refactor numass resolution

dataforge-core/src/main/kotlin/hep/dataforge/tables/ListTable.kt

@@ -136,9 +136,7 @@ class ListTable @JvmOverloads constructor(override val format: TableFormat, poin
          * @throws NamingException
          */
         @Throws(NamingException::class)
-        fun row(vararg values: Any): Builder {
+        fun row(vararg values: Any): Builder = row(ValueMap.of(format.namesAsArray(), *values))
-            return row(ValueMap.of(format.namesAsArray(), *values))
-        }
 
         fun row(values: ValueProvider): Builder {
             val names = format.namesAsArray()
@@ -146,17 +144,12 @@ class ListTable @JvmOverloads constructor(override val format: TableFormat, poin
             return row(ValueMap(map))
         }
 
-        fun row(vararg values: NamedValue): Builder {
+        fun row(vararg values: NamedValue): Builder = row(ValueMap.of(*values))
-            return row(ValueMap.of(*values))
-        }
 
-        fun row(vararg values: Pair<String, Any>): Builder {
+        fun row(vararg values: Pair<String, Any>): Builder =
-            return row(ValueMap.of(values.map { NamedValue.of(it.first, it.second) }))
+            row(ValueMap.of(values.map { NamedValue.of(it.first, it.second) }))
-        }
 
-        fun row(map: Map<String, Any>): Builder {
+        fun row(map: Map<String, Any>): Builder = row(ValueMap.ofMap(map))
-            return row(ValueMap.ofMap(map))
-        }
 
         fun rows(points: Iterable<Values>): Builder {
             for (point in points) {
@@ -170,16 +163,12 @@ class ListTable @JvmOverloads constructor(override val format: TableFormat, poin
             return this
         }
 
-        fun build(): Table {
+        fun build(): ListTable = ListTable(format, points)
-            return ListTable(format, points)
-        }
 
         /**
          * Build table without points name check
          */
-        fun buildUnsafe(): Table {
+        fun buildUnsafe(): Table = ListTable(format, points, true)
-            return ListTable(format, points, true)
-        }
     }
 
     companion object {

dataforge-core/src/main/kotlin/hep/dataforge/tables/Table.kt

@@ -52,8 +52,6 @@ interface Table : NavigableValuesSource, MetaMorph {
      */
     fun getColumn(name: String): Column
 
-
-    @JvmDefault
     override fun toMeta(): Meta {
         val res = MetaBuilder("table")
         res.putNode("format", format.toMeta())

numass-main/src/main/groovy/inr/numass/scripts/ShowTransmission.groovy

@@ -1,77 +0,0 @@
-package inr.numass.scripts
-
-import hep.dataforge.context.Context
-import hep.dataforge.context.Global
-import hep.dataforge.grind.GrindShell
-import hep.dataforge.grind.helpers.PlotHelper
-import hep.dataforge.stat.fit.ParamSet
-import inr.numass.NumassPlugin
-import inr.numass.models.sterile.NumassResolution
-import inr.numass.models.sterile.SterileNeutrinoSpectrum
-
-import static hep.dataforge.grind.Grind.buildMeta
-
-Context ctx = Global.instance()
-ctx.getPlugins().load(FXPlotManager)
-ctx.getPlugins().load(NumassPlugin.class)
-
-GrindShell shell = new GrindShell(ctx)
-
-shell.eval {
-    PlotHelper plot = plots
-
-
-    ParamSet params = new ParamSet(buildMeta {
-        N(value: 2.7e+06, err: 30, lower: 0)
-        bkg(value: 5.0, err: 0.1)
-        E0(value: 18575.0, err: 0.1)
-        mnu2(value: 0, err: 0.01)
-        msterile2(value: 1000**2, err: 1)
-        U2(value: 0.0, err: 1e-3)
-        X(value: 0.0, err: 0.01, lower: 0)
-        trap(value: 1.0, err: 0.05)
-    })
-
-    def meta1 = buildMeta {
-        resolution(width: 8.3e-5, tail: "(0.99797 - 3.05346E-7*D - 5.45738E-10 * D**2 - 6.36105E-14 * D**3)")
-    }
-
-    def meta2 = buildMeta {
-        resolution(width: 8.3e-5, tail: "(0.99797 - 3.05346E-7*D - 5.45738E-10 * D**2 - 6.36105E-14 * D**3)*(1-5e-3*sqrt(E/1000))")
-    }
-
-    def resolution1 = new NumassResolution(
-            ctx,
-            meta1.getMeta("resolution")
-    )
-
-    def resolution2 = new NumassResolution(
-            ctx,
-            meta2.getMeta("resolution")
-    )
-
-    plot.plot(frame: "resolution", from: 13500, to: 19000) { x ->
-        resolution1.value(x, 14000, params)
-    }
-
-    plot.plot(frame: "resolution", from: 13500, to: 19000) { x ->
-        resolution2.value(x, 14000, params)
-    }
-
-    def spectrum1 = new SterileNeutrinoSpectrum(ctx, meta1)
-    def spectrum2 = new SterileNeutrinoSpectrum(ctx, meta2)
-
-    def x = []
-    def y1 = []
-    def y2 = []
-    (13500..19000).step(100).each {
-        x << it
-        y1 << spectrum1.value(it, params)
-        y2 << spectrum2.value(it, params)
-    }
-
-    plot.plot(x, y1, "spectrum1", "spectrum")
-    plot.plot(x, y2, "spectrum2", "spectrum")
-
-}
-

numass-main/src/main/kotlin/inr/numass/models/NBkgSpectrum.kt

@@ -26,7 +26,9 @@ import hep.dataforge.values.Values
  *
  * @author Darksnake
  */
-open class NBkgSpectrum(private val source: ParametricFunction) : AbstractParametricFunction(*combineNamesWithEquals(source.namesAsArray(), *list)) {
+open class NBkgSpectrum(
+    private val source: ParametricFunction,
+) : AbstractParametricFunction(*combineNamesWithEquals(source.namesAsArray(), *list)) {
 
     var counter = MultiCounter(this.javaClass.name)
 
@@ -49,7 +51,7 @@ open class NBkgSpectrum(private val source: ParametricFunction) : AbstractParame
 
     override fun providesDeriv(name: String): Boolean {
         return when (name) {
-            "N","bkg" -> true
+            "N", "bkg" -> true
             else -> this.source.providesDeriv(name)
         }
     }

numass-main/src/main/kotlin/inr/numass/models/sterile/NumassResolution.kt

@@ -13,40 +13,16 @@ import hep.dataforge.values.Values
 import inr.numass.models.ResolutionFunction
 import inr.numass.utils.ExpressionUtils
 import org.apache.commons.math3.analysis.BivariateFunction
-import java.lang.Math.sqrt
+import kotlin.math.sqrt
-import java.util.*
 
 /**
  * @author [Alexander Nozik](mailto:altavir@gmail.com)
  */
-class NumassResolution(context: Context, meta: Meta) : AbstractParametricBiFunction(list) {
+class NumassResolution(
-
+    val resA: Double = 8.3e-5,
-    private val resA: Double = meta.getDouble("A", 8.3e-5)
+    val resB: Double = 0.0,
-    private val resB = meta.getDouble("B", 0.0)
+    val tailFunction: BivariateFunction = ResolutionFunction.getConstantTail(),
-    private val tailFunction: BivariateFunction = when {
+) : AbstractParametricBiFunction(list) {
-        meta.hasValue("tail") -> {
-            val tailFunctionStr = meta.getString("tail")
-            if (tailFunctionStr.startsWith("function::")) {
-                FunctionLibrary.buildFrom(context).buildBivariateFunction(tailFunctionStr.substring(10))
-            } else {
-                BivariateFunction { E, U ->
-                    val binding = HashMap<String, Any>()
-                    binding["E"] = E
-                    binding["U"] = U
-                    binding["D"] = E - U
-                    ExpressionUtils.function(tailFunctionStr, binding)
-                }
-            }
-        }
-        meta.hasValue("tailAlpha") -> {
-            //add polynomial function here
-            val alpha = meta.getDouble("tailAlpha")
-            val beta = meta.getDouble("tailBeta", 0.0)
-            BivariateFunction { E: Double, U: Double -> 1 - (E - U) * (alpha + E / 1000.0 * beta) / 1000.0 }
-
-        }
-        else -> ResolutionFunction.getConstantTail()
-    }
 
     override fun derivValue(parName: String, x: Double, y: Double, set: Values): Double {
         return 0.0
@@ -82,6 +58,35 @@ class NumassResolution(context: Context, meta: Meta) : AbstractParametricBiFunct
     companion object {
 
         private val list = arrayOf<String>() //leaving
+
+        internal fun fromMeta(context: Context, meta: Meta) = NumassResolution(
+            meta.getDouble("A", 8.3e-5),
+            meta.getDouble("B", 0.0),
+            when {
+                meta.hasValue("tail") -> {
+                    val tailFunctionStr = meta.getString("tail")
+                    if (tailFunctionStr.startsWith("function::")) {
+                        FunctionLibrary.buildFrom(context).buildBivariateFunction(tailFunctionStr.substring(10))
+                    } else {
+                        BivariateFunction { E, U ->
+                            val binding = HashMap<String, Any>()
+                            binding["E"] = E
+                            binding["U"] = U
+                            binding["D"] = E - U
+                            ExpressionUtils.function(tailFunctionStr, binding)
+                        }
+                    }
+                }
+                meta.hasValue("tailAlpha") -> {
+                    //add polynomial function here
+                    val alpha = meta.getDouble("tailAlpha")
+                    val beta = meta.getDouble("tailBeta", 0.0)
+                    BivariateFunction { E: Double, U: Double -> 1 - (E - U) * (alpha + E / 1000.0 * beta) / 1000.0 }
+
+                }
+                else -> ResolutionFunction.getConstantTail()
+            }
+        )
     }
 
 }

numass-main/src/main/kotlin/inr/numass/models/sterile/SterileNeutrinoSpectrum.kt

@@ -48,7 +48,7 @@ class SterileNeutrinoSpectrum @JvmOverloads constructor(
         configuration: Meta,
         val source: ParametricBiFunction = NumassBeta(),
         val transmission: ParametricBiFunction = NumassTransmission(context, configuration.getMetaOrEmpty("transmission")),
-        val resolution: ParametricBiFunction = NumassResolution(context, configuration.getMeta("resolution", Meta.empty()))
+        val resolution: ParametricBiFunction = NumassResolution.fromMeta(context, configuration.getMeta("resolution", Meta.empty()))
 ) : AbstractParametricFunction(*list) {
 
 

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

@@ -0,0 +1,155 @@
+/*
+ * 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.models
+
+import hep.dataforge.buildContext
+import hep.dataforge.configure
+import hep.dataforge.fx.FXPlugin
+import hep.dataforge.fx.output.FXOutputManager
+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.plotFrame
+import hep.dataforge.plots.plotFunction
+import hep.dataforge.stat.fit.FitManager
+import hep.dataforge.stat.fit.FitStage
+import hep.dataforge.stat.fit.FitState
+import hep.dataforge.stat.fit.ParamSet
+import hep.dataforge.stat.models.XYModel
+import hep.dataforge.step
+import hep.dataforge.tables.Adapters.X_AXIS
+import hep.dataforge.tables.Table
+import hep.dataforge.values.ValueMap
+import inr.numass.NumassPlugin
+import inr.numass.data.SpectrumAdapter
+import inr.numass.data.SpectrumGenerator
+import inr.numass.models.NBkgSpectrum
+import inr.numass.models.sterile.NumassResolution
+import inr.numass.models.sterile.SterileNeutrinoSpectrum
+import org.apache.commons.math3.analysis.interpolation.SplineInterpolator
+import java.io.PrintWriter
+
+private fun getCustomResolution(): NumassResolution {
+    val correctionDataString = """
+        10	0.376892
+        12	0.1615868
+        13	0.1009648
+        14	0.0677539
+        15	0.0487972
+        16	0.037275
+        17	0.02958922
+        18	0.02511696
+        19	0.02247986
+    """.trimIndent()
+
+    val correctionData = correctionDataString.lines().map { line ->
+        val (u, cor) = line.split("\t")
+        u.toDouble() * 1000 to cor.toDouble()
+    }
+
+    val correctionInterpolation = SplineInterpolator().interpolate(
+        correctionData.map { it.first }.toDoubleArray(),
+        correctionData.map { it.second }.toDoubleArray()
+    )
+    return NumassResolution(tailFunction = { e, _ -> 1.0 - correctionInterpolation.value(e) })
+}
+
+private fun XYModel.plot(name: String, params: ParamSet): Plot {
+    val x = (14000.0..19000.0).step(100.0).toList()
+    val y = x.map { spectrum.value(it, params) }
+    return DataPlot.plot(name, x.toDoubleArray(), y.toDoubleArray())
+}
+
+fun main() {
+
+    val context = buildContext(
+        "NUMASS",
+        NumassPlugin::class.java,
+        FXPlugin::class.java,
+        JFreeChartPlugin::class.java
+    ) {
+        output = FXOutputManager()
+    }
+
+    val params = ParamSet().apply {
+        setPar("N", 8e5, 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", 0.0, 0.01)
+        setPar("trap", 1.0, 0.01)
+    }
+
+    val customResolution = getCustomResolution()
+
+    context.plotFrame("fit", stage = "resolution") {
+        plots.configure {
+            "showLine" to true
+            "showSymbol" to false
+            "showErrors" to false
+            "thickness" to 2.0
+        }
+        plots.setType<DataPlot>()
+
+        plotFunction("custom", 14000.0, 18000.0, 1000) { x ->
+            customResolution.value(x, 14100.0, params)
+        }
+
+        val basicResolution = NumassResolution()
+        plotFunction("basic", 14000.0, 18000.0, 1000) { x ->
+            basicResolution.value(x, 14100.0, params)
+        }
+    }
+
+    val dataSpectrum = NBkgSpectrum(SterileNeutrinoSpectrum(context, Meta.empty(), resolution = customResolution))
+
+    val t = 30 * 50 // time in seconds per point
+
+    val adapter = SpectrumAdapter(Meta.empty())
+    val fm = context.getOrLoad(FitManager::class.java)
+    val x = (14000.0..18500.0).step(100.0).toList()
+    val dataModel = XYModel(Meta.empty(), adapter, dataSpectrum)
+
+    val generator = SpectrumGenerator(dataModel, params, 12316)
+
+    val configuration = x.map { ValueMap.ofPairs(X_AXIS to it, "time" to t) }
+    val data: Table = generator.generateData(configuration)
+
+    val modelSpectrum = NBkgSpectrum(SterileNeutrinoSpectrum(context, Meta.empty(), resolution = NumassResolution()))
+    val fitModel = XYModel(Meta.empty(), adapter, modelSpectrum)
+
+    context.plotFrame("fit", stage = "plots") {
+        plots.configure {
+            "showLine" to true
+            "showSymbol" to false
+            "showErrors" to false
+            "thickness" to 4.0
+        }
+        plots.setType<DataPlot>()
+        +dataModel.plot("Data", params)
+        +fitModel.plot("Fit-start", params)
+    }
+
+    val state = FitState(data, fitModel, params)
+    val res = fm.runStage(state, "QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap")
+    res.printState(PrintWriter(System.out))
+    val resU2 = fm.runStage(res.optState().get(), "QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap", "U2")
+    resU2.printState(PrintWriter(System.out))
+}