Fix volume rendering scaling

build.gradle.kts

@@ -45,7 +45,7 @@ dependencies {
         exclude("org.lwjgl")
     }
 
-    val sceneryVersion = "0.11.0"
+    val sceneryVersion = "0.11.1"
     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
@@ -113,6 +109,7 @@ import sc.iview.ui.CustomPropertyUI
 import sc.iview.ui.MainWindow
 import sc.iview.ui.SwingMainWindow
 import sc.iview.ui.TaskManager
+import ucar.units.ConversionException
 import java.awt.event.WindowListener
 import java.io.IOException
 import java.net.URL
@@ -811,19 +808,14 @@ 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
@@ -1386,18 +1378,26 @@ 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()).first { idx -> image.axis(idx).type().label == axisNames[axisIdx] }
             val inValue = image.axis(d).averageScale(0.0, 1.0)
             if (image.axis(d).unit() == null || d >= axes.size) {
                 voxelDims[axisIdx] = inValue.toFloat()
             } else {
-                val imageAxisUnit = image.axis(d).unit().replace("µ", "u")
-                val sciviewAxisUnit = axis(axisIdx)!!.unit().replace("µ", "u")
+                try {
+                    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()
+                } catch(e: IllegalArgumentException) {
+                    logger.warn(e.message + " - setting voxel scale for dimension $axisIdx to 1.0")
+                    voxelDims[axisIdx] = 1.0f
+                }
 
-                voxelDims[axisIdx] = unitService.value(inValue, imageAxisUnit, sciviewAxisUnit).toFloat()
             }
+
+            logger.debug("Dim for axis $d is ${voxelDims[axisIdx]}")
         }
         return voxelDims
     }
@@ -1513,7 +1513,7 @@ 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 +1534,11 @@ 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/demo/advanced/LoadCremiDatasetAndNeurons.kt

@@ -163,7 +163,7 @@ class LoadCremiDatasetAndNeurons : Command {
 
         val v = sciview.addVolume(nai.third, file.name) {
             origin = Origin.FrontBottomLeft
-            this.spatialOrNull()?.scale = Vector3f(0.08f, 0.08f, 5.0f)
+            this.spatialOrNull()?.scale = Vector3f(8f, 8f, 8f)
             transferFunction = TransferFunction.ramp(0.3f, 0.1f, 0.1f)
             // min 20, max 180, color map fire
 

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

@@ -87,9 +87,10 @@ class LoadFlybrainOutOfCore : Command {
         log.info("Done.")
 
         val transform = AffineTransform3D()
-        val sx = imp.calibration.pixelWidth
-        val sy = imp.calibration.pixelHeight
-        val sz = imp.calibration.pixelDepth  * 10
+        val scaleFactor = 40
+        val sx = imp.calibration.pixelWidth * 40
+        val sy = imp.calibration.pixelHeight * 40
+        val sz = imp.calibration.pixelDepth * 40
         transform[sx, 0.0, 0.0, 0.0, 0.0, sy, 0.0, 0.0, 0.0, 0.0, sz] = 0.0
         val type = UnsignedShortType()
 

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

@@ -32,6 +32,7 @@ import graphics.scenery.*
 import graphics.scenery.attribute.material.HasMaterial
 import graphics.scenery.primitives.Line
 import graphics.scenery.primitives.TextBoard
+import graphics.scenery.volumes.Colormap
 import graphics.scenery.volumes.Colormap.Companion.fromColorTable
 import graphics.scenery.volumes.SlicingPlane
 import graphics.scenery.volumes.Volume
@@ -138,17 +139,8 @@ 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 = "Color map", choices = [], callback = "updateNodeProperties", style = "group:Volume")
-    private var colormapName: String = "Fire.lut"
-
-    @Parameter(label = " ", style = "group:Volume")
-    private var colormap = dummyColorTable
+    @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 = "AO steps", style = NumberWidget.SPINNER_STYLE+"group:Volume", callback = "updateNodeProperties")
     private val occlusionSteps = 0
@@ -234,6 +226,8 @@ class Properties : InteractiveCommand() {
      */
     override fun run() {}
     fun setSceneNode(node: Node?) {
+        Colormap.Companion.lutService = sciView.scijavaContext?.getService(LUTService::class.java)
+
         currentSceneNode = node
         updateCommandFields()
     }
@@ -378,47 +372,31 @@ class Properties : InteractiveCommand() {
             slicingModeInput.setChoices(slicingMethods)
             slicingMode = slicingModeChoices[Volume.SlicingMode.values().indexOf(node .slicingMode)].toString()
 
-            val lutNameItem = info.getMutableInput("colormapName", String::class.java)
-            lutNameItem.choices = sciView.getAvailableLUTs()
-            val cachedColormapName = node.metadata["sciview.colormapName"] as? String
-
-            if(cachedColormapName != null && sciView.getLUT(cachedColormapName) != null) {
-                colormapName = cachedColormapName
-            }
-
-            try {
-                val cm = sciView.getLUT(colormapName)
-                // Ensure the node matches
-                node.colormap = fromColorTable(cm)
-                node.metadata["sciview.colormapName"] = colormapName
-
-                colormap = cm
-            } catch (ioe: IOException) {
-                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 {
+                // Warning! The java.lang prefix needs to be here, otherwise the compiler
+                // reverts to the Kotlin types and you'll end up with interesting error messages
+                // like "float does not match type float" ;-)
                 maybeRemoveInput("timepoint", java.lang.Integer::class.java)
                 maybeRemoveInput("playPauseButton", Button::class.java)
                 maybeRemoveInput("playSpeed", java.lang.Integer::class.java)
             }
 
             maybeRemoveInput("colour", ColorRGB::class.java)
         } else {
+            // Warning! The java.lang prefix needs to be here, otherwise the compiler
+            // reverts to the Kotlin types and you'll end up with interesting error messages
+            // like "float does not match type float" ;-)
+            maybeRemoveInput("pixelToWorldRatio", java.lang.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("colormap", ColorTable::class.java)
             maybeRemoveInput("colormapName", String::class.java)
@@ -489,7 +467,7 @@ 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
@@ -530,22 +508,13 @@ class Properties : InteractiveCommand() {
             node.intensity = intensity
         }
         if (node is Volume) {
-            try {
-                val cm = sciView.getLUT(colormapName)
-                node.colormap = fromColorTable(cm!!)
-                node.metadata["sciview.colormapName"] = colormapName
-                log.info("Setting new colormap to $colormapName / $cm")
-
-                colormap = cm
-            } catch (ioe: IOException) {
-                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()
@@ -624,32 +593,7 @@ class Properties : InteractiveCommand() {
     companion object {
         private const val PI_NEG = "-3.142"
         private const val PI_POS = "3.142"
-        private var dummyColorTable: ColorTable? = null
 
         private val inputModuleMaps = ConcurrentHashMap<ModuleItem<*>, Module>()
-
-        init {
-            dummyColorTable = object : ColorTable {
-                override fun lookupARGB(v: Double, v1: Double, v2: Double): Int {
-                    return 0
-                }
-
-                override fun getComponentCount(): Int {
-                    return 0
-                }
-
-                override fun getLength(): Int {
-                    return 0
-                }
-
-                override fun get(i: Int, i1: Int): Int {
-                    return 0
-                }
-
-                override fun getResampled(i: Int, i1: Int, i2: Int): Int {
-                    return 0
-                }
-            }
-        }
     }
 }