add cli parser to fit.kt

numass-workspace/build.gradle.kts

@@ -2,7 +2,7 @@ plugins {
     id("space.kscience.gradle.jvm")
     id("com.github.johnrengelman.shadow") version "7.1.2"
     `maven-publish`
-//    application
+    application
 }
 
 kotlin {
@@ -32,5 +32,5 @@ kscience{
 }
 
 //application {
-//    mainClass.set("ru.inr.mass.scripts.Spectrum_serverKt")
+//    mainClass.set("ru.inr.mass.scripts.Get_spectrumKt")
 //}

numass-workspace/src/main/kotlin/ru/inr/mass/scripts/fit.kt

@@ -1,5 +1,17 @@
 package ru.inr.mass.scripts
 
+import com.github.ajalt.clikt.core.CliktCommand
+import com.github.ajalt.clikt.core.context
+import com.github.ajalt.clikt.output.MordantHelpFormatter
+import com.github.ajalt.clikt.parameters.arguments.argument
+import com.github.ajalt.clikt.parameters.arguments.help
+import com.github.ajalt.clikt.parameters.options.default
+import com.github.ajalt.clikt.parameters.options.help
+import com.github.ajalt.clikt.parameters.options.option
+import com.github.ajalt.clikt.parameters.options.prompt
+import com.github.ajalt.clikt.parameters.types.double
+import com.github.ajalt.clikt.parameters.types.int
+import kotlinx.coroutines.runBlocking
 import ru.inr.mass.models.*
 import ru.inr.mass.workspace.buffer
 import ru.inr.mass.workspace.fitWith
@@ -37,47 +49,79 @@ fun parse(filename: String): XYErrorColumnarData<Double, Double, Double> {
         errors.map { it }.asBuffer()
     )
 }
+class Args : CliktCommand() {
 
-//@OptIn(UnstableKMathAPI::class)
+    init {
-@UnstableKMathAPI
+        context {
-suspend fun main() {
+            helpFormatter = { MordantHelpFormatter(it, showDefaultValues = true) }
+        }
+    }
 
-//    val fitParams = FitParams().main(args);
+    val spectrum: String by argument().help("path to spectrum TSV file")
 
+    val norm: Double by option().double().default(8.311751921319484E8).help("NBkgSpectrum.norm")
+    val bkg: Double by option().double().default(1612.626961212948).help("NBkgSpectrum.bkg")
+
+    val mnu2: Double by option().double().default(0.0).help("NumassBeta.mnu2")
+    val e0: Double by option().double().default(18572.0).help("NumassBeta.e0")
+    val msterile2: Double by option().double().default(0.0.pow(2)).help("NumassBeta.msterile2")
+    val u2: Double by option().double().default(1e-2).help("NumassBeta.u2")
+
+    val thickness: Double by option().double().default(0.3).help("NumassTransmission.thickness")
+    val trap: Double by option().double().default(1.0).help("NumassTransmission.trap")
+
+    @UnstableKMathAPI
+    override fun run() {
+        val fitParams: Map<Symbol, Double> = mapOf(
+            NBkgSpectrum.norm to norm,
+            NBkgSpectrum.bkg to bkg,
+            NumassBeta.mnu2 to mnu2,
+            NumassBeta.e0 to e0,
+            NumassBeta.msterile2 to msterile2,
+            NumassBeta.u2 to u2,
+            NumassTransmission.thickness to thickness,
+            NumassTransmission.trap to trap
+        )
+
+        runBlocking {
+            process(spectrum, fitParams)
+        }
+    }
+}
+
+fun main(args: Array<String>) = Args().main(args)
+
+suspend fun fitNumassSpectrum(data: XYErrorColumnarData<Double, Double, Double>, initial: Map<Symbol, Double>): XYFit {
     val spectrum: NBkgSpectrum = SterileNeutrinoSpectrum(
 //        fss = FSS.default,
-          transmission = NumassTransmission(NumassTransmission.trapFunction),
+        transmission = NumassTransmission(NumassTransmission.trapFunction),
 //        resolution = NumassResolution(1.7e-4)
     ).withNBkg()
 
-    val args: Map<Symbol, Double> = mapOf(
+    return data.fitWith(
-        NBkgSpectrum.norm to 8.84e8,
-        NBkgSpectrum.bkg to -1.702,
-        NumassBeta.mnu2 to 0.0,
-        NumassBeta.e0 to 18572.0,
-        NumassBeta.msterile2 to 0.0.pow(2),
-        NumassBeta.u2 to 1e-2,
-        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 }
-
-    val data = parse("/home/chernov/projects/notebooks/manual-fit/06.10.2023")
-
-    val fit: XYFit = data.fitWith(
         optimizer = QowOptimizer,
         modelExpression = spectrum,
-        startingPoint = args,
+        startingPoint = initial,
-        OptimizationParameters(NumassBeta.e0, NBkgSpectrum.norm, NBkgSpectrum.bkg),
+        OptimizationParameters(NumassBeta.e0, NBkgSpectrum.norm, NBkgSpectrum.bkg,
+//            NumassTransmission.trap
+        ),
         OptimizationIterations(20)
     )
+}
+
+
+@UnstableKMathAPI
+suspend fun process(spectrumFile: String, fitParams: Map<Symbol, Double>) {
+
+    val data = parse(spectrumFile)
+
+    val spectrum: NBkgSpectrum = SterileNeutrinoSpectrum(
+//        fss = FSS.default,
+        transmission = NumassTransmission(NumassTransmission.trapFunction),
+//        resolution = NumassResolution(1.7e-4)
+    ).withNBkg()
+
+    val fit = fitNumassSpectrum(data, fitParams)
 
     println(fit.resultPoint)
 
@@ -95,11 +139,15 @@ suspend fun main() {
             scatter {
                 name = "Initial"
                 mode = ScatterMode.lines
-                x.buffer = 12000.0..18600.0 step 50.0
+                x.buffer = data.x
-                y.numbers = x.doubles.map { spectrum(it, args + fit.resultPoint) }
+                y.numbers = x.doubles.map { spectrum(it, fitParams + fit.resultPoint) }
-                File("/home/chernov/projects/notebooks/manual-fit/04.10.2023-fit").printWriter().use { out ->
+                File(spectrumFile + "-fit").printWriter().use { out ->
-                    y.numbers.forEach {
+                    out.println("U_sp\tcounts\tresidials")
-                        out.println(it)
+
+                    data.indices.map{
+                        val value = spectrum(data.x[it], fitParams + fit.resultPoint)
+                        val dif = data.y[it] - value
+                        out.println("${data.x[it]}\t${data.y[it]}\t${dif/data.yErr[it]}")
                     }
                 }
             }
@@ -107,7 +155,7 @@ suspend fun main() {
                 name = "Fit"
                 mode = ScatterMode.lines
                 x.buffer = 12000.0..18600.0 step 10.0
-                y.numbers = x.doubles.map { spectrum(it, args + fit.resultPoint) }
+                y.numbers = x.doubles.map { spectrum(it, fitParams + fit.resultPoint) }
             }
         }
         plot{
@@ -116,7 +164,7 @@ suspend fun main() {
                 mode = ScatterMode.markers
                 x.buffer = data.x
                 y.numbers = data.indices.map{
-                    val value = spectrum(data.x[it], args + fit.resultPoint)
+                    val value = spectrum(data.x[it], fitParams + fit.resultPoint)
                     val dif = data.y[it] - value
                     dif/data.yErr[it]
                 }
@@ -125,7 +173,7 @@ suspend fun main() {
         plot{
             histogram {
                     x.numbers = data.indices.map{
-                        val value = spectrum(data.x[it], args + fit.resultPoint)
+                        val value = spectrum(data.x[it], fitParams + fit.resultPoint)
                         val dif = data.y[it] - value
                         dif/data.yErr[it]
                     }
@@ -138,7 +186,7 @@ suspend fun main() {
                 mode = ScatterMode.lines
                 x.buffer = data.x
                 y.numbers = data.indices.map {
-                    val value = spectrum(data.x[it], args + fit.resultPoint)
+                    val value = spectrum(data.x[it], fitParams + fit.resultPoint)
                     val dif = data.y[it] - value
                     dif / data.yErr[it]
                 }

numass-workspace/src/main/kotlin/ru/inr/mass/scripts/get-spectrum.kt

@@ -1,31 +1,76 @@
 package ru.inr.mass.scripts
 
+import com.github.ajalt.clikt.core.CliktCommand
+import com.github.ajalt.clikt.core.context
+import com.github.ajalt.clikt.output.MordantHelpFormatter
+import com.github.ajalt.clikt.parameters.arguments.argument
+import com.github.ajalt.clikt.parameters.arguments.help
+import com.github.ajalt.clikt.parameters.options.default
+import com.github.ajalt.clikt.parameters.options.help
+import com.github.ajalt.clikt.parameters.options.option
+import com.github.ajalt.clikt.parameters.types.double
 import kotlinx.coroutines.Dispatchers
 import kotlinx.coroutines.async
 import kotlinx.coroutines.runBlocking
 import ru.inr.mass.models.*
+import space.kscience.kmath.data.XYErrorColumnarData
+import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.operations.toTypedArray
 import space.kscience.kmath.real.plus
 import space.kscience.kmath.real.step
+import space.kscience.plotly.models.HoverMode
+import kotlin.math.pow
 
-fun main(args: Array<String>) {
+private class CalcSpectrum : CliktCommand() {
-    val cli = args.map { it.toDouble() }
 
-    val args: Map<Symbol, Double> = mapOf(
+    init {
-        NBkgSpectrum.norm to cli[0],
+        context {
-        NBkgSpectrum.bkg to cli[1],
+            helpFormatter = { MordantHelpFormatter(it, showDefaultValues = true) }
-        NumassBeta.mnu2 to cli[2],
+        }
-        NumassBeta.e0 to cli[3],
+    }
-        NumassBeta.msterile2 to cli[4],
+
-        NumassBeta.u2 to cli[5],
+    val spectrum: String by argument().help("path to spectrum TSV file")
-        NumassTransmission.thickness to cli[6],
+
-        NumassTransmission.trap to cli[7]
+    val norm: Double by option().double().default(8.84e8).help("NBkgSpectrum.norm")
-    )
+    val bkg: Double by option().double().default(-1.702).help("NBkgSpectrum.bkg")
+
+    val mnu2: Double by option().double().default(0.0).help("NumassBeta.mnu2")
+    val e0: Double by option().double().default(18572.0).help("NumassBeta.e0")
+    val msterile2: Double by option().double().default(0.0.pow(2)).help("NumassBeta.msterile2")
+    val u2: Double by option().double().default(1e-2).help("NumassBeta.u2")
+
+    val thickness: Double by option().double().default(0.3).help("NumassTransmission.thickness")
+    val trap: Double by option().double().default(1.0).help("NumassTransmission.trap")
+
+    @UnstableKMathAPI
+    override fun run() {
+        val fitParams: Map<Symbol, Double> = mapOf(
+            NBkgSpectrum.norm to norm,
+            NBkgSpectrum.bkg to bkg,
+            NumassBeta.mnu2 to mnu2,
+            NumassBeta.e0 to e0,
+            NumassBeta.msterile2 to msterile2,
+            NumassBeta.u2 to u2,
+            NumassTransmission.thickness to thickness,
+            NumassTransmission.trap to trap
+        )
+
+        runBlocking {
+            calcSpectrum(spectrum, fitParams)
+        }
+    }
+}
+
+fun main(args: Array<String>) = CalcSpectrum().main(args)
+
+suspend fun calcSpectrum(spectrumFile: String, fitParams: Map<Symbol, Double>) {
+
+    val data = parse(spectrumFile)
+
+    val range = data.x.toTypedArray();
 
     runBlocking(Dispatchers.Default) {
-        val range = (12000.0..16000.0 step 50.0).toTypedArray()
-            .plus((16100.0..18600.0 step 100.0).toTypedArray());
 
         val handles = range.map {
 
@@ -34,7 +79,7 @@ fun main(args: Array<String>) {
                     transmission = NumassTransmission(NumassTransmission.trapFunction),
                 ).withNBkg()
 
-                val res = spectrum.invoke(it, args)
+                val res = spectrum.invoke(it, fitParams)
                 return@async res
             }
         }