Add methods to access volume data for algorithms like marching cubes

src/main/java/sc/iview/commands/process/VolumeMarchingCubes.java

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+/*-
+ * #%L
+ * Scenery-backed 3D visualization package for ImageJ.
+ * %%
+ * Copyright (C) 2016 - 2024 sciview developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package sc.iview.commands.process;
+
+import graphics.scenery.Group;
+import graphics.scenery.Mesh;
+import graphics.scenery.Node;
+import graphics.scenery.volumes.Volume;
+import net.imagej.mesh.MeshConnectedComponents;
+import net.imagej.mesh.RemoveDuplicateVertices;
+import net.imagej.ops.OpService;
+import net.imagej.ops.geom.geom3d.mesh.BitTypeVertexInterpolator;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
+import net.imglib2.type.logic.BitType;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.view.IntervalView;
+import org.joml.Vector3f;
+import org.scijava.command.Command;
+import org.scijava.log.LogService;
+import org.scijava.plugin.Menu;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.ui.DialogPrompt;
+import org.scijava.ui.UIService;
+import sc.iview.SciView;
+import sc.iview.process.MeshConverter;
+import sc.iview.process.VolumeExtensionsKt;
+
+import static sc.iview.commands.MenuWeights.PROCESS;
+import static sc.iview.commands.MenuWeights.PROCESS_ISOSURFACE;
+
+/**
+ * Command to create a mesh from the active Volume using VolumeUtils/VolumeExtensions
+ * @param <T> a RealType
+ *
+ * @author You-Name-Here
+ */
+@Plugin(type = Command.class, menuRoot = "SciView", //
+        menu = {@Menu(label = "Process", weight = PROCESS), //
+                @Menu(label = "Volume Marching Cubes", weight = PROCESS_ISOSURFACE)})
+public class VolumeMarchingCubes implements Command {
+
+    @Parameter
+    private OpService ops;
+
+    @Parameter
+    private SciView sciView;
+
+    @Parameter
+    private UIService ui;
+
+    @Parameter
+    private LogService log;
+
+    @Parameter(label = "Threshold", min = "1", max = "255", stepSize = "1")
+    private int threshold = 1;
+
+    @Override
+    public void run() {
+        Node active = sciView.getActiveNode();
+
+        if (!(active instanceof Volume)) {
+            ui.showDialog("The active node needs to be a volume.", DialogPrompt.MessageType.ERROR_MESSAGE);
+            return;
+        }
+
+        Volume volume = (Volume) active;
+
+        // Use the new extension methods to get the current view of the volume
+        IntervalView<UnsignedByteType> view = VolumeExtensionsKt.getCurrentView(volume);
+
+        if (view == null) {
+            ui.showDialog("Could not access volume data. Make sure this is a valid volume.", 
+                    DialogPrompt.MessageType.ERROR_MESSAGE);
+            return;
+        }
+
+        log.info("Creating mesh from volume at timepoint: " + volume.getCurrentTimepoint());
+
+        // Use the threshold value to create a binary image
+        Img<BitType> bitImg = (Img<BitType>) ops.threshold().apply(view, new UnsignedByteType(threshold));
+
+        // Apply marching cubes algorithm
+        net.imagej.mesh.Mesh mesh = (net.imagej.mesh.Mesh) ops.geom().marchingCubes(
+                bitImg, (double) threshold, new BitTypeVertexInterpolator());
+
+        // Process the mesh
+        net.imagej.mesh.Mesh meshes = RemoveDuplicateVertices.calculate(mesh, 0);
+
+        // Create a group to hold the mesh components
+        Group group = new Group();
+        group.setName("Mesh from volume at timepoint: " + volume.getCurrentTimepoint());
+
+        // Add each connected component as a separate mesh
+        for (net.imagej.mesh.Mesh m : MeshConnectedComponents.iterable(meshes)) {
+            Mesh ready = MeshConverter.toScenery(m);
+            ready.material().setWireframe(true);
+            ready.material().setDiffuse(new Vector3f(1f, 0.7f, 0.5f));
+            group.addChild(ready);
+        }
+
+        // Add the group to the scene
+        sciView.addNode(group, volume);
+    }
+}

src/main/kotlin/sc/iview/process/README.md

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+# SciView Volume Data Access Utilities
+
+This module provides utilities for accessing the original data stored in Volume objects.
+
+## VolumeUtils
+
+The `VolumeUtils` class provides static methods for accessing volume data:
+
+- `getOriginalRandomAccessibleInterval(volume)`: Returns the original RandomAccessibleInterval data stored in a Volume.
+- `getCurrentView(volume)`: Returns an IntervalView representing the current timepoint of a volume.
+
+## Volume Extensions
+
+For more convenient usage, extension methods are provided for the Volume class:
+
+- `volume.getOriginalRandomAccessibleInterval<T>()`: Extension method to get the original data.
+- `volume.getCurrentView<T>()`: Extension method to get the current view based on the timepoint.
+
+## Usage Example
+
+Here's a simple example of using these utilities to apply a marching cubes algorithm to a Volume:
+
+```kotlin
+// Get the current Volume
+val volume = sciView.activeNode as Volume
+
+// Get the current view based on the timepoint
+val view = volume.getCurrentView<UnsignedByteType>()
+
+// Apply your processing
+val bitImg = ops.threshold().apply(view, UnsignedByteType(1)) as Img<BitType>
+val mesh = ops.geom().marchingCubes(bitImg, 1.0, BitTypeVertexInterpolator())
+
+// Convert to scenery mesh
+val sceneryMesh = MeshConverter.toScenery(mesh)
+
+// Add to scene
+sciView.addNode(sceneryMesh)
+```
+
+See the `VolumeMarchingCubes` command for a complete example.

src/main/kotlin/sc/iview/process/VolumeExtensions.kt

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+/*-
+ * #%L
+ * Scenery-backed 3D visualization package for ImageJ.
+ * %%
+ * Copyright (C) 2016 - 2024 sciview developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package sc.iview.process
+
+import graphics.scenery.volumes.Volume
+import net.imglib2.RandomAccessibleInterval
+import net.imglib2.view.IntervalView
+
+/**
+ * Extension functions for the Volume class
+ * 
+ * @author You-Name-Here
+ */
+
+/**
+ * Gets the original data source of a Volume as a RandomAccessibleInterval
+ * 
+ * @return The original RandomAccessibleInterval, or null if not available
+ */
+@Suppress("UNCHECKED_CAST")
+fun <T> Volume.getOriginalRandomAccessibleInterval(): RandomAccessibleInterval<T>? {
+    return VolumeUtils.getOriginalRandomAccessibleInterval(this)
+}
+
+/**
+ * Gets the current view of a Volume based on the current timepoint
+ * 
+ * @return An IntervalView representing the current timepoint of the volume, or null if not available
+ */
+@Suppress("UNCHECKED_CAST")
+fun <T> Volume.getCurrentView(): IntervalView<T>? {
+    return VolumeUtils.getCurrentView(this)
+}

src/main/kotlin/sc/iview/process/VolumeUtils.kt

@@ -0,0 +1,73 @@
+/*-
+ * #%L
+ * Scenery-backed 3D visualization package for ImageJ.
+ * %%
+ * Copyright (C) 2016 - 2024 sciview developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package sc.iview.process
+
+import graphics.scenery.volumes.Volume
+import net.imglib2.RandomAccessibleInterval
+import net.imglib2.view.IntervalView
+import net.imglib2.view.Views
+import org.scijava.log.LogService
+
+/**
+ * Utility methods for working with Volumes
+ * 
+ * @author You-Name-Here
+ */
+object VolumeUtils {
+    /**
+     * Gets the original data source of a Volume as a RandomAccessibleInterval
+     *
+     * @param volume The volume to get the original data from
+     * @return The original RandomAccessibleInterval, or null if not available
+     */
+    @Suppress("UNCHECKED_CAST")
+    fun <T> getOriginalRandomAccessibleInterval(volume: Volume): RandomAccessibleInterval<T>? {
+        return volume.metadata["RandomAccessibleInterval"] as? RandomAccessibleInterval<T>
+    }
+
+    /**
+     * Gets the current view of a Volume based on the current timepoint
+     *
+     * @param volume The volume to get the current view from
+     * @return An IntervalView representing the current timepoint of the volume, or null if not available
+     */
+    @Suppress("UNCHECKED_CAST")
+    fun <T> getCurrentView(volume: Volume): IntervalView<T>? {
+        val originalRAI = getOriginalRandomAccessibleInterval<T>(volume) ?: return null
+
+        // Check if the original data is time-series (has more than 3 dimensions)
+        return if (originalRAI.numDimensions() > 3) {
+            // Create a view for the current timepoint by fixing the 4th dimension (time)
+            Views.hyperSlice(originalRAI, 3, volume.currentTimepoint.toLong()) as IntervalView<T>
+        } else {
+            // If it's not a time-series, just return the original data as an IntervalView
+            Views.interval(originalRAI, originalRAI) as IntervalView<T>
+        }
+    }
+}