Mercurial > hg > orthanc-java

annotate Samples/MammographyDeepLearning/src/main/java/Main.java @ 42:b04559283a1d

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updated Stone Web viewer to newer snapshot
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 31 Aug 2024 12:00:40 +0200
parents 08ea8401f7b2
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 ai.djl.ndarray.NDArray;
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26 import ai.djl.ndarray.NDManager;
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27 import be.uclouvain.orthanc.Callbacks;
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28 import be.uclouvain.orthanc.ChangeType;
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29 import be.uclouvain.orthanc.Functions;
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30 import be.uclouvain.orthanc.HttpMethod;
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31 import be.uclouvain.orthanc.ResourceType;
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32 import be.uclouvain.orthanc.RestOutput;
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33 import org.apache.commons.compress.utils.IOUtils;
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34 import org.json.JSONArray;
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35 import org.json.JSONObject;
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36
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37 import java.awt.image.BufferedImage;
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38 import java.io.IOException;
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39 import java.io.InputStream;
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40 import java.nio.charset.StandardCharsets;
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41 import java.security.NoSuchAlgorithmException;
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42 import java.util.HashMap;
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43 import java.util.List;
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44 import java.util.Map;
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45 import java.util.concurrent.ExecutorService;
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46 import java.util.concurrent.Executors;
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47 import java.util.zip.ZipEntry;
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48 import java.util.zip.ZipFile;
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49
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50 public class Main {
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51 private static final String MODEL_PATH = "2024-03-08-retina_res50_trained_08_03.torchscript";
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52 private static final String STONE_VERSION = "2024-08-31-StoneWebViewer-DICOM-SR";
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53 private static final String STONE_PATH = "2024-08-31-StoneWebViewer-DICOM-SR.zip";
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55 private static ZipFile stone;
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56 private static NDManager manager;
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57 private static RetinaNet retinaNet;
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58 private static Map<String, String> mimeTypes = new HashMap<>();
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59
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60 static {
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61 ExecutorService executor = Executors.newSingleThreadExecutor();
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62 try {
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63 OrthancConnection.download(MODEL_PATH, executor,
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64 "https://orthanc.uclouvain.be/downloads/cross-platform/orthanc-mammography/models/" + MODEL_PATH,
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65 146029397L, "b3de8f562de683bc3515fe93ae102fd4");
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66 OrthancConnection.download(STONE_PATH, executor,
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67 "https://github.com/jodogne/orthanc-mammography/raw/master/viewer/" + STONE_PATH,
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68 4815178L, "86b52a17f86e4769d12e9ae680c4a99f");
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69 } catch (IOException | NoSuchAlgorithmException | InterruptedException e) {
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70 throw new RuntimeException(e);
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71 } finally {
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72 executor.shutdown();
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73 }
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74
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75 try {
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76 stone = new ZipFile(STONE_PATH);
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77 } catch (IOException e) {
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78 throw new RuntimeException(e);
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79 }
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80
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81 Functions.logWarning("Initializing Deep Java Library");
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82 manager = NDManager.newBaseManager();
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83
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84 Functions.logWarning("Loading RetinaNet model");
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85 try {
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86 retinaNet = new RetinaNet(MODEL_PATH);
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87 } catch (Exception e) {
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88 throw new RuntimeException(e);
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89 }
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90
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91 Functions.logWarning("RetinaNet model is ready");
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92
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93 mimeTypes.put("css", "text/css");
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94 mimeTypes.put("gif", "image/gif");
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95 mimeTypes.put("html", "text/html");
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96 mimeTypes.put("jpeg", "image/jpeg");
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97 mimeTypes.put("js", "text/javascript");
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98 mimeTypes.put("png", "image/png");
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99
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100 try (InputStream stream = Main.class.getResourceAsStream("OrthancExplorer.js")) {
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101 byte[] content = IOUtils.toByteArray(stream);
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102 Functions.extendOrthancExplorer(new String(content, StandardCharsets.UTF_8));
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103 } catch (IOException e) {
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104 throw new RuntimeException(e);
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105 }
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106
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107 Callbacks.register(new Callbacks.OnChange() {
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108 @Override
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109 public void call(ChangeType changeType, ResourceType resourceType, String resourceId) {
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110 switch (changeType) {
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111 case ORTHANC_STARTED:
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112 OrthancConnection connection = OrthancConnection.createForPlugin();
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113 try {
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114 if (!connection.isOrthancVersionAbove(1, 12, 5)) {
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115 throw new RuntimeException("Your version of Orthanc must be >= 1.12.5 to run this plugin");
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116 }
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117
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118 JSONArray plugins = new JSONArray(connection.doGetAsString("/plugins"));
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119
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120 boolean hasDicomWeb = false;
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121 for (int i = 0; i < plugins.length() && !hasDicomWeb; i++) {
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122 if (plugins.getString(i).equals("dicom-web")) {
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123 hasDicomWeb = true;
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124 }
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125 }
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126
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127 if (!hasDicomWeb) {
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128 throw new RuntimeException("The DICOMweb plugin is required, but is not installed");
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129 }
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130 } catch (IOException | InterruptedException e) {
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131 throw new RuntimeException(e);
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132 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
133
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
134 break;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
135
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136 case ORTHANC_STOPPED:
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137 Functions.logWarning("Finalizing Deep Java Library");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138 if (retinaNet != null) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
139 retinaNet.close();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
140 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
141
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142 if (manager != null) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143 manager.close();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
144 }
43923934e934 added sample: deep learning for mammography
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 System.gc();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147 System.runFinalization();
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148 break;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 default:
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 break;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154 });
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156 Callbacks.register("/java-mammography-apply", new Callbacks.OnRestRequest() {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
157 @Override
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 public void call(RestOutput output,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 HttpMethod method,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 String uri,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 String[] regularExpressionGroups,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162 Map<String, String> headers,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163 Map<String, String> getParameters,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 byte[] body) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 if (method != HttpMethod.POST) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166 output.sendMethodNotAllowed("POST");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167 return;
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 JSONObject request = new JSONObject(new String(body, StandardCharsets.UTF_8));
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 String instanceId = request.getString("instance");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173 if (instanceId == null) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 throw new RuntimeException("Missing instance identifier");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 Functions.logWarning("Applying RetinaNet to instance: " + instanceId);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178 OrthancConnection connection = OrthancConnection.createForPlugin();
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 try {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181 BufferedImage image = connection.getGrayscaleFrame(instanceId, 0);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 double largestSide = Math.max(image.getWidth(), image.getHeight());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 BufferedImage resized = ImageProcessing.resizeImage(image,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 (int) Math.round((double) image.getWidth() * 2048.0 / largestSide),
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186 (int) Math.round((double) image.getHeight() * 2048.0 / largestSide));
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188 double aspectRatio = (double) image.getWidth() / (double) resized.getWidth();
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 NDArray grayscale = ImageProcessing.imageToTensor(manager, resized);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191 grayscale = ImageProcessing.standardize(grayscale);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
192
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
193 NDArray rgb = grayscale.concat(grayscale).concat(grayscale); // Create a "RGB" image from grayscale pixel values
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
194 List<Detection> detections = retinaNet.apply(rgb);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
196 JSONObject created = DicomToolbox.createDicomSR(connection, instanceId, detections, aspectRatio);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
197
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
198 String id = created.getString("ID");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 Functions.logWarning("Detection results stored in DICOM-SR instance: " + id);
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 output.answerBuffer(created.toString().getBytes(StandardCharsets.UTF_8), "application/json");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202 } catch (Exception e) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203 throw new RuntimeException(e);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206 });
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 Callbacks.register("/java-mammography-viewer/(.*)", new Callbacks.OnRestRequest() {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 @Override
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210 public void call(RestOutput output,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 HttpMethod method,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 String uri,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 String[] regularExpressionGroups,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 Map<String, String> headers,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215 Map<String, String> getParameters,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
216 byte[] body) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
217 if (method != HttpMethod.GET) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218 output.sendMethodNotAllowed("GET");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 return;
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
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
222 String path = regularExpressionGroups[0];
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223 int dot = path.lastIndexOf(".");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 if (dot < 0) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225 output.sendHttpStatus((short) 404, new byte[0]);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 } else {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227 String extension = path.substring(dot + 1);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228 String mime = mimeTypes.getOrDefault(extension, "application/octet-stream");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230 ZipEntry entry = stone.getEntry(STONE_VERSION + "/" + path);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231 if (entry == null) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
232 output.sendHttpStatus((short) 404, new byte[0]);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233 } else {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 try (InputStream stream = stone.getInputStream(entry)) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 output.answerBuffer(IOUtils.toByteArray(stream), mime);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236 } catch (IOException e) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237 throw new RuntimeException(e);
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 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242 });
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
244 }