Mercurial > hg > orthanc-java

annotate Samples/MammographyDeepLearning/src/main/java/Main.java @ 28:43923934e934

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added sample: deep learning for mammography
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 12 Jun 2024 13:58:29 +0200
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children 08ea8401f7b2
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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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23
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24
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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.JSONObject;
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35
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36 import java.awt.image.BufferedImage;
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37 import java.io.IOException;
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38 import java.io.InputStream;
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39 import java.nio.charset.StandardCharsets;
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40 import java.security.NoSuchAlgorithmException;
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41 import java.util.HashMap;
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42 import java.util.List;
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43 import java.util.Map;
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44 import java.util.concurrent.ExecutorService;
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45 import java.util.concurrent.Executors;
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46 import java.util.zip.ZipEntry;
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47 import java.util.zip.ZipFile;
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48
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49 public class Main {
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50 private static final String MODEL_PATH = "2024-03-08-retina_res50_trained_08_03.torchscript";
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51 private static final String STONE_VERSION = "2024-03-15-StoneWebViewer-DICOM-SR";
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52 private static final String STONE_PATH = "2024-03-15-StoneWebViewer-DICOM-SR.zip";
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53
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54 private static ZipFile stone;
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55 private static NDManager manager;
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56 private static RetinaNet retinaNet;
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57 private static Map<String, String> mimeTypes = new HashMap<>();
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58
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59 static {
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60 ExecutorService executor = Executors.newSingleThreadExecutor();
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61 try {
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62 OrthancConnection.download("2024-03-08-retina_res50_trained_08_03.torchscript", executor,
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63 "https://orthanc.uclouvain.be/downloads/cross-platform/orthanc-mammography/models/2024-03-08-retina_res50_trained_08_03.torchscript",
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64 146029397L, "b3de8f562de683bc3515fe93ae102fd4");
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65 OrthancConnection.download("2024-03-15-StoneWebViewer-DICOM-SR.zip", executor,
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66 "https://github.com/jodogne/orthanc-mammography/raw/master/viewer/2024-03-15-StoneWebViewer-DICOM-SR.zip",
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67 4742571L, "de952da6fc74a9d4b78ca5064a6a7318");
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68 } catch (IOException | NoSuchAlgorithmException | InterruptedException e) {
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69 throw new RuntimeException(e);
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70 } finally {
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71 executor.shutdown();
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72 }
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73
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74 try {
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75 stone = new ZipFile(STONE_PATH);
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76 } catch (IOException e) {
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77 throw new RuntimeException(e);
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78 }
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79
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80 Functions.logWarning("Initializing Deep Java Library");
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81 manager = NDManager.newBaseManager();
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82
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83 Functions.logWarning("Loading RetinaNet model");
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84 try {
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85 retinaNet = new RetinaNet(MODEL_PATH);
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86 } catch (Exception e) {
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87 throw new RuntimeException(e);
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88 }
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89
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90 Functions.logWarning("RetinaNet model is ready");
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91
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92 mimeTypes.put("css", "text/css");
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93 mimeTypes.put("gif", "image/gif");
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94 mimeTypes.put("html", "text/html");
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95 mimeTypes.put("jpeg", "image/jpeg");
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96 mimeTypes.put("js", "text/javascript");
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97 mimeTypes.put("png", "image/png");
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98
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99 try (InputStream stream = Main.class.getResourceAsStream("OrthancExplorer.js")) {
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100 byte[] content = IOUtils.toByteArray(stream);
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101 Functions.extendOrthancExplorer(new String(content, StandardCharsets.UTF_8));
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102 } catch (IOException e) {
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103 throw new RuntimeException(e);
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104 }
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105
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106 Callbacks.register(new Callbacks.OnChange() {
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107 @Override
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108 public void call(ChangeType changeType, ResourceType resourceType, String resourceId) {
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109 switch (changeType) {
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110 case ORTHANC_STARTED:
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111 OrthancConnection connection = OrthancConnection.createForPlugin();
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112 try {
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113 if (!connection.isOrthancVersionAbove(1, 12, 5)) {
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114 throw new RuntimeException("Your version of Orthanc must be >= 1.12.5 to run this plugin");
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115 }
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116 } catch (IOException | InterruptedException e) {
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117 throw new RuntimeException(e);
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118 }
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119
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120 break;
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121
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122 case ORTHANC_STOPPED:
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123 Functions.logWarning("Finalizing Deep Java Library");
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124 if (retinaNet != null) {
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125 retinaNet.close();
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126 }
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127
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128 if (manager != null) {
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129 manager.close();
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130 }
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131
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132 System.gc();
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133 System.runFinalization();
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134 break;
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diff changeset
135
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136 default:
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137 break;
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 }
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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
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142 Callbacks.register("/java-mammography-apply", new Callbacks.OnRestRequest() {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143 @Override
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
144 public void call(RestOutput output,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
145 HttpMethod method,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 String uri,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147 String[] regularExpressionGroups,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148 Map<String, String> headers,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 Map<String, String> getParameters,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 byte[] body) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 if (method != HttpMethod.POST) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152 output.sendMethodNotAllowed("POST");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153 return;
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 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
157
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 String instanceId = request.getString("instance");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 if (instanceId == null) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 throw new RuntimeException("Missing instance identifier");
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
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163 Functions.logWarning("Applying RetinaNet to instance: " + instanceId);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 OrthancConnection connection = OrthancConnection.createForPlugin();
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 try {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167 BufferedImage image = connection.getGrayscaleFrame(instanceId, 0);
43923934e934 added sample: deep learning for mammography
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parents:
diff changeset
168
43923934e934 added sample: deep learning for mammography
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parents:
diff changeset
169 double largestSide = Math.max(image.getWidth(), image.getHeight());
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 BufferedImage resized = ImageProcessing.resizeImage(image,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 (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
172 (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
173
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 double aspectRatio = (double) image.getWidth() / (double) resized.getWidth();
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 NDArray grayscale = ImageProcessing.imageToTensor(manager, resized);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 grayscale = ImageProcessing.standardize(grayscale);
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 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
180 List<Detection> detections = retinaNet.apply(rgb);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182 JSONObject created = DicomToolbox.createDicomSR(connection, instanceId, detections, aspectRatio);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 String id = created.getString("ID");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 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
186
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 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
188 } catch (Exception e) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
189 throw new RuntimeException(e);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191 }
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
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
194 Callbacks.register("/java-mammography-viewer/(.*)", new Callbacks.OnRestRequest() {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195 @Override
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
196 public void call(RestOutput output,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
197 HttpMethod method,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
198 String uri,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 String[] regularExpressionGroups,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
200 Map<String, String> headers,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
201 Map<String, String> getParameters,
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202 byte[] body) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203 if (method != HttpMethod.GET) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 output.sendMethodNotAllowed("GET");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 return;
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 String path = regularExpressionGroups[0];
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 int dot = path.lastIndexOf(".");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210 if (dot < 0) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 output.sendHttpStatus((short) 404, new byte[0]);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 } else {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 String extension = path.substring(dot + 1);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 String mime = mimeTypes.getOrDefault(extension, "application/octet-stream");
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
216 ZipEntry entry = stone.getEntry(STONE_VERSION + "/" + path);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
217 if (entry == null) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218 output.sendHttpStatus((short) 404, new byte[0]);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 } else {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220 try (InputStream stream = stone.getInputStream(entry)) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 output.answerBuffer(IOUtils.toByteArray(stream), mime);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
222 } catch (IOException e) {
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223 throw new RuntimeException(e);
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 }
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 }
43923934e934 added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230 }