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Migrate model to MPP

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This commit is contained in:
Alexander Nozik 2021-01-29 19:23:16 +03:00
parent edcc3e4956
commit 71e55ed5fc
19 changed files with 174 additions and 271 deletions
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2
build.gradle.kts
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@ -8,7 +8,7 @@ allprojects {
}
group = "ru.inr.mass"
version = "0.1.0"
version = "0.1.0-SNAPSHOT"
}
val dataforgeVersion by extra("0.3.0-dev-2")

15
numass-data-model/build.gradle.kts
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@ -1,14 +1,21 @@
plugins {
kotlin("jvm")
kotlin("multiplatform")
id("ru.mipt.npm.kscience")
}
kscience{
kscience {
publish()
}
val dataforgeVersion: String by rootProject.extra
dependencies {
api("hep.dataforge:dataforge-context:$dataforgeVersion")
kotlin.sourceSets {
commonMain {
dependencies {
api("hep.dataforge:dataforge-context:$dataforgeVersion")
api("org.jetbrains.kotlinx:kotlinx-datetime:0.1.1")
}
}
}

9
numass-data-model/src/main/kotlin/ru/inr/mass/data/api/MetaBlock.kt → numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/MetaBlock.kt
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@ -2,11 +2,10 @@ package ru.inr.mass.data.api
import kotlinx.coroutines.flow.Flow
import kotlinx.coroutines.flow.asFlow
import kotlinx.coroutines.flow.flatMap
import kotlinx.coroutines.flow.flatMapConcat
import java.time.Duration
import java.time.Instant
import java.util.stream.Stream
import kotlinx.datetime.Instant
import kotlin.time.Duration
import kotlin.time.nanoseconds
public interface ParentBlock : NumassBlock {
public val blocks: List<NumassBlock>
@ -27,7 +26,7 @@ public class MetaBlock(override val blocks: List<NumassBlock>) : ParentBlock {
get() = blocks.first().startTime
override val length: Duration
get() = Duration.ofNanos(blocks.stream().mapToLong { block -> block.length.toNanos() }.sum())
get() = blocks.sumOf { it.length.inNanoseconds }.nanoseconds
override val events: Flow<NumassEvent>
get() = blocks.sortedBy { it.startTime }.asFlow().flatMapConcat { it.events }

24
numass-data-model/src/main/kotlin/ru/inr/mass/data/api/NumassBlock.kt → numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/NumassBlock.kt
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@ -19,8 +19,10 @@ package ru.inr.mass.data.api
import kotlinx.coroutines.flow.Flow
import kotlinx.coroutines.flow.asFlow
import kotlinx.coroutines.flow.emptyFlow
import java.time.Duration
import java.time.Instant
import kotlinx.datetime.DateTimeUnit
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> {
@ -46,7 +48,7 @@ public class NumassEvent(amplitude: Short, timeOffset: Long, public val owner: N
public val channel: Int get() = owner.channel
public val time: Instant get() = owner.startTime.plusNanos(timeOffset)
public val time: Instant get() = owner.startTime.plus(timeOffset, DateTimeUnit.NANOSECOND)
}
@ -103,12 +105,14 @@ public class SimpleBlock(
override val events: Flow<NumassEvent> get() = eventList.asFlow()
public companion object {
public suspend fun produce(
startTime: Instant,
length: Duration,
producer: suspend () -> Iterable<OrphanNumassEvent>,
): SimpleBlock {
return SimpleBlock(startTime, length, producer())
}
}
}
public suspend fun SimpleBlock(
startTime: Instant,
length: Duration,
producer: suspend () -> Iterable<OrphanNumassEvent>,
): SimpleBlock {
return SimpleBlock(startTime, length, producer())
}

19
numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/NumassFrame.kt Normal file
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@ -0,0 +1,19 @@
package ru.inr.mass.data.api
import kotlinx.datetime.Instant
import kotlin.time.Duration
/**
* The continuous frame of digital detector data
* Created by darksnake on 06-Jul-17.
* @param time The absolute start time of the frame
* @param tickSize The time interval per tick
* @param signal The buffered signal shape in ticks
*/
public class NumassFrame(
public val time: Instant,
public val tickSize: Duration,
public val signal: ShortArray,
) {
public val length: Duration get() = tickSize * signal.size
}

14
numass-data-model/src/main/kotlin/ru/inr/mass/data/api/NumassPoint.kt → numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/NumassPoint.kt
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@ -22,11 +22,10 @@ import hep.dataforge.names.toName
import hep.dataforge.provider.Provider
import kotlinx.coroutines.flow.Flow
import kotlinx.coroutines.flow.asFlow
import kotlinx.coroutines.flow.flatMap
import kotlinx.coroutines.flow.flatMapConcat
import java.time.Duration
import java.time.Instant
import java.util.stream.Stream
import kotlinx.datetime.Instant
import kotlin.time.Duration
import kotlin.time.nanoseconds
/**
* Created by darksnake on 06-Jul-17.
@ -76,7 +75,7 @@ public interface NumassPoint : ParentBlock, Provider {
* @return
*/
override val startTime: Instant
get() = meta[START_TIME_KEY]?.long?.let { Instant.ofEpochMilli(it) } ?: firstBlock.startTime
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
@ -84,8 +83,7 @@ public interface NumassPoint : ParentBlock, Provider {
* @return
*/
override val length: Duration
get() = Duration.ofNanos(blocks.stream().filter { it.channel == 0 }.mapToLong { it -> it.length.toNanos() }
.sum())
get() = blocks.filter { it.channel == 0 }.sumOf { it.length.inNanoseconds }.nanoseconds
/**
* Get all events it all blocks as a single sequence
@ -111,6 +109,8 @@ public interface NumassPoint : ParentBlock, Provider {
override val isSequential: Boolean
get() = channels.size == 1
override fun toString(): String
public companion object {
public const val NUMASS_BLOCK_TARGET: String = "block"
public const val NUMASS_CHANNEL_TARGET: String = "channel"

4
numass-data-model/src/main/kotlin/ru/inr/mass/data/api/NumassSet.kt → numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/NumassSet.kt
View File

@ -11,7 +11,7 @@ import hep.dataforge.meta.long
import hep.dataforge.names.Name
import hep.dataforge.names.toName
import hep.dataforge.provider.Provider
import java.time.Instant
import kotlinx.datetime.Instant
/**
* A single set of numass measurements together with metadata.
@ -31,7 +31,7 @@ public interface NumassSet : Iterable<NumassPoint>, Provider {
*/
public val startTime: Instant
get() = meta[NumassPoint.START_TIME_KEY].long?.let {
Instant.ofEpochMilli(it)
Instant.fromEpochMilliseconds(it)
} ?: firstPoint.startTime
//suspend fun getHvData(): Table?

4
numass-data-model/src/main/kotlin/ru/inr/mass/data/api/SignalProcessor.kt → numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/SignalProcessor.kt
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@ -1,11 +1,11 @@
package ru.inr.mass.data.api
import java.util.stream.Stream
import kotlinx.coroutines.flow.Flow
/**
* An ancestor to numass frame analyzers
* Created by darksnake on 07.07.2017.
*/
public interface SignalProcessor {
public fun analyze(frame: NumassFrame): Stream<NumassEvent>
public fun analyze(frame: NumassFrame): Flow<NumassEvent>
}

20
numass-data-model/src/commonMain/kotlin/ru/inr/mass/data/api/SimpleNumassPoint.kt Normal file
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@ -0,0 +1,20 @@
package ru.inr.mass.data.api
import hep.dataforge.meta.Meta
/**
* A simple static implementation of NumassPoint
* Created by darksnake on 08.07.2017.
*/
public class SimpleNumassPoint(
override val blocks: List<NumassBlock>,
override val meta: Meta,
override val isSequential: Boolean = true,
) : NumassPoint {
init {
check(blocks.isNotEmpty()){"No blocks in a point"}
}
override fun toString(): String = "SimpleNumassPoint(index = ${index}, hv = $voltage)"
}

27
numass-data-model/src/main/kotlin/ru/inr/mass/data/api/NumassFrame.kt
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@ -1,27 +0,0 @@
package ru.inr.mass.data.api
import java.nio.ShortBuffer
import java.time.Duration
import java.time.Instant
/**
* The continuous frame of digital detector data
* Created by darksnake on 06-Jul-17.
*/
public class NumassFrame(
/**
* The absolute start time of the frame
*/
public val time: Instant,
/**
* The time interval per tick
*/
public val tickSize: Duration,
/**
* The buffered signal shape in ticks
*/
public val signal: ShortBuffer) {
public val length: Duration
get() = tickSize.multipliedBy(signal.capacity().toLong())
}

30
numass-data-model/src/main/kotlin/ru/inr/mass/data/api/SimpleNumassPoint.kt
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@ -1,30 +0,0 @@
package ru.inr.mass.data.api
import hep.dataforge.meta.Meta
import hep.dataforge.meta.MetaBuilder
/**
* A simple static implementation of NumassPoint
* Created by darksnake on 08.07.2017.
*/
public class SimpleNumassPoint(
override val blocks: List<NumassBlock>,
override val meta: Meta,
override val isSequential: Boolean = true,
) : NumassPoint {
// /**
// * Input blocks must be sorted
// * @param voltage
// * @param blocks
// */
// constructor(blocks: Collection<NumassBlock>, voltage: Double) :
// this(blocks.sortedBy { it.startTime }, MetaBuilder("point").setValue(NumassPoint.HV_KEY, voltage))
init {
if (blocks.isEmpty()) {
throw IllegalArgumentException("No blocks in collection")
}
}
}

3
numass-data-proto/build.gradle.kts
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@ -12,8 +12,7 @@ val dataforgeVersion: String by rootProject.extra
dependencies {
api(project(":numass-data-model"))
api("hep.dataforge:dataforge-workspace:$dataforgeVersion")
implementation("javax.annotation:javax.annotation-api:1.3.1")
api("hep.dataforge:dataforge-io:$dataforgeVersion")
}
wire{

52
numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/NumassFileEnvelope.kt
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@ -1,52 +0,0 @@
///*
// * Copyright 2018 Alexander Nozik.
// *
// * Licensed under the Apache License, Version 2.0 (the "License");
// * you may not use this file except in compliance with the License.
// * You may obtain a copy of the License at
// *
// * http://www.apache.org/licenses/LICENSE-2.0
// *
// * Unless required by applicable law or agreed to in writing, software
// * distributed under the License is distributed on an "AS IS" BASIS,
// * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// * See the License for the specific language governing permissions and
// * limitations under the License.
// */
//
//package ru.inr.mass.data.proto
//
//import hep.dataforge.meta.Meta
//import hep.dataforge.storage.files.MutableFileEnvelope
//import java.nio.ByteBuffer
//import java.nio.file.Files
//import java.nio.file.Path
//import java.nio.file.StandardOpenOption
//
//class NumassFileEnvelope(path: Path) : MutableFileEnvelope(path) {
//
// private val tag by lazy { Files.newByteChannel(path, StandardOpenOption.READ).use { NumassEnvelopeType.LegacyTag().read(it) } }
//
// override val dataOffset: Long by lazy { (tag.length + tag.metaSize).toLong() }
//
// override var dataLength: Int
// get() = tag.dataSize
// set(value) {
// if (value > Int.MAX_VALUE) {
// throw RuntimeException("Too large data block")
// }
// tag.dataSize = value
// if (channel.write(tag.toBytes(), 0L) < tag.length) {
// throw error("Tag is not overwritten.")
// }
// }
//
//
// override val meta: Meta by lazy {
// val buffer = ByteBuffer.allocate(tag.metaSize).also {
// channel.read(it, tag.length.toLong())
// }
// tag.metaType.reader.readBuffer(buffer)
// }
//}
//

40
numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/ProtoNumassPoint.kt
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@ -20,16 +20,21 @@ import hep.dataforge.io.Envelope
import hep.dataforge.meta.*
import kotlinx.coroutines.flow.*
import kotlinx.coroutines.runBlocking
import kotlinx.datetime.DateTimeUnit
import kotlinx.datetime.Instant
import kotlinx.datetime.plus
import kotlinx.io.asInputStream
import kotlinx.io.readByteArray
import okio.ByteString
import org.slf4j.LoggerFactory
import ru.inr.mass.data.api.*
import java.io.ByteArrayInputStream
import java.io.ByteArrayOutputStream
import java.io.InputStream
import java.time.Duration
import java.time.Instant
import java.util.zip.Inflater
import kotlin.time.Duration
import kotlin.time.milliseconds
import kotlin.time.nanoseconds
/**
* Protobuf based numass point
@ -60,14 +65,15 @@ internal class ProtoNumassPoint(
override val startTime: Instant
get() = meta["start_time"].long?.let {
Instant.ofEpochMilli(it)
Instant.fromEpochMilliseconds(it)
} ?: super.startTime
override val length: Duration
get() = meta["acquisition_time"].double?.let {
Duration.ofMillis((it * 1000).toLong())
(it * 1000).toLong().milliseconds
} ?: super.length
override fun toString(): String = "ProtoNumassPoint(index = ${index}, hv = $voltage)"
public companion object {
@ -119,23 +125,23 @@ public class ProtoBlock(
) : NumassBlock {
override val startTime: Instant
get(){
get() {
val nanos = block.time
val seconds = Math.floorDiv(nanos, 1e9.toInt().toLong())
val reminder = (nanos % 1e9).toInt()
return Instant.ofEpochSecond(seconds, reminder.toLong())
return Instant.fromEpochSeconds(seconds, reminder.toLong())
}
override val length: Duration = when {
block.length > 0 -> Duration.ofNanos(block.length)
block.length > 0 -> block.length.nanoseconds
parent?.meta["acquisition_time"] != null ->
Duration.ofMillis((parent?.meta["acquisition_time"].double ?: 0.0 * 1000).toLong())
(parent?.meta["acquisition_time"].double ?: 0.0 * 1000).milliseconds
else -> {
LoggerFactory.getLogger(javaClass)
.error("No length information on block. Trying to infer from first and last events")
val times = runBlocking { events.map { it.timeOffset }.toList() }
val nanos = (times.maxOrNull()!! - times.minOrNull()!!)
Duration.ofNanos(nanos)
nanos.nanoseconds
}
}
@ -158,14 +164,22 @@ public class ProtoBlock(
emptyFlow()
}
private fun ByteString.toShortArray(): ShortArray{
val shortBuffer = asByteBuffer().asShortBuffer()
return if(shortBuffer.hasArray()){
shortBuffer.array()
} else {
ShortArray(shortBuffer.limit()){shortBuffer.get(it)}
}
}
override val frames: Flow<NumassFrame>
get() {
val tickSize = Duration.ofNanos(block.bin_size)
val tickSize = block.bin_size.nanoseconds
return block.frames.asFlow().map { frame ->
val time = startTime.plusNanos(frame.time)
val frameData = frame.data_.asByteBuffer()
NumassFrame(time, tickSize, frameData.asShortBuffer())
val time = startTime.plus(frame.time, DateTimeUnit.NANOSECOND)
val frameData = frame.data_
NumassFrame(time, tickSize, frameData.toShortArray())
}
}
}

116
numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/TaggedNumassEnvelopeFormat.kt
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@ -104,7 +104,7 @@ internal class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeFo
IOFormat.NAME_KEY put name.toString()
}
public companion object : EnvelopeFormatFactory {
companion object : EnvelopeFormatFactory {
private const val START_SEQUENCE = "#!"
private const val END_SEQUENCE = "!#\r\n"
@ -170,118 +170,4 @@ internal class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeFo
override fun readObject(input: Input): Envelope = default.readObject(input)
}
}
///**
// * An envelope type for legacy numass tags. Reads legacy tag and writes DF02 tags
// */
//object NumassEnvelopeType : EnvelopeFormatFactory {
//
// override val code: Int = DefaultEnvelopeType.DEFAULT_ENVELOPE_CODE
//
// override val name: String = "numass"
//
// override fun description(): String = "Numass legacy envelope"
//
// /**
// * Read as legacy
// */
// override fun getReader(properties: Map<String, String>): EnvelopeReader {
// return NumassEnvelopeReader()
// }
//
// /**
// * Write as default
// */
// override fun getWriter(properties: Map<String, String>): EnvelopeWriter {
// return DefaultEnvelopeWriter(this, MetaType.resolve(properties))
// }
//
// class LegacyTag : EnvelopeTag() {
// override val startSequence: ByteArray
// get() = LEGACY_START_SEQUENCE
//
// override val endSequence: ByteArray
// get() = LEGACY_END_SEQUENCE
//
// /**
// * Get the length of tag in bytes. -1 means undefined size in case tag was modified
// *
// * @return
// */
// override val length: Int
// get() = 30
//
// /**
// * Read leagscy version 1 tag without leading tag head
// *
// * @param buffer
// * @return
// * @throws IOException
// */
// override fun readHeader(buffer: ByteBuffer): Map<String, Value> {
// val res = HashMap<String, Value>()
//
// val type = buffer.getInt(2)
// res[Envelope.TYPE_PROPERTY] = Value.of(type)
//
// val metaTypeCode = buffer.getShort(10)
// val metaType = MetaType.resolve(metaTypeCode)
//
// if (metaType != null) {
// res[Envelope.META_TYPE_PROPERTY] = metaType.name.parseValue()
// } else {
// LoggerFactory.getLogger(EnvelopeTag::class.java).warn("Could not resolve meta type. Using default")
// }
//
// val metaLength = Integer.toUnsignedLong(buffer.getInt(14))
// res[Envelope.META_LENGTH_PROPERTY] = Value.of(metaLength)
// val dataLength = Integer.toUnsignedLong(buffer.getInt(22))
// res[Envelope.DATA_LENGTH_PROPERTY] = Value.of(dataLength)
// return res
// }
// }
//
// private class NumassEnvelopeReader : DefaultEnvelopeReader() {
// override fun newTag(): EnvelopeTag {
// return LegacyTag()
// }
// }
//
// companion object {
// val INSTANCE = NumassEnvelopeType()
//
// val LEGACY_START_SEQUENCE = byteArrayOf('#'.toByte(), '!'.toByte())
// val LEGACY_END_SEQUENCE = byteArrayOf('!'.toByte(), '#'.toByte(), '\r'.toByte(), '\n'.toByte())
//
// /**
// * Replacement for standard type infer to include legacy type
// *
// * @param path
// * @return
// */
// fun infer(path: Path): EnvelopeType? {
// return try {
// FileChannel.open(path, StandardOpenOption.READ).use {
// val buffer = it.map(FileChannel.MapMode.READ_ONLY, 0, 6)
// when {
// //TODO use templates from appropriate types
// buffer.get(0) == '#'.toByte() && buffer.get(1) == '!'.toByte() -> INSTANCE
// buffer.get(0) == '#'.toByte() && buffer.get(1) == '!'.toByte() &&
// buffer.get(4) == 'T'.toByte() && buffer.get(5) == 'L'.toByte() -> TaglessEnvelopeType.INSTANCE
// buffer.get(0) == '#'.toByte() && buffer.get(1) == '~'.toByte() -> DefaultEnvelopeType.INSTANCE
// else -> null
// }
// }
// } catch (ex: Exception) {
// LoggerFactory.getLogger(EnvelopeType::class.java).warn("Could not infer envelope type of file {} due to exception: {}", path, ex)
// null
// }
//
// }
//
// }
//
//}

20
numass-workspace/build.gradle.kts Normal file
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@ -0,0 +1,20 @@
plugins {
kotlin("jvm")
id("ru.mipt.npm.kscience")
}
kscience{
application()
publish()
}
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")
dependencies {
implementation(project(":numass-data-proto"))
implementation("hep.dataforge:dataforge-workspace:$dataforgeVersion")
implementation("kscience.plotlykt:plotlykt-core:$plotlyVersion")
implementation("kscience.kmath:kmath-histograms:$kmathVersion")
}

33
numass-workspace/src/main/kotlin/ru/inr/mass/workspace/AmplitudeSpectrum.kt Normal file
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@ -0,0 +1,33 @@
@file:Suppress("EXPERIMENTAL_API_USAGE")
package ru.inr.mass.workspace
import hep.dataforge.context.logger
import kotlinx.coroutines.flow.collect
import kotlinx.coroutines.runBlocking
import kscience.kmath.histogram.UnivariateHistogram
import ru.inr.mass.data.api.NumassPoint
/**
* Build an amplitude spectrum
*/
fun NumassPoint.spectrum(): UnivariateHistogram =
UnivariateHistogram.uniform(1.0) {
runBlocking {
events.collect { put(it.channel.toDouble()) }
}
}
fun Collection<NumassPoint>.spectrum(): UnivariateHistogram {
if (distinctBy { it.voltage }.size != 1) {
numass.logger.warn { "Spectrum is generated from points with different hv value: $this" }
}
return UnivariateHistogram.uniform(1.0) {
runBlocking {
this@spectrum.forEach { point ->
point.events.collect { put(it.channel.toDouble()) }
}
}
}
}

10
numass-workspace/src/main/kotlin/ru/inr/mass/workspace/workspace.kt Normal file
View File

@ -0,0 +1,10 @@
package ru.inr.mass.workspace
import hep.dataforge.workspace.Workspace
import ru.inr.mass.data.proto.NumassProtoPlugin
val numass = Workspace {
context("numass") {
plugin(NumassProtoPlugin)
}
}

1
settings.gradle.kts
View File

@ -36,3 +36,4 @@ pluginManagement {
include("numass-data-model")
include("numass-data-proto")
include("numass-workspace")