minor fixes

numass-core/src/main/kotlin/inr/numass/data/analyzers/TimeAnalyzer.kt

@@ -26,13 +26,19 @@ import hep.dataforge.values.Value
 import hep.dataforge.values.ValueMap
 import hep.dataforge.values.ValueType
 import hep.dataforge.values.Values
+import inr.numass.data.analyzers.NumassAnalyzer.Companion.COUNT_KEY
+import inr.numass.data.analyzers.NumassAnalyzer.Companion.COUNT_RATE_ERROR_KEY
+import inr.numass.data.analyzers.NumassAnalyzer.Companion.COUNT_RATE_KEY
+import inr.numass.data.analyzers.NumassAnalyzer.Companion.LENGTH_KEY
 import inr.numass.data.api.*
 import inr.numass.data.api.NumassPoint.Companion.HV_KEY
 import java.util.*
 import java.util.concurrent.atomic.AtomicLong
 import java.util.stream.Stream
+import kotlin.math.sqrt
 import kotlin.streams.asSequence
 import kotlin.streams.asStream
+import kotlin.streams.toList
 
 
 /**
@@ -56,12 +62,7 @@ class TimeAnalyzer @JvmOverloads constructor(private val processor: SignalProces
 
         val res = getEventsWithDelay(block, config).asSequence().chunked(chunkSize) {
             analyzeSequence(it.asSequence(), t0)
-        }.reduce(this::combineBlockResults) ?: ValueMap.ofPairs(
+        }.toList().average()
-                NumassAnalyzer.LENGTH_KEY to 0,
-                NumassAnalyzer.COUNT_KEY to 0,
-                NumassAnalyzer.COUNT_RATE_KEY to 0,
-                NumassAnalyzer.COUNT_RATE_ERROR_KEY to 0
-        )
 
         return ValueMap.Builder(res)
                 .putValue(NumassAnalyzer.WINDOW_KEY, arrayOf(loChannel, upChannel))
@@ -92,15 +93,7 @@ class TimeAnalyzer @JvmOverloads constructor(private val processor: SignalProces
                 NumassAnalyzer.COUNT_RATE_KEY to countRate,
                 NumassAnalyzer.COUNT_RATE_ERROR_KEY to countRateError
         )
-//        ValueMap.of(NAME_LIST,
+
-//                length,
-//                count,
-//                countRate,
-//                countRateError,
-//                arrayOf(loChannel, upChannel),
-//                block.startTime,
-//                t0.toDouble() / 1000.0
-//        )
     }
 
     override fun analyzeParent(point: ParentBlock, config: Meta): Values {
@@ -108,7 +101,7 @@ class TimeAnalyzer @JvmOverloads constructor(private val processor: SignalProces
         val res = point.blocks.stream()
                 .filter { it.events.findAny().isPresent }// filter for empty blocks
                 .map { it -> analyze(it, config) }
-                .reduce(null) { v1, v2 -> this.combineBlockResults(v1, v2) }
+                .toList().average()
 
         val map = HashMap(res.asMap())
         if (point is NumassPoint) {
@@ -118,38 +111,21 @@ class TimeAnalyzer @JvmOverloads constructor(private val processor: SignalProces
     }
 
     /**
-     * Combine two blocks from the same point into one
+     * Combine multiple blocks from the same point into one
      *
-     * @param v1
-     * @param v2
      * @return
      */
-    private fun combineBlockResults(v1: Values?, v2: Values?): Values? {
+    private fun List<Values>.average(): Values {
-        if (v1 == null) {
-            return v2
-        }
-        if (v2 == null) {
-            return v1
-        }
 
+        val totalTime = sumByDouble { it.getDouble(LENGTH_KEY) }
+        val countRate = sumByDouble { it.getDouble(COUNT_RATE_KEY) * it.getDouble(LENGTH_KEY) } / totalTime
+        val countRateDispersion = sumByDouble { Math.pow(it.getDouble(COUNT_RATE_ERROR_KEY) * it.getDouble(LENGTH_KEY) / totalTime, 2.0) }
 
-        val t1 = v1.getDouble(NumassAnalyzer.LENGTH_KEY)
+        return ValueMap.Builder(first())
-        val t2 = v2.getDouble(NumassAnalyzer.LENGTH_KEY)
+                .putValue(LENGTH_KEY, totalTime)
-        val cr1 = v1.getDouble(NumassAnalyzer.COUNT_RATE_KEY)
+                .putValue(COUNT_KEY, sumBy { it.getInt(COUNT_KEY) })
-        val cr2 = v2.getDouble(NumassAnalyzer.COUNT_RATE_KEY)
+                .putValue(COUNT_RATE_KEY, countRate)
-        val err1 = v1.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY)
+                .putValue(COUNT_RATE_ERROR_KEY, sqrt(countRateDispersion))
-        val err2 = v2.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY)
-
-        val countRate = (t1 * cr1 + t2 * cr2) / (t1 + t2)
-
-        val countRateErr = Math.sqrt(Math.pow(t1 * err1 / (t1 + t2), 2.0) + Math.pow(t2 * err2 / (t1 + t2), 2.0))
-
-
-        return ValueMap.Builder(v1)
-                .putValue(NumassAnalyzer.LENGTH_KEY, t1 + t2)
-                .putValue(NumassAnalyzer.COUNT_KEY, v1.getInt(NumassAnalyzer.COUNT_KEY) + v2.getInt(NumassAnalyzer.COUNT_KEY))
-                .putValue(NumassAnalyzer.COUNT_RATE_KEY, countRate)
-                .putValue(NumassAnalyzer.COUNT_RATE_ERROR_KEY, countRateErr)
                 .build()
     }
 

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

@@ -82,7 +82,7 @@ class SimpleBlock(
 
     private val eventList = runBlocking { producer(this@SimpleBlock).toList()}
 
-    override val frames: Stream<NumassFrame> = Stream.empty()
+    override val frames: Stream<NumassFrame> get() = Stream.empty()
 
     override val events: Stream<NumassEvent>
         get() = eventList.stream()

numass-main/src/main/groovy/inr/numass/scripts/times/AnalyzePoint.groovy

@@ -1,76 +0,0 @@
-package inr.numass.scripts.times
-
-import hep.dataforge.context.Context
-import hep.dataforge.context.Global
-import hep.dataforge.data.DataSet
-import hep.dataforge.fx.plots.FXPlotManager
-import hep.dataforge.grind.Grind
-import hep.dataforge.grind.GrindShell
-import hep.dataforge.meta.Meta
-import inr.numass.NumassPlugin
-import inr.numass.actions.TimeAnalyzerAction
-import inr.numass.data.NumassDataUtils
-import inr.numass.data.api.NumassPoint
-import inr.numass.data.api.NumassSet
-import inr.numass.data.api.SimpleNumassPoint
-import inr.numass.data.storage.NumassStorageFactory
-
-/**
- * Created by darksnake on 27-Jun-17.
- */
-
-
-Context ctx = Global.instance()
-ctx.getPluginManager().load(FXPlotManager)
-ctx.getPluginManager().load(NumassPlugin)
-
-new GrindShell(ctx).eval {
-
-    def storage = NumassStorageFactory.buildLocal(ctx, "D:\\Work\\Numass\\data\\2017_05\\Fill_2", true, false);
-
-    Meta meta = Grind.buildMeta(binNum: 200, inverted: true) {
-        window(lo: 500, up: 3000)
-        plot(showErrors: false)
-    }
-
-    //def sets = ((2..14) + (22..31)).collect { "set_$it" }
-    def sets = (2..14).collect { "set_$it" }
-    //def sets = (16..31).collect { "set_$it" }
-    //def sets = (20..28).collect { "set_$it" }
-
-    def loaders = sets.collect { set ->
-        storage.provide("loader::$set", NumassSet.class).orElse(null)
-    }.findAll { it != null }
-
-    def hvs = [14000d]//[14000d, 14200d, 14600d, 14800d, 15000d, 15200d, 15400d, 15600d, 15800d]
-
-    def all = NumassDataUtils.join("sum", loaders)
-
-    def builder = DataSet.builder(NumassPoint)
-
-    hvs.each { hv ->
-        builder.putStatic("point_${hv as int}", new SimpleNumassPoint(hv, all.points.filter {
-            it.voltage == hv
-        }.collect()));
-    }
-
-    def data = builder.build()
-
-//    def hv = 14000;
-//    def dataBuilder = DataSet.builder(NumassPoint)
-//
-//    StorageUtils.loaderStream(storage, false)
-//                .filter { it.value instanceof NumassSet }
-//                .forEach { pair ->
-//        (pair.value as NumassSet).optPoint(hv).ifPresent {
-//            dataBuilder.putData(pair.key, it, it.meta);
-//        }
-//    }
-//    def data = dataBuilder.build()
-
-    def result = new TimeAnalyzerAction().run(ctx, data, meta);
-
-    result.computeAll();
-
-//    storage.close()
-}

numass-main/src/main/groovy/inr/numass/scripts/times/TestAnalyzer.groovy

@@ -1,44 +0,0 @@
-package inr.numass.scripts.times
-
-import hep.dataforge.context.Context
-import hep.dataforge.context.Global
-import hep.dataforge.fx.plots.FXPlotManager
-import hep.dataforge.grind.GrindShell
-import hep.dataforge.meta.Meta
-import inr.numass.NumassPlugin
-import inr.numass.actions.TimeAnalyzerAction
-import inr.numass.data.GeneratorKt
-import inr.numass.data.api.SimpleNumassPoint
-import org.apache.commons.math3.random.JDKRandomGenerator
-
-import java.time.Instant
-
-/**
- * Created by darksnake on 27-Jun-17.
- */
-
-
-Context ctx = Global.INSTANCE
-ctx.getPluginManager().load(FXPlotManager)
-ctx.getPluginManager().load(NumassPlugin.class)
-
-new GrindShell(ctx).eval {
-
-    double cr = 30e3;
-    long length = 30e9;
-    def num = 5;
-    def dt = 6.5
-
-
-
-    def blocks = (1..num).collect {
-        def chain = GeneratorKt.generateEvents(cr, new JDKRandomGenerator(),{10000})
-        GeneratorKt.generateBlock(Instant.now().plusNanos(it * length), length, chain)
-    }
-
-    def point = new SimpleNumassPoint(10000, blocks)
-
-    def meta = Meta.empty()//Grind.buildMeta(plotHist: false)
-
-    new TimeAnalyzerAction().simpleRun(point, meta);
-}

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

@@ -13,6 +13,7 @@ import hep.dataforge.tables.Table
 import hep.dataforge.values.ValueType
 import inr.numass.data.analyzers.NumassAnalyzer
 import inr.numass.data.analyzers.TimeAnalyzer
+import inr.numass.data.analyzers.TimeAnalyzer.Companion.T0_KEY
 import inr.numass.data.api.NumassPoint
 
 /**
@@ -39,9 +40,10 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
 
         val pm = context[PlotPlugin::class.java];
 
-        val trueCR = analyzer.analyze(input, inputMeta).getDouble("cr")
+        val initialEstimate = analyzer.analyze(input, inputMeta)
+        val trueCR = initialEstimate.getDouble("cr")
 
-        log.report("The expected count rate for 30 us delay is $trueCR")
+        log.report("The expected count rate for ${initialEstimate.getDouble(T0_KEY)} us delay is $trueCR")
 
         val binNum = inputMeta.getInt("binNum", 1000);
         val binSize = inputMeta.getDouble("binSize", 1.0 / trueCR * 10 / binNum * 1e6)
@@ -92,7 +94,16 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
                 configure(inputMeta.getMetaOrEmpty("plot"))
             }
 
-            pm.getPlotFrame(name, "stat-method").add(statPlot)
+            pm.getPlotFrame(name, "stat-method")
+                    .configure {
+                        "xAxis" to {
+                            "title" to "delay"
+                            "units" to "us"
+                        }
+                        "yAxis" to {
+                            "title" to "Relative count rate"
+                        }
+                    }.add(statPlot)
 
             (1..100).map { inputMeta.getDouble("t0Step", 1000.0) * it }.map { t ->
                 val result = analyzer.analyze(input, inputMeta.builder.setValue("t0", t))
@@ -103,7 +114,7 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
                 } else {
                     1.0
                 }
-                if(Thread.currentThread().isInterrupted){
+                if (Thread.currentThread().isInterrupted) {
                     throw InterruptedException()
                 }
                 statPlot.append(

numass-main/src/main/kotlin/inr/numass/data/Generator.kt

@@ -87,7 +87,7 @@ fun buildBunchChain(
             BunchState(0, 0),
             OrphanNumassEvent(rnd.amp(null, 0), 0)) { event ->
         if (event.timeOffset >= bunchEnd) {
-            bunchStart = bunchEnd + (rnd.nextDeltaTime(bunchRate)).toLong()
+            bunchStart = bunchEnd + rnd.nextDeltaTime(bunchRate)
             bunchEnd = bunchStart + (bunchLength * 1e9).toLong()
             OrphanNumassEvent(rnd.amp(null, 0), bunchStart)
         } else {
@@ -112,105 +112,3 @@ fun mergeEventChains(vararg chains: Chain<OrphanNumassEvent>): Chain<OrphanNumas
         poll()
     }
 }
-//
-//
-///**
-// * @param S - intermediate state of generator
-// */
-//abstract class ChainGenerator<S> {
-//
-//    protected abstract fun next(event: NumassEvent?, state: S = buildState()): NumassEvent
-//
-//    fun buildSequence(): Sequence<NumassEvent> {
-//        val state = buildState()
-//        return generateSequence(seed = null) { event: NumassEvent? ->
-//            next(event, state)
-//        }
-//    }
-//
-//    protected abstract fun buildState(): S
-//
-//    fun generateBlock(start: Instant, length: Long): NumassBlock {
-//        val events = buildSequence().takeWhile { it.timeOffset < length }.toList()
-//        return SimpleBlock(start, Duration.ofNanos(length), events)
-//    }
-//}
-//
-//
-//class SimpleChainGenerator(
-//        val cr: Double,
-//        private val rnd: RandomGenerator = JDKRandomGenerator(),
-//        private val amp: RandomGenerator.(NumassEvent?, Long) -> Short = { _, _ -> ((nextDouble() + 2.0) * 100).toShort() }
-//) : ChainGenerator<Unit>() {
-//
-//    override fun buildState() {
-//        return Unit
-//    }
-//
-//    override fun next(event: NumassEvent?, state: Unit): NumassEvent {
-//        return if (event == null) {
-//            NumassEvent(rnd.amp(null, 0), Instant.EPOCH, 0)
-//        } else {
-//            val deltaT = rnd.nextDeltaTime(cr)
-//            NumassEvent(rnd.amp(event, deltaT), event.blockTime, event.timeOffset + deltaT)
-//        }
-//    }
-//
-//    fun next(event: NumassEvent?): NumassEvent {
-//        return next(event, Unit)
-//    }
-//}
-//
-//class BunchGenerator(
-//        private val cr: Double,
-//        private val bunchRate: Double,
-//        private val bunchLength: RandomGenerator.() -> Long,
-//        private val rnd: RandomGenerator = JDKRandomGenerator(),
-//        private val amp: RandomGenerator.(NumassEvent?, Long) -> Short = { _, _ -> ((nextDouble() + 2.0) * 100).toShort() }
-//) : ChainGenerator<BunchGenerator.BunchState>() {
-//
-//    private val internalGenerator = SimpleChainGenerator(cr, rnd, amp)
-//
-//    class BunchState(var bunchStart: Long = 0, var bunchEnd: Long = 0)
-//
-//    override fun next(event: NumassEvent?, state: BunchState): NumassEvent {
-//        if (event?.timeOffset ?: 0 >= state.bunchEnd) {
-//            state.bunchStart = state.bunchEnd + (rnd.nextExp(bunchRate) * 1e9).toLong()
-//            state.bunchEnd = state.bunchStart + rnd.bunchLength()
-//            return NumassEvent(rnd.amp(null, 0), Instant.EPOCH, state.bunchStart)
-//        } else {
-//            return internalGenerator.next(event)
-//        }
-//    }
-//
-//    override fun buildState(): BunchState {
-//        return BunchState(0, 0)
-//    }
-//}
-//
-//
-//class MergingGenerator(private vararg val generators: ChainGenerator<*>) : ChainGenerator<MergingGenerator.MergingState>() {
-//
-//    inner class MergingState {
-//        val queue: PriorityQueue<Pair<Sequence<NumassEvent>, NumassEvent>> =
-//                PriorityQueue(Comparator.comparing<Pair<Sequence<NumassEvent>, NumassEvent>, Long> { it.second.timeOffset })
-//
-//        init {
-//            generators.forEach { generator ->
-//                val sequence = generator.buildSequence()
-//                queue.add(Pair(sequence, sequence.iterator().next()))
-//            }
-//        }
-//    }
-//
-//    override fun next(event: NumassEvent?, state: MergingState): NumassEvent {
-//        val pair = state.queue.poll()
-//        state.queue.add(Pair(pair.first, pair.first.iterator().next()))
-//        return pair.second
-//    }
-//
-//    override fun buildState(): MergingState {
-//        return MergingState()
-//    }
-//}
-//

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

@@ -19,12 +19,13 @@ fun main(args: Array<String>) {
         dataDir = "D:\\Work\\Numass\\data\\2018_04"
     }
 
-    val storage = NumassStorageFactory.buildLocal(context, "Fill_2", true, false);
+    val storage = NumassStorageFactory.buildLocal(context, "Fill_3", true, false);
 
     val meta = buildMeta {
+        "t0" to 3000
         "binNum" to 200
-        "t0Step" to 1000
+        "t0Step" to 100
-        "chunkSize" to 1000
+        "chunkSize" to 3000
         node("window") {
             "lo" to 0
             "up" to 4000
@@ -33,7 +34,7 @@ fun main(args: Array<String>) {
     }
 
     //def sets = ((2..14) + (22..31)).collect { "set_$it" }
-    val sets = (5..6).map { "set_$it" }
+    val sets = (2..12).map { "set_$it" }
     //def sets = (16..31).collect { "set_$it" }
     //def sets = (20..28).collect { "set_$it" }
 
@@ -41,7 +42,7 @@ fun main(args: Array<String>) {
         storage.provide("loader::$set", NumassSet::class.java).orElse(null)
     }.filter { it != null }
 
-    val hvs = listOf(15000.0)//, 15000d, 15200d, 15400d, 15600d, 15800d]
+    val hvs = listOf(12000.0, 14000.0, 16000.0)//, 15000d, 15200d, 15400d, 15600d, 15800d]
 
     val all = NumassDataUtils.join("sum", loaders)
 

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

@@ -0,0 +1,56 @@
+package inr.numass.scripts.timeanalysis
+
+import hep.dataforge.fx.plots.FXPlotManager
+import hep.dataforge.kodex.buildMeta
+import hep.dataforge.maths.chain.MarkovChain
+import inr.numass.NumassPlugin
+import inr.numass.actions.TimeAnalyzerAction
+import inr.numass.data.api.OrphanNumassEvent
+import inr.numass.data.api.SimpleNumassPoint
+import inr.numass.data.api.timeOffset
+import inr.numass.data.generateBlock
+import org.apache.commons.math3.random.JDKRandomGenerator
+import org.apache.commons.math3.random.RandomGenerator
+import java.lang.Math.exp
+import java.time.Instant
+
+fun main(args: Array<String>) {
+    FXPlotManager().startGlobal()
+    NumassPlugin().startGlobal()
+
+    val cr = 10e3;
+    val length = 30e9.toLong();
+    val num = 20;
+    val dt = 6.5
+
+    val rnd = JDKRandomGenerator()
+
+    fun RandomGenerator.nextExp(mean: Double): Double {
+        return -mean * Math.log(1 - nextDouble())
+    }
+
+    fun RandomGenerator.nextDeltaTime(cr: Double): Long {
+        return (nextExp(1.0 / cr) * 1e9).toLong()
+    }
+
+
+    val chain = MarkovChain(OrphanNumassEvent(1000, 0)) { event ->
+        val deltaT = rnd.nextDeltaTime(cr * exp(- event.timeOffset / 1e11))
+        OrphanNumassEvent(1000, event.timeOffset + deltaT)
+    }
+
+    val blocks = (1..num).map {
+        generateBlock(Instant.now().plusNanos(it * length), length, chain)
+    }
+
+    val point = SimpleNumassPoint(blocks, 12000.0)
+
+    val meta = buildMeta {
+        "t0" to 3000
+        "binNum" to 200
+        "t0Step" to 200
+        "chunkSize" to 5000
+    }
+
+    TimeAnalyzerAction().simpleRun(point, meta);
+}