minor update

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

@@ -46,13 +46,12 @@ abstract class AbstractAnalyzer @JvmOverloads constructor(private val processor:
     override fun getEvents(block: NumassBlock, meta: Meta): Stream<NumassEvent> {
         val loChannel = meta.getInt("window.lo", 0)
         val upChannel = meta.getInt("window.up", Integer.MAX_VALUE)
-        var res = getAllEvents(block).filter { event ->
+        //        if (meta.getBoolean("sort", false)) {
+//            res = res.sorted(compareBy { it.timeOffset })
+//        }
+        return getAllEvents(block).filter { event ->
             event.amplitude.toInt() in loChannel..(upChannel - 1)
         }
-        if (meta.getBoolean("sort", false)) {
-            res = res.sorted(compareBy { it.timeOffset })
-        }
-        return res
     }
 
     protected fun getAllEvents(block: NumassBlock): Stream<NumassEvent> {

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

@@ -22,7 +22,7 @@ import kotlin.streams.asStream
  * Plot time analysis graphics
  */
 @ValueDefs(
-        ValueDef(key = "normalize", type = arrayOf(ValueType.BOOLEAN), def = "true", info = "Normalize t0 dependencies"),
+        ValueDef(key = "normalize", type = arrayOf(ValueType.BOOLEAN), def = "false", info = "Normalize t0 dependencies"),
         ValueDef(key = "t0", type = arrayOf(ValueType.NUMBER), def = "30e3", info = "The default t0 in nanoseconds"),
         ValueDef(key = "window.lo", type = arrayOf(ValueType.NUMBER), def = "0", info = "Lower boundary for amplitude window"),
         ValueDef(key = "window.up", type = arrayOf(ValueType.NUMBER), def = "10000", info = "Upper boundary for amplitude window"),
@@ -40,13 +40,15 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
     override fun execute(context: Context, name: String, input: NumassPoint, inputMeta: Laminate): Table {
         val log = getLog(context, name);
 
-        val initialEstimate = analyzer.analyze(input, inputMeta)
+        val analyzerMeta = inputMeta.getMetaOrEmpty("analyzer")
-        val trueCR = initialEstimate.getDouble("cr")
 
-        log.report("The expected count rate for ${initialEstimate.getDouble(T0_KEY)} us delay is $trueCR")
+        val initialEstimate = analyzer.analyze(input, analyzerMeta)
+        val cr = initialEstimate.getDouble("cr")
+
+        log.report("The expected count rate for ${initialEstimate.getDouble(T0_KEY)} us delay is $cr")
 
         val binNum = inputMeta.getInt("binNum", 1000);
-        val binSize = inputMeta.getDouble("binSize", 1.0 / trueCR * 10 / binNum * 1e6)
+        val binSize = inputMeta.getDouble("binSize", 1.0 / cr * 10 / binNum * 1e6)
 
         val histogram = UnivariateHistogram.buildUniform(0.0, binSize * binNum, binSize)
                 .fill(analyzer
@@ -72,7 +74,7 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
 
 
             val functionPlot = XYFunctionPlot.plot(name + "_theory", 0.0, binSize * binNum) {
-                trueCR / 1e6 * initialEstimate.getInt(NumassAnalyzer.COUNT_KEY) * binSize * Math.exp(-it * trueCR / 1e6)
+                cr / 1e6 * initialEstimate.getInt(NumassAnalyzer.COUNT_KEY) * binSize * Math.exp(-it * cr / 1e6)
             }
 
             context.plot("histogram", name, listOf(histogramPlot, functionPlot)) {
@@ -106,15 +108,19 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
                 }
             }
 
-            (1..100).map { inputMeta.getDouble("t0Step", 1000.0) * it }.map { t ->
+            val minT0 = inputMeta.getDouble("t0.min", 0.0)
-                val result = analyzer.analyze(input, inputMeta.builder.setValue("t0", t))
+            val maxT0 = inputMeta.getDouble("t0.max", 1e9 / cr)
+            val steps = inputMeta.getInt("t0.steps", 100)
 
-
+            val norm = if (inputMeta.getBoolean("normalize", false)) {
-                val norm = if (inputMeta.getBoolean("normalize", true)) {
+                cr
-                    trueCR
             } else {
                 1.0
             }
+
+            (0..steps).map { minT0 + (maxT0-minT0)/steps*it }.map { t ->
+                val result = analyzer.analyze(input, analyzerMeta.builder.setValue("t0", t))
+
                 if (Thread.currentThread().isInterrupted) {
                     throw InterruptedException()
                 }

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

@@ -1,115 +0,0 @@
-package inr.numass.data
-
-import hep.dataforge.maths.chain.Chain
-import hep.dataforge.maths.chain.MarkovChain
-import hep.dataforge.maths.chain.StatefulChain
-import hep.dataforge.stat.defaultGenerator
-import hep.dataforge.tables.Table
-import inr.numass.data.analyzers.NumassAnalyzer.Companion.CHANNEL_KEY
-import inr.numass.data.analyzers.NumassAnalyzer.Companion.COUNT_RATE_KEY
-import inr.numass.data.api.NumassBlock
-import inr.numass.data.api.OrphanNumassEvent
-import inr.numass.data.api.SimpleBlock
-import kotlinx.coroutines.experimental.channels.takeWhile
-import kotlinx.coroutines.experimental.channels.toList
-import org.apache.commons.math3.distribution.EnumeratedRealDistribution
-import org.apache.commons.math3.random.RandomGenerator
-import java.time.Duration
-import java.time.Instant
-
-private fun RandomGenerator.nextExp(mean: Double): Double {
-    return -mean * Math.log(1 - nextDouble())
-}
-
-private fun RandomGenerator.nextDeltaTime(cr: Double): Long {
-    return (nextExp(1.0 / cr) * 1e9).toLong()
-}
-
-suspend fun Chain<OrphanNumassEvent>.generateBlock(start: Instant, length: Long): NumassBlock {
-    return SimpleBlock.produce(start, Duration.ofNanos(length)) {
-        channel.takeWhile { it.timeOffset < length }.toList()
-    }
-}
-
-internal val defaultAmplitudeGenerator: RandomGenerator.(OrphanNumassEvent?, Long) -> Short = { _, _ -> ((nextDouble() + 2.0) * 100).toShort() }
-
-/**
- * Generate an event chain with fixed count rate
- * @param cr = count rate in Hz
- * @param rnd = random number generator
- * @param amp amplitude generator for the chain. The receiver is rng, first argument is the previous event and second argument
- * is the delay between the next event. The result is the amplitude in channels
- */
-fun generateEvents(
-        cr: Double,
-        rnd: RandomGenerator = defaultGenerator,
-        amp: RandomGenerator.(OrphanNumassEvent?, Long) -> Short = defaultAmplitudeGenerator): Chain<OrphanNumassEvent> {
-    return MarkovChain(OrphanNumassEvent(rnd.amp(null, 0), 0)) { event ->
-        val deltaT = rnd.nextDeltaTime(cr)
-        OrphanNumassEvent(rnd.amp(event, deltaT), event.timeOffset + deltaT)
-    }
-}
-
-/**
- * Generate a chain using provided spectrum for amplitudes
- */
-fun generateEvents(
-        cr: Double,
-        rnd: RandomGenerator = defaultGenerator,
-        spectrum: Table): Chain<OrphanNumassEvent> {
-
-    val channels = DoubleArray(spectrum.size())
-    val values = DoubleArray(spectrum.size())
-    for (i in 0 until spectrum.size()) {
-        channels[i] = spectrum.get(CHANNEL_KEY, i).double
-        values[i] = spectrum.get(COUNT_RATE_KEY, i).double
-    }
-    val distribution = EnumeratedRealDistribution(channels, values)
-
-    return generateEvents(cr, rnd) { _, _ -> distribution.sample().toShort() }
-}
-
-private data class BunchState(var bunchStart: Long = 0, var bunchEnd: Long = 0)
-
-/**
- * The chain of bunched events
- * @param cr count rate of events inside bunch
- * @param bunchRate number of bunches per second
- * @param bunchLength the length of bunch
- */
-fun buildBunchChain(
-        cr: Double,
-        bunchRate: Double,
-        bunchLength: Double,
-        rnd: RandomGenerator = defaultGenerator,
-        amp: RandomGenerator.(OrphanNumassEvent?, Long) -> Short = defaultAmplitudeGenerator
-): Chain<OrphanNumassEvent> {
-    return StatefulChain(
-            BunchState(0, 0),
-            OrphanNumassEvent(rnd.amp(null, 0), 0)) { event ->
-        if (event.timeOffset >= bunchEnd) {
-            bunchStart = bunchEnd + rnd.nextDeltaTime(bunchRate)
-            bunchEnd = bunchStart + (bunchLength * 1e9).toLong()
-            OrphanNumassEvent(rnd.amp(null, 0), bunchStart)
-        } else {
-            val deltaT = rnd.nextDeltaTime(cr)
-            OrphanNumassEvent(rnd.amp(event, deltaT), event.timeOffset + deltaT)
-        }
-    }
-}
-
-private class MergingState(private val chains: List<Chain<OrphanNumassEvent>>) {
-    suspend fun poll(): OrphanNumassEvent {
-        val next = chains.minBy { it.value.timeOffset } ?: chains.first()
-        val res = next.value
-        next.next()
-        return res
-    }
-
-}
-
-fun mergeEventChains(vararg chains: Chain<OrphanNumassEvent>): Chain<OrphanNumassEvent> {
-    return StatefulChain(MergingState(listOf(*chains)), OrphanNumassEvent(0, 0)) {
-        poll()
-    }
-}

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

@@ -0,0 +1,141 @@
+package inr.numass.data
+
+import hep.dataforge.maths.chain.Chain
+import hep.dataforge.maths.chain.MarkovChain
+import hep.dataforge.maths.chain.StatefulChain
+import hep.dataforge.stat.defaultGenerator
+import hep.dataforge.tables.Table
+import inr.numass.data.analyzers.NumassAnalyzer.Companion.CHANNEL_KEY
+import inr.numass.data.analyzers.NumassAnalyzer.Companion.COUNT_RATE_KEY
+import inr.numass.data.api.NumassBlock
+import inr.numass.data.api.OrphanNumassEvent
+import inr.numass.data.api.SimpleBlock
+import kotlinx.coroutines.experimental.channels.asReceiveChannel
+import kotlinx.coroutines.experimental.channels.takeWhile
+import kotlinx.coroutines.experimental.channels.toList
+import org.apache.commons.math3.distribution.EnumeratedRealDistribution
+import org.apache.commons.math3.random.RandomGenerator
+import java.time.Duration
+import java.time.Instant
+
+private fun RandomGenerator.nextExp(mean: Double): Double {
+    return -mean * Math.log(1 - nextDouble())
+}
+
+private fun RandomGenerator.nextDeltaTime(cr: Double): Long {
+    return (nextExp(1.0 / cr) * 1e9).toLong()
+}
+
+suspend fun Sequence<OrphanNumassEvent>.generateBlock(start: Instant, length: Long): NumassBlock {
+    return SimpleBlock.produce(start, Duration.ofNanos(length)) {
+        asReceiveChannel().takeWhile { it.timeOffset < length }.toList()
+    }
+}
+
+private class MergingState(private val chains: List<Chain<OrphanNumassEvent>>) {
+    suspend fun poll(): OrphanNumassEvent {
+        val next = chains.minBy { it.value.timeOffset } ?: chains.first()
+        val res = next.value
+        next.next()
+        return res
+    }
+
+}
+
+/**
+ * Merge event chains in ascending time order
+ */
+fun List<Chain<OrphanNumassEvent>>.merge(): Chain<OrphanNumassEvent> {
+    return StatefulChain(MergingState(this), OrphanNumassEvent(0, 0)) {
+        poll()
+    }
+}
+
+/**
+ * Apply dead time based on event that caused it
+ */
+fun Chain<OrphanNumassEvent>.withDeadTime(deadTime: (OrphanNumassEvent) -> Long): Chain<OrphanNumassEvent> {
+    return MarkovChain(this.value) {
+        val start = this.value
+        val dt = deadTime(start)
+        do {
+            val next = next()
+        } while (next.timeOffset - start.timeOffset < dt)
+        this.value
+    }
+}
+
+object NumassGenerator {
+
+    val defaultAmplitudeGenerator: RandomGenerator.(OrphanNumassEvent?, Long) -> Short = { _, _ -> ((nextDouble() + 2.0) * 100).toShort() }
+
+    /**
+     * Generate an event chain with fixed count rate
+     * @param cr = count rate in Hz
+     * @param rnd = random number generator
+     * @param amp amplitude generator for the chain. The receiver is rng, first argument is the previous event and second argument
+     * is the delay between the next event. The result is the amplitude in channels
+     */
+    fun generateEvents(
+            cr: Double,
+            rnd: RandomGenerator = defaultGenerator,
+            amp: RandomGenerator.(OrphanNumassEvent?, Long) -> Short = defaultAmplitudeGenerator): Chain<OrphanNumassEvent> {
+        return MarkovChain(OrphanNumassEvent(rnd.amp(null, 0), 0)) { event ->
+            val deltaT = rnd.nextDeltaTime(cr)
+            OrphanNumassEvent(rnd.amp(event, deltaT), event.timeOffset + deltaT)
+        }
+    }
+
+    fun mergeEventChains(vararg chains: Chain<OrphanNumassEvent>): Chain<OrphanNumassEvent> {
+        return listOf(*chains).merge()
+    }
+
+
+    private data class BunchState(var bunchStart: Long = 0, var bunchEnd: Long = 0)
+
+    /**
+     * The chain of bunched events
+     * @param cr count rate of events inside bunch
+     * @param bunchRate number of bunches per second
+     * @param bunchLength the length of bunch
+     */
+    fun generateBunches(
+            cr: Double,
+            bunchRate: Double,
+            bunchLength: Double,
+            rnd: RandomGenerator = defaultGenerator,
+            amp: RandomGenerator.(OrphanNumassEvent?, Long) -> Short = defaultAmplitudeGenerator
+    ): Chain<OrphanNumassEvent> {
+        return StatefulChain(
+                BunchState(0, 0),
+                OrphanNumassEvent(rnd.amp(null, 0), 0)) { event ->
+            if (event.timeOffset >= bunchEnd) {
+                bunchStart = bunchEnd + rnd.nextDeltaTime(bunchRate)
+                bunchEnd = bunchStart + (bunchLength * 1e9).toLong()
+                OrphanNumassEvent(rnd.amp(null, 0), bunchStart)
+            } else {
+                val deltaT = rnd.nextDeltaTime(cr)
+                OrphanNumassEvent(rnd.amp(event, deltaT), event.timeOffset + deltaT)
+            }
+        }
+    }
+
+    /**
+     * Generate a chain using provided spectrum for amplitudes
+     */
+    fun generateEvents(
+            cr: Double,
+            rnd: RandomGenerator = defaultGenerator,
+            spectrum: Table): Chain<OrphanNumassEvent> {
+
+        val channels = DoubleArray(spectrum.size())
+        val values = DoubleArray(spectrum.size())
+        for (i in 0 until spectrum.size()) {
+            channels[i] = spectrum.get(CHANNEL_KEY, i).double
+            values[i] = spectrum.get(COUNT_RATE_KEY, i).double
+        }
+        val distribution = EnumeratedRealDistribution(channels, values)
+
+        return generateEvents(cr, rnd) { _, _ -> distribution.sample().toShort() }
+    }
+}

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

@@ -50,7 +50,7 @@ class PileUpSimulator {
 
     constructor(length: Long, rnd: RandomGenerator, countRate: Double) {
         this.rnd = rnd
-        generator = generateEvents(countRate, rnd)
+        generator = NumassGenerator.generateEvents(countRate, rnd)
         this.pointLength = length
     }
 

numass-main/src/main/kotlin/inr/numass/scripts/Bunches.kt

@@ -2,11 +2,9 @@ package inr.numass.scripts
 
 import hep.dataforge.kodex.buildMeta
 import inr.numass.actions.TimeAnalyzerAction
+import inr.numass.data.NumassGenerator
 import inr.numass.data.api.SimpleNumassPoint
-import inr.numass.data.buildBunchChain
 import inr.numass.data.generateBlock
-import inr.numass.data.generateEvents
-import inr.numass.data.mergeEventChains
 import kotlinx.coroutines.experimental.channels.produce
 import kotlinx.coroutines.experimental.channels.toList
 import kotlinx.coroutines.experimental.runBlocking
@@ -21,10 +19,10 @@ fun main(args: Array<String>) {
 
     val blockchannel = produce {
         (1..num).forEach {
-            val regularChain = generateEvents(cr)
+            val regularChain = NumassGenerator.generateEvents(cr)
-            val bunchChain = buildBunchChain(40.0, 0.01, 5.0)
+            val bunchChain = NumassGenerator.generateBunches(40.0, 0.01, 5.0)
 
-            send(mergeEventChains(regularChain, bunchChain).generateBlock(start.plusNanos(it * length), length))
+            send(NumassGenerator.mergeEventChains(regularChain, bunchChain).generateBlock(start.plusNanos(it * length), length))
         }
     }
 

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

@@ -64,6 +64,8 @@ fun main(args: Array<String>) {
     val histogram = SimpleHistogram(arrayOf(0.0, 0.0), arrayOf(20.0, 100.0))
     histogram.fill(
             TimeAnalyzer().getEventsWithDelay(point, meta)
+                    .filter { it.second <10000 }
+                    .filter { it.first.channel == 0 }
                     .map { arrayOf(it.first.amplitude.toDouble(), it.second.toDouble()/1e3) }
                     .asStream()
     )

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

@@ -6,17 +6,14 @@ import hep.dataforge.kodex.buildMeta
 import hep.dataforge.kodex.coroutineContext
 import hep.dataforge.kodex.generate
 import hep.dataforge.kodex.join
-import hep.dataforge.maths.chain.MarkovChain
 import hep.dataforge.plots.jfreechart.JFreeChartPlugin
 import inr.numass.NumassPlugin
 import inr.numass.actions.TimeAnalyzerAction
+import inr.numass.data.NumassGenerator
 import inr.numass.data.analyzers.TimeAnalyzer
-import inr.numass.data.api.OrphanNumassEvent
 import inr.numass.data.api.SimpleNumassPoint
 import inr.numass.data.generateBlock
-import org.apache.commons.math3.random.JDKRandomGenerator
+import inr.numass.data.withDeadTime
-import org.apache.commons.math3.random.RandomGenerator
-import java.lang.Math.exp
 import java.time.Instant
 
 fun main(args: Array<String>) {
@@ -29,27 +26,11 @@ fun main(args: Array<String>) {
     val num = 2
     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 start = Instant.now()
 
-
     val point = (1..num).map {
         Global.generate {
-            MarkovChain(OrphanNumassEvent(1000, 0)) { event ->
+            NumassGenerator.generateEvents(cr).withDeadTime { (dt*1000).toLong() }.generateBlock(start.plusNanos(it * length), length)
-                val deltaT = rnd.nextDeltaTime(cr * exp(- event.timeOffset.toDouble() / 5e10))
-                //val deltaT = rnd.nextDeltaTime(cr)
-                OrphanNumassEvent(1000, event.timeOffset + deltaT)
-            }.generateBlock(start.plusNanos(it * length), length)
         }
     }.join(Global.coroutineContext) { blocks ->
         SimpleNumassPoint(blocks, 12000.0)
@@ -57,12 +38,14 @@ fun main(args: Array<String>) {
 
 
     val meta = buildMeta {
+        "analyzer" to {
             "t0" to 3000
-        "binNum" to 200
-        "t0Step" to 200
             "chunkSize" to 5000
             "mean" to TimeAnalyzer.AveragingMethod.ARITHMETIC
         }
+        "binNum" to 200
+        "t0.max" to 1e4
+    }
 
     TimeAnalyzerAction().simpleRun(point, meta);
 }

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

@@ -0,0 +1,72 @@
+/*
+ * Copyright  2018 Alexander Nozik.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+package inr.numass.scripts.timeanalysis
+
+import hep.dataforge.context.Global
+import hep.dataforge.fx.output.FXOutputManager
+import hep.dataforge.kodex.buildMeta
+import hep.dataforge.kodex.coroutineContext
+import hep.dataforge.kodex.generate
+import hep.dataforge.kodex.join
+import hep.dataforge.plots.jfreechart.JFreeChartPlugin
+import inr.numass.NumassPlugin
+import inr.numass.actions.TimeAnalyzerAction
+import inr.numass.data.NumassGenerator
+import inr.numass.data.api.SimpleNumassPoint
+import inr.numass.data.generateBlock
+import inr.numass.data.withDeadTime
+import java.time.Instant
+
+fun main(args: Array<String>) {
+    Global.output = FXOutputManager()
+    JFreeChartPlugin().startGlobal()
+    NumassPlugin().startGlobal()
+
+    val cr = 3.0
+    val length = (30000 *1e9).toLong()
+    val num = 1
+    val dt = 6.5
+
+    val start = Instant.now()
+
+    val point = (1..num).map {
+        Global.generate {
+            val events = NumassGenerator
+                    .generateEvents(cr)
+
+            val bunches = NumassGenerator
+                    .generateBunches(6.0, 0.001, 5.0)
+
+            val discharges = NumassGenerator
+                    .generateBunches(50.0,0.001,0.1)
+
+            NumassGenerator.mergeEventChains(events, bunches, discharges).withDeadTime { (dt * 1000).toLong() }.generateBlock(start.plusNanos(it * length), length)
+        }
+    }.join(Global.coroutineContext) { blocks ->
+        SimpleNumassPoint(blocks, 18000.0)
+    }.get()
+
+
+    val meta = buildMeta {
+        "analyzer" to {
+            "t0" to 30000
+        }
+        "binNum" to 200
+    }
+
+    TimeAnalyzerAction().simpleRun(point, meta);
+}