Refactor Numass API

build.gradle.kts

@@ -11,7 +11,7 @@ allprojects {
     version = "0.1.0-SNAPSHOT"
 }
 
-val dataforgeVersion by extra("0.3.0-dev-2")
+val dataforgeVersion by extra("0.3.0-dev-3")
 
 apiValidation{
     validationDisabled = true

numass-data-model/build.gradle.kts

@@ -13,6 +13,7 @@ kotlin.sourceSets {
     commonMain {
         dependencies {
             api("hep.dataforge:dataforge-context:$dataforgeVersion")
+            api("hep.dataforge:dataforge-data:$dataforgeVersion")
             api("org.jetbrains.kotlinx:kotlinx-datetime:0.1.1")
         }
     }

numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/MetaBlock.kt

@@ -1,35 +1,37 @@
 package ru.inr.mass.data.api
 
-import kotlinx.coroutines.flow.Flow
-import kotlinx.coroutines.flow.asFlow
-import kotlinx.coroutines.flow.flatMapConcat
+import kotlinx.coroutines.flow.*
 import kotlinx.datetime.Instant
 import kotlin.time.Duration
 import kotlin.time.nanoseconds
 
 public interface ParentBlock : NumassBlock {
-    public val blocks: List<NumassBlock>
+
+    public fun flowBlocks(): Flow<NumassBlock>
 
     /**
-     * If true, the sub-blocks a considered to be isSequential, if not, the sub-blocks are parallel
+     * If true, the sub-blocks a considered to be sequential, if not, the sub-blocks are parallel
      */
-    public val isSequential: Boolean get() = true
+    public val sequential: Boolean get() = true
 }
 
 /**
  * A block constructed from a set of other blocks. Internal blocks are not necessary subsequent. Blocks are automatically sorted.
  * Created by darksnake on 16.07.2017.
  */
-public class MetaBlock(override val blocks: List<NumassBlock>) : ParentBlock {
+public class MetaBlock(private val blocks: List<NumassBlock>) : ParentBlock {
+
+    override fun flowBlocks(): Flow<NumassBlock> = blocks.asFlow()
 
     override val startTime: Instant
         get() = blocks.first().startTime
 
-    override val length: Duration
-        get() = blocks.sumOf { it.length.inNanoseconds }.nanoseconds
+    override suspend fun getLength(): Duration = blocks.sumOf { it.getLength().inNanoseconds }.nanoseconds
 
     override val events: Flow<NumassEvent>
-        get() = blocks.sortedBy { it.startTime }.asFlow().flatMapConcat { it.events }
+        get() = flow {
+            blocks.sortedBy { it.startTime }.forEach { emitAll(it.events) }
+        }
 
     override val frames: Flow<NumassFrame>
         get() = blocks.sortedBy { it.startTime }.asFlow().flatMapConcat { it.frames }

numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/NumassBlock.kt

@@ -24,8 +24,10 @@ import kotlinx.datetime.Instant
 import kotlinx.datetime.plus
 import kotlin.time.Duration
 
-public open class OrphanNumassEvent(public val amplitude: Short, public val timeOffset: Long) :
-    Comparable<OrphanNumassEvent> {
+public open class OrphanNumassEvent(
+    public val amplitude: Short,
+    public val timeOffset: Long,
+) : Comparable<OrphanNumassEvent> {
     public operator fun component1(): Short = amplitude
     public operator fun component2(): Long = timeOffset
 
@@ -43,14 +45,15 @@ public open class OrphanNumassEvent(public val amplitude: Short, public val time
  * @property owner an owner block for this event
  *
  */
-public class NumassEvent(amplitude: Short, timeOffset: Long, public val owner: NumassBlock) :
-    OrphanNumassEvent(amplitude, timeOffset) {
+public class NumassEvent(
+    amplitude: Short,
+    timeOffset: Long,
+    public val owner: NumassBlock,
+) : OrphanNumassEvent(amplitude, timeOffset)
 
-    public val channel: Int get() = owner.channel
+public val NumassEvent.channel: Int get() = owner.channel
 
-    public val time: Instant get() = owner.startTime.plus(timeOffset, DateTimeUnit.NANOSECOND)
-
-}
+public fun NumassEvent.getTime(): Instant = owner.startTime.plus(timeOffset, DateTimeUnit.NANOSECOND)
 
 
 /**
@@ -69,7 +72,7 @@ public interface NumassBlock {
     /**
      * The length of the block
      */
-    public val length: Duration
+    public suspend fun getLength(): Duration
 
     /**
      * Stream of isolated events. Could be empty
@@ -94,10 +97,12 @@ public fun OrphanNumassEvent.adopt(parent: NumassBlock): NumassEvent {
  */
 public class SimpleBlock(
     override val startTime: Instant,
-    override val length: Duration,
+    private val length: Duration,
     rawEvents: Iterable<OrphanNumassEvent>,
 ) : NumassBlock {
 
+    override suspend fun getLength(): Duration = length
+
     private val eventList by lazy { rawEvents.map { it.adopt(this) } }
 
     override val frames: Flow<NumassFrame> get() = emptyFlow()

numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/NumassPoint.kt

@@ -16,31 +16,26 @@
 
 package ru.inr.mass.data.api
 
-import hep.dataforge.meta.*
-import hep.dataforge.names.Name
-import hep.dataforge.names.toName
-import hep.dataforge.provider.Provider
-import kotlinx.coroutines.flow.Flow
-import kotlinx.coroutines.flow.asFlow
-import kotlinx.coroutines.flow.flatMapConcat
-import kotlinx.datetime.Instant
+import hep.dataforge.meta.Meta
+import hep.dataforge.meta.double
+import hep.dataforge.meta.get
+import hep.dataforge.meta.int
+import kotlinx.coroutines.flow.*
 import kotlin.time.Duration
 import kotlin.time.nanoseconds
 
 /**
  * Created by darksnake on 06-Jul-17.
  */
-public interface NumassPoint : ParentBlock, Provider {
+public interface NumassPoint : ParentBlock {
 
     public val meta: Meta
 
-    override val blocks: List<NumassBlock>
-
     /**
      * Distinct map of channel number to corresponding grouping block
      */
-    public val channels: Map<Int, NumassBlock>
-        get() = blocks.toList().groupBy { it.channel }.mapValues { entry ->
+    public suspend fun getChannels(): Map<Int, NumassBlock> =
+        flowBlocks().toList().groupBy { it.channel }.mapValues { entry ->
             if (entry.value.size == 1) {
                 entry.value.first()
             } else {
@@ -48,66 +43,35 @@ public interface NumassPoint : ParentBlock, Provider {
             }
         }
 
-    override fun content(target: String): Map<Name, Any> = when (target) {
-        NUMASS_BLOCK_TARGET -> blocks.mapIndexed { index, numassBlock ->
-            "block[$index]".toName() to numassBlock
-        }.toMap()
-        NUMASS_CHANNEL_TARGET -> channels.mapKeys { "channel[${it.key}]".toName() }
-        else -> super.content(target)
-    }
-
     /**
      * Get the voltage setting for the point
-     *
-     * @return
      */
     public val voltage: Double get() = meta[HV_KEY].double ?: 0.0
 
     /**
      * Get the index for this point in the set
-     * @return
      */
     public val index: Int get() = meta[INDEX_KEY].int ?: -1
 
-    /**
-     * Get the starting time from meta or from first block
-     *
-     * @return
-     */
-    override val startTime: Instant
-        get() = meta[START_TIME_KEY]?.long?.let { Instant.fromEpochMilliseconds(it) } ?: firstBlock.startTime
-
     /**
      * Get the length key of meta or calculate length as a sum of block lengths. The latter could be a bit slow
-     *
-     * @return
      */
-    override val length: Duration
-        get() = blocks.filter { it.channel == 0 }.sumOf { it.length.inNanoseconds }.nanoseconds
+    override suspend fun getLength(): Duration =
+        flowBlocks().filter { it.channel == 0 }.toList().sumOf { it.getLength().inNanoseconds }.nanoseconds
 
     /**
      * Get all events it all blocks as a single sequence
-     *
-     *
      * Some performance analysis of different stream concatenation approaches is given here: https://www.techempower.com/blog/2016/10/19/efficient-multiple-stream-concatenation-in-java/
-     *
-     *
-     * @return
      */
-    override val events: Flow<NumassEvent>
-        get() = blocks.asFlow().flatMapConcat { it.events }
+    override val events: Flow<NumassEvent> get() = flowBlocks().flatMapConcat { it.events }
 
     /**
      * Get all frames in all blocks as a single sequence
-     *
-     * @return
      */
-    override val frames: Flow<NumassFrame>
-        get() = blocks.asFlow().flatMapConcat { it.frames }
+    override val frames: Flow<NumassFrame> get() = flowBlocks().flatMapConcat { it.frames }
 
 
-    override val isSequential: Boolean
-        get() = channels.size == 1
+    public suspend fun isSequential(): Boolean = getChannels().size == 1
 
     override fun toString(): String
 
@@ -126,5 +90,5 @@ public interface NumassPoint : ParentBlock, Provider {
  * Get the first block if it exists. Throw runtime exception otherwise.
  *
  */
-public val NumassPoint.firstBlock: NumassBlock
-    get() = blocks.firstOrNull() ?: throw RuntimeException("The point is empty")
+public suspend fun NumassPoint.getFirstBlock(): NumassBlock =
+    flowBlocks().firstOrNull() ?: throw RuntimeException("The point is empty")

numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/NumassSet.kt

@@ -29,10 +29,9 @@ public interface NumassSet : Iterable<NumassPoint>, Provider {
      *
      * @return
      */
-    public val startTime: Instant
-        get() = meta[NumassPoint.START_TIME_KEY].long?.let {
-            Instant.fromEpochMilliseconds(it)
-        } ?: firstPoint.startTime
+    public suspend fun getStartTime(): Instant = meta[NumassPoint.START_TIME_KEY].long?.let {
+        Instant.fromEpochMilliseconds(it)
+    } ?: firstPoint.startTime
 
     //suspend fun getHvData(): Table?
 

numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/SimpleNumassPoint.kt

@@ -1,20 +1,26 @@
 package ru.inr.mass.data.api
 
 import hep.dataforge.meta.Meta
+import kotlinx.coroutines.flow.Flow
+import kotlinx.coroutines.flow.asFlow
+import kotlinx.datetime.Instant
 
 /**
  * A simple static implementation of NumassPoint
  * Created by darksnake on 08.07.2017.
  */
 public class SimpleNumassPoint(
-    override val blocks: List<NumassBlock>,
+    private val blocks: List<NumassBlock>,
     override val meta: Meta,
-    override val isSequential: Boolean = true,
+    override val startTime: Instant = Instant.DISTANT_PAST,
+    override val sequential: Boolean = true,
 ) : NumassPoint {
+
     init {
-        check(blocks.isNotEmpty()){"No blocks in a point"}
+        check(blocks.isNotEmpty()) { "No blocks in a point" }
     }
 
-    override fun toString(): String = "SimpleNumassPoint(index = ${index}, hv = $voltage)"
+    override fun flowBlocks(): Flow<NumassBlock> = blocks.asFlow()
 
+    override fun toString(): String = "SimpleNumassPoint(index = ${index}, hv = $voltage)"
 }

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

@@ -45,18 +45,17 @@ internal class ProtoNumassPoint(
     private val protoBuilder: () -> Point,
 ) : NumassPoint {
 
-    private val proto: Point get() = protoBuilder()
+    val point by lazy(protoBuilder)
 
-    override val blocks: List<NumassBlock>
-        get() = proto.channels.flatMap { channel ->
-            channel.blocks
-                .map { block -> ProtoBlock(channel.id.toInt(), block, this) }
-                .sortedBy { it.startTime }
-        }
+    override fun flowBlocks() = point.channels.flatMap { channel ->
+        channel.blocks
+            .map { block -> ProtoNumassBlock(channel.id.toInt(), block, this) }
+            .sortedBy { it.startTime }
+    }.asFlow()
 
-    override val channels: Map<Int, NumassBlock>
-        get() = proto.channels.groupBy { it.id.toInt() }.mapValues { entry ->
-            MetaBlock(entry.value.flatMap { it.blocks }.map { ProtoBlock(entry.key, it, this) })
+    override suspend fun getChannels(): Map<Int, NumassBlock> =
+        point.channels.groupBy { it.id.toInt() }.mapValues { entry ->
+            MetaBlock(entry.value.flatMap { it.blocks }.map { ProtoNumassBlock(entry.key, it, this) })
         }
 
     override val voltage: Double get() = meta["external_meta.HV1_value"].double ?: super.voltage
@@ -66,12 +65,11 @@ internal class ProtoNumassPoint(
     override val startTime: Instant
         get() = meta["start_time"].long?.let {
             Instant.fromEpochMilliseconds(it)
-        } ?: super.startTime
+        } ?: Instant.DISTANT_PAST
 
-    override val length: Duration
-        get() = meta["acquisition_time"].double?.let {
-            (it * 1000).toLong().milliseconds
-        } ?: super.length
+    override suspend fun getLength(): Duration = meta["acquisition_time"].double?.let {
+        (it * 1000).toLong().milliseconds
+    } ?: super.getLength()
 
     override fun toString(): String = "ProtoNumassPoint(index = ${index}, hv = $voltage)"
 
@@ -118,10 +116,10 @@ internal class ProtoNumassPoint(
 }
 
 
-public class ProtoBlock(
+public class ProtoNumassBlock(
     override val channel: Int,
     private val block: Point.Channel.Block,
-    parent: NumassPoint? = null,
+    private val parent: NumassPoint? = null,
 ) : NumassBlock {
 
     override val startTime: Instant
@@ -132,7 +130,7 @@ public class ProtoBlock(
             return Instant.fromEpochSeconds(seconds, reminder.toLong())
         }
 
-    override val length: Duration = when {
+    override suspend fun getLength(): Duration = when {
         block.length > 0 -> block.length.nanoseconds
         parent?.meta["acquisition_time"] != null ->
             (parent?.meta["acquisition_time"].double ?: 0.0 * 1000).milliseconds
@@ -164,12 +162,12 @@ public class ProtoBlock(
             emptyFlow()
         }
 
-    private fun ByteString.toShortArray(): ShortArray{
+    private fun ByteString.toShortArray(): ShortArray {
         val shortBuffer = asByteBuffer().asShortBuffer()
-        return if(shortBuffer.hasArray()){
+        return if (shortBuffer.hasArray()) {
             shortBuffer.array()
         } else {
-            ShortArray(shortBuffer.limit()){shortBuffer.get(it)}
+            ShortArray(shortBuffer.limit()) { shortBuffer.get(it) }
         }
     }
 

numass-data-proto/src/test/kotlin/ru/inr/mass/data/proto/TestNumassDirectory.kt

@@ -22,7 +22,7 @@ class TestNumassDirectory {
         assertEquals(ListValue.EMPTY, testSet.meta["comments"].value)
         assertEquals(31, testSet.points.size)
         val point22 = testSet.points.find { it.index == 22 }!!
-        point22.blocks
+        point22.flowBlocks()
         assertEquals("2018-04-13T21:56:09", point22.meta["end_time"].string)
     }
 }

numass-workspace/build.gradle.kts

@@ -1,13 +1,17 @@
 plugins {
     kotlin("jvm")
     id("ru.mipt.npm.kscience")
+    id("com.github.johnrengelman.shadow") version "6.1.0"
 }
 
-kscience{
-    application()
+kscience {
     publish()
 }
 
+kotlin {
+    explicitApi = null
+}
+
 val dataforgeVersion: String by rootProject.extra
 val plotlyVersion: String by rootProject.extra("0.3.1-dev-5")
 val kmathVersion: String by rootProject.extra("0.2.0-dev-6")
@@ -17,4 +21,5 @@ dependencies {
     implementation("hep.dataforge:dataforge-workspace:$dataforgeVersion")
     implementation("kscience.plotlykt:plotlykt-core:$plotlyVersion")
     implementation("kscience.kmath:kmath-histograms:$kmathVersion")
+    implementation("kscience.kmath:kmath-for-real:$kmathVersion")
 }

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

@@ -1,11 +1,14 @@
 package ru.inr.mass.workspace
 
+import hep.dataforge.data.await
+import hep.dataforge.names.toName
+import kscience.plotly.Plotly
 import kscience.plotly.makeFile
-import ru.inr.mass.data.proto.readNumassDirectory
-import java.nio.file.Path
 
-fun main() {
-    val dataPath = Path.of("D:\\Work\\Numass\\data\\2018_04\\Adiabacity_19\\set_4\\")
-    val testSet = NUMASS.context.readNumassDirectory(dataPath)
-    testSet.plotlyPage().makeFile()
+suspend fun main() {
+    val repo = readNumassRepository("D:\\Work\\Numass\\data\\2018_04")
+    //val dataPath = Path.of("D:\\Work\\Numass\\data\\2018_04\\Adiabacity_19\\set_4\\")
+    //val testSet = NUMASS.context.readNumassDirectory(dataPath)
+    val testSet = repo.getData("Adiabacity_19.set_4".toName())!!.await()
+    Plotly.numassDirectory(testSet).makeFile()
 }

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

@@ -6,17 +6,21 @@ import hep.dataforge.context.logger
 import kotlinx.coroutines.flow.collect
 import kotlinx.coroutines.runBlocking
 import kscience.kmath.histogram.UnivariateHistogram
+import kscience.kmath.structures.RealBuffer
+import kscience.kmath.structures.asBuffer
 import ru.inr.mass.data.api.NumassPoint
 
 /**
  * Build an amplitude spectrum
  */
-fun NumassPoint.spectrum(): UnivariateHistogram =
-    UnivariateHistogram.uniform(1.0) {
-        runBlocking {
-            events.collect { put(it.amplitude.toDouble()) }
-        }
+fun NumassPoint.spectrum(): UnivariateHistogram = UnivariateHistogram.uniform(1.0) {
+    runBlocking {
+        events.collect { put(it.amplitude.toDouble()) }
     }
+}
+
+operator fun UnivariateHistogram.component1(): RealBuffer = map {it.position}.toDoubleArray().asBuffer()
+operator fun UnivariateHistogram.component2(): RealBuffer = map { it.value }.toDoubleArray().asBuffer()
 
 fun Collection<NumassPoint>.spectrum(): UnivariateHistogram {
     if (distinctBy { it.voltage }.size != 1) {

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

@@ -1,6 +1,38 @@
 package ru.inr.mass.workspace
 
+import hep.dataforge.data.ActiveDataTree
+import hep.dataforge.data.DataTree
+import hep.dataforge.data.emitStatic
+import hep.dataforge.names.Name
+import hep.dataforge.names.NameToken
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.withContext
 import ru.inr.mass.data.proto.NumassDirectorySet
 import ru.inr.mass.data.proto.readNumassDirectory
+import java.nio.file.Files
+import java.nio.file.Path
+import kotlin.io.path.ExperimentalPathApi
+import kotlin.io.path.exists
+import kotlin.io.path.isDirectory
+import kotlin.io.path.relativeTo
+import kotlin.streams.toList
 
-fun readNumassDirectory(path: String): NumassDirectorySet = NUMASS.context.readNumassDirectory(path)
+fun readNumassDirectory(path: String): NumassDirectorySet = NUMASS.context.readNumassDirectory(path)
+
+@OptIn(ExperimentalPathApi::class)
+suspend fun readNumassRepository(path: String): DataTree<NumassDirectorySet> = ActiveDataTree {
+    val basePath = Path.of(path)
+    @Suppress("BlockingMethodInNonBlockingContext")
+    withContext(Dispatchers.IO) {
+        Files.walk(Path.of(path)).filter {
+            it.isDirectory() && it.resolve("meta").exists()
+        }.toList().forEach { childPath ->
+            val name = Name(childPath.relativeTo(basePath).map { segment ->
+                NameToken(segment.fileName.toString())
+            })
+            val value = NUMASS.context.readNumassDirectory(childPath)
+            emitStatic(name, value, value.meta)
+        }
+    }
+    //TODO add file watcher
+}

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

@@ -39,19 +39,19 @@ fun Plot.hvData(data: List<HVEntry>): Trace = scatter {
     y.numbers = data.map { it.value }
 }
 
-fun NumassDirectorySet.plotlyPage(binSize: Int = 20, range: IntRange = 0..2000): PlotlyPage = Plotly.page {
+fun Plotly.numassDirectory(set: NumassDirectorySet, binSize: Int = 20, range: IntRange = 0..2000): PlotlyPage = Plotly.page {
     h1 {
-        +"Numass point set $path"
+        +"Numass point set ${set.path}"
     }
     h2 {
         +"Amplitude spectrum"
     }
     plot {
-        points.sortedBy { it.index }.forEach {
+        set.points.sortedBy { it.index }.forEach {
             amplitudeSpectrum(it, binSize, range)
         }
     }
-    getHvData()?.let { entries ->
+    set.getHvData()?.let { entries ->
         h2 {
             +"HV"
         }