WIP: OpenOrganelle demo

src/main/kotlin/sc/iview/commands/demo/advanced/LoadOpenOrganelle.kt

@@ -0,0 +1,123 @@
+/*-
+ * #%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.demo.advanced
+
+import bdv.util.volatiles.VolatileViews
+import graphics.scenery.Origin
+import graphics.scenery.volumes.Colormap
+import graphics.scenery.volumes.Volume
+import net.imagej.lut.LUTService
+import net.imagej.ops.OpService
+import net.imglib2.FinalInterval
+import net.imglib2.Interval
+import net.imglib2.RandomAccessibleInterval
+import net.imglib2.converter.Converters
+import net.imglib2.img.Img
+import net.imglib2.img.array.ArrayImgs
+import net.imglib2.img.cell.CellImgFactory
+import net.imglib2.loops.LoopBuilder
+import net.imglib2.type.numeric.ARGBType
+import net.imglib2.type.numeric.integer.UnsignedByteType
+import net.imglib2.type.numeric.real.FloatType
+import net.imglib2.type.volatiles.VolatileUnsignedByteType
+import net.imglib2.view.Views
+import org.embl.mobie.io.ome.zarr.openers.OMEZarrS3Opener
+import org.joml.Vector3f
+import org.joml.Vector4f
+import org.scijava.command.Command
+import org.scijava.command.CommandService
+import org.scijava.log.LogService
+import org.scijava.plugin.Menu
+import org.scijava.plugin.Parameter
+import org.scijava.plugin.Plugin
+import org.scijava.ui.UIService
+import sc.iview.SciView
+import sc.iview.commands.MenuWeights
+import net.imglib2.converter.Converter
+import net.imglib2.type.numeric.integer.UnsignedIntType
+import net.imglib2.type.numeric.integer.UnsignedShortType
+import net.imglib2.type.volatiles.VolatileUnsignedIntType
+import net.imglib2.type.volatiles.VolatileUnsignedShortType
+import org.embl.mobie.io.openorganelle.OpenOrganelleS3Opener
+
+@Plugin(type = Command::class,
+        label = "Load Open Organelle demo",
+        menuRoot = "SciView",
+        menu = [Menu(label = "Demo", weight = MenuWeights.DEMO),
+            Menu(label = "Advanced", weight = MenuWeights.DEMO_ADVANCED),
+            Menu(label = "Load Open Organelle demo", weight = MenuWeights.DEMO_ADVANCED_CREMI)])
+class LoadOpenOrganelle : Command {
+    @Parameter
+    private lateinit var log: LogService
+
+    @Parameter
+    private lateinit var sciview: SciView
+
+    @Parameter
+    private lateinit var lut: LUTService
+
+    override fun run() {
+        val reader = OMEZarrS3Opener(
+                "https://janelia-cosem.s3.amazonaws.com",
+                "us-west-2",
+                "jrc_hela-2")
+        OpenOrganelleS3Opener.setLogging(true)
+        val image = reader.readKey("jrc_hela-2.n5/em/fibsem-uint16")
+
+        // Assume the data is of UnsignedIntType
+        //
+        val rai = image.getSequenceDescription().getImgLoader()
+
+        //val colormapVolume = lut.loadLUT(lut.findLUTs().get("Grays.lut"))
+
+        // Wrap the RandomAccessibleInterval with VolatileViews for tiled rendering
+        //val volatileRai = VolatileViews.wrapAsVolatile(rai) as RandomAccessibleInterval<VolatileUnsignedShortType>
+
+        // Create and configure the volume
+//        val volume = Volume.fromRAI(
+//                rai,
+//                VolatileUnsignedShortType(),
+//                name = "My image",
+//                hub = sciview.hub
+//        )
+
+//        sciview.addNode(volume)
+    }
+
+    companion object {
+        @Throws(Exception::class)
+        @JvmStatic
+        fun main(args: Array<String>) {
+            val sv = SciView.create()
+            val command = sv.scijavaContext!!.getService(CommandService::class.java)
+            val argmap = HashMap<String, Any>()
+            command.run(LoadOpenOrganelle::class.java, true, argmap)
+        }
+    }
+}