Add VolumeUtils for slice positioning, clean up examples accordingly

scenerygraphics · Jan 30, 2024 · 1064d30 · 1064d30
1 parent e78bb91
commit 1064d30
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Showing 8 changed files with 55 additions and 59 deletions.
diff --git a/src/main/kotlin/graphics/scenery/RichNode.kt b/src/main/kotlin/graphics/scenery/RichNode.kt
@@ -13,23 +13,4 @@ open class RichNode(override var name: String = "Node") : DefaultNode (name), Ha
         addMaterial()
         addSpatial()
     }
-
-    /**
-     * Positions [volumes] back-to-back without gaps, using their pixel-to-world ratio. Can, e.g., be used
-     * with [fromPathRawSplit] to load volume files greater than 2 GiB into sliced partitions and place
-     * the partitions back-to-back, emulating a single large volume in the scene.
-     */
-    fun positionVolumeSlices(volumes: List<Volume>) {
-        val pixelToWorld = volumes.first().pixelToWorldRatio
-
-        var sliceIndex = 0
-        volumes.forEach { volume ->
-            val currentSlices = volume.getDimensions().z
-            logger.debug("Volume partition with z slices: $currentSlices")
-            volume.pixelToWorldRatio = pixelToWorld
-
-            volume.spatial().position = Vector3f(0f, 0f, 1.0f * (sliceIndex) * pixelToWorld)
-            sliceIndex += currentSlices
-        }
-    }
 }
diff --git a/src/main/kotlin/graphics/scenery/utils/extensions/VolumeUtils.kt b/src/main/kotlin/graphics/scenery/utils/extensions/VolumeUtils.kt
@@ -0,0 +1,25 @@
+package graphics.scenery.utils.extensions
+
+import graphics.scenery.RichNode
+import graphics.scenery.volumes.Volume
+import graphics.scenery.volumes.Volume.Companion.fromPathRawSplit
+import org.joml.Vector3f
+
+/**
+ * Positions [volumes] back-to-back without gaps, using their pixel-to-world ratio. Can, e.g., be used
+ * with [fromPathRawSplit] to load volume files greater than 2 GiB into sliced partitions and place
+ * the partitions back-to-back, emulating a single large volume in the scene.
+ */
+fun RichNode.positionVolumeSlices(volumes: List<Volume>) {
+    val pixelToWorld = volumes.first().pixelToWorldRatio
+
+    var sliceIndex = 0
+    volumes.forEach { volume ->
+        val currentSlices = volume.getDimensions().z
+        logger.debug("Volume partition with z slices: $currentSlices")
+        volume.pixelToWorldRatio = pixelToWorld
+
+        volume.spatial().position = Vector3f(0f, 0f, 1.0f * (sliceIndex) * pixelToWorld)
+        sliceIndex += currentSlices
+    }
+}
diff --git a/src/main/kotlin/graphics/scenery/volumes/Volume.kt b/src/main/kotlin/graphics/scenery/volumes/Volume.kt
@@ -36,6 +36,7 @@ import graphics.scenery.numerics.Random
 import graphics.scenery.utils.lazyLogger
 import graphics.scenery.utils.extensions.times
 import graphics.scenery.utils.forEachIndexedAsync
+import graphics.scenery.volumes.Volume.Companion.fromPathRawSplit
 import graphics.scenery.volumes.Volume.VolumeDataSource.SpimDataMinimalSource
 import io.scif.SCIFIO
 import io.scif.filters.ReaderFilter
@@ -982,11 +983,26 @@ open class Volume(
         }
 
         /**
-         * Reads raw volumetric data from a [file].
+         * Reads raw volumetric data from a [file], assuming the input
+         * data is 16bit Unsigned Int.
          *
          * Returns the new volume.
          */
-        @JvmStatic @JvmOverloads
+        @JvmStatic
+        fun <T: RealType<T>> fromPathRaw(
+            file: Path,
+            hub: Hub
+        ): BufferedVolume {
+            return fromPathRaw(file, hub, UnsignedShortType())
+        }
+
+        /**
+         * Reads raw volumetric data from a [file], with the [type] being
+         * explicitly specified.
+         *
+         * Returns the new volume.
+         */
+        @JvmStatic
         fun <T: RealType<T>> fromPathRaw(
             file: Path,
             hub: Hub,
@@ -1109,3 +1125,4 @@ open class Volume(
     }
 }
 
+
diff --git a/src/test/kotlin/graphics/scenery/tests/examples/cluster/ClusterExample.kt b/src/test/kotlin/graphics/scenery/tests/examples/cluster/ClusterExample.kt
@@ -1,27 +1,19 @@
 package graphics.scenery.tests.examples.cluster
 
-import org.joml.Vector3f
 import graphics.scenery.*
 import graphics.scenery.backends.Renderer
-import graphics.scenery.controls.InputHandler
 import graphics.scenery.controls.TrackedStereoGlasses
-import graphics.scenery.net.NodePublisher
-import graphics.scenery.net.NodeSubscriber
 import graphics.scenery.numerics.Random
 import graphics.scenery.primitives.Cone
 import graphics.scenery.proteins.Protein
 import graphics.scenery.proteins.RibbonDiagram
-import graphics.scenery.utils.Statistics
 import graphics.scenery.utils.extensions.minus
 import graphics.scenery.volumes.BufferedVolume
 import graphics.scenery.volumes.Colormap
 import graphics.scenery.volumes.TransferFunction
 import graphics.scenery.volumes.Volume
-import net.imglib2.type.numeric.integer.UnsignedByteType
-import net.imglib2.type.numeric.integer.UnsignedShortType
-import org.scijava.ui.behaviour.ClickBehaviour
+import org.joml.Vector3f
 import java.nio.file.Paths
-import kotlin.concurrent.thread
 import kotlin.math.PI
 import kotlin.math.floor
 import kotlin.math.roundToInt
@@ -103,7 +95,7 @@ class ClusterExample: SceneryBase("Clustered Volume Rendering example") {
        val volume: BufferedVolume
        val croc = false
        if(croc) {
-           volume = Volume.fromPathRaw(Paths.get(basepath + "Croc/104B_08_side1_647_25p.raw"), hub, UnsignedShortType())
+           volume = Volume.fromPathRaw(Paths.get(basepath + "Croc/104B_08_side1_647_25p.raw"), hub)
 
            volume.name = "volume"
            volume.colormap = Colormap.get("viridis") // jet, hot, rainbow, plasma, grays
@@ -120,7 +112,7 @@ class ClusterExample: SceneryBase("Clustered Volume Rendering example") {
            //volume.transferFunction.addControlPoint(0.1f, 0.5f)
            scene.addChild(volume)
        } else {
-           volume = Volume.fromPathRaw(Paths.get(basepath + "droso-royer-autopilot-transposed"), hub, UnsignedShortType())
+           volume = Volume.fromPathRaw(Paths.get(basepath + "droso-royer-autopilot-transposed"), hub)
 
            volume.name = "volume"
            volume.colormap = Colormap.get("hot") // jet, hot, rainbow, plasma, grays

diff --git a/src/test/kotlin/graphics/scenery/tests/examples/cluster/DemoReelExample.kt b/src/test/kotlin/graphics/scenery/tests/examples/cluster/DemoReelExample.kt
@@ -12,8 +12,6 @@ import graphics.scenery.attribute.material.Material
 import graphics.scenery.volumes.Colormap
 import graphics.scenery.volumes.TransferFunction
 import graphics.scenery.volumes.Volume
-import net.imglib2.type.numeric.integer.UnsignedByteType
-import net.imglib2.type.numeric.integer.UnsignedShortType
 import org.scijava.ui.behaviour.ClickBehaviour
 import java.nio.file.Paths
 import kotlin.concurrent.thread
@@ -71,8 +69,7 @@ class DemoReelExample: SceneryBase("Demo Reel") {
 
         val histoneVolume = Volume.fromPathRaw(
             Paths.get("$driveLetter:/ssd-backup-inauguration/CAVE_DATA/histones-isonet/stacks/default/"),
-            hub,
-            UnsignedShortType()
+            hub
         )
         histoneVolume.transferFunction = TransferFunction.ramp(0.1f, 1.0f)
         histoneVolume.colormap = Colormap.get("hot")
@@ -82,8 +79,7 @@ class DemoReelExample: SceneryBase("Demo Reel") {
 
         val drosophilaVolume = Volume.fromPathRaw(
             Paths.get("$driveLetter:/ssd-backup-inauguration/CAVE_DATA/droso-royer-autopilot-transposed/"),
-            hub,
-            UnsignedShortType()
+            hub
         )
         drosophilaVolume.spatial {
             rotation.rotateX(1.57f)
@@ -96,8 +92,7 @@ class DemoReelExample: SceneryBase("Demo Reel") {
 
         val retinaVolume = Volume.fromPathRaw(
             Paths.get("$driveLetter:/ssd-backup-inauguration/CAVE_DATA/retina_test2/"),
-            hub,
-            UnsignedShortType()
+            hub
         )
         retinaScene.addChild(retinaVolume)
         retinaScene.visible = false

diff --git a/src/test/kotlin/graphics/scenery/tests/examples/cluster/GiovannisExample.kt b/src/test/kotlin/graphics/scenery/tests/examples/cluster/GiovannisExample.kt
@@ -1,32 +1,21 @@
 package graphics.scenery.tests.examples.cluster
 
-import org.joml.Vector3f
 import graphics.scenery.*
 import graphics.scenery.backends.Renderer
-import graphics.scenery.controls.InputHandler
 import graphics.scenery.controls.TrackedStereoGlasses
 import graphics.scenery.controls.behaviours.GamepadClickBehaviour
 import graphics.scenery.controls.behaviours.GamepadRotationControl
-import graphics.scenery.net.NodePublisher
-import graphics.scenery.net.NodeSubscriber
-import graphics.scenery.numerics.Random
 import graphics.scenery.proteins.Protein
 import graphics.scenery.proteins.RibbonDiagram
-import graphics.scenery.utils.Statistics
-import graphics.scenery.utils.extensions.minus
 import graphics.scenery.volumes.BufferedVolume
 import graphics.scenery.volumes.Colormap
 import graphics.scenery.volumes.TransferFunction
 import graphics.scenery.volumes.Volume
-import net.imglib2.type.numeric.integer.UnsignedByteType
-import net.imglib2.type.numeric.integer.UnsignedShortType
 import net.java.games.input.Component
-import org.scijava.ui.behaviour.ClickBehaviour
+import org.joml.Vector3f
 import java.nio.file.Paths
 import kotlin.concurrent.thread
 import kotlin.math.PI
-import kotlin.math.floor
-import kotlin.math.roundToInt
 
 /**
  * Example to demonstrate rendering on a cluster. Will display a grid of geometric options,
@@ -105,7 +94,7 @@ class GiovannisExample: SceneryBase("Clustered Volume Rendering example, Giovann
 
         val croc = true
         if(croc) {
-            volume = Volume.fromPathRaw(Paths.get(basepath + "Croc/104B_08_side1_647_25p.raw"), hub, UnsignedShortType())
+            volume = Volume.fromPathRaw(Paths.get(basepath + "Croc/104B_08_side1_647_25p.raw"), hub)
 
             volume.name = "volume"
             volume.colormap = Colormap.get("hot") // jet, hot, rainbow, plasma, grays
@@ -125,7 +114,7 @@ class GiovannisExample: SceneryBase("Clustered Volume Rendering example, Giovann
             scene.addChild(volume)
             volume.origin = Origin.FrontBottomLeft
         } else {
-            volume = Volume.fromPathRaw(Paths.get(basepath + "droso-royer-autopilot-transposed"), hub, UnsignedShortType())
+            volume = Volume.fromPathRaw(Paths.get(basepath + "droso-royer-autopilot-transposed"), hub)
 
             volume.name = "volume"
             volume.colormap = Colormap.get("hot") // jet, hot, rainbow, plasma, grays

diff --git a/src/test/kotlin/graphics/scenery/tests/examples/volumes/SplitVolumeExample.kt b/src/test/kotlin/graphics/scenery/tests/examples/volumes/SplitVolumeExample.kt
@@ -4,6 +4,7 @@ import graphics.scenery.*
 import graphics.scenery.backends.Renderer
 import graphics.scenery.controls.TrackedStereoGlasses
 import graphics.scenery.attribute.material.Material
+import graphics.scenery.utils.extensions.positionVolumeSlices
 import graphics.scenery.volumes.Colormap
 import graphics.scenery.volumes.TransferFunction
 import graphics.scenery.volumes.Volume
@@ -50,8 +51,6 @@ class SplitVolumeExample: SceneryBase("Split volume data", 1280, 720) {
         val parent = pair.first as RichNode
         val volumeList = pair.second
 
-//        Volume.positionSlices(volumeList, volumeList.first().pixelToWorldRatio)
-
         parent.positionVolumeSlices(volumeList)
 
         volumeList.forEachIndexed{ i, volume->

diff --git a/src/test/kotlin/graphics/scenery/tests/examples/volumes/VolumeExample.kt b/src/test/kotlin/graphics/scenery/tests/examples/volumes/VolumeExample.kt
@@ -7,8 +7,6 @@ import graphics.scenery.attribute.material.Material
 import graphics.scenery.volumes.Colormap
 import graphics.scenery.volumes.TransferFunction
 import graphics.scenery.volumes.Volume
-import net.imglib2.type.numeric.integer.UnsignedByteType
-import net.imglib2.type.numeric.integer.UnsignedShortType
 import org.joml.Vector3f
 import java.nio.file.Paths
 import kotlin.concurrent.thread
@@ -48,7 +46,7 @@ class VolumeExample: SceneryBase("Volume Rendering example", 1280, 720) {
         s.material().diffuse = Vector3f(0.0f, 0.0f, 0.0f)
         scene.addChild(s)
 
-        val volume = Volume.fromPathRaw(Paths.get(getDemoFilesPath() + "/volumes/box-iso/"), hub, UnsignedShortType())
+        val volume = Volume.fromPathRaw(Paths.get(getDemoFilesPath() + "/volumes/box-iso/"), hub)
         volume.name = "volume"
         volume.colormap = Colormap.get("viridis")
         volume.spatial {