Merge pull request #22 from ksugar/dev

0.6.0 -> 0.7.0

README.md

@@ -1,5 +1,8 @@
 # QuPath extension SAM
 
+### New release v0.7: SAM2-based 2D+T tracking and 3D segmentation are supported now!
+<img src="https://github.com/ksugar/qupath-extension-sam/releases/download/assets/sam2-sequence-demo.gif" width="768">
+
 <img src="https://github.com/ksugar/samapi/releases/download/assets/qupath-samapi.gif" width="768">
 
 <img src="https://github.com/ksugar/samapi/releases/download/assets/qupath-sam-multipoint-live.gif" width="768">
@@ -12,7 +15,7 @@ This is a part of the following paper. Please [cite](#citation) it when you use
 
 ## Install
 
-Drag and drop [the extension file](https://github.com/ksugar/qupath-extension-sam/releases/download/v0.6.0/qupath-extension-sam-0.6.0.jar) to [QuPath](https://qupath.github.io) and restart it.
+Drag and drop [the extension file](https://github.com/ksugar/qupath-extension-sam/releases/download/v0.7.0/qupath-extension-sam-0.7.0.jar) to [QuPath](https://qupath.github.io) and restart it.
 
 Since QuPath v0.5.0, you can install the extension from the extension manager dialog by specifying `Owner` and `Repository` as shown below.
 
@@ -30,7 +33,7 @@ To update the `qupath-extension-sam`, follow the following instructions.
 
 1. Open extensions directory from `Extensions` > `Installed extensions` > `Open extensions directory`
    ![](https://github.com/ksugar/qupath-extension-sam/releases/download/assets/open-extensions-directory.png)
-2. Replace `qupath-extension-sam-x.y.z.jar` with [the latest version of the extension file](https://github.com/ksugar/qupath-extension-sam/releases/download/v0.6.0/qupath-extension-sam-0.6.0.jar). If you are using QuPath v0.4.x, you need to install [the extension file for QuPath v0.4.x](https://github.com/ksugar/qupath-extension-sam/releases/download/v0.4.1/qupath-extension-sam-0.4.1.jar), which is now deprecated.
+2. Replace `qupath-extension-sam-x.y.z.jar` with [the latest version of the extension file](https://github.com/ksugar/qupath-extension-sam/releases/download/v0.7.0/qupath-extension-sam-0.7.0.jar). If you are using QuPath v0.4.x, you need to install [the extension file for QuPath v0.4.x](https://github.com/ksugar/qupath-extension-sam/releases/download/v0.4.1/qupath-extension-sam-0.4.1.jar), which is now deprecated.
 3. Restart QuPath application.
 
 Please note that you need to also update the [samapi](https://github.com/ksugar/samapi/tree/v0.5.0) server.  
@@ -173,8 +176,11 @@ If you select a class in `Auto set` in the Annotations tab, it is used for a new
 
 ## Updates
 
+### v0.7.0
+- Support 2D+T tracking and 3D segmentation with [SAM2](https://ai.meta.com/sam2/) models, available with the [samapi](https://github.com/ksugar/samapi) server `v0.6.0` and above.
+
 ### v0.6.0
-- Support [SAM2](https://ai.meta.com/sam2/) models. The SAM2 models are available from the [samapi](https://github.com/ksugar/samapi) server `v0.5.0` and above.
+- Support [SAM2](https://ai.meta.com/sam2/) models, available with the [samapi](https://github.com/ksugar/samapi) server `v0.5.0` and above.
 - Use the current view for the encoder input in the rectangle mode.
 
 ### v0.5.0

build.gradle

@@ -13,7 +13,7 @@ plugins {
 ext.moduleName = 'org.elephant.sam.qupath'
 
 // TODO: Define the extension version & provide a short description
-version = "0.6.0"
+version = "0.7.0"
 description = 'QuPath extension for Segment Anything Model (SAM)'
 
 // TODO: Specify the QuPath version, compatible with the extension.

src/main/java/org/elephant/sam/SAMExtension.java

@@ -61,7 +61,7 @@ public GitHubRepo getRepository() {
 
 	@Override
 	public Version getQuPathVersion() {
-		return Version.parse("0.6.0");
+		return Version.parse("0.7.0");
 	}
 
 }

src/main/java/org/elephant/sam/Utils.java

@@ -5,9 +5,12 @@
 import com.google.gson.JsonObject;
 
 import org.elephant.sam.entities.SAMOutput;
+import org.elephant.sam.http.MultipartBodyBuilder;
 import org.locationtech.jts.geom.Coordinate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+
+import qupath.lib.awt.common.AwtTools;
 import qupath.lib.common.GeneralTools;
 import qupath.lib.geom.Point2;
 import qupath.lib.gui.images.servers.RenderedImageServer;
@@ -18,6 +21,7 @@
 import qupath.lib.objects.PathObjectTools;
 import qupath.lib.objects.classes.PathClass;
 import qupath.lib.regions.ImagePlane;
+import qupath.lib.regions.ImageRegion;
 import qupath.lib.regions.RegionRequest;
 import qupath.lib.roi.RectangleROI;
 import qupath.lib.roi.interfaces.ROI;
@@ -92,10 +96,14 @@ private static PathObject parsePathObject(Gson gson, JsonElement element) {
         if (jsonObj.has("properties")) {
             // Set quality from properties if we can
             JsonObject properties = jsonObj.get("properties").getAsJsonObject();
-            JsonElement quality = properties.has("quality") ? properties.get("quality") : null;
+            JsonElement quality = properties.get("quality");
             if (quality != null && quality.isJsonPrimitive()) {
                 pathObject.getMeasurementList().put(SAM_QUALITY_MEASUREMENT, quality.getAsDouble());
             }
+            JsonElement objectId = properties.get("object_idx");
+            if (objectId != null && objectId.isJsonPrimitive()) {
+                pathObject.setPathClass(PathClass.getInstance(objectId.getAsString()));
+            }
         }
         return pathObject;
     }
@@ -154,7 +162,11 @@ public static PathObject applyTransformAndClassification(PathObject pathObject,
         }
         if (plane != null && !Objects.equals(plane, pathObject.getROI().getImagePlane()))
             pathObject = PathObjectTools.updatePlane(pathObject, plane, true, false);
-        pathObject.setPathClass(pathClass);
+        if (pathClass == PathClass.NULL_CLASS) {
+            pathObject.resetPathClass();
+        } else if (pathClass != null) {
+            pathObject.setPathClass(pathClass);
+        }
         return pathObject;
     }
 
@@ -214,6 +226,43 @@ public static ImageServer<BufferedImage> createRenderedServer(QuPathViewer viewe
                 .build();
     }
 
+    /**
+     * Get a region request for the viewer, intersected with the rendered server.
+     * 
+     * @param viewer
+     * @param renderedServer
+     * @return the region request
+     */
+    public static RegionRequest getViewerRegion(QuPathViewer viewer, ImageServer<BufferedImage> renderedServer) {
+        return getViewerRegion(viewer, renderedServer, viewer.getZPosition(), viewer.getTPosition());
+    }
+
+    /**
+     * Get a region request for the viewer, intersected with the rendered server.
+     * 
+     * @param viewer
+     * @param renderedServer
+     * @param z
+     * @param t
+     * @return the region request
+     */
+    public static RegionRequest getViewerRegion(QuPathViewer viewer, ImageServer<BufferedImage> renderedServer, int z,
+            int t) {
+        if (renderedServer == null) {
+            try {
+                renderedServer = Utils.createRenderedServer(viewer);
+            } catch (IOException e) {
+                logger.error("Failed to create rendered server", e);
+            }
+        }
+        // Find the region and downsample currently used within the viewer
+        ImageRegion region = AwtTools.getImageRegion(viewer.getDisplayedRegionShape(), z, t);
+        RegionRequest viewerRegion = RegionRequest.createInstance(renderedServer.getPath(),
+                viewer.getDownsampleFactor(), region);
+        viewerRegion = viewerRegion.intersect2D(0, 0, renderedServer.getWidth(), renderedServer.getHeight());
+        return viewerRegion;
+    }
+
     /**
      * Encode a BufferedImage as a base64-encoded PNG.
      * 
@@ -333,4 +382,30 @@ public static boolean isPotentialPromptObject(PathObject pathObject) {
         return pathObject.isAnnotation() && pathObject.hasROI() && !pathObject.getROI().isEmpty();
     }
 
+    /**
+     * Converts a BufferedImage to a JPEG byte array.
+     *
+     * @param image
+     *            The BufferedImage to convert.
+     * @return A byte array containing the JPEG data.
+     * @throws IOException
+     *             If an error occurs during writing.
+     */
+    public static byte[] bufferedImageToJpegBytes(BufferedImage image) throws IOException {
+        try (ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
+            ImageIO.write(image, "jpg", baos);
+            return baos.toByteArray();
+        }
+    }
+
+    public static byte[] createImageUploadMultipartBody(String boundary, String dirname, String filename,
+            BufferedImage image)
+            throws IOException {
+        byte[] imageBytes = bufferedImageToJpegBytes(image);
+        final MultipartBodyBuilder builder = new MultipartBodyBuilder(boundary);
+        builder.addFormField("dirname", dirname);
+        builder.addFilePart("file", filename, "image/jpeg", imageBytes);
+        return builder.build();
+    }
+
 }