Add HV and plots for set

numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/HVEntry.kt

@@ -0,0 +1,27 @@
+package ru.inr.mass.data.proto
+
+import hep.dataforge.io.Envelope
+import hep.dataforge.meta.get
+import hep.dataforge.meta.string
+import kotlinx.datetime.Instant
+import kotlinx.datetime.toInstant
+import kotlinx.io.text.forEachUtf8Line
+
+public data class HVEntry(val timestamp: Instant, val value: Double, val channel: Int = 1) {
+    public companion object {
+        public fun readString(line: String): HVEntry {
+            val (timeStr, channelStr, valueStr) = line.split(' ')
+            return HVEntry(timeStr.toInstant(), valueStr.toDouble(), channelStr.toInt())
+        }
+
+        public fun readEnvelope(envelope: Envelope): List<HVEntry> {
+            check(envelope.meta["type"].string == "voltage"){"Expecting voltage type envelope"}
+            return buildList {
+                envelope.data?.read {
+                    forEachUtf8Line { str -> add(readString(str)) }
+                }
+            }
+        }
+    }
+}
+

numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/NumassDirectorySet.kt

@@ -23,7 +23,7 @@ public class NumassDirectorySet internal constructor(
     override val meta: Meta by lazy {
         val metaFilePath = path / "meta"
         if (metaFilePath.exists()) {
-            val envelope = context.io.readEnvelopeFile(metaFilePath) ?: error("Envelope could not be read from $metaFilePath")
+            val envelope = context.io.readEnvelopeFile(metaFilePath)
             envelope.meta
         } else {
             context.logger.warn { "Meta file does not exist for Numass set $metaFilePath" }
@@ -31,7 +31,7 @@ public class NumassDirectorySet internal constructor(
         }
     }
 
-    override val points: List<NumassPoint> by lazy<List<NumassPoint>> {
+    override val points: List<NumassPoint> by lazy {
         Files.list(path).filter {
             it.fileName.name.startsWith("p")
         }.map { pointPath ->
@@ -43,11 +43,22 @@ public class NumassDirectorySet internal constructor(
             }
         }.toList().filterNotNull()
     }
+
+    @OptIn(DFExperimental::class)
+    public val hvData: List<HVEntry>? get(){
+        val hvFile = path/"voltage"
+        return if( hvFile.exists()){
+            val envelope = context.io.readEnvelopeFile(hvFile)
+            HVEntry.readEnvelope(envelope)
+        } else {
+            null
+        }
+    }
 }
 
 @OptIn(DFExperimental::class)
 public fun Context.readNumassPointFile(path: Path): NumassPoint? {
-    val envelope = io.readEnvelopeFile(path) ?: error("Envelope could not be read from $path")
+    val envelope = io.readEnvelopeFile(path)
     return ProtoNumassPoint.fromEnvelope(envelope)
 }
 

numass-workspace/numass.json

@@ -0,0 +1,34 @@
+{
+    "imports": [
+        "kscience.plotly.*",
+        "kscience.plotly.models.*",
+        "kscience.plotly.JupyterPlotly",
+        "hep.dataforge.meta.*",
+        "kotlinx.html.*",
+        "ru.inr.mass.workspace.*"
+    ],
+    "repositories": [
+        "*mavenLocal",
+        "https://dl.bintray.com/mipt-npm/dataforge",
+        "https://dl.bintray.com/mipt-npm/kscience",
+        "https://dl.bintray.com/mipt-npm/dev"
+    ],
+    "properties": {
+        "v": "0.1.0-SNAPSHOT"
+    },
+    "link": "https://mipt-npm.jetbrains.space/p/numass/code/numass",
+    "dependencies": [
+        "ru.inr.mass:numass-workspace:$v"
+    ],
+    "init": [
+        "DISPLAY(HTML(JupyterPlotly.loadJs().toString()))",
+        "DISPLAY(HTML(\"<p>Plotly.kt jupyter integration is in the development phase. Expect glitches!</p>\"))"
+    ],
+    "renderers": {
+        "kscience.plotly.HtmlFragment": "HTML($it.toString())",
+        "kscience.plotly.Plot": "HTML(JupyterPlotly.renderPlot($it))",
+        "kscience.plotly.PlotlyFragment": "HTML(JupyterPlotly.renderFragment($it))",
+        "kscience.plotly.PlotlyPage": "HTML(JupyterPlotly.renderPage($it), true)",
+        "ru.inr.mass.data.proto.NumassDirectorySet": "HTML(JupyterPlotly.renderPage(${it.plotlyPage}), true)"
+    }
+}

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

@@ -20,7 +20,7 @@ fun NumassPoint.spectrum(): UnivariateHistogram =
 
 fun Collection<NumassPoint>.spectrum(): UnivariateHistogram {
     if (distinctBy { it.voltage }.size != 1) {
-        numass.logger.warn { "Spectrum is generated from points with different hv value: $this" }
+        NUMASS.logger.warn { "Spectrum is generated from points with different hv value: $this" }
     }
 
     return UnivariateHistogram.uniform(1.0) {
@@ -30,4 +30,17 @@ fun Collection<NumassPoint>.spectrum(): UnivariateHistogram {
             }
         }
     }
+}
+
+/**
+ * Re-shape the spectrum with the increased bin size and range. Throws a error if new bin is smaller than before.
+ */
+fun UnivariateHistogram.reShape(
+    binSize: Int,
+    channelRange: IntRange,
+): UnivariateHistogram = UnivariateHistogram.uniform(binSize.toDouble()) {
+    this@reShape.filter { it.position.toInt() in channelRange }.forEach { bin ->
+        if(bin.size > binSize.toDouble()) error("Can't reShape the spectrum with increased binning")
+        putMany(bin.position, bin.value.toLong())
+    }
 }

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

@@ -0,0 +1,6 @@
+package ru.inr.mass.workspace
+
+import ru.inr.mass.data.proto.NumassDirectorySet
+import ru.inr.mass.data.proto.readNumassDirectory
+
+fun readNumassDirectory(path: String): NumassDirectorySet = NUMASS.context.readNumassDirectory(path)

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

@@ -0,0 +1,62 @@
+package ru.inr.mass.workspace
+
+import kotlinx.html.h1
+import kotlinx.html.h2
+import kscience.kmath.histogram.UnivariateHistogram
+import kscience.kmath.misc.UnstableKMathAPI
+import kscience.plotly.*
+import kscience.plotly.models.Bar
+import kscience.plotly.models.Scatter
+import kscience.plotly.models.Trace
+import ru.inr.mass.data.api.NumassPoint
+import ru.inr.mass.data.proto.HVEntry
+import ru.inr.mass.data.proto.NumassDirectorySet
+
+@OptIn(UnstableKMathAPI::class)
+fun Trace.fromSpectrum(histogram: UnivariateHistogram) {
+    x.numbers = histogram.map { it.position }
+    y.numbers = histogram.map { it.value }
+}
+
+/**
+ *
+ */
+@OptIn(UnstableKMathAPI::class)
+fun Plot.spectrum(name: String, histogram: UnivariateHistogram): Bar = bar {
+    this.name = name
+    fromSpectrum(histogram)
+}
+
+fun Plot.amplitudeSpectrum(point: NumassPoint, binSize: Int = 20, range: IntRange = 0..4096, name: String = point.toString()): Bar = bar {
+    spectrum(name, point.spectrum().reShape(binSize, range))
+}
+
+/**
+ * Generate a plot from hv data
+ */
+fun Plot.hvData(data: List<HVEntry>): Scatter = scatter {
+    x.strings = data.map { it.timestamp.toString() }
+    y.numbers = data.map { it.value }
+}
+
+fun NumassDirectorySet.plotlyPage(binSize: Int = 20, range: IntRange = 0..4096): PlotlyPage = Plotly.page {
+    h1 {
+        +"Numass point set $path"
+    }
+    h2{
+        +"Amplitude spectrum"
+    }
+    plot {
+        points.forEach {
+            amplitudeSpectrum(it,binSize, range)
+        }
+    }
+    hvData?.let {entries->
+        h2{
+            +"HV"
+        }
+        plot {
+            hvData(entries)
+        }
+    }
+}

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

@@ -3,8 +3,8 @@ package ru.inr.mass.workspace
 import hep.dataforge.workspace.Workspace
 import ru.inr.mass.data.proto.NumassProtoPlugin
 
-val numass = Workspace {
+val NUMASS = Workspace {
-    context("numass") {
+    context("NUMASS") {
         plugin(NumassProtoPlugin)
     }
 }