Update numass to match dev

build.gradle

@@ -1,11 +1,17 @@
 buildscript {
-    ext.kotlin_version = "1.2.30"
+    ext.kotlin_version = "1.2.31"
-}
+    repositories {
+        jcenter()
+        maven {
+            url  "https://dl.bintray.com/kotlin/kotlin-eap"
+        }
+    }
 
-plugins {
+    dependencies {
-    id "org.jetbrains.kotlin.jvm" version "1.2.30" apply false
+        classpath "org.jetbrains.dokka:dokka-gradle-plugin:0.9.16"
+        classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlin_version"
+    }
 }
-
 allprojects{
     apply plugin: 'idea'
     apply plugin: 'java'

numass-control/cryotemp/src/main/kotlin/inr/numass/control/cryotemp/PKT8Channel.kt

@@ -16,12 +16,12 @@
 
 package inr.numass.control.cryotemp
 
+import hep.dataforge.Named
 import hep.dataforge.kodex.buildMeta
 import hep.dataforge.kodex.stringValue
 import hep.dataforge.meta.Meta
 import hep.dataforge.meta.MetaBuilder
 import hep.dataforge.meta.Metoid
-import hep.dataforge.names.Named
 
 
 internal fun createChannel(name: String): PKT8Channel =
@@ -51,11 +51,7 @@ internal fun createChannel(meta: Meta): PKT8Channel {
  */
 class PKT8Channel(override val meta: Meta, private val func: (Double) -> Double) : Named, Metoid {
 
-    private val _name: String by meta.stringValue()
+    override val name: String by meta.stringValue()
-
-    override fun getName(): String {
-        return _name
-    }
 
     fun description(): String {
         return meta.getString("description", "")

numass-core/src/main/kotlin/inr/numass/data/NumassDataUtils.kt

@@ -19,7 +19,7 @@ import kotlin.streams.asSequence
  * Created by darksnake on 30-Jan-17.
  */
 object NumassDataUtils {
-    fun join(name: String, sets: Collection<NumassSet>): NumassSet {
+    fun join(setName: String, sets: Collection<NumassSet>): NumassSet {
         return object : NumassSet {
             override val points: Stream<out NumassPoint> by lazy {
                 val points = sets.stream().flatMap<NumassPoint> { it.points }
@@ -33,9 +33,7 @@ object NumassDataUtils {
                 metaBuilder
             }
 
-            override fun getName(): String {
+            override val name = setName
-                return name
-            }
         }
     }
 

numass-core/src/main/kotlin/inr/numass/data/api/NumassSet.kt

@@ -5,9 +5,9 @@
  */
 package inr.numass.data.api
 
+import hep.dataforge.Named
 import hep.dataforge.kodex.toList
 import hep.dataforge.meta.Metoid
-import hep.dataforge.names.Named
 import hep.dataforge.providers.Provider
 import hep.dataforge.providers.Provides
 import hep.dataforge.providers.ProvidesNames

numass-core/src/main/kotlin/inr/numass/data/legacy/NumassDatFile.kt

@@ -23,7 +23,7 @@ import java.util.stream.Stream
  * Created by darksnake on 08.07.2017.
  */
 class NumassDatFile @Throws(IOException::class)
-constructor(private val name: String, private val path: Path, meta: Meta) : NumassSet {
+constructor(override val name: String, private val path: Path, meta: Meta) : NumassSet {
     override val meta: Meta
 
     private val hVdev: Double
@@ -57,10 +57,6 @@ constructor(private val name: String, private val path: Path, meta: Meta) : Numa
                 .build()
     }
 
-    override fun getName(): String {
-        return name
-    }
-
     private fun hasUset(): Boolean {
         return meta.getBoolean("dat.uSet", true)
     }

numass-core/src/main/kotlin/inr/numass/data/storage/NumassDataFactory.kt

@@ -2,7 +2,7 @@ package inr.numass.data.storage
 
 import hep.dataforge.context.Context
 import hep.dataforge.data.DataFactory
-import hep.dataforge.data.DataTree
+import hep.dataforge.data.DataNodeEditor
 import hep.dataforge.meta.Meta
 import hep.dataforge.storage.commons.StorageManager
 import hep.dataforge.storage.commons.StorageUtils
@@ -13,12 +13,10 @@ import inr.numass.data.api.NumassSet
  */
 class NumassDataFactory : DataFactory<NumassSet>(NumassSet::class.java) {
 
-    override fun getName(): String {
+    override val name= "numass"
-        return "numass"
-    }
 
 
-    override fun fill(builder: DataTree.Builder<NumassSet>, context: Context, meta: Meta) {
+    override fun fill(builder: DataNodeEditor<NumassSet>, context: Context, meta: Meta) {
         val newMeta = meta.builder.setValue("type", "numass")
         val storage = context.load(StorageManager::class.java, Meta.empty()).buildStorage(newMeta)
         StorageUtils.loaderStream(storage).forEach { loader ->

numass-main/src/main/java/inr/numass/WorkspaceTest.java

@@ -1,32 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass;
-
-import hep.dataforge.meta.MetaBuilder;
-import hep.dataforge.storage.commons.StorageDataFactory;
-import hep.dataforge.workspace.BasicWorkspace;
-import hep.dataforge.workspace.Workspace;
-
-/**
- *
- * @author Alexander Nozik
- */
-public class WorkspaceTest {
-
-    /**
-     * @param args the command line arguments
-     */
-    public static void main(String[] args) {
-        
-        String storagepath = "D:\\Work\\Numass\\data\\";
-        Workspace workspace = BasicWorkspace.builder()
-                .setContext(Numass.buildContext())
-                .data("", new StorageDataFactory(), new MetaBuilder("storage").putValue("path", storagepath))
-                
-                .build();
-    }
-    
-}

numass-main/src/main/kotlin/inr/numass/NumassUtils.kt

@@ -152,8 +152,8 @@ object NumassUtils {
      * @return
      */
     fun setToNode(set: NumassSet): DataNode<Any> {
-        val builder = DataSet.builder()
+        val builder = DataSet.edit()
-        builder.setName(set.name)
+        builder.name = set.name
         set.points.forEach { point ->
             val pointMeta = MetaBuilder("point")
                     .putValue("voltage", point.voltage)

numass-main/src/main/kotlin/inr/numass/WorkspaceTest.kt

@@ -0,0 +1,32 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package inr.numass
+
+import hep.dataforge.meta.MetaBuilder
+import hep.dataforge.storage.commons.StorageDataFactory
+import hep.dataforge.workspace.BasicWorkspace
+
+/**
+ *
+ * @author Alexander Nozik
+ */
+object WorkspaceTest {
+
+    /**
+     * @param args the command line arguments
+     */
+    @JvmStatic
+    fun main(args: Array<String>) {
+
+        val storagepath = "D:\\Work\\Numass\\data\\"
+
+        val workspace = BasicWorkspace.builder().apply {
+            this.context = Numass.buildContext()
+            data("", StorageDataFactory(), MetaBuilder("storage").putValue("path", storagepath))
+        }.build()
+    }
+
+}

numass-main/src/main/kotlin/inr/numass/actions/SummaryAction.kt

@@ -37,9 +37,11 @@ import java.util.*
  */
 @TypedActionDef(name = "summary", inputType = FitState::class, outputType = Table::class, info = "Generate summary for fit results of different datasets.")
 @ValueDef(name = "parnames", multiple = true, required = true, info = "List of names of parameters for which summary should be done")
-class SummaryAction : ManyToOneAction<FitState, Table>() {
+object SummaryAction : ManyToOneAction<FitState, Table>() {
 
-    protected override fun buildGroups(context: Context, input: DataNode<FitState>, actionMeta: Meta): List<DataNode<FitState>> {
+    const val SUMMARY_NAME = "sumName"
+
+    override fun buildGroups(context: Context, input: DataNode<FitState>, actionMeta: Meta): List<DataNode<FitState>> {
         val meta = inputMeta(context, input.meta, actionMeta)
         val groups: List<DataNode<FitState>>
         if (meta.hasValue("grouping.byValue")) {
@@ -108,9 +110,4 @@ class SummaryAction : ManyToOneAction<FitState, Table>() {
         super.afterGroup(context, groupName, outputMeta, output)
     }
 
-    companion object {
-
-        val SUMMARY_NAME = "sumName"
-    }
-
 }

numass-main/src/main/kotlin/inr/numass/actions/TimeAnalyzerAction.kt

@@ -63,7 +63,7 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
 
         if (inputMeta.getBoolean("plotHist", true)) {
 
-            val histPlot = pm.getPlotFrame(getName(), "histogram");
+            val histPlot = pm.getPlotFrame(name, "histogram");
 
             histPlot.configure {
                 node("xAxis") {
@@ -99,7 +99,7 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
                 configure(inputMeta.getMetaOrEmpty("plot"))
             }
 
-            pm.getPlotFrame(getName(), "stat-method").add(statPlot)
+            pm.getPlotFrame(name, "stat-method").add(statPlot)
 
             (1..100).map { inputMeta.getDouble("t0Step", 1000.0) * it }.map { t ->
                 val result = analyzer.analyze(input, inputMeta.builder.setValue("t0", t))

numass-main/src/main/kotlin/inr/numass/actions/TimeSpectrumAction.kt

@@ -68,7 +68,7 @@ class TimeSpectrumAction : OneToOneAction<NumassPoint, Table>() {
 
         if (inputMeta.getBoolean("plotHist", true)) {
 
-            val histPlot = pm.getPlotFrame(getName(), "histogram");
+            val histPlot = pm.getPlotFrame(name, "histogram");
 
             histPlot.configure {
                 node("xAxis") {
@@ -105,7 +105,7 @@ class TimeSpectrumAction : OneToOneAction<NumassPoint, Table>() {
                 configure(inputMeta.getMetaOrEmpty("plot"))
             }
 
-            pm.getPlotFrame(getName(), "stat-method").add(statPlot)
+            pm.getPlotFrame(name, "stat-method").add(statPlot)
 
             (1..100).map { 1000 * it }.map { t ->
                 val result = analyzer.analyze(input, buildMeta {

numass-main/src/main/kotlin/inr/numass/actions/TransformDataAction.kt

@@ -1,15 +1,17 @@
 package inr.numass.actions
 
+import hep.dataforge.Named
 import hep.dataforge.actions.OneToOneAction
 import hep.dataforge.context.Context
 import hep.dataforge.description.NodeDef
 import hep.dataforge.description.TypedActionDef
 import hep.dataforge.description.ValueDef
 import hep.dataforge.description.ValueDefs
+import hep.dataforge.isAnonymous
 import hep.dataforge.meta.Laminate
 import hep.dataforge.meta.Meta
 import hep.dataforge.meta.MetaUtils
-import hep.dataforge.names.Named
+
 import hep.dataforge.tables.ColumnFormat
 import hep.dataforge.tables.ColumnTable
 import hep.dataforge.tables.ListColumn
@@ -49,6 +51,8 @@ class TransformDataAction : OneToOneAction<Table, Table>() {
         if (meta.hasValue("correction")) {
             val correction = meta.getString("correction")
             corrections.add(object : Correction {
+                override val name: String = ""
+
                 override fun corr(point: Values): Double {
                     return pointExpression(correction, point)
                 }
@@ -60,7 +64,7 @@ class TransformDataAction : OneToOneAction<Table, Table>() {
 
         for (correction in corrections) {
             //adding correction columns
-            if (!correction.isAnonimous) {
+            if (!correction.isAnonymous) {
                 table = table.buildColumn(ColumnFormat.build(correction.name, NUMBER)) { correction.corr(it) }
                 if (correction.hasError()) {
                     table = table.buildColumn(ColumnFormat.build(correction.name + ".err", NUMBER)) { correction.corrErr(it) }
@@ -69,8 +73,8 @@ class TransformDataAction : OneToOneAction<Table, Table>() {
         }
 
         // adding original count rate and error columns
-        table = table.addColumn(ListColumn(ColumnFormat.build(COUNT_RATE_KEY + ".orig", NUMBER), table.getColumn(COUNT_RATE_KEY).stream()))
+        table = table.addColumn(ListColumn(ColumnFormat.build("$COUNT_RATE_KEY.orig", NUMBER), table.getColumn(COUNT_RATE_KEY).stream()))
-        table = table.addColumn(ListColumn(ColumnFormat.build(COUNT_RATE_ERROR_KEY + ".orig", NUMBER), table
+        table = table.addColumn(ListColumn(ColumnFormat.build("$COUNT_RATE_ERROR_KEY.orig", NUMBER), table
                 .getColumn(COUNT_RATE_ERROR_KEY).stream()))
 
         val cr = ArrayList<Double>()
@@ -99,7 +103,7 @@ class TransformDataAction : OneToOneAction<Table, Table>() {
         val res = table.addColumn(ListColumn.build(table.getColumn(COUNT_RATE_KEY).format, cr.stream()))
                 .addColumn(ListColumn.build(table.getColumn(COUNT_RATE_ERROR_KEY).format, crErr.stream()))
 
-        context.io.output(name, getName()).push(NumassUtils.wrap(res, meta))
+        context.io.output(name, name).push(NumassUtils.wrap(res, meta))
         return res
     }
 
@@ -112,9 +116,7 @@ class TransformDataAction : OneToOneAction<Table, Table>() {
         val expr = corrMeta.getString("value")
         val errExpr = corrMeta.getString("err", "")
         return object : Correction {
-            override fun getName(): String {
+            override val name=corrMeta.getString("name", corrMeta.name)
-                return corrMeta.getString("name", corrMeta.name)
-            }
 
             override fun corr(point: Values): Double {
                 return pointExpression(expr, point)
@@ -136,10 +138,6 @@ class TransformDataAction : OneToOneAction<Table, Table>() {
 
     private interface Correction : Named {
 
-        override fun getName(): String {
-            return ""
-        }
-
         /**
          * correction coefficient
          *

numass-main/src/main/kotlin/inr/numass/scripts/timeanalysis/AnalyzePoint.kt

@@ -45,7 +45,7 @@ fun main(args: Array<String>) {
 
     val all = NumassDataUtils.join("sum", loaders)
 
-    val data = DataSet.builder(NumassPoint::class.java).apply {
+    val data = DataSet.edit(NumassPoint::class).apply {
         hvs.forEach { hv ->
             putStatic(
                     "point_${hv.toInt()}",

numass-main/src/main/kotlin/inr/numass/subthreshold/Threshold.kt

@@ -46,7 +46,7 @@ object Threshold {
 
         val analyzer = TimeAnalyzer();
 
-        val data = DataSet.builder(NumassPoint::class.java).also { dataBuilder ->
+        val data = DataSet.edit(NumassPoint::class).also { dataBuilder ->
             sets.sortedBy { it.startTime }
                     .flatMap { set -> set.points.toList() }
                     .groupBy { it.voltage }

numass-main/src/main/kotlin/inr/numass/tasks/NumassFitScanSummaryTask.kt

@@ -27,12 +27,12 @@ import inr.numass.NumassUtils
 class NumassFitScanSummaryTask : AbstractTask<Table>() {
 
     override fun run(model: TaskModel, data: DataNode<*>): DataNode<Table> {
-        val builder = DataSet.builder(Table::class.java)
+        val builder = DataSet.edit(Table::class)
         val action = FitSummaryAction()
         val input = data.checked(FitResult::class.java)
         input.nodeStream()
                 .filter { it -> it.getSize(false) > 0 }
-                .forEach { node -> builder.putData(node.name, action.run(model.context, node, model.meta).data) }
+                .forEach { node -> builder.putData(node.name, action.run(model.context, node, model.meta).data!!) }
         return builder.build()
     }
 
@@ -41,9 +41,7 @@ class NumassFitScanSummaryTask : AbstractTask<Table>() {
     }
 
 
-    override fun getName(): String {
+    override val name = "scansum"
-        return "scansum"
-    }
 
     @TypedActionDef(name = "sterileSummary", inputType = FitResult::class, outputType = Table::class)
     private inner class FitSummaryAction : ManyToOneAction<FitResult, Table>() {

numass-main/src/main/kotlin/inr/numass/tasks/NumassFitScanTask.kt

@@ -21,7 +21,7 @@ import java.util.stream.Collectors
 /**
  * @author Alexander Nozik
  */
-class NumassFitScanTask : AbstractTask<FitResult>() {
+object NumassFitScanTask : AbstractTask<FitResult>() {
 
 
     override fun run(model: TaskModel, data: DataNode<*>): DataNode<FitResult> {
@@ -39,7 +39,7 @@ class NumassFitScanTask : AbstractTask<FitResult>() {
         }
 
         val action = FitAction()
-        val resultBuilder = DataTree.builder(FitResult::class.java)
+        val resultBuilder = DataTree.edit(FitResult::class)
         val sourceNode = data.checked(Table::class.java)
 
         //do fit
@@ -53,7 +53,7 @@ class NumassFitScanTask : AbstractTask<FitResult>() {
                 val resultName = String.format("%s[%s=%s]", table.name, scanParameter, `val`.stringValue())
                 //                overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", table.getName(), scanParameter, val.stringValue()));
 
-                if (overrideMeta.hasMeta("params." + scanParameter)) {
+                if (overrideMeta.hasMeta("params.$scanParameter")) {
                     overrideMeta.setValue("params.$scanParameter.value", `val`)
                 } else {
                     overrideMeta.getMetaList("params.param").stream()
@@ -62,7 +62,7 @@ class NumassFitScanTask : AbstractTask<FitResult>() {
                 }
                 //                Data<Table> newData = new Data<Table>(data.getGoal(),data.type(),overrideMeta);
                 val node = action.run(model.context, DataNode.of(resultName, table, Meta.empty()), overrideMeta)
-                resultBuilder.putData(table.name + ".fit_" + i, node.data)
+                resultBuilder.putData(table.name + ".fit_" + i, node.data!!)
             }
         }
 
@@ -76,8 +76,6 @@ class NumassFitScanTask : AbstractTask<FitResult>() {
         model.dependsOn("filter", meta)
     }
 
-    override fun getName(): String {
+    override val name = "fitscan"
-        return "fitscan"
-    }
 
 }

numass-main/src/main/kotlin/inr/numass/tasks/NumassFitSummaryTask.kt

@@ -16,33 +16,24 @@
 
 package inr.numass.tasks
 
-import hep.dataforge.actions.Action
 import hep.dataforge.data.DataNode
 import hep.dataforge.meta.Meta
 import hep.dataforge.stat.fit.FitState
 import hep.dataforge.tables.Table
-import hep.dataforge.workspace.tasks.SingleActionTask
+import hep.dataforge.workspace.tasks.AbstractTask
 import hep.dataforge.workspace.tasks.TaskModel
 import inr.numass.actions.SummaryAction
 
 /**
  * Created by darksnake on 16-Sep-16.
  */
-class NumassFitSummaryTask : SingleActionTask<FitState, Table>() {
+object NumassFitSummaryTask : AbstractTask<Table>() {
-    override fun getName(): String {
+    override val name: String = "summary"
-        return "summary"
-    }
 
-    override fun getAction(model: TaskModel): Action<FitState, Table> {
+    override fun run(model: TaskModel, data: DataNode<*>): DataNode<out Table> {
-        return SummaryAction()
+        val actionMeta = model.meta.getMeta("summary")
-    }
+        val checkedData = data.getCheckedNode("fit", FitState::class.java)
-
+        return SummaryAction.run(model.context, checkedData, actionMeta)
-    override fun gatherNode(data: DataNode<*>): DataNode<FitState> {
-        return data.getCheckedNode("fit", FitState::class.java)
-    }
-
-    override fun transformMeta(model: TaskModel): Meta {
-        return model.meta.getMeta("summary")
     }
 
     override fun buildModel(model: TaskModel.Builder, meta: Meta) {

numass-main/src/main/kotlin/inr/numass/tasks/NumassTasks.kt

@@ -42,7 +42,7 @@ val selectTask = task("select") {
         data("*")
         configure(meta.getMetaOrEmpty("data"))
     }
-    transform<NumassSet, NumassSet> { data ->
+    transform<NumassSet> { data ->
         logger.info("Starting selection from data node with size ${data.size}")
         CustomDataFilter(meta).filter<NumassSet>(data.checked(NumassSet::class.java)).also {
             logger.info("Selected ${it.size} elements")
@@ -80,13 +80,13 @@ val monitorTableTask = task("monitor") {
                     }
                     plots + DataPlot.plot(name, Adapters.buildXYAdapter("timestamp", "cr", "crErr"), res)
                 }.also { frame ->
-                            if (frame is JFreeChartFrame) {
+                    if (frame is JFreeChartFrame) {
-                                //add set markers
+                        //add set markers
-                                addSetMarkers(frame, data.values)
+                        addSetMarkers(frame, data.values)
-                            }
+                    }
-                            context.io.output(name, stage = "numass.monitor", type = "dfp").push(PlotFrame.Wrapper().wrap(frame))
+                    context.io.output(name, stage = "numass.monitor", type = "dfp").push(PlotFrame.Wrapper().wrap(frame))
 
-                        }
+                }
             }
         }
 
@@ -139,8 +139,8 @@ val mergeEmptyTask = task("empty") {
                 .setValue("merge." + MERGE_NAME, meta.getString("merge." + MERGE_NAME, "") + "_empty");
         dependsOn(mergeTask, newMeta)
     }
-    transform<Table, Table> { data ->
+    transform<Table> { data ->
-        val builder = DataSet.builder(Table::class.java)
+        val builder = DataSet.edit(Table::class)
         data.forEach {
             builder.putData(it.name + "_empty", it.anonymize());
         }
@@ -154,12 +154,13 @@ val subtractEmptyTask = task("dif") {
         dependsOn(mergeTask, meta, "data")
         dependsOn(mergeEmptyTask, meta, "empty")
     }
-    transform<Table, Table> { data ->
+    transform<Table> { data ->
-        val builder = DataTree.builder(Table::class.java)
+        val builder = DataTree.edit(Table::class)
-        val rootNode = data.getCheckedNode<Table>("data", Table::class.java)
+        val rootNode = data.getCheckedNode("data", Table::class.java)
-        val empty = data.getCheckedNode<Table>("empty", Table::class.java).data
+        val empty = data.getCheckedNode("empty", Table::class.java).data
+                ?: throw RuntimeException("No empty data found")
 
-        rootNode.forEachData(Table::class.java, { input ->
+        rootNode.visit(Table::class.java, { input ->
             val resMeta = buildMeta {
                 putNode("data", input.meta)
                 putNode("empty", empty.meta)
@@ -170,7 +171,7 @@ val subtractEmptyTask = task("dif") {
 
             res.goal.onComplete { r, _ ->
                 if (r != null) {
-                    context.io.output(input.name + "_subtract", stage = "numass.merge").push(NumassUtils.wrap(r,resMeta))
+                    context.io.output(input.name + "_subtract", stage = "numass.merge").push(NumassUtils.wrap(r, resMeta))
                 }
             }
 

numass-viewer/src/main/kotlin/inr/numass/viewer/NumassDataCache.kt

@@ -12,7 +12,7 @@ import java.util.stream.Stream
  * Cached numass data
  * Created by darksnake on 23-Jun-17.
  */
-class NumassDataCache(val data: NumassSet) : NumassSet {
+class NumassDataCache(private val data: NumassSet) : NumassSet {
     //private val cachedDescription: String by lazy { data.description }
     override val meta: Meta by lazy { data.meta }
     private val cachedPoints: List<NumassPoint> by lazy { data.points.collect(Collectors.toList()) }
@@ -22,12 +22,5 @@ class NumassDataCache(val data: NumassSet) : NumassSet {
     override val points: Stream<NumassPoint>
         get() = cachedPoints.stream()
 
-//    override fun getDescription(): String {
+    override val name: String = data.name
-//        return cachedDescription
-//    }
-
-
-    override fun getName(): String {
-        return data.name;
-    }
 }