Mercurial > hg > orthanc-java
comparison Samples/MammographyDeepLearning/src/main/java/Main.java @ 28:43923934e934
added sample: deep learning for mammography
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 12 Jun 2024 13:58:29 +0200 |
parents | |
children | 08ea8401f7b2 |
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27:4a750ca9461e | 28:43923934e934 |
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1 /** | |
2 * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium | |
3 * SPDX-License-Identifier: GPL-3.0-or-later | |
4 **/ | |
5 | |
6 /** | |
7 * Java plugin for Orthanc | |
8 * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium | |
9 * | |
10 * This program is free software: you can redistribute it and/or | |
11 * modify it under the terms of the GNU General Public License as | |
12 * published by the Free Software Foundation, either version 3 of the | |
13 * License, or (at your option) any later version. | |
14 * | |
15 * This program is distributed in the hope that it will be useful, but | |
16 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
18 * General Public License for more details. | |
19 * | |
20 * You should have received a copy of the GNU General Public License | |
21 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
22 **/ | |
23 | |
24 | |
25 import ai.djl.ndarray.NDArray; | |
26 import ai.djl.ndarray.NDManager; | |
27 import be.uclouvain.orthanc.Callbacks; | |
28 import be.uclouvain.orthanc.ChangeType; | |
29 import be.uclouvain.orthanc.Functions; | |
30 import be.uclouvain.orthanc.HttpMethod; | |
31 import be.uclouvain.orthanc.ResourceType; | |
32 import be.uclouvain.orthanc.RestOutput; | |
33 import org.apache.commons.compress.utils.IOUtils; | |
34 import org.json.JSONObject; | |
35 | |
36 import java.awt.image.BufferedImage; | |
37 import java.io.IOException; | |
38 import java.io.InputStream; | |
39 import java.nio.charset.StandardCharsets; | |
40 import java.security.NoSuchAlgorithmException; | |
41 import java.util.HashMap; | |
42 import java.util.List; | |
43 import java.util.Map; | |
44 import java.util.concurrent.ExecutorService; | |
45 import java.util.concurrent.Executors; | |
46 import java.util.zip.ZipEntry; | |
47 import java.util.zip.ZipFile; | |
48 | |
49 public class Main { | |
50 private static final String MODEL_PATH = "2024-03-08-retina_res50_trained_08_03.torchscript"; | |
51 private static final String STONE_VERSION = "2024-03-15-StoneWebViewer-DICOM-SR"; | |
52 private static final String STONE_PATH = "2024-03-15-StoneWebViewer-DICOM-SR.zip"; | |
53 | |
54 private static ZipFile stone; | |
55 private static NDManager manager; | |
56 private static RetinaNet retinaNet; | |
57 private static Map<String, String> mimeTypes = new HashMap<>(); | |
58 | |
59 static { | |
60 ExecutorService executor = Executors.newSingleThreadExecutor(); | |
61 try { | |
62 OrthancConnection.download("2024-03-08-retina_res50_trained_08_03.torchscript", executor, | |
63 "https://orthanc.uclouvain.be/downloads/cross-platform/orthanc-mammography/models/2024-03-08-retina_res50_trained_08_03.torchscript", | |
64 146029397L, "b3de8f562de683bc3515fe93ae102fd4"); | |
65 OrthancConnection.download("2024-03-15-StoneWebViewer-DICOM-SR.zip", executor, | |
66 "https://github.com/jodogne/orthanc-mammography/raw/master/viewer/2024-03-15-StoneWebViewer-DICOM-SR.zip", | |
67 4742571L, "de952da6fc74a9d4b78ca5064a6a7318"); | |
68 } catch (IOException | NoSuchAlgorithmException | InterruptedException e) { | |
69 throw new RuntimeException(e); | |
70 } finally { | |
71 executor.shutdown(); | |
72 } | |
73 | |
74 try { | |
75 stone = new ZipFile(STONE_PATH); | |
76 } catch (IOException e) { | |
77 throw new RuntimeException(e); | |
78 } | |
79 | |
80 Functions.logWarning("Initializing Deep Java Library"); | |
81 manager = NDManager.newBaseManager(); | |
82 | |
83 Functions.logWarning("Loading RetinaNet model"); | |
84 try { | |
85 retinaNet = new RetinaNet(MODEL_PATH); | |
86 } catch (Exception e) { | |
87 throw new RuntimeException(e); | |
88 } | |
89 | |
90 Functions.logWarning("RetinaNet model is ready"); | |
91 | |
92 mimeTypes.put("css", "text/css"); | |
93 mimeTypes.put("gif", "image/gif"); | |
94 mimeTypes.put("html", "text/html"); | |
95 mimeTypes.put("jpeg", "image/jpeg"); | |
96 mimeTypes.put("js", "text/javascript"); | |
97 mimeTypes.put("png", "image/png"); | |
98 | |
99 try (InputStream stream = Main.class.getResourceAsStream("OrthancExplorer.js")) { | |
100 byte[] content = IOUtils.toByteArray(stream); | |
101 Functions.extendOrthancExplorer(new String(content, StandardCharsets.UTF_8)); | |
102 } catch (IOException e) { | |
103 throw new RuntimeException(e); | |
104 } | |
105 | |
106 Callbacks.register(new Callbacks.OnChange() { | |
107 @Override | |
108 public void call(ChangeType changeType, ResourceType resourceType, String resourceId) { | |
109 switch (changeType) { | |
110 case ORTHANC_STARTED: | |
111 OrthancConnection connection = OrthancConnection.createForPlugin(); | |
112 try { | |
113 if (!connection.isOrthancVersionAbove(1, 12, 5)) { | |
114 throw new RuntimeException("Your version of Orthanc must be >= 1.12.5 to run this plugin"); | |
115 } | |
116 } catch (IOException | InterruptedException e) { | |
117 throw new RuntimeException(e); | |
118 } | |
119 | |
120 break; | |
121 | |
122 case ORTHANC_STOPPED: | |
123 Functions.logWarning("Finalizing Deep Java Library"); | |
124 if (retinaNet != null) { | |
125 retinaNet.close(); | |
126 } | |
127 | |
128 if (manager != null) { | |
129 manager.close(); | |
130 } | |
131 | |
132 System.gc(); | |
133 System.runFinalization(); | |
134 break; | |
135 | |
136 default: | |
137 break; | |
138 } | |
139 } | |
140 }); | |
141 | |
142 Callbacks.register("/java-mammography-apply", new Callbacks.OnRestRequest() { | |
143 @Override | |
144 public void call(RestOutput output, | |
145 HttpMethod method, | |
146 String uri, | |
147 String[] regularExpressionGroups, | |
148 Map<String, String> headers, | |
149 Map<String, String> getParameters, | |
150 byte[] body) { | |
151 if (method != HttpMethod.POST) { | |
152 output.sendMethodNotAllowed("POST"); | |
153 return; | |
154 } | |
155 | |
156 JSONObject request = new JSONObject(new String(body, StandardCharsets.UTF_8)); | |
157 | |
158 String instanceId = request.getString("instance"); | |
159 if (instanceId == null) { | |
160 throw new RuntimeException("Missing instance identifier"); | |
161 } | |
162 | |
163 Functions.logWarning("Applying RetinaNet to instance: " + instanceId); | |
164 OrthancConnection connection = OrthancConnection.createForPlugin(); | |
165 | |
166 try { | |
167 BufferedImage image = connection.getGrayscaleFrame(instanceId, 0); | |
168 | |
169 double largestSide = Math.max(image.getWidth(), image.getHeight()); | |
170 BufferedImage resized = ImageProcessing.resizeImage(image, | |
171 (int) Math.round((double) image.getWidth() * 2048.0 / largestSide), | |
172 (int) Math.round((double) image.getHeight() * 2048.0 / largestSide)); | |
173 | |
174 double aspectRatio = (double) image.getWidth() / (double) resized.getWidth(); | |
175 | |
176 NDArray grayscale = ImageProcessing.imageToTensor(manager, resized); | |
177 grayscale = ImageProcessing.standardize(grayscale); | |
178 | |
179 NDArray rgb = grayscale.concat(grayscale).concat(grayscale); // Create a "RGB" image from grayscale pixel values | |
180 List<Detection> detections = retinaNet.apply(rgb); | |
181 | |
182 JSONObject created = DicomToolbox.createDicomSR(connection, instanceId, detections, aspectRatio); | |
183 | |
184 String id = created.getString("ID"); | |
185 Functions.logWarning("Detection results stored in DICOM-SR instance: " + id); | |
186 | |
187 output.answerBuffer(created.toString().getBytes(StandardCharsets.UTF_8), "application/json"); | |
188 } catch (Exception e) { | |
189 throw new RuntimeException(e); | |
190 } | |
191 } | |
192 }); | |
193 | |
194 Callbacks.register("/java-mammography-viewer/(.*)", new Callbacks.OnRestRequest() { | |
195 @Override | |
196 public void call(RestOutput output, | |
197 HttpMethod method, | |
198 String uri, | |
199 String[] regularExpressionGroups, | |
200 Map<String, String> headers, | |
201 Map<String, String> getParameters, | |
202 byte[] body) { | |
203 if (method != HttpMethod.GET) { | |
204 output.sendMethodNotAllowed("GET"); | |
205 return; | |
206 } | |
207 | |
208 String path = regularExpressionGroups[0]; | |
209 int dot = path.lastIndexOf("."); | |
210 if (dot < 0) { | |
211 output.sendHttpStatus((short) 404, new byte[0]); | |
212 } else { | |
213 String extension = path.substring(dot + 1); | |
214 String mime = mimeTypes.getOrDefault(extension, "application/octet-stream"); | |
215 | |
216 ZipEntry entry = stone.getEntry(STONE_VERSION + "/" + path); | |
217 if (entry == null) { | |
218 output.sendHttpStatus((short) 404, new byte[0]); | |
219 } else { | |
220 try (InputStream stream = stone.getInputStream(entry)) { | |
221 output.answerBuffer(IOUtils.toByteArray(stream), mime); | |
222 } catch (IOException e) { | |
223 throw new RuntimeException(e); | |
224 } | |
225 } | |
226 } | |
227 } | |
228 }); | |
229 } | |
230 } |