Fix derivative for the spectrum and introduce fit example

2023-01-24 21:07:04 +03:00 · 2023-01-24 21:07:04 +03:00 · 43d79db6bb
commit 43d79db6bb
parent 26f5e7461c
11 changed files with 42 additions and 33 deletions
--- a/build.gradle.kts
+++ b/build.gradle.kts
@ -1,4 +1,5 @@
-import space.kscience.gradle.*
+import space.kscience.gradle.useApache2Licence
+import space.kscience.gradle.useSPCTeam

 plugins {
    id("space.kscience.gradle.project")
@ -17,7 +18,7 @@ allprojects {

 val dataforgeVersion by extra("0.6.0-dev-15")
 val tablesVersion: String by extra("0.2.0-dev-3")
-val kmathVersion by extra("0.3.1-dev-6")
+val kmathVersion by extra("0.3.1-dev-9")
 val visionForgeVersion: String by rootProject.extra("0.3.0-dev-6")


--- a/gradle.properties
+++ b/gradle.properties
@ -13,4 +13,4 @@ org.gradle.parallel=true
 org.gradle.jvmargs=-XX:MaxMetaspaceSize=1G

 toolsVersion=0.13.3-kotlin-1.7.20
-compose.version=1.2.1
+compose.version=1.2.2
--- a/kotlin-js-store/yarn.lock
+++ b/kotlin-js-store/yarn.lock
--- a/numass-data-server/build.gradle.kts
+++ b/numass-data-server/build.gradle.kts
@ -24,6 +24,7 @@ kotlin {
                implementation(project(":numass-data-model"))
                implementation("space.kscience:visionforge-core:$visionForgeVersion")
                implementation("space.kscience:visionforge-plotly:$visionForgeVersion")
+                implementation(compose.runtime)
            }
        }
        jvmMain {
--- a/numass-data-server/src/jvmMain/kotlin/ru/inr/mass/data/server/serverExtensions.kt
+++ b/numass-data-server/src/jvmMain/kotlin/ru/inr/mass/data/server/serverExtensions.kt
@ -2,11 +2,8 @@ package ru.inr.mass.data.server

 import space.kscience.dataforge.context.Context
 import space.kscience.dataforge.misc.DFExperimental
-import space.kscience.visionforge.html.HtmlVisionFragment
-import space.kscience.visionforge.html.ResourceLocation
-import space.kscience.visionforge.html.VisionPage
-import space.kscience.visionforge.html.importScriptHeader
-import space.kscience.visionforge.makeFile
+import space.kscience.visionforge.html.*
+import space.kscience.visionforge.visionManager
 import java.awt.Desktop
 import java.nio.file.Path

@ -19,7 +16,7 @@ public fun Context.makeNumassWebFile(
    show: Boolean = true,
    content: HtmlVisionFragment,
 ): Unit {
-    val actualPath = VisionPage(this, content = content).makeFile(path) { actualPath: Path ->
+    val actualPath = VisionPage(visionManager, content = content).makeFile(path) { actualPath: Path ->
        mapOf(
            "title" to VisionPage.title(title),
            "numassWeb" to VisionPage.importScriptHeader("js/numass-web.js", resourceLocation, actualPath)
--- a/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NBkgSpectrum.kt
+++ b/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NBkgSpectrum.kt
@ -32,8 +32,8 @@ public class NBkgSpectrum(public val source: Spectrum) : DifferentiableSpectrum
    override fun derivativeOrNull(symbols: List<Symbol>): Spectrum? = when {
        symbols.isEmpty() -> this
        symbols.size == 1 -> when (symbols.first()) {
-            norm -> Spectrum { x, arguments -> source(x, arguments) + (arguments[bkg] ?: 0.0) }
-            bkg -> Spectrum { x, arguments -> (arguments[norm] ?: 1.0) * source(x, arguments) }
+            norm -> Spectrum { x, arguments -> source(x, arguments) }
+            bkg -> Spectrum { x, _ -> 1.0 }
            else -> (source as? DifferentiableSpectrum)?.derivativeOrNull(symbols)?.let { NBkgSpectrum(it) }
        }
        else -> null
--- a/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassBeta.kt
+++ b/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassBeta.kt
@ -3,6 +3,8 @@
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
+@file:Suppress("PARAMETER_NAME_CHANGED_ON_OVERRIDE")
+
 package ru.inr.mass.models

 import space.kscience.kmath.expressions.Symbol
--- a/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassResolution.kt
+++ b/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassResolution.kt
@ -12,6 +12,8 @@ import kotlin.math.sqrt
 /**
 * @author [Alexander Nozik](mailto:altavir@gmail.com)
 */
+
+@Suppress("PARAMETER_NAME_CHANGED_ON_OVERRIDE")
 public class NumassResolution(
    public val resA: Double = 8.3e-5,
    public val resB: Double = 0.0,
@ -43,12 +45,12 @@ public class NumassResolution(
 //        else -> ResolutionFunction.getConstantTail()
 //    }

-    private fun getValueFast(E: Double, U: Double): Double {
-        val delta = resA * E
+    private fun getValueFast(e: Double, u: Double): Double {
+        val delta = resA * e
        return when {
-            E - U < 0 -> 0.0
-            E - U > delta -> tailFunction(E, U)
-            else -> (E - U) / delta
+            e - u < 0 -> 0.0
+            e - u > delta -> tailFunction(e, u)
+            else -> (e - u) / delta
        }
    }

@ -57,15 +59,15 @@ public class NumassResolution(
    override val x: Symbol get() = e
    override val y: Symbol get() = u

-    override fun invoke(E: Double, U: Double, arguments: Map<Symbol, Double>): Double {
+    override fun invoke(e: Double, u: Double, arguments: Map<Symbol, Double>): Double {
        if (resB <= 0) {
-            return this.getValueFast(E, U)
+            return this.getValueFast(e, u)
        }
-        val delta = resA * E
+        val delta = resA * e
        return when {
-            E - U < 0 -> 0.0
-            E - U > delta -> tailFunction(E, U)
-            else -> (1 - sqrt(1 - (E - U) / E * resB)) / (1 - sqrt(1 - resA * resB))
+            e - u < 0 -> 0.0
+            e - u > delta -> tailFunction(e, u)
+            else -> (1 - sqrt(1 - (e - u) / e * resB)) / (1 - sqrt(1 - resA * resB))
        }
    }

--- a/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassTransmission.kt
+++ b/numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassTransmission.kt
@ -274,13 +274,13 @@ public class NumassTransmission(
         * Значение полной производной функции потерь с учетом всех неисчезающих
         * порядков
         *
-         * @param X
+         * @param thickness
         * @param eIn
         * @param eOut
         * @return
         */
-        private fun getTotalLossDeriv(X: Double, eIn: Double, eOut: Double): Double {
-            val probs = getLossProbDerivs(X)
+        private fun getTotalLossDeriv(thickness: Double, eIn: Double, eOut: Double): Double {
+            val probs = getLossProbDerivs(thickness)

            var sum = 0.0
            for (i in 1 until probs.size) {
@ -399,8 +399,8 @@ public class NumassTransmission(
 //            return getSingleScatterFunction(exPos, ionPos, exW, ionW, exIonRatio)
 //        }

-        public val trapFunction: (Double, Double) -> Double = { Ei: Double, Ef: Double ->
-            val eps = Ei - Ef
+        public val trapFunction: (Double, Double) -> Double = { ei: Double, ef: Double ->
+            val eps = ei - ef
            if (eps > 10) {
                1.86e-04 * exp(-eps / 25.0) + 5.5e-05
            } else {
--- a/numass-workspace/src/main/kotlin/ru/inr/mass/scripts/fit.kt
+++ b/numass-workspace/src/main/kotlin/ru/inr/mass/scripts/fit.kt
@ -5,6 +5,7 @@ import ru.inr.mass.workspace.buffer
 import ru.inr.mass.workspace.fitWith
 import ru.inr.mass.workspace.generate
 import space.kscience.kmath.expressions.Symbol
+import space.kscience.kmath.expressions.derivative
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.operations.asSequence
 import space.kscience.kmath.optimization.*
@ -28,10 +29,14 @@ suspend fun main() {
        NumassBeta.e0 to 18575.0,
        NumassBeta.msterile2 to 1000.0.pow(2),
        NumassBeta.u2 to 1e-2,
-        NumassTransmission.thickness to 0.1,
+        NumassTransmission.thickness to 0.3,
        NumassTransmission.trap to 1.0
    )

+    listOf(NBkgSpectrum.norm, NBkgSpectrum.bkg, NumassBeta.e0).forEach {
+        println("$it: ${spectrum.derivative(it).invoke(14000.0, args)}")
+    }
+
    val timePerPoint = 30.0

    val strategy = (12000.0..19000.0 step 100.0).asSequence().associateWith { timePerPoint }
@ -41,11 +46,12 @@ suspend fun main() {
    val fit: XYFit = generatedData.fitWith(
        optimizer = QowOptimizer,
        modelExpression = spectrum,
-        startingPoint = args,
-        OptimizationParameters(NBkgSpectrum.norm, NBkgSpectrum.bkg, NumassBeta.e0)
+        startingPoint = args + mapOf(NBkgSpectrum.norm to 8.1e5),
+        OptimizationParameters(NBkgSpectrum.norm, NBkgSpectrum.bkg, NumassBeta.e0),
+        OptimizationIterations(20)
    )

-    val fitResult = fit.resultPoint
+    println("Chi squared/dof: ${fit.chiSquaredOrNull}/${fit.dof}")

    Plotly.plot {
        scatter {
@ -66,7 +72,7 @@ suspend fun main() {
            name = "Fit"
            mode = ScatterMode.lines
            x.buffer = 12000.0..18600.0 step 10.0
-            y.numbers = x.doubles.map { spectrum(it, fitResult) }
+            y.numbers = x.doubles.map { spectrum(it, args + fit.resultPoint) }
        }
    }.makeFile()
 }
--- a/numass-workspace/src/main/kotlin/ru/inr/mass/workspace/dataUtils.kt
+++ b/numass-workspace/src/main/kotlin/ru/inr/mass/workspace/dataUtils.kt
@ -11,8 +11,8 @@ import space.kscience.kmath.misc.FeatureSet
 import space.kscience.kmath.misc.Loggable
 import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.optimization.*
+import space.kscience.kmath.random.RandomGenerator
 import space.kscience.kmath.samplers.PoissonSampler
-import space.kscience.kmath.stat.RandomGenerator
 import space.kscience.kmath.stat.next
 import space.kscience.kmath.structures.asBuffer
 import kotlin.math.sqrt