Minor changes

build.gradle

@@ -1,5 +1,5 @@
 buildscript {
-    ext.kotlin_version = "1.2.61"
+    ext.kotlin_version = "1.2.70"
     repositories {
         jcenter()
         maven {

numass-control/dante/src/main/kotlin/inr/numass/control/dante/DanteTest.kt

@@ -23,7 +23,7 @@ import hep.dataforge.meta.KMetaBuilder
 import hep.dataforge.meta.buildMeta
 import hep.dataforge.nullable
 import hep.dataforge.plots.data.DataPlot
-import hep.dataforge.plots.output.plot
+import hep.dataforge.plots.output.plotFrame
 import hep.dataforge.tables.Adapters
 import inr.numass.data.analyzers.NumassAnalyzer
 import inr.numass.data.analyzers.SimpleAnalyzer
@@ -78,7 +78,7 @@ fun NumassBlock.plotAmplitudeSpectrum(plotName: String = "spectrum", frameName:
     val lo = meta.optNumber("window.lo").nullable?.toInt()
     val up = meta.optNumber("window.up").nullable?.toInt()
     val data = SimpleAnalyzer().getAmplitudeSpectrum(this, meta.getMetaOrEmpty("spectrum")).withBinning(binning, lo, up)
-    context.plot(plotName) {
+    context.plotFrame(plotName) {
         val valueAxis = if (meta.getBoolean("normalize", false)) {
             NumassAnalyzer.COUNT_RATE_KEY
         } else {

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

@@ -23,7 +23,7 @@ import hep.dataforge.meta.KMetaBuilder
 import hep.dataforge.meta.buildMeta
 import hep.dataforge.nullable
 import hep.dataforge.plots.data.DataPlot
-import hep.dataforge.plots.output.plot
+import hep.dataforge.plots.output.plotFrame
 import hep.dataforge.tables.Adapters
 import inr.numass.data.analyzers.NumassAnalyzer
 import inr.numass.data.analyzers.SmartAnalyzer
@@ -37,7 +37,7 @@ fun NumassBlock.plotAmplitudeSpectrum(plotName: String = "spectrum", frameName:
     val lo = meta.optNumber("window.lo").nullable?.toInt()
     val up = meta.optNumber("window.up").nullable?.toInt()
     val data = SmartAnalyzer().getAmplitudeSpectrum(this, meta.getMetaOrEmpty("spectrum")).withBinning(binning, lo, up)
-    context.plot(plotName) {
+    context.plotFrame(plotName) {
         val valueAxis = if (meta.getBoolean("normalize", false)) {
             NumassAnalyzer.COUNT_RATE_KEY
         } else {

numass-main/src/main/kotlin/inr/numass/models/mc/BetaSampler.kt

@@ -4,7 +4,7 @@ import hep.dataforge.context.Global
 import hep.dataforge.maths.chain.Chain
 import hep.dataforge.meta.buildMeta
 import hep.dataforge.plots.data.XYFunctionPlot
-import hep.dataforge.plots.output.plot
+import hep.dataforge.plots.output.plotFrame
 import hep.dataforge.stat.PolynomialDistribution
 import hep.dataforge.stat.fit.ParamSet
 import inr.numass.NumassPlugin
@@ -46,7 +46,7 @@ fun main(args: Array<String>) {
         50 * distribution.density(18600.0 - it)
     }
 
-    Global.plot("beta") {
+    Global.plotFrame("beta") {
         add(spectrumPlot)
         add(distributionPlot)
     }

numass-main/src/main/kotlin/inr/numass/models/misc/LossCalculator.kt

@@ -124,7 +124,7 @@ object LossCalculator {
      * @param X
      * @return
      */
-    fun getLossProbabilities(x: Double): List<Double> {
+    fun calculateLossProbabilities(x: Double): List<Double> {
         val res = ArrayList<Double>()
         var prob: Double
         if (x > 0) {
@@ -151,6 +151,8 @@ object LossCalculator {
         return res
     }
 
+    fun getLossProbabilities(x: Double): List<Double> = lossProbCache.getOrPut(x) { calculateLossProbabilities(x) }
+
     fun getLossProbability(order: Int, X: Double): Double {
         if (order == 0) {
             return if (X > 0) {

numass-main/src/main/kotlin/inr/numass/scripts/models/IntegralSpectrum.kt

@@ -24,7 +24,7 @@ import hep.dataforge.meta.Meta
 import hep.dataforge.plots.Plot
 import hep.dataforge.plots.data.DataPlot
 import hep.dataforge.plots.jfreechart.JFreeChartPlugin
-import hep.dataforge.plots.output.plot
+import hep.dataforge.plots.output.plotFrame
 import hep.dataforge.stat.fit.FitManager
 import hep.dataforge.stat.fit.FitStage
 import hep.dataforge.stat.fit.FitState
@@ -127,7 +127,7 @@ fun main(args: Array<String>) {
     }
 
 
-    context.plot("fit", stage = "plots") {
+    context.plotFrame("fit", stage = "plots") {
         plots.configure {
             "showLine" to true
             "showSymbol" to false

numass-main/src/main/kotlin/inr/numass/scripts/threshold/FitWithPower.kt

@@ -0,0 +1,66 @@
+/*
+ * 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.threshold
+
+import hep.dataforge.buildContext
+import hep.dataforge.fx.output.FXOutputManager
+import hep.dataforge.io.DirectoryOutput
+import hep.dataforge.io.plus
+import hep.dataforge.meta.buildMeta
+import hep.dataforge.nullable
+import hep.dataforge.plots.data.DataPlot
+import hep.dataforge.plots.jfreechart.JFreeChartPlugin
+import hep.dataforge.plots.plotData
+import hep.dataforge.storage.files.FileStorage
+import hep.dataforge.tables.Adapters
+import inr.numass.NumassPlugin
+import inr.numass.data.api.NumassSet
+import inr.numass.data.storage.NumassDirectory
+import inr.numass.displayChart
+import inr.numass.subthreshold.Threshold
+
+fun main(args: Array<String>) {
+    val context = buildContext("NUMASS", NumassPlugin::class.java, JFreeChartPlugin::class.java) {
+        rootDir = "D:\\Work\\Numass\\sterile\\2017_05"
+        dataDir = "D:\\Work\\Numass\\data\\2017_05"
+        output = FXOutputManager() + DirectoryOutput()
+    }
+
+    val storage = NumassDirectory.read(context, "Fill_2") as? FileStorage ?: error("Storage not found")
+
+    val meta = buildMeta {
+        "delta" to -200
+        "method" to "pow"
+        "t0" to 15e3
+        "window.lo" to 400
+        "window.up" to 1600
+    }
+
+    val frame = displayChart("correction").apply {
+        plots.setType<DataPlot>()
+    }
+
+    listOf("set_2", "set_3", "set_4", "set_5").forEach { setName ->
+        val set = storage.provide(setName, NumassSet::class.java).nullable ?: error("Set does not exist")
+
+        val correctionTable = Threshold.calculateSubThreshold(set, meta).filter {
+            it.getDouble("correction") in (1.0..1.2)
+        }
+
+        frame.plotData(setName, correctionTable, Adapters.buildXYAdapter("U", "correction"))
+    }
+}

numass-main/src/main/kotlin/inr/numass/scripts/tristan/FitTextTristanFiles.kt

@@ -0,0 +1,162 @@
+/*
+ * 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.tristan
+
+import hep.dataforge.buildContext
+import hep.dataforge.configure
+import hep.dataforge.data.DataNode
+import hep.dataforge.fx.output.FXOutputManager
+import hep.dataforge.io.ColumnedDataReader
+import hep.dataforge.io.DirectoryOutput
+import hep.dataforge.io.output.stream
+import hep.dataforge.io.plus
+import hep.dataforge.meta.Meta
+import hep.dataforge.meta.buildMeta
+import hep.dataforge.plots.data.DataPlot
+import hep.dataforge.plots.jfreechart.JFreeChartPlugin
+import hep.dataforge.plots.output.plotFrame
+import hep.dataforge.stat.fit.FitHelper
+import hep.dataforge.stat.fit.ParamSet
+import hep.dataforge.tables.*
+import hep.dataforge.values.ValueType
+import inr.numass.NumassPlugin
+import inr.numass.actions.MergeDataAction
+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.NumassPoint.Companion.HV_KEY
+import java.io.PrintWriter
+import java.nio.file.Files
+import java.util.function.Predicate
+
+fun main(args: Array<String>) {
+    val context = buildContext("NUMASS") {
+        plugin<NumassPlugin>()
+        plugin<JFreeChartPlugin>()
+        rootDir = "D:\\Work\\Numass\\TristanText\\"
+        dataDir = "D:\\Work\\Numass\\TristanText\\data\\"
+        output = FXOutputManager() + DirectoryOutput()
+    }
+    context.load<NumassPlugin>()
+
+
+    val tables = DataNode.build<Table> {
+        name = "tristan"
+        Files.list(context.dataDir).forEach {
+            val name = ".*(set_\\d+).*".toRegex().matchEntire(it.fileName.toString())!!.groupValues[1]
+            val table = ColumnedDataReader(Files.newInputStream(it), HV_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY).toTable()
+                    .addColumn(LENGTH_KEY, ValueType.NUMBER) { 30 }
+                    .addColumn(COUNT_KEY, ValueType.NUMBER) { getDouble(COUNT_RATE_KEY) * 30 }
+            putStatic(name, table)
+        }
+    }
+    val adapter = Adapters.buildXYAdapter(HV_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY)
+
+    context.plotFrame("raw", "plots") {
+        configure {
+            "legend.show" to false
+        }
+        plots.configure {
+            "showLine" to true
+            "showSymbol" to false
+        }
+        tables.forEach { (key, value) ->
+            add(DataPlot.plot(key, value, adapter))
+        }
+    }
+
+    context.plotFrame("raw_normalized", "plots") {
+        configure {
+            "legend.show" to false
+        }
+        plots.configure {
+            "showLine" to true
+            "showSymbol" to false
+        }
+        tables.forEach { (key, table) ->
+            val norming = table.find { it.getDouble(HV_KEY) == 13000.0 }!!.getDouble(COUNT_RATE_KEY)
+            val normalizedTable = table
+                    .replaceColumn(COUNT_RATE_KEY) { getDouble(COUNT_RATE_KEY) / norming }
+                    .replaceColumn(COUNT_RATE_ERROR_KEY) { getDouble(COUNT_RATE_ERROR_KEY) / norming }
+            add(DataPlot.plot(key, normalizedTable, adapter))
+        }
+    }
+
+    val merge = MergeDataAction.runGroup(context, tables, Meta.empty()).get()
+
+    val filtered = Tables.filter(merge,
+            Predicate {
+                val hv = it.getDouble(HV_KEY)
+                hv > 12200.0 && (hv < 15500 || hv > 16500)
+            }
+    )
+
+    context.plotFrame("merge", "plots") {
+        plots.configure {
+            "showLine" to true
+            "showSymbol" to false
+        }
+        add(DataPlot.plot("merge", merge, adapter))
+    }
+
+    val meta = buildMeta {
+        "model" to {
+            "modelName" to "sterile"
+            "resolution" to {
+                "width" to 8.3e-5
+                "tail" to "function::numass.resolutionTail.2017.mod"
+            }
+            "transmission" to {
+                "trapping" to "function::numass.trap.nominal"
+            }
+        }
+        "stage" to { "freePars" to listOf("N", "bkg", "E0") }
+    }
+
+    val params = ParamSet().apply {
+        setPar("N", 4e4, 6.0, 0.0, Double.POSITIVE_INFINITY)
+        setPar("bkg", 2.0, 0.03)
+        setPar("E0", 18575.0, 1.0)
+        setPar("mnu2", 0.0, 1.0)
+        setParValue("msterile2", (1000 * 1000).toDouble())
+        setPar("U2", 0.0, 1e-3)
+        setPar("X", 0.1, 0.01)
+        setPar("trap", 1.0, 0.01)
+    }
+
+    context.output["numass.fit", "text"].stream.use { out ->
+        val log = context.history.getChronicle("log")
+        val writer = PrintWriter(out)
+        writer.printf("%n*** META ***%n")
+        writer.println(meta.toString())
+        writer.flush()
+        FitHelper(context)
+                .fit(filtered, meta)
+                .setListenerStream(out)
+                .report(log)
+                .apply {
+                    params(params)
+                }.run()
+
+        writer.println()
+        log.entries.forEach { entry -> writer.println(entry.toString()) }
+        writer.println()
+
+    }
+
+}

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

@@ -11,11 +11,14 @@ import hep.dataforge.tables.ListTable
 import hep.dataforge.tables.Table
 import hep.dataforge.values.ValueMap
 import hep.dataforge.values.Values
+import inr.numass.data.analyzers.NumassAnalyzer
 import inr.numass.data.analyzers.NumassAnalyzer.Companion.CHANNEL_KEY
 import inr.numass.data.analyzers.NumassAnalyzer.Companion.COUNT_RATE_KEY
+import inr.numass.data.analyzers.SmartAnalyzer
 import inr.numass.data.analyzers.TimeAnalyzer
 import inr.numass.data.analyzers.withBinning
 import inr.numass.data.api.NumassPoint
+import inr.numass.data.api.NumassSet
 import inr.numass.data.api.SimpleNumassPoint
 import inr.numass.data.storage.NumassDataLoader
 import inr.numass.data.storage.NumassDirectory
@@ -137,6 +140,7 @@ object Threshold {
     }
 
 
+
     /**
      * Exponential function $a e^{\frac{x}{\sigma}}$
      */
@@ -226,9 +230,12 @@ object Threshold {
         }
     }
 
-    fun calculateSubThreshold(spectra: Map<Double, Table>, config: Meta): Table {
+    fun calculateSubThreshold(set: NumassSet, config: Meta, analyzer: NumassAnalyzer = SmartAnalyzer()): Table {
         return ListTable.Builder().apply {
-            spectra.forEach { voltage, spectrum -> row(calculateSubThreshold(spectrum, voltage, config)) }
+            set.forEach{
+                val spectrum = analyzer.getAmplitudeSpectrum(it,config)
+                row(calculateSubThreshold(spectrum,it.voltage,config))
+            }
         }.build()
     }
 

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

@@ -16,6 +16,7 @@ import hep.dataforge.plots.data.XYFunctionPlot
 import hep.dataforge.plots.jfreechart.JFreeChartFrame
 import hep.dataforge.plots.output.PlotOutput
 import hep.dataforge.plots.output.plot
+import hep.dataforge.plots.output.plotFrame
 import hep.dataforge.stat.fit.FitHelper
 import hep.dataforge.stat.fit.FitResult
 import hep.dataforge.stat.models.XYModel
@@ -351,7 +352,7 @@ val histogramTask = task("histogram") {
         context.output.render(table, stage = "numass.histogram", name = name, meta = meta)
 
         if (meta.getBoolean("plot", false)) {
-            context.plot("$name.plot", stage = "numass.histogram") {
+            context.plotFrame("$name.plot", stage = "numass.histogram") {
                 plots.setType<DataPlot>()
                 plots.configure {
                     "showSymbol" to false