--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Samples/MammographyDeepLearning/src/main/java/Main.java	Wed Jun 12 13:58:29 2024 +0200
@@ -0,0 +1,230 @@
+/**
+ * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium
+ * SPDX-License-Identifier: GPL-3.0-or-later
+ **/
+
+/**
+ * Java plugin for Orthanc
+ * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+import ai.djl.ndarray.NDArray;
+import ai.djl.ndarray.NDManager;
+import be.uclouvain.orthanc.Callbacks;
+import be.uclouvain.orthanc.ChangeType;
+import be.uclouvain.orthanc.Functions;
+import be.uclouvain.orthanc.HttpMethod;
+import be.uclouvain.orthanc.ResourceType;
+import be.uclouvain.orthanc.RestOutput;
+import org.apache.commons.compress.utils.IOUtils;
+import org.json.JSONObject;
+
+import java.awt.image.BufferedImage;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.security.NoSuchAlgorithmException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+public class Main {
+    private static final String MODEL_PATH = "2024-03-08-retina_res50_trained_08_03.torchscript";
+    private static final String STONE_VERSION = "2024-03-15-StoneWebViewer-DICOM-SR";
+    private static final String STONE_PATH = "2024-03-15-StoneWebViewer-DICOM-SR.zip";
+
+    private static ZipFile stone;
+    private static NDManager manager;
+    private static RetinaNet retinaNet;
+    private static Map<String, String> mimeTypes = new HashMap<>();
+
+    static {
+        ExecutorService executor = Executors.newSingleThreadExecutor();
+        try {
+            OrthancConnection.download("2024-03-08-retina_res50_trained_08_03.torchscript", executor,
+                    "https://orthanc.uclouvain.be/downloads/cross-platform/orthanc-mammography/models/2024-03-08-retina_res50_trained_08_03.torchscript",
+                    146029397L, "b3de8f562de683bc3515fe93ae102fd4");
+            OrthancConnection.download("2024-03-15-StoneWebViewer-DICOM-SR.zip", executor,
+                    "https://github.com/jodogne/orthanc-mammography/raw/master/viewer/2024-03-15-StoneWebViewer-DICOM-SR.zip",
+                    4742571L, "de952da6fc74a9d4b78ca5064a6a7318");
+        } catch (IOException | NoSuchAlgorithmException | InterruptedException e) {
+            throw new RuntimeException(e);
+        } finally {
+            executor.shutdown();
+        }
+
+        try {
+            stone = new ZipFile(STONE_PATH);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+
+        Functions.logWarning("Initializing Deep Java Library");
+        manager = NDManager.newBaseManager();
+
+        Functions.logWarning("Loading RetinaNet model");
+        try {
+            retinaNet = new RetinaNet(MODEL_PATH);
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
+
+        Functions.logWarning("RetinaNet model is ready");
+
+        mimeTypes.put("css", "text/css");
+        mimeTypes.put("gif", "image/gif");
+        mimeTypes.put("html", "text/html");
+        mimeTypes.put("jpeg", "image/jpeg");
+        mimeTypes.put("js", "text/javascript");
+        mimeTypes.put("png", "image/png");
+
+        try (InputStream stream = Main.class.getResourceAsStream("OrthancExplorer.js")) {
+            byte[] content = IOUtils.toByteArray(stream);
+            Functions.extendOrthancExplorer(new String(content, StandardCharsets.UTF_8));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+
+        Callbacks.register(new Callbacks.OnChange() {
+            @Override
+            public void call(ChangeType changeType, ResourceType resourceType, String resourceId) {
+                switch (changeType) {
+                    case ORTHANC_STARTED:
+                        OrthancConnection connection = OrthancConnection.createForPlugin();
+                        try {
+                            if (!connection.isOrthancVersionAbove(1, 12, 5)) {
+                                throw new RuntimeException("Your version of Orthanc must be >= 1.12.5 to run this plugin");
+                            }
+                        } catch (IOException | InterruptedException e) {
+                            throw new RuntimeException(e);
+                        }
+
+                        break;
+
+                    case ORTHANC_STOPPED:
+                        Functions.logWarning("Finalizing Deep Java Library");
+                        if (retinaNet != null) {
+                            retinaNet.close();
+                        }
+
+                        if (manager != null) {
+                            manager.close();
+                        }
+
+                        System.gc();
+                        System.runFinalization();
+                        break;
+
+                    default:
+                        break;
+                }
+            }
+        });
+
+        Callbacks.register("/java-mammography-apply", new Callbacks.OnRestRequest() {
+            @Override
+            public void call(RestOutput output,
+                             HttpMethod method,
+                             String uri,
+                             String[] regularExpressionGroups,
+                             Map<String, String> headers,
+                             Map<String, String> getParameters,
+                             byte[] body) {
+                if (method != HttpMethod.POST) {
+                    output.sendMethodNotAllowed("POST");
+                    return;
+                }
+
+                JSONObject request = new JSONObject(new String(body, StandardCharsets.UTF_8));
+
+                String instanceId = request.getString("instance");
+                if (instanceId == null) {
+                    throw new RuntimeException("Missing instance identifier");
+                }
+
+                Functions.logWarning("Applying RetinaNet to instance: " + instanceId);
+                OrthancConnection connection = OrthancConnection.createForPlugin();
+
+                try {
+                    BufferedImage image = connection.getGrayscaleFrame(instanceId, 0);
+
+                    double largestSide = Math.max(image.getWidth(), image.getHeight());
+                    BufferedImage resized = ImageProcessing.resizeImage(image,
+                            (int) Math.round((double) image.getWidth() * 2048.0 / largestSide),
+                            (int) Math.round((double) image.getHeight() * 2048.0 / largestSide));
+
+                    double aspectRatio = (double) image.getWidth() / (double) resized.getWidth();
+
+                    NDArray grayscale = ImageProcessing.imageToTensor(manager, resized);
+                    grayscale = ImageProcessing.standardize(grayscale);
+
+                    NDArray rgb = grayscale.concat(grayscale).concat(grayscale);  // Create a "RGB" image from grayscale pixel values
+                    List<Detection> detections = retinaNet.apply(rgb);
+
+                    JSONObject created = DicomToolbox.createDicomSR(connection, instanceId, detections, aspectRatio);
+
+                    String id = created.getString("ID");
+                    Functions.logWarning("Detection results stored in DICOM-SR instance: " + id);
+
+                    output.answerBuffer(created.toString().getBytes(StandardCharsets.UTF_8), "application/json");
+                } catch (Exception e) {
+                    throw new RuntimeException(e);
+                }
+            }
+        });
+
+        Callbacks.register("/java-mammography-viewer/(.*)", new Callbacks.OnRestRequest() {
+            @Override
+            public void call(RestOutput output,
+                             HttpMethod method,
+                             String uri,
+                             String[] regularExpressionGroups,
+                             Map<String, String> headers,
+                             Map<String, String> getParameters,
+                             byte[] body) {
+                if (method != HttpMethod.GET) {
+                    output.sendMethodNotAllowed("GET");
+                    return;
+                }
+
+                String path = regularExpressionGroups[0];
+                int dot = path.lastIndexOf(".");
+                if (dot < 0) {
+                    output.sendHttpStatus((short) 404, new byte[0]);
+                } else {
+                    String extension = path.substring(dot + 1);
+                    String mime = mimeTypes.getOrDefault(extension, "application/octet-stream");
+
+                    ZipEntry entry = stone.getEntry(STONE_VERSION + "/" + path);
+                    if (entry == null) {
+                        output.sendHttpStatus((short) 404, new byte[0]);
+                    } else {
+                        try (InputStream stream = stone.getInputStream(entry)) {
+                            output.answerBuffer(IOUtils.toByteArray(stream), mime);
+                        } catch (IOException e) {
+                            throw new RuntimeException(e);
+                        }
+                    }
+                }
+            }
+        });
+    }
+}