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This commit is contained in:
Alexander Nozik 2018-04-14 21:50:57 +03:00
parent 7e676681b7
commit 73dd8cb4eb
11 changed files with 166 additions and 83 deletions
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6
numass-core/src/main/kotlin/inr/numass/data/analyzers/NumassAnalyzer.kt
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@ -199,9 +199,11 @@ fun Table.withBinning(binSize: Int, loChannel: Int? = null, upChannel: Int? = nu
.addNumber("binSize")
val builder = ListTable.Builder(format)
var chan = loChannel ?: this.getColumn(NumassAnalyzer.CHANNEL_KEY).stream().mapToInt { it.intValue() }.min().orElse(0)
var chan = loChannel
?: this.getColumn(NumassAnalyzer.CHANNEL_KEY).stream().mapToInt { it.intValue() }.min().orElse(0)
val top = upChannel ?: this.getColumn(NumassAnalyzer.CHANNEL_KEY).stream().mapToInt { it.intValue() }.max().orElse(1)
val top = upChannel
?: this.getColumn(NumassAnalyzer.CHANNEL_KEY).stream().mapToInt { it.intValue() }.max().orElse(1)
while (chan < top - binSize) {
val count = AtomicLong(0)

2
numass-core/src/main/kotlin/inr/numass/data/api/NumassBlock.kt
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@ -62,7 +62,7 @@ interface NumassBlock : Metoid {
typealias OrphanNumassEvent = Pair<Short, Long>
inline fun OrphanNumassEvent.adopt(parent: NumassBlock): NumassEvent {
fun OrphanNumassEvent.adopt(parent: NumassBlock): NumassEvent {
return NumassEvent(this.first, this.second, parent)
}

19
numass-core/src/main/kotlin/inr/numass/data/api/NumassPoint.kt
View File

@ -1,6 +1,9 @@
package inr.numass.data.api
import hep.dataforge.io.envelopes.Envelope
import hep.dataforge.meta.Metoid
import inr.numass.data.storage.ClassicNumassPoint
import inr.numass.data.storage.ProtoNumassPoint
import java.time.Duration
import java.time.Instant
import java.util.stream.Stream
@ -42,7 +45,7 @@ interface NumassPoint : Metoid, NumassBlock {
* @return
*/
override val startTime: Instant
get() = meta.optValue(START_TIME_KEY).map<Instant>{ it.timeValue() }.orElseGet { firstBlock.startTime }
get() = meta.optValue(START_TIME_KEY).map<Instant> { it.timeValue() }.orElseGet { firstBlock.startTime }
/**
* Get the length key of meta or calculate length as a sum of block lengths. The latter could be a bit slow
@ -51,7 +54,7 @@ interface NumassPoint : Metoid, NumassBlock {
*/
override val length: Duration
get() = Duration.ofNanos(
meta.optValue(LENGTH_KEY).map<Long>{ it.longValue() }
meta.optValue(LENGTH_KEY).map<Long> { it.longValue() }
.orElseGet { blocks.mapToLong { it -> it.length.toNanos() }.sum() }
)
@ -65,7 +68,7 @@ interface NumassPoint : Metoid, NumassBlock {
* @return
*/
override val events: Stream<NumassEvent>
get() = blocks.flatMap{ it.events }
get() = blocks.flatMap { it.events }
/**
* Get all frames in all blocks as a single sequence
@ -73,7 +76,7 @@ interface NumassPoint : Metoid, NumassBlock {
* @return
*/
override val frames: Stream<NumassFrame>
get() = blocks.flatMap{ it.frames }
get() = blocks.flatMap { it.frames }
companion object {
@ -81,5 +84,13 @@ interface NumassPoint : Metoid, NumassBlock {
const val LENGTH_KEY = "length"
const val HV_KEY = "voltage"
const val INDEX_KEY = "index"
fun read(envelope: Envelope): NumassPoint {
return if (envelope.dataType?.startsWith("numass.point.classic") ?: envelope.meta.hasValue("split")) {
ClassicNumassPoint(envelope)
} else {
ProtoNumassPoint(envelope)
}
}
}
}

14
numass-core/src/main/kotlin/inr/numass/data/storage/ClassicNumassPoint.kt
View File

@ -22,6 +22,12 @@ import java.util.stream.StreamSupport
*/
class ClassicNumassPoint(private val envelope: Envelope) : NumassPoint {
override val meta: Meta = envelope.meta
override val voltage: Double = meta.getDouble("external_meta.HV1_value", super.voltage)
override val index: Int = meta.getInt("external_meta.point_index", super.index)
override val blocks: Stream<NumassBlock>
get() {
val length: Long = if (envelope.meta.hasValue("external_meta.acquisition_time")) {
@ -36,15 +42,9 @@ class ClassicNumassPoint(private val envelope: Envelope) : NumassPoint {
get() = if (meta.hasValue("start_time")) {
meta.getValue("start_time").timeValue()
} else {
Instant.EPOCH
super.startTime
}
override val meta: Meta = envelope.meta
override val voltage: Double = meta.getDouble("external_meta.HV1_value", 0.0)
override val index: Int = meta.getInt("external_meta.point_index", -1)
//TODO split blocks using meta
private inner class ClassicBlock(

4
numass-core/src/main/kotlin/inr/numass/data/storage/NumassDataLoader.kt
View File

@ -89,7 +89,9 @@ class NumassDataLoader(
override val points: Stream<NumassPoint>
get() {
return pointEnvelopes.map { ClassicNumassPoint(it) }
return pointEnvelopes.map {
NumassPoint.read(it)
}
}
override fun pull(fragmentName: String): Envelope {

2
numass-core/src/main/kotlin/inr/numass/data/storage/NumassStorage.kt
View File

@ -135,7 +135,7 @@ class NumassStorage : FileStorage {
val files = ArrayList<NumassSet>()
Files.list(dataDir).forEach { file ->
if (Files.isRegularFile(file) && file.fileName.toString().toLowerCase().endsWith(".dat")) {
val name = file.fileName.toString()
//val name = file.fileName.toString()
try {
files.add(NumassDatFile(file, Meta.empty()))
} catch (ex: Exception) {

47
numass-core/src/main/kotlin/inr/numass/data/storage/ProtoNumassPoint.kt
View File

@ -4,6 +4,8 @@ import hep.dataforge.context.Context
import hep.dataforge.context.Global
import hep.dataforge.io.envelopes.Envelope
import hep.dataforge.kodex.buildMeta
import hep.dataforge.kodex.toList
import hep.dataforge.meta.Laminate
import hep.dataforge.meta.Meta
import inr.numass.data.NumassProto
import inr.numass.data.api.NumassBlock
@ -12,6 +14,7 @@ import inr.numass.data.api.NumassFrame
import inr.numass.data.api.NumassPoint
import inr.numass.data.dataStream
import inr.numass.data.legacy.NumassFileEnvelope
import org.slf4j.LoggerFactory
import java.io.IOException
import java.nio.file.Path
import java.time.Duration
@ -39,13 +42,25 @@ class ProtoNumassPoint(private val envelope: Envelope) : NumassPoint {
get() = point.channelsList.stream()
.flatMap { channel ->
channel.blocksList.stream()
.map { block -> ProtoBlock(channel.id.toInt(), block) }
.map { block -> ProtoBlock(channel.id.toInt(), block, this) }
.sorted(Comparator.comparing<ProtoBlock, Instant> { it.startTime })
}
override val meta: Meta = envelope.meta
override val voltage: Double = meta.getDouble("external_meta.HV1_value", super.voltage)
override val index: Int = meta.getInt("external_meta.point_index", super.index)
override val startTime: Instant
get() = if (meta.hasValue("start_time")) {
meta.getValue("start_time").timeValue()
} else {
super.startTime
}
companion object {
fun readFile(path: Path): ProtoNumassPoint {
return ProtoNumassPoint(NumassFileEnvelope.open(path, true))
@ -63,25 +78,27 @@ class ProtoNumassPoint(private val envelope: Envelope) : NumassPoint {
}
}
class ProtoBlock(val channel: Int, private val block: NumassProto.Point.Channel.Block) : NumassBlock {
class ProtoBlock(val channel: Int, private val block: NumassProto.Point.Channel.Block, parent: NumassBlock? = null) : NumassBlock {
override val meta: Meta by lazy {
buildMeta {
val blockMeta = buildMeta {
"channel" to channel
}
return@lazy parent?.let { Laminate(blockMeta, parent.meta) } ?: blockMeta
}
override val startTime: Instant
get() = ProtoNumassPoint.ofEpochNanos(block.time)
override val length: Duration
get() = if (meta.hasMeta("params")) {
Duration.ofNanos((meta.getDouble("params.b_size") / meta.getDouble("params.sample_freq") * 1e9).toLong())
} else if (meta.hasValue("length")) {
Duration.ofNanos(meta.getValue("length").longValue())
} else {
Duration.ZERO
override val length: Duration = when {
block.length > 0 -> Duration.ofNanos(block.length)
meta.hasValue("acquisition_time") -> Duration.ofMillis((meta.getDouble("acquisition_time") * 1000).toLong())
else -> {
LoggerFactory.getLogger(javaClass).error("No length information on block. Trying to infer from first and last events")
val times = events.map { it.timeOffset }.toList()
val nanos = (times.max()!! - times.min()!!)
Duration.ofNanos(nanos)
}
}
override val events: Stream<NumassEvent>
get() = if (block.hasEvents()) {
@ -94,13 +111,7 @@ class ProtoBlock(val channel: Int, private val block: NumassProto.Point.Channel.
override val frames: Stream<NumassFrame>
get() {
val tickSize = if (meta.hasMeta("params")) {
Duration.ofNanos((1e9 / meta.getInt("params.sample_freq")).toLong())
} else if (meta.hasValue("tick_length")) {
Duration.ofNanos(meta.getInt("tick_length").toLong())
} else {
Duration.ofNanos(1)
}
val tickSize = Duration.ofNanos(block.binSize)
return block.framesList.stream().map { frame ->
val time = startTime.plusNanos(frame.time)
val data = frame.data.asReadOnlyByteBuffer()

44
numass-main/src/main/kotlin/inr/numass/scripts/tristan/ProtoPoint.kt Normal file
View File

@ -0,0 +1,44 @@
/*
* 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 inr.numass.scripts.tristan
import hep.dataforge.context.Global
import hep.dataforge.kodex.toList
import inr.numass.data.api.NumassPoint
import inr.numass.data.channel
import inr.numass.data.storage.NumassDataLoader
import inr.numass.data.storage.NumassStorageFactory
fun main(args: Array<String>) {
val storage = NumassStorageFactory.buildLocal(Global, "D:\\Work\\Numass\\data\\2018_04\\Adiabacity_19\\", true, false)
val set = storage.optLoader("set_4").get() as NumassDataLoader
set.points.forEach { point ->
if (point.voltage == 18700.0) {
println("${point.index}:")
point.blocks.forEach {
println("\t${it.channel}: events: ${it.events.count()}, time: ${it.length}")
}
}
}
val point: NumassPoint = set.points.filter { it.index == 18 }.findFirst().get()
(0..99).forEach { bin ->
val times = point.events.filter { it.amp > 0 }.map { it.timeOffset }.toList()
val count = times.filter { it > bin.toDouble() / 10 * 1e9 && it < (bin + 1).toDouble() / 10 * 1e9 }.count()
println("${bin.toDouble() / 10.0}: $count")
}
}

2
numass-viewer/build.gradle
View File

@ -12,7 +12,7 @@ if (!hasProperty('mainClass')) {
mainClassName = mainClass
version = "0.5.0"
version = "0.5.1 - SNAPSHOT"
description = "The viewer for numass data"

72
numass-viewer/src/main/kotlin/inr/numass/viewer/AmplitudeView.kt
View File

@ -6,8 +6,11 @@ import hep.dataforge.fx.runGoal
import hep.dataforge.fx.ui
import hep.dataforge.goals.Goal
import hep.dataforge.kodex.configure
import hep.dataforge.kodex.toList
import hep.dataforge.meta.Meta
import hep.dataforge.plots.PlotFrame
import hep.dataforge.plots.PlotGroup
import hep.dataforge.plots.Plottable
import hep.dataforge.plots.data.DataPlot
import hep.dataforge.plots.jfreechart.JFreeChartFrame
import hep.dataforge.tables.Adapters
@ -15,7 +18,10 @@ import hep.dataforge.tables.Table
import inr.numass.data.analyzers.NumassAnalyzer
import inr.numass.data.analyzers.SimpleAnalyzer
import inr.numass.data.analyzers.withBinning
import inr.numass.data.api.MetaBlock
import inr.numass.data.api.NumassBlock
import inr.numass.data.api.NumassPoint
import inr.numass.data.channel
import javafx.beans.Observable
import javafx.beans.binding.DoubleBinding
import javafx.beans.property.SimpleBooleanProperty
@ -30,7 +36,7 @@ import java.util.concurrent.ConcurrentHashMap
class AmplitudeView(
private val analyzer: NumassAnalyzer = SimpleAnalyzer(),
private val cache: MutableMap<NumassPoint, Table> = ConcurrentHashMap()
private val cache: MutableMap<NumassBlock, Table> = ConcurrentHashMap()
) : View(title = "Numass amplitude spectrum plot", icon = ImageView(dfIcon)) {
private val frame: PlotFrame = JFreeChartFrame().configure {
@ -45,9 +51,17 @@ class AmplitudeView(
"units" to "Hz"
}
"legend.showComponent" to false
}.apply {
plots.configure {
"connectionType" to "step"
"thickness" to 2
"showLine" to true
"showSymbol" to false
"showErrors" to false
}.setType(DataPlot::class)
}
val binningProperty = SimpleObjectProperty<Int>(20)
val binningProperty = SimpleObjectProperty(20)
var binning by binningProperty
val normalizeProperty = SimpleBooleanProperty(true)
@ -68,7 +82,7 @@ class AmplitudeView(
}
private val data: ObservableMap<String, NumassPoint> = FXCollections.observableHashMap()
private val plots: ObservableMap<String, Goal<DataPlot>> = FXCollections.observableHashMap()
private val plots: ObservableMap<String, Goal<Plottable>> = FXCollections.observableHashMap()
val isEmpty = booleanBinding(data) { data.isEmpty() }
@ -83,7 +97,6 @@ class AmplitudeView(
}
init {
data.addListener { _: Observable ->
invalidate()
@ -106,7 +119,7 @@ class AmplitudeView(
/**
* Calculate or get spectrum from the immutable
*/
private suspend fun getSpectrum(point: NumassPoint): Table {
private fun getSpectrum(point: NumassBlock): Table {
return cache.computeIfAbsent(point) { analyzer.getAmplitudeSpectrum(point, Meta.empty()) }
}
@ -114,33 +127,56 @@ class AmplitudeView(
* Put or replace current plot with name `key`
*/
fun add(key: String, point: NumassPoint) {
data.put(key, point)
data[key] = point
}
fun addAll(data: Map<String, NumassPoint>) {
this.data.putAll(data);
}
/**
* Distinct map of channel number to corresponding grouping block
*/
private fun NumassPoint.getChannels(): Map<Int, NumassBlock> {
return blocks.toList().groupBy { it.channel ?: 0 }.mapValues { entry ->
if (entry.value.size == 1) {
entry.value.first()
} else {
MetaBlock(entry.value)
}
}
}
private fun invalidate() {
data.forEach { key, point ->
plots.computeIfAbsent(key) {
runGoal("loadAmplitudeSpectrum_$key") {
runGoal<Plottable>("loadAmplitudeSpectrum_$key") {
val valueAxis = if (normalize) {
NumassAnalyzer.COUNT_RATE_KEY
} else {
NumassAnalyzer.COUNT_KEY
}
DataPlot.plot(
key,
Adapters.buildXYAdapter(NumassAnalyzer.CHANNEL_KEY, valueAxis),
getSpectrum(point).withBinning(binning)
).configure {
"connectionType" to "step"
"thickness" to 2
"showLine" to true
"showSymbol" to false
"showErrors" to false
"JFreeChart.cache" to true
val adapter = Adapters.buildXYAdapter(NumassAnalyzer.CHANNEL_KEY, valueAxis)
val channels = point.getChannels()
return@runGoal if (channels.size == 1) {
DataPlot.plot(
key,
adapter,
getSpectrum(point).withBinning(binning)
)
} else {
val group = PlotGroup.typed<DataPlot>(key)
channels.forEach { key, block ->
val plot = DataPlot.plot(
key.toString(),
adapter,
getSpectrum(block).withBinning(binning)
)
group.add(plot)
}
group
}
} ui { plot ->
frame.add(plot)

37
numass-viewer/src/main/kotlin/inr/numass/viewer/StorageView.kt
View File

@ -9,6 +9,7 @@ import hep.dataforge.storage.api.Loader
import hep.dataforge.storage.api.Storage
import hep.dataforge.storage.api.TableLoader
import hep.dataforge.storage.commons.StorageManager
import hep.dataforge.tables.Table
import inr.numass.NumassProperties
import inr.numass.data.api.NumassPoint
import inr.numass.data.api.NumassSet
@ -29,6 +30,7 @@ import org.controlsfx.control.StatusBar
import tornadofx.*
import java.io.File
import java.net.URI
import java.util.concurrent.ConcurrentHashMap
import kotlin.streams.toList
class StorageView(private val context: Context = Global) : View(title = "Numass storage", icon = ImageView(dfIcon)) {
@ -43,8 +45,10 @@ class StorageView(private val context: Context = Global) : View(title = "Numass
private val statusBar = StatusBar();
private val ampView: AmplitudeView by inject();
private val spectrumView: SpectrumView by inject();
private val cache: MutableMap<NumassPoint, Table> = ConcurrentHashMap()
private val ampView: AmplitudeView by inject(params = mapOf("cache" to cache));
private val spectrumView: SpectrumView by inject(params = mapOf("cache" to cache));
private val hvView: HVView by inject();
private val scView: SlowControlView by inject();
@ -122,7 +126,7 @@ class StorageView(private val context: Context = Global) : View(title = "Numass
isSelected = false
LogFragment().apply {
addLogHandler(context.logger)
bindWindow(this@togglebutton, selectedProperty())
bindWindow(this@togglebutton)
}
}
}
@ -263,15 +267,6 @@ class StorageView(private val context: Context = Global) : View(title = "Numass
else -> throw IllegalArgumentException("Unknown content type: ${content::class.java}");
}
// private fun getSetName(value: NumassSet): String {
// return if (value is NumassDataLoader) {
// value.path
// } else {
// value.name
// }
// }
private fun loadDirectory(path: URI) {
statusBar.text = "Loading storage: $path"
runGoal("loadDirectory[$path]") {
@ -289,22 +284,4 @@ class StorageView(private val context: Context = Global) : View(title = "Numass
}
}
// fun setRootStorage(root: Storage) {
// runGoal("loadStorage[${root.name}]") {
// title = "Fill data to UI (" + root.name + ")"
// progress = -1.0
// runLater { statusBar.progress = -1.0 }
//
// message = "Loading numass storage tree..."
//
// runLater {
// storage = root
// }
//
// // callback.setProgress(1, 1);
// runLater { statusBar.progress = 0.0 }
// message = "Numass storage tree loaded."
// progress = 1.0
// }
// }
}