23
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24
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25 import be.uclouvain.orthanc.ResourceType;
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26 import org.hl7.fhir.r5.model.*;
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27 import org.json.JSONArray;
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28 import org.json.JSONObject;
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29
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30 import java.nio.charset.StandardCharsets;
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31 import java.util.ArrayList;
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32 import java.util.HashMap;
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33 import java.util.List;
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34 import java.util.Map;
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35
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36 public class OrthancResource {
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37 private ResourceType type;
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38 private String id;
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39 private String lastUpdate;
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40 private Map<String, String> tags;
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41 private List<String> children;
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42
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43 public OrthancResource(JSONObject info) {
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44 String s = info.getString("Type");
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45 if (s.equals("Patient")) {
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46 type = ResourceType.PATIENT;
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47 } else if (s.equals("Study")) {
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48 type = ResourceType.STUDY;
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49 } else if (s.equals("Series")) {
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50 type = ResourceType.SERIES;
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51 } else if (s.equals("Instance")) {
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52 type = ResourceType.INSTANCE;
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53 } else {
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54 throw new RuntimeException("Unknown resource type");
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55 }
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56
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57 id = info.getString("ID");
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58 lastUpdate = info.optString("LastUpdate");
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59 tags = new HashMap<>();
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60 addToDictionary(tags, info.getJSONObject("MainDicomTags"));
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61
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62 if (type != ResourceType.INSTANCE) {
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63 String childKey;
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64 switch (type) {
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65 case PATIENT:
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66 childKey = "Studies";
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67 break;
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68 case STUDY:
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69 childKey = "Series";
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70 addToDictionary(tags, info.getJSONObject("PatientMainDicomTags"));
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71 break;
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72 case SERIES:
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73 childKey = "Instances";
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74 break;
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75 default:
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76 throw new RuntimeException();
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77 }
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78
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79 children = new ArrayList<>();
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80 addToListOfStrings(children, info.getJSONArray(childKey));
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81 }
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82 }
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83
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84 static public void addToDictionary(Map<String, String> target,
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85 JSONObject source) {
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86 for (String key : source.keySet()) {
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87 target.put(key, source.getString(key));
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88 }
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89 }
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90
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91 static public void addToListOfStrings(List<String> target,
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92 JSONArray source) {
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93 for (int i = 0; i < source.length(); i++) {
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94 target.add(source.getString(i));
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95 }
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96 }
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97
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98 public ResourceType getType() {
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99 return type;
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100 }
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101
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102 public String getId() {
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103 return id;
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104 }
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105
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106 public String getLastUpdate() {
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107 return lastUpdate;
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108 }
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109
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110 public Map<String, String> getTags() {
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111 return tags;
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112 }
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113
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114 public List<String> getChildren() {
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115 if (type == ResourceType.INSTANCE) {
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116 throw new RuntimeException("A DICOM instance has no child");
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117 } else {
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118 return children;
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119 }
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120 }
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121
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122 public static List<OrthancResource> find(IOrthancConnection connection,
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123 ResourceType type,
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124 Map<String, String> tags,
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125 boolean caseSensitive) {
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126 JSONObject query = new JSONObject();
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127 for (Map.Entry<String, String> entry : tags.entrySet()) {
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128 query.put(entry.getKey(), entry.getValue());
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129 }
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130
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131 JSONObject request = new JSONObject();
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132 request.put("Expand", true);
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133 request.put("Query", query);
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134 request.put("Short", true);
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135 request.put("CaseSensitive", caseSensitive);
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136
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137 switch (type) {
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138 case PATIENT:
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139 request.put("Level", "Patient");
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140 break;
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141 case STUDY:
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142 request.put("Level", "Study");
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143 break;
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144 case SERIES:
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145 request.put("Level", "Series");
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146 break;
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147 case INSTANCE:
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148 request.put("Level", "Instance");
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149 break;
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150 default:
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151 throw new RuntimeException();
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152 }
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153
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154 byte[] response = connection.doPost("/tools/find", request.toString().getBytes(StandardCharsets.UTF_8));
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155
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156 JSONArray arr = new JSONArray(new String(response, StandardCharsets.UTF_8));
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157
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158 List<OrthancResource> result = new ArrayList<>();
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159 for (int i = 0; i < arr.length(); i++) {
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160 result.add(new OrthancResource(arr.getJSONObject(i)));
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161 }
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162
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163 return result;
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164 }
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165
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166
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167 public Patient getFhirPatient() {
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168 if (type != ResourceType.PATIENT) {
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169 throw new RuntimeException("Not a patient");
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170 }
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171
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172 Patient patient = new Patient();
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173 patient.setId(getTags().getOrDefault(Toolbox.TAG_PATIENT_ID, ""));
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174
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175 String birthDate = getTags().getOrDefault(Toolbox.TAG_PATIENT_BIRTH_DATE, "");
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176 if (birthDate != null) {
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177 patient.setBirthDate(Toolbox.parseDicomDate(birthDate));
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178 }
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179
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180 String patientName = getTags().getOrDefault(Toolbox.TAG_PATIENT_NAME, "");
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181 if (!patientName.isEmpty()) {
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182 patient.addName();
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183 HumanName name = patient.getName().get(0);
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184
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185 String[] parts = patientName.split("\\^");
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186
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187 // https://dicom.nema.org/medical/dicom/current/output/chtml/part19/sect_10.2.html
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188 // https://www.hl7.org/fhir/datatypes.html#HumanName
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189 if (parts.length > 0) {
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190 name.setFamily(parts[0]);
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191 }
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192 for (int i = 1; i < parts.length; i++) {
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193 name.addGiven(parts[i]);
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194 }
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195 }
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196
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197 String sex = getTags().getOrDefault(Toolbox.TAG_PATIENT_SEX, "");
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198 if (sex.equals("M")) {
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199 patient.setGender(Enumerations.AdministrativeGender.MALE);
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200 } else if (sex.equals("F")) {
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201 patient.setGender(Enumerations.AdministrativeGender.FEMALE);
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202 }
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203
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204 return patient;
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205 }
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206
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207 public ImagingStudy getFhirStudy(IOrthancConnection orthanc) {
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208 if (type != ResourceType.STUDY) {
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209 throw new RuntimeException("Not a study");
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210 }
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211
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212 boolean hasDicomWeb = IOrthancConnection.hasPluginInstalled(orthanc, "dicom-web");
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213
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214 // https://build.fhir.org/imagingstudy-example.json.html
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215
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216 ImagingStudy study = new ImagingStudy();
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217 study.setId(getTags().getOrDefault(Toolbox.TAG_STUDY_INSTANCE_UID, ""));
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218 study.setStatus(ImagingStudy.ImagingStudyStatus.AVAILABLE);
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219
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220 if (hasDicomWeb) {
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221 study.addEndpoint(Toolbox.createLocalReference("Endpoint", EndpointProvider.ID));
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222 }
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223
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diff changeset
224 study.setSubject(Toolbox.createLocalReference("Patient", getTags().getOrDefault(Toolbox.TAG_PATIENT_ID, "")));
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225
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diff changeset
226 String studyDate = getTags().getOrDefault(Toolbox.TAG_STUDY_DATE, "");
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227 if (!studyDate.isEmpty()) {
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diff changeset
228 study.setStarted(Toolbox.parseDicomDate(studyDate));
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229 }
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diff changeset
230
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diff changeset
231 study.addIdentifier();
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diff changeset
232 study.getIdentifier().get(0).setSystem("urn:dicom:uid");
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diff changeset
233 study.getIdentifier().get(0).setValue("urn:oid:" + study.getId());
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234
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235 study.setNumberOfSeries(getChildren().size());
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diff changeset
236
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diff changeset
237 int countInstances = 0;
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238
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diff changeset
239 Map<String, String> shortTags = new HashMap<>();
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diff changeset
240 shortTags.put("short", "");
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241
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diff changeset
242 Map<String, String> expand = new HashMap<>();
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diff changeset
243 expand.put("expand", "");
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diff changeset
244
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diff changeset
245 for (int i = 0; i < getChildren().size(); i++) {
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246 String seriesUri = "/series/" + getChildren().get(i);
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parents:
diff changeset
247 OrthancResource orthancSeries = new OrthancResource(IOrthancConnection.getJSONObject(orthanc, seriesUri, shortTags));
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248
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diff changeset
249 ImagingStudy.ImagingStudySeriesComponent fhirSeries = study.addSeries();
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parents:
diff changeset
250 fhirSeries.setUid(orthancSeries.getTags().getOrDefault(Toolbox.TAG_SERIES_INSTANCE_UID, ""));
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251
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diff changeset
252 String modality = orthancSeries.getTags().getOrDefault(Toolbox.TAG_MODALITY, "");
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253 if (!modality.isEmpty()) {
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diff changeset
254 fhirSeries.setModality(Toolbox.createDicomCodeableConcept(modality));
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255 }
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diff changeset
256
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diff changeset
257 String seriesDescription = orthancSeries.getTags().getOrDefault(Toolbox.TAG_SERIES_DESCRIPTION, "");
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258 if (!seriesDescription.isEmpty()) {
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diff changeset
259 fhirSeries.setDescription(seriesDescription);
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260 }
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261
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262 String seriesNumber = orthancSeries.getTags().getOrDefault(Toolbox.TAG_SERIES_NUMBER, "");
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parents:
diff changeset
263 if (!seriesNumber.isEmpty()) {
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diff changeset
264 fhirSeries.setNumber(Integer.parseInt(seriesNumber));
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265 }
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diff changeset
266
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diff changeset
267 fhirSeries.setNumberOfInstances(orthancSeries.getChildren().size());
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268
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diff changeset
269 for (int j = 0; j < orthancSeries.getChildren().size(); j++) {
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270 String instanceUri = "/instances/" + orthancSeries.getChildren().get(j);
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diff changeset
271 OrthancResource orthancInstance = new OrthancResource(IOrthancConnection.getJSONObject(orthanc, instanceUri, shortTags));
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272
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273 JSONObject instanceMetadata = IOrthancConnection.getJSONObject(orthanc, instanceUri + "/metadata", expand);
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274
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275 ImagingStudy.ImagingStudySeriesInstanceComponent fhirInstance = fhirSeries.addInstance();
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276 fhirInstance.setUid(orthancInstance.getTags().getOrDefault(Toolbox.TAG_SOP_INSTANCE_UID, ""));
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diff changeset
277
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diff changeset
278 String instanceNumber = orthancInstance.getTags().getOrDefault(Toolbox.TAG_INSTANCE_NUMBER, "");
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279 if (!instanceNumber.isEmpty()) {
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280 fhirInstance.setNumber(Integer.parseInt(instanceNumber));
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281 }
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282
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283 String sopClassUid = instanceMetadata.optString("SopClassUid", "");
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284 if (!sopClassUid.isEmpty()) {
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285 fhirInstance.setSopClass(new Coding("urn:ietf:rfc:3986", "urn:oid:" + sopClassUid, ""));
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286 }
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287 }
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288
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289 countInstances += orthancSeries.getChildren().size();
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290 }
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291
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292 study.setNumberOfInstances(countInstances);
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293
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294 return study;
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295 }
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296 }