Merge pull request #499 from scenerygraphics/lut-fixes

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

@@ -112,6 +112,7 @@ import sc.iview.ui.TaskManager
 import tpietzsch.example2.VolumeViewerOptions
 import java.awt.event.WindowListener
 import java.io.IOException
+import java.net.URL
 import java.nio.ByteBuffer
 import java.nio.FloatBuffer
 import java.time.LocalDate
@@ -122,6 +123,9 @@ import java.util.function.Consumer
 import java.util.function.Function
 import java.util.function.Predicate
 import java.util.stream.Collectors
+import kotlin.collections.ArrayList
+import kotlin.collections.HashMap
+import kotlin.collections.LinkedHashMap
 import javax.swing.JOptionPane
 import kotlin.math.cos
 import kotlin.math.sin
@@ -134,6 +138,7 @@ import kotlin.math.sin
 // we suppress unused warnings here because @Parameter-annotated fields
 // get updated automatically by SciJava.
 class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
+
     val sceneryPanel = arrayOf<SceneryPanel?>(null)
 
     /*
@@ -216,6 +221,11 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
      * Set the SciJava Display
      */  var display: Display<*>? = null
 
+    /**
+     * List of available LUTs for caching
+     */
+    private var availableLUTs = LinkedHashMap<String, URL>()
+
     /**
      * Return the current SceneryJPanel. This is necessary for custom context menus
      * @return panel the current SceneryJPanel
@@ -899,6 +909,7 @@ class SciView : SceneryBase, CalibratedRealInterval<CalibratedAxis> {
         n.let {
             objectService.addObject(n)
             eventService.publish(NodeAddedEvent(n))
+            (mainWindow as SwingMainWindow).nodePropertyEditor.updateProperties(n, rebuild = true)
         }
         return n
     }
@@ -1418,7 +1429,8 @@ fun deleteNode(node: Node?, activePublish: Boolean = true) {
                                        numTimepoints: Int,
                                        name: String = "Volume",
                                        vararg voxelDimensions: Float,
-                                       block: Volume.() -> Unit = {}): Volume {
+                                       block: Volume.() -> Unit = {},
+                                       colormapName: String = "Fire.lut"): Volume {
         var timepoints = numTimepoints
         var cacheControl: CacheControl? = null
 
@@ -1462,6 +1474,10 @@ fun deleteNode(node: Node?, activePublish: Boolean = true) {
         val bg = BoundingGrid()
         bg.node = v
 
+        // Set default colormap
+        v.metadata["sciview.colormapName"] = colormapName
+        v.colormap = Colormap.fromColorTable(getLUT(colormapName))
+
         imageToVolumeMap[image] = v
         return addNode(v, block = block)
     }
@@ -1745,6 +1761,41 @@ fun deleteNode(node: Node?, activePublish: Boolean = true) {
         println(scijavaContext!!.serviceIndex)
     }
 
+    /**
+     * Return the color table corresponding to the [lutName]
+     * @param lutName a String represening an ImageJ style LUT name, like Fire.lut
+     * @return a [ColorTable] corresponding to the LUT or null if LUT not available
+     */
+    fun getLUT(lutName: String = "Fire.lut"): ColorTable {
+        try {
+            refreshLUTs()
+            var lutResult = availableLUTs[lutName]
+            return lutService.loadLUT(lutResult)
+        } catch (e: IOException) {
+            log.error("LUT $lutName not available")
+            e.printStackTrace()
+            throw e
+        }
+    }
+
+    /**
+     * Refresh the cache of available LUTs fetched from LutService
+     */
+    private fun refreshLUTs() {
+        if(availableLUTs.isEmpty()) {
+            availableLUTs.putAll(lutService.findLUTs().entries.sortedBy { it.key }.map { it.key to it.value })
+        }
+    }
+
+    /**
+     * Return a list of available LUTs/colormaps
+     * @return a list of LUT names
+     */
+    fun getAvailableLUTs(): List<String> {
+        refreshLUTs()
+        return availableLUTs.map {entry -> entry.key}
+    }
+
     companion object {
         //bounds for the controls
         const val FPSSPEED_MINBOUND_SLOW = 0.01f

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

@@ -224,8 +224,6 @@ class Properties : InteractiveCommand() {
     @Parameter
     private lateinit var log: LogService
 
-    private var availableLUTs = LinkedHashMap<String, URL>()
-
     /**
      * Nothing happens here, as cancelling the dialog is not possible.
      */
@@ -242,13 +240,6 @@ class Properties : InteractiveCommand() {
     }
 
     protected fun initValues() {
-        if (colormap == null) {
-            try {
-                lutService.loadLUT(availableLUTs["Red.lut"])
-            } catch (ioe: IOException) {
-                System.err.println("IOException while loading Red.lut")
-            }
-        }
         rebuildSceneObjectChoiceList()
         refreshSceneNodeInDialog()
         updateCommandFields()
@@ -345,10 +336,6 @@ class Properties : InteractiveCommand() {
     /** Updates command fields to match current scene node properties.  */
     @Suppress("PLATFORM_CLASS_MAPPED_TO_KOTLIN")
     fun updateCommandFields() {
-        if(availableLUTs.isEmpty()) {
-            availableLUTs.putAll(lutService.findLUTs().entries.sortedBy { it.key }.map { it.key to it.value })
-        }
-
         val node = currentSceneNode ?: return
 
         fieldsUpdating = true
@@ -397,13 +384,24 @@ class Properties : InteractiveCommand() {
             slicingMode = slicingModeChoices[Volume.SlicingMode.values().indexOf(node .slicingMode)].toString()
 
             val lutNameItem = info.getMutableInput("colormapName", String::class.java)
-            lutNameItem.choices = availableLUTs.keys.toMutableList()
-            val cachedColormapName = node.metadata["sciview.colormap-name"] as? String
+            lutNameItem.choices = sciView.getAvailableLUTs()
+            val cachedColormapName = node.metadata["sciview.colormapName"] as? String
 
-            if(cachedColormapName != null && availableLUTs[cachedColormapName] != null) {
+            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")
+            }
+
             min = node.converterSetups[0].displayRangeMin.toInt()
             max = node.converterSetups[0].displayRangeMax.toInt()
 
@@ -538,9 +536,9 @@ class Properties : InteractiveCommand() {
                 node.renderingMethod = Volume.RenderingMethod.values()[mode]
             }
             try {
-                val cm = lutService.loadLUT(availableLUTs[colormapName])
-                node.colormap = fromColorTable(cm)
-                node.metadata["sciview.colormap-name"] = colormapName
+                val cm = sciView.getLUT(colormapName)
+                node.colormap = fromColorTable(cm!!)
+                node.metadata["sciview.colormapName"] = colormapName
                 log.info("Setting new colormap to $colormapName / $cm")
 
                 colormap = cm

src/main/kotlin/sc/iview/commands/view/SetLUT.kt

@@ -29,21 +29,22 @@
 package sc.iview.commands.view
 
 import graphics.scenery.Node
-import net.imagej.lut.LUTService
-import net.imglib2.display.AbstractArrayColorTable
 import net.imglib2.display.ColorTable
 import org.scijava.command.Command
+import org.scijava.command.CommandService
 import org.scijava.command.DynamicCommand
 import org.scijava.plugin.Menu
 import org.scijava.plugin.Parameter
 import org.scijava.plugin.Plugin
+import org.scijava.prefs.PrefService
 import sc.iview.SciView
 import sc.iview.commands.MenuWeights.VIEW
 import sc.iview.commands.MenuWeights.VIEW_SET_LUT
+import sc.iview.commands.demo.basic.VolumeRenderDemo
 import java.io.IOException
-import java.net.URL
 import java.util.*
 
+
 /**
  * Command to set the currently used Look Up Table (LUT). This is a colormap for the volume.
  *
@@ -55,38 +56,49 @@ class SetLUT : DynamicCommand() {
     @Parameter
     private lateinit var sciView: SciView
 
-    @Parameter
-    private lateinit var lutService: LUTService
-
     @Parameter(label = "Node")
     private lateinit var node: Node
 
-    @Parameter(label = "Selected LUT", choices = [], callback = "lutNameChanged")
+    @Parameter(label = "Selected LUT", choices = [], callback = "lutNameChanged", initializer = "initLutName")
     private lateinit var lutName: String
 
     @Parameter(label = "LUT Selection")
     private lateinit var colorTable: ColorTable
 
+    @Parameter
+    private lateinit var prefs: PrefService
+
+    protected fun initLutName() {
+        lutName = "Fire.lut"
+    }
+
     protected fun lutNameChanged() {
-        val lutNameItem = info.getMutableInput("lutName", String::class.java)
         try {
-            colorTable = lutService.loadLUT(lutService.findLUTs()[lutNameItem.toString()])
+            colorTable = sciView.getLUT(lutName)!!
         } catch (e: IOException) {
             e.printStackTrace()
+        } catch (e: Exception) {
+            e.printStackTrace()
         }
     }
 
     override fun initialize() {
+        val lutNameItem = info.getMutableInput("lutName", String::class.java)
+        lutNameItem.choices = sciView.getAvailableLUTs()
+
+        var persistLutName = prefs.get(SetLUT::class.java, "lutName");
+
         try {
-            colorTable = lutService.loadLUT(lutService.findLUTs()["Red.lut"])
+            colorTable = sciView.getLUT(persistLutName)!!
         } catch (e: IOException) {
             e.printStackTrace()
         }
-        val lutNameItem = info.getMutableInput("lutName", String::class.java)
-        lutNameItem.choices = ArrayList(lutService.findLUTs().keys)
     }
 
     override fun run() {
+        node.metadata["sciview.colormapName"] = lutName
         sciView.setColormap(node, colorTable)
+        // Trigger an update to the UI for the colormap
+        sciView.publishNode(node)
     }
 }

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

@@ -281,7 +281,7 @@ class SwingNodePropertyEditor(private val sciView: SciView) : UIComponent<JPanel
     private val updateLock = ReentrantLock()
 
     /** Generates a properties panel for the given node.  */
-    fun updateProperties(sceneNode: Node?) {
+    fun updateProperties(sceneNode: Node?, rebuild: Boolean = false) {
         if (sceneNode == null) {
             try {
                 if (updateLock.tryLock() || updateLock.tryLock(200, TimeUnit.MILLISECONDS)) {
@@ -295,7 +295,7 @@ class SwingNodePropertyEditor(private val sciView: SciView) : UIComponent<JPanel
         }
         try {
             if (updateLock.tryLock() || updateLock.tryLock(200, TimeUnit.MILLISECONDS)) {
-                if (currentNode === sceneNode && currentProperties != null) {
+                if (!rebuild && currentNode === sceneNode && currentProperties != null) {
                     currentProperties!!.updateCommandFields()
                     inputPanel.refresh()
                     updateLock.unlock()
@@ -347,6 +347,7 @@ class SwingNodePropertyEditor(private val sciView: SciView) : UIComponent<JPanel
                     textArea.text = "<html><pre>$stackTrace</pre>"
                     updatePropertiesPanel(textArea)
                 }
+
                 updateLock.unlock()
             }
         } catch (e: InterruptedException) {
@@ -418,9 +419,7 @@ class SwingNodePropertyEditor(private val sciView: SciView) : UIComponent<JPanel
         if (newPath != null) {
             tree.selectionPath = newPath
             tree.scrollPathToVisible(newPath)
-            if (node !== sciView.activeNode) {
-                updateProperties(node)
-            }
+            updateProperties(node)
         }
     }