Mercurial > hg > orthanc-java

annotate Samples/FHIR/src/main/java/OrthancResource.java @ 15:b69bc09e2969

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 26 Oct 2023 13:51:32 +0200
parents 0dc05fe76bd5
children 1c407ba1d311
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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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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 private 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 boolean hasPaging,
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127 int since,
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128 int limit) {
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129 JSONObject query = new JSONObject();
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130 for (Map.Entry<String, String> entry : tags.entrySet()) {
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131 query.put(entry.getKey(), entry.getValue());
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132 }
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133
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134 JSONObject request = new JSONObject();
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135 request.put("Expand", true);
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136 request.put("Query", query);
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137 request.put("Short", true);
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138 request.put("CaseSensitive", caseSensitive);
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139
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140 if (hasPaging) {
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141 request.put("Since", since);
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142 request.put("Limit", limit);
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143 }
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144
11
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145 switch (type) {
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146 case PATIENT:
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147 request.put("Level", "Patient");
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148 break;
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149 case STUDY:
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150 request.put("Level", "Study");
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151 break;
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152 case SERIES:
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153 request.put("Level", "Series");
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154 break;
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155 case INSTANCE:
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156 request.put("Level", "Instance");
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157 break;
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158 default:
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159 throw new RuntimeException();
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160 }
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161
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162 byte[] response = connection.doPost("/tools/find", request.toString().getBytes(StandardCharsets.UTF_8));
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163
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164 JSONArray arr = new JSONArray(new String(response, StandardCharsets.UTF_8));
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165
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166 List<OrthancResource> result = new ArrayList<>();
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167 for (int i = 0; i < arr.length(); i++) {
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168 result.add(new OrthancResource(arr.getJSONObject(i)));
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169 }
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170
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171 return result;
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172 }
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173
14
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diff changeset
174 public static List<OrthancResource> find(IOrthancConnection connection,
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175 ResourceType type,
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176 Map<String, String> tags,
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diff changeset
177 boolean caseSensitive,
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diff changeset
178 int since,
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diff changeset
179 int limit) {
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diff changeset
180 return find(connection, type, tags, caseSensitive, true, since, limit);
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181 }
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182
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diff changeset
183 public static List<OrthancResource> find(IOrthancConnection connection,
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184 ResourceType type,
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diff changeset
185 Map<String, String> tags,
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diff changeset
186 boolean caseSensitive) {
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187 return find(connection, type, tags, caseSensitive, false, 0, 0);
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188 }
11
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189
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190 public Patient getFhirPatient() {
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191 if (type != ResourceType.PATIENT) {
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192 throw new RuntimeException("Not a patient");
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193 }
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194
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195 Patient patient = new Patient();
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196 patient.setId(getTags().getOrDefault(Toolbox.TAG_PATIENT_ID, ""));
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197
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198 String birthDate = getTags().getOrDefault(Toolbox.TAG_PATIENT_BIRTH_DATE, "");
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199 if (birthDate != null) {
15
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200 try {
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201 patient.setBirthDate(Toolbox.parseDicomDate(birthDate));
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202 } catch (IllegalArgumentException e) {
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diff changeset
203 // Ignore incorrect dates
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diff changeset
204 }
11
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205 }
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206
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207 String patientName = getTags().getOrDefault(Toolbox.TAG_PATIENT_NAME, "");
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208 if (!patientName.isEmpty()) {
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diff changeset
209 patient.addName();
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210 HumanName name = patient.getName().get(0);
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diff changeset
211
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212 String[] parts = patientName.split("\\^");
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213
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parents:
diff changeset
214 // https://dicom.nema.org/medical/dicom/current/output/chtml/part19/sect_10.2.html
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diff changeset
215 // https://www.hl7.org/fhir/datatypes.html#HumanName
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diff changeset
216 if (parts.length > 0) {
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diff changeset
217 name.setFamily(parts[0]);
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diff changeset
218 }
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diff changeset
219 for (int i = 1; i < parts.length; i++) {
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diff changeset
220 name.addGiven(parts[i]);
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diff changeset
221 }
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diff changeset
222 }
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diff changeset
223
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diff changeset
224 String sex = getTags().getOrDefault(Toolbox.TAG_PATIENT_SEX, "");
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parents:
diff changeset
225 if (sex.equals("M")) {
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diff changeset
226 patient.setGender(Enumerations.AdministrativeGender.MALE);
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diff changeset
227 } else if (sex.equals("F")) {
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diff changeset
228 patient.setGender(Enumerations.AdministrativeGender.FEMALE);
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diff changeset
229 }
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parents:
diff changeset
230
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parents:
diff changeset
231 return patient;
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parents:
diff changeset
232 }
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diff changeset
233
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diff changeset
234 public ImagingStudy getFhirStudy(IOrthancConnection orthanc) {
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parents:
diff changeset
235 if (type != ResourceType.STUDY) {
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parents:
diff changeset
236 throw new RuntimeException("Not a study");
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parents:
diff changeset
237 }
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diff changeset
238
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 boolean hasDicomWeb = IOrthancConnection.hasPluginInstalled(orthanc, "dicom-web");
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240
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diff changeset
241 // https://build.fhir.org/imagingstudy-example.json.html
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diff changeset
242
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parents:
diff changeset
243 ImagingStudy study = new ImagingStudy();
8d876a4f541b added sample FHIR server
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
244 study.setId(getTags().getOrDefault(Toolbox.TAG_STUDY_INSTANCE_UID, ""));
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parents:
diff changeset
245 study.setStatus(ImagingStudy.ImagingStudyStatus.AVAILABLE);
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parents:
diff changeset
246
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parents:
diff changeset
247 if (hasDicomWeb) {
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diff changeset
248 study.addEndpoint(Toolbox.createLocalReference("Endpoint", EndpointProvider.ID));
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parents:
diff changeset
249 }
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parents:
diff changeset
250
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 study.setSubject(Toolbox.createLocalReference("Patient", getTags().getOrDefault(Toolbox.TAG_PATIENT_ID, "")));
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parents:
diff changeset
252
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diff changeset
253 String studyDate = getTags().getOrDefault(Toolbox.TAG_STUDY_DATE, "");
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parents:
diff changeset
254 if (!studyDate.isEmpty()) {
15
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diff changeset
255 try {
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
256 study.setStarted(Toolbox.parseDicomDate(studyDate));
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 14
diff changeset
257 } catch (IllegalArgumentException e) {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 14
diff changeset
258 // Ignore incorrect dates
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 14
diff changeset
259 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 14
diff changeset
260 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 14
diff changeset
261
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 14
diff changeset
262 String studyDescription = getTags().getOrDefault(Toolbox.TAG_STUDY_DESCRIPTION, "");
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 14
diff changeset
263 if (!studyDescription.isEmpty()) {
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
264 study.setDescription(studyDescription);
11
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parents:
diff changeset
265 }
8d876a4f541b added sample FHIR server
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diff changeset
266
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parents:
diff changeset
267 study.addIdentifier();
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parents:
diff changeset
268 study.getIdentifier().get(0).setSystem("urn:dicom:uid");
8d876a4f541b added sample FHIR server
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parents:
diff changeset
269 study.getIdentifier().get(0).setValue("urn:oid:" + study.getId());
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parents:
diff changeset
270
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parents:
diff changeset
271 study.setNumberOfSeries(getChildren().size());
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parents:
diff changeset
272
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parents:
diff changeset
273 int countInstances = 0;
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parents:
diff changeset
274
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parents:
diff changeset
275 Map<String, String> shortTags = new HashMap<>();
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parents:
diff changeset
276 shortTags.put("short", "");
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parents:
diff changeset
277
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parents:
diff changeset
278 Map<String, String> expand = new HashMap<>();
8d876a4f541b added sample FHIR server
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parents:
diff changeset
279 expand.put("expand", "");
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parents:
diff changeset
280
8d876a4f541b added sample FHIR server
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
281 for (int i = 0; i < getChildren().size(); i++) {
8d876a4f541b added sample FHIR server
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parents:
diff changeset
282 String seriesUri = "/series/" + getChildren().get(i);
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parents:
diff changeset
283 OrthancResource orthancSeries = new OrthancResource(IOrthancConnection.getJSONObject(orthanc, seriesUri, shortTags));
8d876a4f541b added sample FHIR server
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parents:
diff changeset
284
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285 ImagingStudy.ImagingStudySeriesComponent fhirSeries = study.addSeries();
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286 fhirSeries.setUid(orthancSeries.getTags().getOrDefault(Toolbox.TAG_SERIES_INSTANCE_UID, ""));
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287
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288 String modality = orthancSeries.getTags().getOrDefault(Toolbox.TAG_MODALITY, "");
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289 if (!modality.isEmpty()) {
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290 fhirSeries.setModality(Toolbox.createDicomCodeableConcept(modality));
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291 }
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292
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293 String seriesDescription = orthancSeries.getTags().getOrDefault(Toolbox.TAG_SERIES_DESCRIPTION, "");
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294 if (!seriesDescription.isEmpty()) {
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295 fhirSeries.setDescription(seriesDescription);
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296 }
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297
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298 String seriesNumber = orthancSeries.getTags().getOrDefault(Toolbox.TAG_SERIES_NUMBER, "");
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299 if (!seriesNumber.isEmpty()) {
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300 fhirSeries.setNumber(Integer.parseInt(seriesNumber));
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301 }
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302
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303 fhirSeries.setNumberOfInstances(orthancSeries.getChildren().size());
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304
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305 for (int j = 0; j < orthancSeries.getChildren().size(); j++) {
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306 String instanceUri = "/instances/" + orthancSeries.getChildren().get(j);
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307 OrthancResource orthancInstance = new OrthancResource(IOrthancConnection.getJSONObject(orthanc, instanceUri, shortTags));
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308
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309 JSONObject instanceMetadata = IOrthancConnection.getJSONObject(orthanc, instanceUri + "/metadata", expand);
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310
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311 ImagingStudy.ImagingStudySeriesInstanceComponent fhirInstance = fhirSeries.addInstance();
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312 fhirInstance.setUid(orthancInstance.getTags().getOrDefault(Toolbox.TAG_SOP_INSTANCE_UID, ""));
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313
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314 String instanceNumber = orthancInstance.getTags().getOrDefault(Toolbox.TAG_INSTANCE_NUMBER, "");
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315 if (!instanceNumber.isEmpty()) {
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316 fhirInstance.setNumber(Integer.parseInt(instanceNumber));
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317 }
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318
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319 String sopClassUid = instanceMetadata.optString("SopClassUid", "");
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320 if (!sopClassUid.isEmpty()) {
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321 fhirInstance.setSopClass(new Coding("urn:ietf:rfc:3986", "urn:oid:" + sopClassUid, ""));
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322 }
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323 }
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324
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325 countInstances += orthancSeries.getChildren().size();
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326 }
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327
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328 study.setNumberOfInstances(countInstances);
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329
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330 return study;
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331 }
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332 }