Fix volume rendering scaling

build.gradle.kts

@@ -45,7 +45,7 @@ dependencies {
         exclude("org.lwjgl")
     }
 
-    val sceneryVersion = "0.11.0"
+    val sceneryVersion = "4e8f7ed"
     api("graphics.scenery:scenery:$sceneryVersion") {
         version { strictly(sceneryVersion) }
         exclude("org.biojava.thirdparty", "forester")

src/main/kotlin/sc/iview/SciView.kt

@@ -63,7 +63,6 @@ import graphics.scenery.volumes.Volume.Companion.fromXML
 import graphics.scenery.volumes.Volume.Companion.setupId
 import graphics.scenery.volumes.Volume.VolumeDataSource.RAISource
 import io.scif.SCIFIOService
-import io.scif.services.DatasetIOService
 import net.imagej.Dataset
 import net.imagej.ImageJService
 import net.imagej.axis.CalibratedAxis
@@ -81,12 +80,9 @@ import net.imglib2.img.Img
 import net.imglib2.img.array.ArrayImgs
 import net.imglib2.realtransform.AffineTransform3D
 import net.imglib2.type.numeric.ARGBType
-import net.imglib2.type.numeric.NumericType
 import net.imglib2.type.numeric.RealType
 import net.imglib2.type.numeric.integer.UnsignedByteType
 import net.imglib2.view.Views
-import org.janelia.saalfeldlab.n5.N5FSReader
-import org.janelia.saalfeldlab.n5.imglib2.N5Utils
 import org.joml.Quaternionf
 import org.joml.Vector3f
 import org.scijava.Context
@@ -811,19 +807,14 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
                     is Mesh -> addMesh(data, name = name)
                     is PointCloud -> addPointCloud(data, name)
                     is graphics.scenery.Mesh -> addMesh(data, name = name)
-                    is Dataset -> addVolume(data, floatArrayOf(1.0f, 1.0f, 1.0f))
-                    //            is RandomAccessibleInterval<*> -> {
-                    //                val t = data.randomAccess().get()
-                    //                addVolume(data, source, floatArrayOf(1.0f, 1.0f, 1.0f))
-                    //            }
+                    is Dataset -> addVolume(data)
                     is List<*> -> {
-                        val list = data
-                        require(!list.isEmpty()) { "Data source '$source' appears empty." }
-                        val element = list[0]
+                        require(data.isNotEmpty()) { "Data source '$source' appears empty." }
+                        val element = data[0]
                         if(element is RealLocalizable) {
                             // NB: For now, we assume all elements will be RealLocalizable.
                             // Highly likely to be the case, barring antagonistic importers.
-                            val points = list as List<RealLocalizable>
+                            val points = data as List<RealLocalizable>
                             addPointCloud(points, name)
                         } else {
                             val type = if(element == null) "<null>" else element.javaClass.name
@@ -1386,17 +1377,19 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
      */
     fun getSciviewScale(image: Dataset): FloatArray {
         val voxelDims = FloatArray(3)
-        var axisNames = arrayOf("X", "Y", "Z")
+        val axisNames = arrayOf("X", "Y", "Z")
         for (axisIdx in voxelDims.indices) {
-            var d = (0 until image.numDimensions()).filter { idx -> image.axis(idx).type().label == axisNames[axisIdx] }.first()
+            val d = (0 until image.numDimensions()).filter { idx -> image.axis(idx).type().label == axisNames[axisIdx] }.first()
             val inValue = image.axis(d).averageScale(0.0, 1.0)
             if (image.axis(d).unit() == null || d >= axes.size) {
+                logger.debug("Dim for axis $d is ${inValue.toFloat()}")
                 voxelDims[axisIdx] = inValue.toFloat()
             } else {
                 val imageAxisUnit = image.axis(d).unit().replace("µ", "u")
                 val sciviewAxisUnit = axis(axisIdx)!!.unit().replace("µ", "u")
 
                 voxelDims[axisIdx] = unitService.value(inValue, imageAxisUnit, sciviewAxisUnit).toFloat()
+                logger.debug("Dim for axis $d is ${voxelDims[axisIdx]}")
             }
         }
         return voxelDims
@@ -1513,7 +1506,7 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
         image.min(minPt)
         imageRA.setPosition(minPt)
         val voxelType = imageRA.get()!!.createVariable() as T
-        println("addVolume " + image.numDimensions() + " interval " + image as Interval)
+        logger.info("Adding ${image.numDimensions()}-dimensional volume with type ${voxelType.javaClass.simpleName} (${image as Interval}) with voxel dimensions ${voxelDimensions.joinToString("/")}")
 
         //int numTimepoints = 1;
         if (image.numDimensions() > 3) {
@@ -1534,11 +1527,11 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
         val options = VolumeViewerOptions()
         val v: Volume = RAIVolume(ds, options, hub)
         // Note we override scenery's default scale of mm
-        // v.pixelToWorldRatio = 0.1f
+//        v.pixelToWorldRatio = 0.01f
         v.name = name
         v.metadata["sources"] = sources
         v.metadata["VoxelDimensions"] = voxelDimensions
-        v.spatial().scale = Vector3f(voxelDimensions[0], voxelDimensions[1], voxelDimensions[2]) * v.pixelToWorldRatio
+        v.spatial().scale = Vector3f(voxelDimensions[0], voxelDimensions[1], voxelDimensions[2])
         val tf = v.transferFunction
         val rampMin = 0f
         val rampMax = 0.1f

src/main/kotlin/sc/iview/commands/add/AddVolume.kt

@@ -83,13 +83,13 @@ class AddVolume : Command {
 
     private fun <RealType> splitChannels(img: Img<RealType>, splitChannelDimension: Int): List<RandomAccessibleInterval<RealType>> {
         // Ensure we're safe in the dimension we choose
-        var splitDim = max(min(img.numDimensions() - 1, splitChannelDimension), 0)
+        val splitDim = max(min(img.numDimensions() - 1, splitChannelDimension), 0)
 
         val numChannels = img.dimension(splitDim)
         val channelIntervals = mutableListOf<RandomAccessibleInterval<RealType>>()
 
         for (channel in 0 until numChannels) {
-            val interval = Views.hyperSlice(img, splitDim, channel.toLong()) as RandomAccessibleInterval<RealType>
+            val interval = Views.hyperSlice(img, splitDim, channel) as RandomAccessibleInterval<RealType>
             channelIntervals.add(interval)
         }
 
@@ -101,13 +101,13 @@ class AddVolume : Command {
             setVoxelDimension()
 
         if (splitChannels && image.numDimensions() > 3) {
-            var splitDim = ((0 until image.numDimensions()).filter { d -> (image.imgPlus.axis(d) as CalibratedAxis).type().label == "Channel" }).first()
-            var channels = splitChannels(image, splitDim)
+            val splitDim = ((0 until image.numDimensions()).filter { d -> (image.imgPlus.axis(d) as CalibratedAxis).type().label == "Channel" }).first()
+            val channels = splitChannels(image, splitDim)
 
             for (ch in channels.indices) {
-                var channel = channels[ch]
-                var v = sciView.addVolume(channel as RandomAccessibleInterval<out RealType<*>>, name = image.name + "-ch$ch", voxelDimensions = floatArrayOf(voxelWidth, voxelHeight, voxelDepth), block = {})
-                var lut = splitChannelLuts[ch % splitChannelLuts.size]
+                val channel = channels[ch]
+                val v = sciView.addVolume(channel as RandomAccessibleInterval<out RealType<*>>, name = image.name + "-ch$ch", voxelDimensions = floatArrayOf(voxelWidth, voxelHeight, voxelDepth), block = {})
+                val lut = splitChannelLuts[ch % splitChannelLuts.size]
                 sciView.setColormap(v, lut)
             }
         } else {

src/main/kotlin/sc/iview/commands/edit/Properties.kt

@@ -138,11 +138,8 @@ class Properties : InteractiveCommand() {
     @Parameter(label = "Speed", min = "1", max = "10", style = NumberWidget.SCROLL_BAR_STYLE + ",group:Volume", persist = false)
     private var playSpeed = 4
 
-    @Parameter(label = "Min", callback = "updateNodeProperties", style = "group:Volume")
-    private var min = 0
-
-    @Parameter(label = "Max", callback = "updateNodeProperties", style = "group:Volume")
-    private var max = 255
+    @Parameter(label = "Pixel-to-world ratio", min = "0.00001f", max = "1000000.0f", style = NumberWidget.SPINNER_STYLE + ",group:Volume", persist = false, callback = "updateNodeProperties")
+    private var pixelToWorldRatio: Float = 0.001f
 
     @Parameter(label = "Color map", choices = [], callback = "updateNodeProperties", style = "group:Volume")
     private var colormapName: String = "Fire.lut"
@@ -397,33 +394,30 @@ class Properties : InteractiveCommand() {
                 log.error("Could not load LUT $colormapName")
             }
 
+            pixelToWorldRatio = node.pixelToWorldRatio
             dimensions = "${node.getDimensions().x}x${node.getDimensions().y}x${node.getDimensions().z}"
 
-            min = node.converterSetups[0].displayRangeMin.toInt()
-            max = node.converterSetups[0].displayRangeMax.toInt()
-
             val maxTimepoint = node.timepointCount - 1
             if(maxTimepoint > 0) {
                 timepoint = node.currentTimepoint
-                val timepointInput = info.getMutableInput("timepoint", java.lang.Integer::class.java)
-                timepointInput.minimumValue = java.lang.Integer.valueOf(0) as java.lang.Integer
-                timepointInput.maximumValue = java.lang.Integer.valueOf(maxTimepoint) as java.lang.Integer
+                val timepointInput = info.getMutableInput("timepoint", Integer::class.java)
+                timepointInput.minimumValue = Integer.valueOf(0) as Integer
+                timepointInput.maximumValue = Integer.valueOf(maxTimepoint) as Integer
             } else {
-                maybeRemoveInput("timepoint", java.lang.Integer::class.java)
+                maybeRemoveInput("timepoint", Integer::class.java)
                 maybeRemoveInput("playPauseButton", Button::class.java)
-                maybeRemoveInput("playSpeed", java.lang.Integer::class.java)
+                maybeRemoveInput("playSpeed", Integer::class.java)
             }
 
             maybeRemoveInput("colour", ColorRGB::class.java)
         } else {
+            maybeRemoveInput("pixelToWorldRatio", Float::class.java)
             maybeRemoveInput("slicingMode", String::class.java)
-            maybeRemoveInput("min", java.lang.Integer::class.java)
-            maybeRemoveInput("max", java.lang.Integer::class.java)
-            maybeRemoveInput("timepoint", java.lang.Integer::class.java)
+            maybeRemoveInput("timepoint", Integer::class.java)
             maybeRemoveInput("colormap", ColorTable::class.java)
             maybeRemoveInput("colormapName", String::class.java)
             maybeRemoveInput("playPauseButton", Button::class.java)
-            maybeRemoveInput("playSpeed", java.lang.Integer::class.java)
+            maybeRemoveInput("playSpeed", Integer::class.java)
             maybeRemoveInput("dimensions", java.lang.String::class.java)
         }
 
@@ -489,7 +483,7 @@ class Properties : InteractiveCommand() {
         if (node is Line){
             edgeWidth = node.edgeWidth.toInt()
         } else {
-            maybeRemoveInput("edgeWidth", java.lang.Integer::class.java)
+            maybeRemoveInput("edgeWidth", Integer::class.java)
         }
 
         name = node.name
@@ -541,11 +535,12 @@ class Properties : InteractiveCommand() {
                 log.error("Could not load LUT $colormapName")
             }
             node.goToTimepoint(timepoint)
-            node.converterSetups[0].setDisplayRange(min.toDouble(), max.toDouble())
             val slicingModeIndex = slicingModeChoices.indexOf(Volume.SlicingMode.valueOf(slicingMode))
             if (slicingModeIndex != -1) {
                 node.slicingMode = Volume.SlicingMode.values()[slicingModeIndex]
             }
+            node.pixelToWorldRatio = pixelToWorldRatio
+            node.spatial().needsUpdateWorld = true
         }
         if (node is Camera) {
             val scene = node.getScene()

src/main/kotlin/sc/iview/ui/SwingMainWindow.kt

@@ -32,8 +32,8 @@ import com.formdev.flatlaf.FlatLightLaf
 import graphics.scenery.Node
 import graphics.scenery.SceneryElement
 import graphics.scenery.backends.Renderer
-import graphics.scenery.utils.lazyLogger
 import graphics.scenery.utils.SceneryJPanel
+import graphics.scenery.utils.lazyLogger
 import org.joml.Vector2f
 import org.scijava.menu.MenuService
 import org.scijava.ui.swing.menu.SwingJMenuBarCreator
@@ -42,14 +42,19 @@ import sc.iview.SciViewService
 import sc.iview.SplashLabel
 import sc.iview.Utils
 import java.awt.*
+import java.awt.datatransfer.DataFlavor
+import java.awt.dnd.DnDConstants
+import java.awt.dnd.DropTarget
+import java.awt.dnd.DropTargetDropEvent
 import java.awt.event.*
+import java.io.File
 import java.util.*
 import javax.script.ScriptException
 import javax.swing.*
-import javax.swing.Timer
 import kotlin.concurrent.thread
 import kotlin.math.roundToInt
 
+
 /**
  * Class for Swing-based main window.
  *
@@ -243,6 +248,31 @@ class SwingMainWindow(val sciview: SciView) : MainWindow {
             glassPane.repaint()
 
             sciview.sceneryPanel[0] = sceneryJPanel
+
+            // attach drag-and-drop handler to enable dropping of e.g. volume files onto the viewport
+            sceneryJPanel.dropTarget = object: DropTarget() {
+                override fun drop(evt: DropTargetDropEvent?) {
+                    if(evt == null) {
+                        return
+                    }
+
+                    try {
+                        evt.acceptDrop(DnDConstants.ACTION_COPY)
+                        val files = evt.transferable.getTransferData(DataFlavor.javaFileListFlavor) as? List<File>
+                            ?: return
+
+                        files.forEach { file ->
+                            logger.info("$file dropped onto sciview, trying to open 👍")
+                            sciview.open(file.absolutePath)
+                        }
+
+                        evt.dropComplete(true)
+                    } catch(ex: Exception) {
+                        ex.printStackTrace()
+                    }
+                }
+            }
+
             val renderer = Renderer.createRenderer(
                     sciview.hub,
                     sciview.applicationName,