wip: working toward figure

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

@@ -64,24 +64,15 @@ class LoadMandelbulbOutOfCore : Command {
         val maxIter = 32 // Example maximum iterations
         val order = 8 // Example Mandelbulb order
 
-
         // Define max scale level
-        val maxScale = 7 // Adjust this value to test rendering at different scales
-
+        val maxScale = 8 // Adjust this value to test rendering at different scales
 
         // Desired grid size at the finest resolution level
-
-        // Desired grid size at the finest resolution level
-        val desiredFinestGridSize = 8 // Define as per your requirement
-
-
-        // Compute the base grid size
+        val desiredFinestGridSize = 8
 
         // Compute the base grid size
         val baseGridSize = desiredFinestGridSize * Math.pow(2.0, (maxScale - 1).toDouble()).toInt()
 
-        // Generate resolutions and corresponding grid sizes
-
         // Generate resolutions and corresponding grid sizes
         val resolutions = Array(maxScale) { DoubleArray(3) }
         val gridSizes = IntArray(maxScale)

src/main/kotlin/sc/iview/commands/demo/advanced/LoadN5OutOfCore.kt

@@ -0,0 +1,89 @@
+package sc.iview.commands.demo.advanced
+
+import bdv.util.volatiles.VolatileViews
+import graphics.scenery.BoundingGrid
+import graphics.scenery.PointLight
+import graphics.scenery.volumes.TransferFunction
+import graphics.scenery.volumes.Volume
+import net.imglib2.RandomAccessibleInterval
+import net.imglib2.type.volatiles.VolatileUnsignedShortType
+import net.imglib2.type.numeric.integer.UnsignedShortType
+import org.janelia.saalfeldlab.n5.N5FSReader
+import org.janelia.saalfeldlab.n5.imglib2.N5Utils
+import org.joml.Vector3f
+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 sc.iview.SciView
+import sc.iview.commands.MenuWeights
+
+@Plugin(type = Command::class,
+        label = "Load N5 Out-of-Core demo",
+        menuRoot = "SciView",
+        menu = [Menu(label = "Demo", weight = MenuWeights.DEMO),
+            Menu(label = "Advanced", weight = MenuWeights.DEMO_ADVANCED),
+            Menu(label = "Load Mandelbulb Out-of-Core demo", weight = MenuWeights.DEMO_ADVANCED)])
+class LoadN5OutOfCore : Command {
+    @Parameter
+    private lateinit var sciview: SciView
+
+    @Parameter
+    private lateinit var log: LogService
+
+    override fun run() {
+        // Load data from N5
+        val n5path = "/Users/kharrington/Library/CloudStorage/Dropbox/sciview_data/data/test_n5_error/input-multiscale.n5"
+        val datasetName = "setup0/timepoint0/s0"
+
+        log.info("Loading N5 data from $n5path with dataset $datasetName")
+
+        val ooc: RandomAccessibleInterval<UnsignedShortType> = N5Utils.openVolatile(N5FSReader(n5path), datasetName)
+        val wrapped = VolatileViews.wrapAsVolatile(ooc)
+
+        // When loading datasets with multiple resolution levels, it's important to use Volatile types
+        // here, such as VolatileUnsignedShortType, otherwise loading volume blocks will not work correctly.
+        @Suppress("UNCHECKED_CAST")
+        val volume = Volume.fromRAI(
+                wrapped as RandomAccessibleInterval<VolatileUnsignedShortType>,
+                VolatileUnsignedShortType(),
+                name = "N5 OOC",
+                hub = sciview.hub
+        )
+        volume.converterSetups.first().setDisplayRange(25.0, 512.0)
+        volume.transferFunction = TransferFunction.ramp(0.01f, 0.03f)
+        volume.spatial().scale = Vector3f(20.0f)
+        sciview.addNode(volume)
+
+        log.info("Volume added to the scene")
+
+        val lights = (0 until 3).map {
+            PointLight(radius = 15.0f)
+        }
+
+        lights.mapIndexed { i, light ->
+            light.spatial().position = Vector3f(2.0f * i - 4.0f, i - 1.0f, 0.0f)
+            light.emissionColor = Vector3f(1.0f, 1.0f, 1.0f)
+            light.intensity = 50.0f
+            sciview.addNode(light)
+        }
+
+        val newBg = BoundingGrid()
+        newBg.node = volume
+        sciview.publishNode(newBg)
+
+        log.info("Lights added to the scene")
+    }
+
+    companion object {
+        @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(LoadN5OutOfCore::class.java, true, argmap)
+        }
+    }
+}