Mercurial > hg > orthanc-java

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improved import of JNI in cmake
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 06 Sep 2024 13:53:54 +0200
parents 43923934e934
children
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1 /**
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2 * SPDX-FileCopyrightText: 2023-2024 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) 2023-2024 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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25 import org.json.JSONArray;
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26 import org.json.JSONObject;
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28 import java.io.IOException;
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29 import java.util.List;
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31 public class DicomToolbox {
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32 private static final String MAPPING_RESOURCE = "0008,0105";
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33 private static final String REFERENCED_SOP_CLASS_UID = "0008,1150";
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34 private static final String REFERENCED_SOP_INSTANCE_UID = "0008,1155";
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35 private static final String REFERENCED_SOP_SEQUENCE = "0008,1199";
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36
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37 private static final String CONTENT_TEMPLATE_SEQUENCE = "0040,a504";
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38 private static final String TEMPLATE_IDENTIFIER = "0040,db00";
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39 private static final String RELATIONSHIP_TYPE = "0040,a010";
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40 private static final String CONCEPT_NAME_CODE_SEQUENCE = "0040,a043";
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41 private static final String VALUE_TYPE = "0040,a040";
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42 private static final String CONCEPT_CODE_SEQUENCE = "0040,a168";
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43 private static final String CONTINUITY_OF_CONTENT = "0040,a050";
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44 private static final String CONTENT_SEQUENCE = "0040,a730";
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45 private static final String TEXT_VALUE_ATTRIBUTE = "0040,a160";
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46 private static final String UID_ATTRIBUTE = "0040,a124";
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47 private static final String MEASURED_VALUE_SEQUENCE = "0040,a300";
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48 private static final String MEASUREMENT_UNITS_CODE_SEQUENCE = "0040,08ea";
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49 private static final String FLOATING_POINT_VALUE = "0040,a161";
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50 private static final String NUMERIC_VALUE = "0040,a30a";
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51 private static final String GRAPHIC_DATA = "0070,0022";
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52 private static final String GRAPHIC_TYPE = "0070,0023";
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53
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54 static JSONObject createDicomSR(OrthancConnection client,
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55 String instance,
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56 List<Detection> detections,
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57 double aspectRatio) throws IOException, InterruptedException {
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58 final JSONObject instanceTags = client.doGetAsJsonObject("/instances/" + instance + "/tags?short");
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59 final String trackingUid = client.doGetAsString("/tools/generate-uid?level=instance");
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61 String instanceStudy = client.doGetAsJsonObject("/instances/" + instance + "/study").getString("ID");
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63 // https://dicom.nema.org/medical/dicom/2024a/output/chtml/part16/chapter_A.html#sect_TID_1500
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64 // Sample TID 1500: https://dicom.nema.org/medical/dicom/current/output/chtml/part21/sect_a.7.2.html
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67 JSONObject json = new JSONObject();
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68 json.put("Parent", instanceStudy);
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69
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70 JSONObject tags = new JSONObject();
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71 tags.put("0008,0016", "1.2.840.10008.5.1.4.1.1.88.33"); // SOP Class UID
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72 tags.put("0008,0060", "SR"); // Modality
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73 tags.put("0008,0070", ""); // Manufacturer
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74 tags.put("0008,1111", new JSONArray()); // Referenced Performed Procedure Step Sequence is type 2 (required but can be empty)
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75 tags.put("0020,0011", "1"); // Series number
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76 tags.put("0020,0013", "1"); // Instance number
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77 tags.put("0040,a040", "CONTAINER"); // Value type for SR: https://dicom.nema.org/medical/dicom/2024a/output/chtml/part03/sect_C.17.3.html
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78
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79 // CID 7021 Measurement Report Document Title: https://dicom.nema.org/medical/dicom/2024a/output/chtml/part16/sect_CID_7021.html
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80 tags.append("0040,a043", new DicomCode("126000", "DCM", "Imaging Measurement Report").toJson());
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81
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82 tags.put("0040,a050", "CONTINUOUS"); // Continuity of content
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83 tags.put("0040,a372", new JSONArray()); // Performed procedure code sequence
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84
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85 // Current Requested Procedure Evidence: References to the StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID, and SOPClassUID
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86 tags.append("0040,a375", new JSONObject().
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87 put("0020,000d", instanceTags.getString("0020,000d")).
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88 append("0008,1115", new JSONObject().
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89 put("0020,000e", instanceTags.getString("0020,000e")).
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90 append("0008,1199", new JSONObject().
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91 put("0008,1150", instanceTags.getString("0008,0016")).
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92 put("0008,1155", instanceTags.getString("0008,0018")))));
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93
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94 tags.put("0040,a491", "PARTIAL"); // Completion flag
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95 tags.put("0040,a493", "UNVERIFIED"); // Verification flag
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96 tags.put("0040,a496", "PRELIMINARY"); // Preliminary flag
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97
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98 // Content template sequence, which indicates TID 1500
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99 setTemplateId(tags, "1500");
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100
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101 JSONArray contentSequence = new JSONArray();
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102 contentSequence.put(createCodeRelationship(
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103 new DicomCode("121049", "DCM", "Language of Content Item and Descendants"),
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104 new DicomCode("en-US", "RFC5646", "English (United States)")));
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105
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106 // This is "procedure_reported" in "highdicom.sr.MeasurementReport()"
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107 contentSequence.put(createCodeRelationship(
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108 new DicomCode("121058", "DCM", "Procedure reported"),
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109 new DicomCode("43468-8", "LN", "XR unspecified body region")));
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110
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111 JSONArray measurementGroups = new JSONArray();
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112
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113 for (Detection detection : detections) {
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114 JSONArray measurements = new JSONArray();
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115 measurements.put(createTextContext(
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116 new DicomCode("112039", "DCM", "Tracking Identifier"),
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117 "Orthanc Deep Learning for Mammography"));
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118
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119 measurements.put(createUidReference(
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120 new DicomCode("112040", "DCM", "Tracking Unique Identifier"),
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121 trackingUid));
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122
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123 measurements.put(createNumericValue(
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124 new DicomCode("111047", "DCM", "Probability of cancer"),
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125 new DicomCode("%", "UCUM", "Percent"),
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126 detection.getScore() * 100.0));
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127
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parents:
diff changeset
128 measurements.put(createRectangle(
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
129 new DicomCode("111030", "DCM", "Image Region"),
43923934e934 added sample: deep learning for mammography
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parents:
diff changeset
130 instanceTags.getString("0008,0016"), instanceTags.getString("0008,0018"),
43923934e934 added sample: deep learning for mammography
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parents:
diff changeset
131 detection.getRectangle(), aspectRatio));
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parents:
diff changeset
132
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parents:
diff changeset
133 JSONObject measurementGroup = createContainer(new DicomCode("125007", "DCM", "Measurement Group"), measurements);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
134 setTemplateId(measurementGroup, "1410");
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parents:
diff changeset
135
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136 measurementGroups.put(measurementGroup);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
139 JSONObject imagingMeasurements = createContainer(new DicomCode("126010", "DCM", "Imaging Measurements"), measurementGroups);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
140 contentSequence.put(imagingMeasurements);
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parents:
diff changeset
141
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142 tags.put("0040,a730", contentSequence);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
144 json.put("Tags", tags);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
145
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 return client.doPostAsJsonObject("/tools/create-dicom", json.toString());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 static public class Point2D {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 private double x;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 private double y;
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parents:
diff changeset
152
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153 public Point2D(double x,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154 double y) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155 this.x = x;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156 this.y = y;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
157 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 public double getX() {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 return x;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163 public double getY() {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 return y;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 public static JSONObject setTemplateId(JSONObject target,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 String templateId) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 if (target.has(CONTENT_TEMPLATE_SEQUENCE)) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 throw new IllegalStateException();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 } else {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173 target.append(CONTENT_TEMPLATE_SEQUENCE, new JSONObject().
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 put(MAPPING_RESOURCE, "DCMR").
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 put(TEMPLATE_IDENTIFIER, templateId));
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176 return target;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
179
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
180 public static JSONObject createCodeRelationship(DicomCode concept,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181 DicomCode referencedCode) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182 JSONObject result = new JSONObject();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 result.put(RELATIONSHIP_TYPE, "HAS CONCEPT MOD");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 result.append(CONCEPT_NAME_CODE_SEQUENCE, concept.toJson());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 result.put(VALUE_TYPE, "CODE");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186 result.append(CONCEPT_CODE_SEQUENCE, referencedCode.toJson());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 return result;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
189
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190 public static JSONObject createContainer(DicomCode concept,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191 JSONArray content) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
192 JSONObject result = new JSONObject();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
193 result.put(RELATIONSHIP_TYPE, "CONTAINS");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
194 result.put(VALUE_TYPE, "CONTAINER");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195 result.append(CONCEPT_NAME_CODE_SEQUENCE, concept.toJson());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
196 result.put(CONTINUITY_OF_CONTENT, "CONTINUOUS");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
197 result.put(CONTENT_SEQUENCE, content);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
198 return result;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
200
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
201 public static JSONObject createTextContext(DicomCode concept,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202 String value) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203 JSONObject result = new JSONObject();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 result.put(RELATIONSHIP_TYPE, "HAS OBS CONTEXT");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 result.put(VALUE_TYPE, "TEXT");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206 result.append(CONCEPT_NAME_CODE_SEQUENCE, concept.toJson());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207 result.put(TEXT_VALUE_ATTRIBUTE, value);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 return result;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 public static JSONObject createUidReference(DicomCode concept,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 String uid) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 JSONObject result = new JSONObject();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 result.put(RELATIONSHIP_TYPE, "HAS OBS CONTEXT");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215 result.put(VALUE_TYPE, "UIDREF");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
216 result.append(CONCEPT_NAME_CODE_SEQUENCE, concept.toJson());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
217 result.put(UID_ATTRIBUTE, uid);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218 return result;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 public static JSONObject createNumericValue(DicomCode concept,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
222 DicomCode unit,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223 double value) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 String ds = String.valueOf(value);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225 if (ds.length() > 16) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 ds = ds.substring(0, 16); // The DS VR must have less than 16 characters
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229 JSONObject result = new JSONObject();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230 result.put(RELATIONSHIP_TYPE, "CONTAINS");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231 result.put(VALUE_TYPE, "NUM");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
232 result.append(CONCEPT_NAME_CODE_SEQUENCE, concept.toJson());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233 result.append(MEASURED_VALUE_SEQUENCE, new JSONObject().
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 append(MEASUREMENT_UNITS_CODE_SEQUENCE, unit.toJson()).
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 put(FLOATING_POINT_VALUE, String.valueOf(value)).
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236 put(NUMERIC_VALUE, ds));
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237 return result;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
240 public static JSONObject createSelectedFromImage(String sopClassUid,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241 String sopInstanceUid) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242 JSONObject result = new JSONObject();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243 result.put(RELATIONSHIP_TYPE, "SELECTED FROM");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
244 result.put(VALUE_TYPE, "IMAGE");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
245 result.append(REFERENCED_SOP_SEQUENCE, new JSONObject().
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
246 put(REFERENCED_SOP_CLASS_UID, sopClassUid).
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
247 put(REFERENCED_SOP_INSTANCE_UID, sopInstanceUid));
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
248 result.append(CONCEPT_NAME_CODE_SEQUENCE, new DicomCode("111040", "DCM", "Original Source").toJson());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
249 return result;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
250 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252 public static JSONObject createPolyline2D(DicomCode concept,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
253 String sopClassUid,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254 String sopInstanceUid,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
255 Point2D vertices[]) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
256 String polyline = new String();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
257 for (int i = 0; i < vertices.length; i++) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
258 if (!polyline.isEmpty()) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
259 polyline = polyline + "\\";
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
260 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
261 polyline += String.valueOf(vertices[i].getX()) + "\\" + String.valueOf(vertices[i].getY());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
262 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
263
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
264 JSONObject result = new JSONObject();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
265 result.put(RELATIONSHIP_TYPE, "CONTAINS");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
266 result.put(VALUE_TYPE, "SCOORD");
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267 result.append(CONCEPT_NAME_CODE_SEQUENCE, concept.toJson());
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268 result.append(CONTENT_SEQUENCE, createSelectedFromImage(sopClassUid, sopInstanceUid));
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269 result.put(GRAPHIC_DATA, polyline); // WARNING: This necessitates Orthanc > 1.12.4: https://orthanc.uclouvain.be/hg/orthanc/rev/dedbf019a707
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270 result.put(GRAPHIC_TYPE, "POLYLINE");
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271 return result;
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272 }
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273
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274 public static JSONObject createRectangle(DicomCode concept,
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275 String sopClassUid,
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276 String sopInstanceUid,
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277 Rectangle rectangle,
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278 double aspectRatio) {
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279 Point2D vertices[] = new Point2D[5];
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280 vertices[0] = new Point2D(rectangle.getX1() * aspectRatio, rectangle.getY1() * aspectRatio);
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281 vertices[1] = new Point2D(rectangle.getX2() * aspectRatio, rectangle.getY1() * aspectRatio);
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282 vertices[2] = new Point2D(rectangle.getX2() * aspectRatio, rectangle.getY2() * aspectRatio);
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283 vertices[3] = new Point2D(rectangle.getX1() * aspectRatio, rectangle.getY2() * aspectRatio);
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284 vertices[4] = new Point2D(rectangle.getX1() * aspectRatio, rectangle.getY1() * aspectRatio);
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285 return createPolyline2D(concept, sopClassUid, sopInstanceUid, vertices);
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286 }
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287 }