Fix fx plugins

dataforge-core/src/main/kotlin/hep/dataforge/workspace/FileBasedWorkspace.kt

@@ -14,7 +14,10 @@ import java.security.MessageDigest
 /**
  * Dynamic workspace that is parsed from file using external algorithm. Workspace is reloaded only if file is changed
  */
-class FileBasedWorkspace(private val path: Path, private val parser: (Path) -> Workspace) : DynamicWorkspace(), AutoCloseable {
+class FileBasedWorkspace(
+    private val path: Path,
+    private val parser: (Path) -> Workspace
+) : DynamicWorkspace(), AutoCloseable {
 
     private var watchJob: Job? = null
 
@@ -28,7 +31,7 @@ class FileBasedWorkspace(private val path: Path, private val parser: (Path) -> W
             watchJob = GlobalScope.launch {
                 while (true) {
                     fileMonitor.pollEvents().forEach {
-                        if(it.context() == path) {
+                        if (it.context() == path) {
                             logger.info("Workspace configuration changed. Invalidating.")
                             invalidate()
                         }
@@ -69,15 +72,19 @@ class FileBasedWorkspace(private val path: Path, private val parser: (Path) -> W
          */
         @JvmOverloads
         @JvmStatic
-        fun build(context: Context, path: Path, transformation: (Workspace.Builder) -> Workspace = { it.build() }): FileBasedWorkspace {
+        fun build(
+            context: Context,
+            path: Path,
+            transformation: (Workspace.Builder) -> Workspace = { it.build() }
+        ): FileBasedWorkspace {
             val fileName = path.fileName.toString()
             return context.serviceStream(WorkspaceParser::class.java)
-                    .filter { parser -> parser.listExtensions().stream().anyMatch { fileName.endsWith(it) } }
+                .filter { parser -> parser.listExtensions().stream().anyMatch { fileName.endsWith(it) } }
-                    .findFirst()
+                .findFirst()
-                    .map { parser ->
+                .map { parser ->
-                        FileBasedWorkspace(path) { p -> transformation(parser.parse(context, p)) }
+                    FileBasedWorkspace(path) { p -> transformation(parser.parse(context, p)) }
-                    }
+                }
-                    .orElseThrow { RuntimeException("Workspace parser for $path not found") }
+                .orElseThrow { RuntimeException("Workspace parser for $path not found") }
         }
 
         fun build(path: Path): Workspace {

dataforge-gui/gui-demo/build.gradle

@@ -1,9 +1,15 @@
 plugins{
     id "application"
     id "com.github.johnrengelman.shadow"
+    id "org.openjfx.javafxplugin"
 }
 apply plugin: 'kotlin'
 
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
+}
+
 if (!hasProperty('mainClass')) {
     ext.mainClass = 'hep.dataforge.plots.demo.DemoApp'//"inr.numass.viewer.test.TestApp"
 }

dataforge-plots/plots-jfc/build.gradle

@@ -1,16 +0,0 @@
-//apply plugin: 'org.openjfx.javafxplugin'
-//
-//javafx {
-//    modules = [ 'javafx.controls' ]
-//}
-
-
-description = 'jFreeChart plugin'
-
-dependencies {
-    api 'org.jfree:jfreesvg:3.3'
-    // https://mvnrepository.com/artifact/org.jfree/jfreechart-fx
-    api group: 'org.jfree', name: 'jfreechart-fx', version: '1.0.1'
-
-    api project(":dataforge-plots")
-}

dataforge-plots/plots-jfc/build.gradle.kts

@@ -0,0 +1,19 @@
+plugins {
+    id("org.openjfx.javafxplugin")
+}
+
+javafx {
+    modules = listOf("javafx.controls")
+    version = "11"
+}
+
+description = "jFreeChart plugin"
+
+dependencies {
+    api("org.jfree:jfreesvg:3.4.2")
+    // https://mvnrepository.com/artifact/org.jfree/org.jfree.chart.fx
+    api(group= "org.jfree", name= "jfreechart-fx", version= "1.0.1")
+
+
+    api(project(":dataforge-plots"))
+}

dataforge-plots/plots-viewer/build.gradle

@@ -1,6 +1,12 @@
 plugins {
     id "com.github.johnrengelman.shadow"
     id 'application'
+    id "org.openjfx.javafxplugin"
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
 }
 
 apply plugin: "kotlin"

grind/grind-terminal/build.gradle

@@ -2,6 +2,12 @@ plugins {
     id 'groovy'
     id 'application'
     id "com.github.johnrengelman.shadow"
+    id "org.openjfx.javafxplugin"
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
 }
 
 

numass-control/build.gradle

@@ -1,3 +1,13 @@
+plugins {
+    id("org.openjfx.javafxplugin")
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
+}
+
+
 dependencies {
     api project(':dataforge-plots:plots-jfc')
     api project(':dataforge-control')

numass-control/cryotemp/build.gradle

@@ -1,3 +1,13 @@
+
+plugins{
+    id "org.openjfx.javafxplugin"
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
+}
+
 apply plugin: 'application'
 apply plugin: 'kotlin'
 

numass-control/gun/build.gradle

@@ -1,17 +1,15 @@
-//
-//plugins {
-//    id 'application'
-//    id 'org.openjfx.javafxplugin' version '0.0.5'
-//}
-//
-//javafx {
-//    modules = [ 'javafx.controls' ]
-//}
 
-plugins {
+plugins{
     id 'application'
+    id "org.openjfx.javafxplugin"
 }
 
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
+}
+
+
 version = "0.1.0"
 
 if (!hasProperty('mainClass')) {

numass-control/magnet/build.gradle

@@ -1,4 +1,13 @@
-apply plugin: 'application'
+
+plugins{
+    id 'application'
+    id "org.openjfx.javafxplugin"
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
+}
 
 version = "0.3.0"
 

numass-control/msp/build.gradle

@@ -1,4 +1,12 @@
-apply plugin: 'application'
+plugins{
+    id 'application'
+    id "org.openjfx.javafxplugin"
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
+}
 
 version = "0.4.0"
 

numass-control/vac/build.gradle

@@ -1,4 +1,12 @@
-apply plugin: 'application'
+plugins{
+    id 'application'
+    id "org.openjfx.javafxplugin"
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
+}
 
 version = "0.6.0"
 

numass-control/vac/src/main/kotlin/inr/numass/control/readvac/MeradatVacDevice.kt

@@ -81,9 +81,9 @@ class MeradatVacDevice(context: Context, meta: Meta) : PortSensor(context, meta)
          * String is Hex String, need to convert in ASCII.
          */
             val bytes = BigInteger(inputString, 16).toByteArray()
-            val checksum = bytes.sumBy { it.toInt() }
+            val checksum = bytes.sumOf { it.toInt() }
             var value = Integer.toHexString(-checksum)
-            value = value.substring(value.length - 2).toUpperCase()
+            value = value.substring(value.length - 2).uppercase()
             if (value.length < 2) {
                 value = "0$value"
             }

numass-control/vac/src/main/kotlin/inr/numass/control/readvac/ThyroContVacDevice.kt

@@ -23,7 +23,7 @@ class ThyroContVacDevice(context: Context, meta: Meta) : PortSensor(context, met
         return GenericPortController(context, port) { it.endsWith("\r") }
     }
 
-    private fun String.checksum(): Char = (sumBy { it.code } % 64 + 64).toChar()
+    private fun String.checksum(): Char = (sumOf { it.code } % 64 + 64).toChar()
 
     private fun wrap(str: String): String = buildString {
         append(str)

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

@@ -59,7 +59,7 @@ abstract class AbstractAnalyzer @JvmOverloads constructor(private val processor:
     protected fun getAllEvents(block: NumassBlock): Stream<NumassEvent> {
         return when {
             block.frames.count() == 0L -> block.events
-            processor == null -> throw IllegalArgumentException("Signal processor needed to analyze frames")
+            processor == null -> block.events//throw IllegalArgumentException("Signal processor needed to analyze frames")
             else -> Stream.concat(block.events, block.frames.flatMap { processor.process(block, it) })
         }
     }

numass-main/build.gradle

@@ -1,6 +1,12 @@
 plugins {
     id 'groovy'
     id 'application'
+    id "org.openjfx.javafxplugin"
+}
+
+javafx {
+    modules = ["javafx.controls", "javafx.web"]
+    version = "11"
 }
 
 apply plugin: 'kotlin'

numass-main/src/main/kotlin/inr/numass/scripts/analysis/test_data.kt

@@ -0,0 +1,29 @@
+package inr.numass.scripts.analysis
+
+import hep.dataforge.context.Global
+import hep.dataforge.fx.output.FXOutputManager
+import hep.dataforge.plots.jfreechart.JFreeChartPlugin
+import inr.numass.data.ProtoNumassPoint
+import java.io.File
+
+fun main() {
+    Global.output = FXOutputManager()
+    JFreeChartPlugin().startGlobal()
+
+    val file = File("C:\\Users\\darksnake\\Desktop\\test-data\\p20211012142003(20s)").toPath()
+    val point = ProtoNumassPoint.readFile(file)
+
+    point.events.forEach {
+        println("channel: ${it.owner.channel}, startTime: ${it.owner.startTime} timeOffset: ${it.timeOffset}\t amp: ${it.amplitude}")
+    }
+
+//    Global.plotFrame("compare") {
+//        plotAmplitudeSpectrum(point, "cut") {
+//            "t0" to 3e3
+//            "sortEvents" to true
+//        }
+//        plotAmplitudeSpectrum(point, "uncut")
+//    }
+//
+//    readLine()
+}

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

@@ -18,6 +18,7 @@ package inr.numass.scripts.models
 
 import hep.dataforge.buildContext
 import hep.dataforge.configure
+import hep.dataforge.data.NamedData
 import hep.dataforge.fx.FXPlugin
 import hep.dataforge.fx.output.FXOutputManager
 import hep.dataforge.meta.Meta
@@ -26,23 +27,23 @@ 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.FitHelper
 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.Adapters
 import hep.dataforge.tables.Table
-import hep.dataforge.values.ValueMap
+import hep.dataforge.workspace.FileBasedWorkspace
 import inr.numass.NumassPlugin
-import inr.numass.data.SpectrumAdapter
+import inr.numass.data.analyzers.NumassAnalyzer
-import inr.numass.data.SpectrumGenerator
+import inr.numass.data.api.NumassPoint
 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
+import java.io.File
 
 private fun getCustomResolution(): NumassResolution {
     val correctionDataString = """
@@ -84,16 +85,19 @@ fun main() {
         JFreeChartPlugin::class.java
     ) {
         output = FXOutputManager()
+        properties {
+            setValue("cache.enabled", false)
+        }
     }
 
     val params = ParamSet().apply {
-        setPar("N", 8e5, 6.0, 0.0, Double.POSITIVE_INFINITY)
+        setPar("N", 8e5, 1e4, 0.0, Double.POSITIVE_INFINITY)
-        setPar("bkg", 2.0, 0.03)
+        setPar("bkg", 3.0, 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("X", 0.1, 0.01)
         setPar("trap", 1.0, 0.01)
     }
 
@@ -122,36 +126,63 @@ fun main() {
 
     val t = 30 * 50 // time in seconds per point
 
-    val adapter = SpectrumAdapter(Meta.empty())
+    val adapter = Adapters.buildXYAdapter(
+        NumassPoint.HV_KEY,
+        NumassAnalyzer.COUNT_RATE_KEY,
+        NumassAnalyzer.COUNT_RATE_ERROR_KEY
+    )
+
     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)
+    // define the data model
-
+    val modifiedModel = XYModel(Meta.empty(), adapter, dataSpectrum)
-    val configuration = x.map { ValueMap.ofPairs(X_AXIS to it, "time" to t) }
-    val data: Table = generator.generateData(configuration)
 
+//    // Simulating data via model
+//    val generator = SpectrumGenerator(dataModel, params, 12316)
+//    val configuration = x.map { ValueMap.ofPairs(X_AXIS to it, "time" to t) }
+//    val simulatedData: Table = generator.generateData(configuration)
+//
+//    // Creating a model which does not know about distortion
     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)
+//    }
+//
+//    //fitting
+//    val state = FitState(simulatedData, fitModel, params)
+//    val res = fm.runStage(state, "QOW", FitStage.TASK_RUN, "N", "E0", "bkg")
+//    res.printState(PrintWriter(System.out))
+//    val resWithTrap = fm.runStage(state, "QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap")
+//    resWithTrap.printState(PrintWriter(System.out))
+//    val resWithU2 = fm.runStage(resWithTrap.optState().get(), "QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap", "U2")
+//    resWithU2.printState(PrintWriter(System.out))
 
-    context.plotFrame("fit", stage = "plots") {
+    // loading real data
-        plots.configure {
+    val configPath = File("D:\\Work\\Numass\\sterile2017_11\\workspace.groovy").toPath()
-            "showLine" to true
+    val workspace = FileBasedWorkspace.build(context, configPath)
-            "showSymbol" to false
+
-            "showErrors" to false
+    val data = workspace.runTask("filter", "fill_2").first() as NamedData<Table>
-            "thickness" to 4.0
+    val table = data.get()
-        }
+
-        plots.setType<DataPlot>()
+    //fitting
-        +dataModel.plot("Data", params)
+    FitHelper(context).fit(table).apply {
-        +fitModel.plot("Fit-start", params)
+        model(modifiedModel)
-    }
+        report("fit")
+        params(params)
+        stage("QOW", FitStage.TASK_RUN, "N", "E0", "bkg")
+        stage("QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap")
+        stage("QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap", "U2")
+    }.run()
 
-    val state = FitState(data, fitModel, params)
-    val res = fm.runStage(state, "QOW", FitStage.TASK_RUN, "N", "E0", "bkg")
-    res.printState(PrintWriter(System.out))
-    val resWithTrap = fm.runStage(state, "QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap")
-    resWithTrap.printState(PrintWriter(System.out))
-    val resWithU2 = fm.runStage(resWithTrap.optState().get(), "QOW", FitStage.TASK_RUN, "N", "E0", "bkg", "trap", "U2")
-    resWithU2.printState(PrintWriter(System.out))
 }