Mercurial > hg > orthanc-java
annotate Samples/MammographyDeepLearning/src/main/java/Main.java @ 28:43923934e934
added sample: deep learning for mammography
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 12 Jun 2024 13:58:29 +0200 |
parents | |
children | 08ea8401f7b2 |
rev | line source |
---|---|
28
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1 /** |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
2 * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
3 * SPDX-License-Identifier: GPL-3.0-or-later |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
4 **/ |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
5 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
6 /** |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
7 * Java plugin for Orthanc |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
8 * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
9 * |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
10 * This program is free software: you can redistribute it and/or |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
11 * modify it under the terms of the GNU General Public License as |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
12 * published by the Free Software Foundation, either version 3 of the |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
13 * License, or (at your option) any later version. |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
14 * |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
15 * This program is distributed in the hope that it will be useful, but |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
16 * WITHOUT ANY WARRANTY; without even the implied warranty of |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
18 * General Public License for more details. |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
19 * |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
20 * You should have received a copy of the GNU General Public License |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
21 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
22 **/ |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
23 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
24 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
25 import ai.djl.ndarray.NDArray; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
26 import ai.djl.ndarray.NDManager; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
27 import be.uclouvain.orthanc.Callbacks; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
28 import be.uclouvain.orthanc.ChangeType; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
29 import be.uclouvain.orthanc.Functions; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
30 import be.uclouvain.orthanc.HttpMethod; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
31 import be.uclouvain.orthanc.ResourceType; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
32 import be.uclouvain.orthanc.RestOutput; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
33 import org.apache.commons.compress.utils.IOUtils; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
34 import org.json.JSONObject; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
35 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
36 import java.awt.image.BufferedImage; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
37 import java.io.IOException; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
38 import java.io.InputStream; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
39 import java.nio.charset.StandardCharsets; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
40 import java.security.NoSuchAlgorithmException; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
41 import java.util.HashMap; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
42 import java.util.List; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
43 import java.util.Map; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
44 import java.util.concurrent.ExecutorService; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
45 import java.util.concurrent.Executors; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
46 import java.util.zip.ZipEntry; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
47 import java.util.zip.ZipFile; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
48 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
49 public class Main { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
50 private static final String MODEL_PATH = "2024-03-08-retina_res50_trained_08_03.torchscript"; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
51 private static final String STONE_VERSION = "2024-03-15-StoneWebViewer-DICOM-SR"; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
52 private static final String STONE_PATH = "2024-03-15-StoneWebViewer-DICOM-SR.zip"; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
53 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
54 private static ZipFile stone; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
55 private static NDManager manager; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
56 private static RetinaNet retinaNet; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
57 private static Map<String, String> mimeTypes = new HashMap<>(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
58 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
59 static { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
60 ExecutorService executor = Executors.newSingleThreadExecutor(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
61 try { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
62 OrthancConnection.download("2024-03-08-retina_res50_trained_08_03.torchscript", executor, |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
63 "https://orthanc.uclouvain.be/downloads/cross-platform/orthanc-mammography/models/2024-03-08-retina_res50_trained_08_03.torchscript", |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
64 146029397L, "b3de8f562de683bc3515fe93ae102fd4"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
65 OrthancConnection.download("2024-03-15-StoneWebViewer-DICOM-SR.zip", executor, |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
66 "https://github.com/jodogne/orthanc-mammography/raw/master/viewer/2024-03-15-StoneWebViewer-DICOM-SR.zip", |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
67 4742571L, "de952da6fc74a9d4b78ca5064a6a7318"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
68 } catch (IOException | NoSuchAlgorithmException | InterruptedException e) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
69 throw new RuntimeException(e); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
70 } finally { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
71 executor.shutdown(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
72 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
73 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
74 try { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
75 stone = new ZipFile(STONE_PATH); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
76 } catch (IOException e) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
77 throw new RuntimeException(e); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
78 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
79 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
80 Functions.logWarning("Initializing Deep Java Library"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
81 manager = NDManager.newBaseManager(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
82 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
83 Functions.logWarning("Loading RetinaNet model"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
84 try { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
85 retinaNet = new RetinaNet(MODEL_PATH); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
86 } catch (Exception e) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
87 throw new RuntimeException(e); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
88 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
89 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
90 Functions.logWarning("RetinaNet model is ready"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
91 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
92 mimeTypes.put("css", "text/css"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
93 mimeTypes.put("gif", "image/gif"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
94 mimeTypes.put("html", "text/html"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
95 mimeTypes.put("jpeg", "image/jpeg"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
96 mimeTypes.put("js", "text/javascript"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
97 mimeTypes.put("png", "image/png"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
98 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
99 try (InputStream stream = Main.class.getResourceAsStream("OrthancExplorer.js")) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
100 byte[] content = IOUtils.toByteArray(stream); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
101 Functions.extendOrthancExplorer(new String(content, StandardCharsets.UTF_8)); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
102 } catch (IOException e) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
103 throw new RuntimeException(e); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
104 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
105 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
106 Callbacks.register(new Callbacks.OnChange() { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
107 @Override |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
108 public void call(ChangeType changeType, ResourceType resourceType, String resourceId) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
109 switch (changeType) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
110 case ORTHANC_STARTED: |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
111 OrthancConnection connection = OrthancConnection.createForPlugin(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
112 try { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
113 if (!connection.isOrthancVersionAbove(1, 12, 5)) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
114 throw new RuntimeException("Your version of Orthanc must be >= 1.12.5 to run this plugin"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
115 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
116 } catch (IOException | InterruptedException e) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
117 throw new RuntimeException(e); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
118 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
119 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
120 break; |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
121 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
122 case ORTHANC_STOPPED: |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
123 Functions.logWarning("Finalizing Deep Java Library"); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
124 if (retinaNet != null) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
125 retinaNet.close(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
126 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
127 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
128 if (manager != null) { |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
129 manager.close(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
130 } |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
131 |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
132 System.gc(); |
43923934e934
added sample: deep learning for mammography
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
133 System.runFinalization(); |
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 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 } |
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 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 |
43923934e934
added sample: deep learning for mammography
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 |
43923934e934
added sample: deep learning for mammography
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
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 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 } |