Minor fixes to storage
This commit is contained in:
parent
c38a346316
commit
804221c859
@ -5,8 +5,7 @@ import hep.dataforge.storage.filestorage.FileEnvelope;
|
||||
import inr.numass.NumassEnvelopeType;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.ByteBuffer;
|
||||
import java.nio.channels.SeekableByteChannel;
|
||||
import java.io.InputStream;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.util.Arrays;
|
||||
@ -20,10 +19,10 @@ public class NumassFileEnvelope extends FileEnvelope {
|
||||
if (!Files.exists(path)) {
|
||||
throw new RuntimeException("File envelope does not exist");
|
||||
}
|
||||
try (SeekableByteChannel channel = Files.newByteChannel(path, READ)) {
|
||||
ByteBuffer header = ByteBuffer.allocate(2);
|
||||
channel.read(header);
|
||||
if (Arrays.equals(header.array(), LEGACY_START_SEQUENCE)) {
|
||||
try (InputStream stream = Files.newInputStream(path, READ)) {
|
||||
byte[] bytes = new byte[2];
|
||||
stream.read(bytes);
|
||||
if (Arrays.equals(bytes, LEGACY_START_SEQUENCE)) {
|
||||
return new NumassFileEnvelope(path, readOnly);
|
||||
} else {
|
||||
return FileEnvelope.open(path, readOnly);
|
||||
|
||||
@ -30,7 +30,7 @@ public class NumassStorageFactory implements StorageType {
|
||||
@NotNull
|
||||
public static FileStorage buildLocal(Context context, Path file, boolean readOnly, boolean monitor) {
|
||||
StorageManager manager = context.loadFeature("hep.dataforge:storage", StorageManager.class);
|
||||
return (FileStorage) manager.buildStorage(buildStorageMeta(file.toUri(),readOnly,monitor));
|
||||
return (FileStorage) manager.buildStorage(buildStorageMeta(file.toUri(), readOnly, monitor));
|
||||
}
|
||||
|
||||
@NotNull
|
||||
@ -57,8 +57,8 @@ public class NumassStorageFactory implements StorageType {
|
||||
int port = meta.getInt("port", 22);
|
||||
SFTPEnvironment env = new SFTPEnvironment()
|
||||
.withUsername(username)
|
||||
.withPassword(meta.getString("password","").toCharArray());
|
||||
FileSystem fs = FileSystems.newFileSystem(uri, env,context.getClassLoader());
|
||||
.withPassword(meta.getString("password", "").toCharArray());
|
||||
FileSystem fs = FileSystems.newFileSystem(uri, env, context.getClassLoader());
|
||||
path = fs.getPath(uri.getPath());
|
||||
} catch (Exception e) {
|
||||
throw new RuntimeException(e);
|
||||
|
||||
@ -124,39 +124,6 @@ interface NumassAnalyzer {
|
||||
return spectrumWithBinning(this,binSize, loChannel, upChannel)
|
||||
}
|
||||
|
||||
/**
|
||||
* Subtract reference spectrum.
|
||||
*
|
||||
* @param sp1
|
||||
* @param sp2
|
||||
* @return
|
||||
*/
|
||||
fun subtractAmplitudeSpectrum(sp1: Table, sp2: Table): Table {
|
||||
val format = TableFormatBuilder()
|
||||
.addNumber(CHANNEL_KEY, X_VALUE_KEY)
|
||||
.addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
|
||||
.addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
|
||||
.build()
|
||||
|
||||
val builder = ListTable.Builder(format)
|
||||
|
||||
sp1.forEach { row1 ->
|
||||
val channel = row1.getDouble(CHANNEL_KEY)
|
||||
val row2 = sp2.rows.asSequence().find { it.getDouble(CHANNEL_KEY) == channel } //t2[channel]
|
||||
if (row2 == null) {
|
||||
throw RuntimeException("Reference for channel $channel not found");
|
||||
|
||||
} else {
|
||||
val value = Math.max(row1.getDouble(COUNT_RATE_KEY) - row2.getDouble(COUNT_RATE_KEY), 0.0)
|
||||
val error1 = row1.getDouble(COUNT_RATE_ERROR_KEY)
|
||||
val error2 = row2.getDouble(COUNT_RATE_ERROR_KEY)
|
||||
val error = Math.sqrt(error1 * error1 + error2 * error2)
|
||||
builder.row(channel, value, error)
|
||||
}
|
||||
}
|
||||
return builder.build()
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@ -262,3 +229,36 @@ fun spectrumWithBinning(spectrum: Table, binSize: Int, loChannel: Int? = null, u
|
||||
}
|
||||
return builder.build()
|
||||
}
|
||||
|
||||
/**
|
||||
* Subtract reference spectrum.
|
||||
*
|
||||
* @param sp1
|
||||
* @param sp2
|
||||
* @return
|
||||
*/
|
||||
fun subtractAmplitudeSpectrum(sp1: Table, sp2: Table): Table {
|
||||
val format = TableFormatBuilder()
|
||||
.addNumber(NumassAnalyzer.CHANNEL_KEY, X_VALUE_KEY)
|
||||
.addNumber(NumassAnalyzer.COUNT_RATE_KEY, Y_VALUE_KEY)
|
||||
.addNumber(NumassAnalyzer.COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
|
||||
.build()
|
||||
|
||||
val builder = ListTable.Builder(format)
|
||||
|
||||
sp1.forEach { row1 ->
|
||||
val channel = row1.getDouble(NumassAnalyzer.CHANNEL_KEY)
|
||||
val row2 = sp2.rows.asSequence().find { it.getDouble(NumassAnalyzer.CHANNEL_KEY) == channel } //t2[channel]
|
||||
if (row2 == null) {
|
||||
throw RuntimeException("Reference for channel $channel not found");
|
||||
|
||||
} else {
|
||||
val value = Math.max(row1.getDouble(NumassAnalyzer.COUNT_RATE_KEY) - row2.getDouble(NumassAnalyzer.COUNT_RATE_KEY), 0.0)
|
||||
val error1 = row1.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY)
|
||||
val error2 = row2.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY)
|
||||
val error = Math.sqrt(error1 * error1 + error2 * error2)
|
||||
builder.row(channel, value, error)
|
||||
}
|
||||
}
|
||||
return builder.build()
|
||||
}
|
||||
@ -138,9 +138,9 @@ class TimeAnalyzer @JvmOverloads constructor(private val processor: SignalProces
|
||||
)
|
||||
private fun getT0(block: NumassBlock, meta: Meta): Int {
|
||||
return if (meta.hasValue("t0")) {
|
||||
meta.getInt("t0")!!
|
||||
meta.getInt("t0")
|
||||
} else if (meta.hasMeta("t0")) {
|
||||
val fraction = meta.getDouble("t0.crFraction")!!
|
||||
val fraction = meta.getDouble("t0.crFraction")
|
||||
val cr = estimateCountRate(block)
|
||||
if (cr < meta.getDouble("t0.minCR", 0.0)) {
|
||||
0
|
||||
@ -169,7 +169,7 @@ class TimeAnalyzer @JvmOverloads constructor(private val processor: SignalProces
|
||||
* @return
|
||||
*/
|
||||
fun getEventsWithDelay(block: NumassBlock, config: Meta): Stream<Pair<NumassEvent, Long>> {
|
||||
val inverted = config.getBoolean("inverted",false)
|
||||
val inverted = config.getBoolean("inverted",true)
|
||||
return super.getEvents(block, config).asSequence().zipWithNext { prev, next ->
|
||||
val delay = Math.max(next.timeOffset - prev.timeOffset, 0)
|
||||
if(inverted){
|
||||
|
||||
@ -21,7 +21,8 @@ import hep.dataforge.tables.Adapters
|
||||
import hep.dataforge.tables.Table
|
||||
import hep.dataforge.tables.TableTransform
|
||||
import inr.numass.NumassPlugin
|
||||
import inr.numass.data.NumassDataUtils
|
||||
import inr.numass.data.analyzers.NumassAnalyzerKt
|
||||
import inr.numass.subthreshold.SubFitKt
|
||||
import javafx.application.Platform
|
||||
|
||||
import static hep.dataforge.grind.Grind.buildMeta
|
||||
@ -33,17 +34,17 @@ ctx.getPluginManager().load(PlotManager)
|
||||
ctx.getPluginManager().load(NumassPlugin)
|
||||
ctx.getPluginManager().load(CachePlugin)
|
||||
|
||||
Meta meta = buildMeta {
|
||||
data(dir: "D:\\Work\\Numass\\data\\2017_05\\Fill_2", mask: "set_.{1,3}")
|
||||
generate(t0: 3e4)
|
||||
Meta meta = buildMeta(t0: 3e4, inverted: false) {
|
||||
data(dir: "D:\\Work\\Numass\\data\\2017_11\\Fill_2", mask: "set_2")
|
||||
subtract(reference: 18500)
|
||||
fit(xLow: 450, xHigh: 700, upper: 3100, binning: 20)
|
||||
fit(xLow: 400, xHigh: 600, upper: 3000, binning: 20)
|
||||
window(lo: 300, up: 3000)
|
||||
}
|
||||
|
||||
|
||||
def shell = new GrindShell(ctx);
|
||||
|
||||
DataNode<Table> spectra = UnderflowUtils.getSpectraMap(shell, meta);
|
||||
DataNode<Table> spectra = SubFitKt.getSpectraMap(ctx, meta).computeAll();
|
||||
|
||||
shell.eval {
|
||||
|
||||
@ -56,7 +57,7 @@ shell.eval {
|
||||
spectraMap = spectra
|
||||
.findAll { it.name != referenceVoltage }
|
||||
.collectEntries {
|
||||
[(it.meta["voltage"]): NumassDataUtils.subtractSpectrum(it.get(), referencePoint)]
|
||||
[(it.meta["voltage"]): NumassAnalyzerKt.subtractAmplitudeSpectrum(it.get(), referencePoint)]
|
||||
}
|
||||
} else {
|
||||
spectraMap = spectra.collectEntries { return [(it.meta["voltage"]): it.get()] }
|
||||
@ -71,7 +72,7 @@ shell.eval {
|
||||
DataPlot.plot(
|
||||
it.key as String,
|
||||
adapter,
|
||||
NumassDataUtils.spectrumWithBinning(it.value as Table, binning)
|
||||
NumassAnalyzerKt.spectrumWithBinning(it.value as Table, binning)
|
||||
)
|
||||
)
|
||||
}
|
||||
@ -85,10 +86,10 @@ shell.eval {
|
||||
|
||||
showPoints(spectraMap.findAll { it.key in [16200d, 16400d, 16800d, 17000d, 17200d, 17700d] })
|
||||
|
||||
[550, 600, 650, 700, 750].each { xHigh ->
|
||||
[500, 550, 600, 650, 700].each { xHigh ->
|
||||
println "Caclculate correctuion for upper linearity bound: ${xHigh}"
|
||||
Table correctionTable = TableTransform.filter(
|
||||
UnderflowFitter.fitAllPoints(
|
||||
SubFitKt.fitAllPoints(
|
||||
spectraMap,
|
||||
meta["fit.xLow"] as int,
|
||||
xHigh,
|
||||
@ -100,7 +101,7 @@ shell.eval {
|
||||
2
|
||||
)
|
||||
|
||||
if (xHigh == 700) {
|
||||
if (xHigh == 600) {
|
||||
ColumnedDataWriter.writeTable(System.out, correctionTable, "underflow parameters")
|
||||
}
|
||||
|
||||
@ -115,10 +116,10 @@ shell.eval {
|
||||
}
|
||||
|
||||
|
||||
[400, 450, 500].each { xLow ->
|
||||
[350, 400, 450].each { xLow ->
|
||||
println "Caclculate correctuion for lower linearity bound: ${xLow}"
|
||||
Table correctionTable = TableTransform.filter(
|
||||
UnderflowFitter.fitAllPoints(
|
||||
SubFitKt.fitAllPoints(
|
||||
spectraMap,
|
||||
xLow,
|
||||
meta["fit.xHigh"] as int,
|
||||
|
||||
@ -1,106 +0,0 @@
|
||||
package inr.numass.scripts.underflow
|
||||
|
||||
import groovy.transform.CompileStatic
|
||||
import hep.dataforge.tables.ListTable
|
||||
import hep.dataforge.tables.Table
|
||||
import hep.dataforge.tables.TableTransform
|
||||
import hep.dataforge.tables.ValueMap
|
||||
import hep.dataforge.values.Values
|
||||
import inr.numass.data.analyzers.NumassAnalyzerKt
|
||||
import org.apache.commons.math3.analysis.ParametricUnivariateFunction
|
||||
import org.apache.commons.math3.exception.DimensionMismatchException
|
||||
import org.apache.commons.math3.fitting.SimpleCurveFitter
|
||||
import org.apache.commons.math3.fitting.WeightedObservedPoint
|
||||
|
||||
import java.util.stream.Collectors
|
||||
|
||||
import static inr.numass.data.analyzers.NumassAnalyzer.CHANNEL_KEY
|
||||
import static inr.numass.data.analyzers.NumassAnalyzer.COUNT_RATE_KEY
|
||||
|
||||
@CompileStatic
|
||||
class UnderflowFitter {
|
||||
|
||||
private static String[] pointNames = ["U", "amp", "expConst", "correction"];
|
||||
|
||||
static Values fitPoint(Double voltage, Table spectrum, int xLow, int xHigh, int upper, int binning) {
|
||||
|
||||
double norm = spectrum.getRows().filter { Values row ->
|
||||
int channel = row.getInt(CHANNEL_KEY);
|
||||
return channel > xLow && channel < upper;
|
||||
}.mapToDouble { it.getValue(COUNT_RATE_KEY).doubleValue() }.sum();
|
||||
|
||||
double[] fitRes = getUnderflowExpParameters(spectrum, xLow, xHigh, binning);
|
||||
double a = fitRes[0];
|
||||
double sigma = fitRes[1];
|
||||
|
||||
return ValueMap.of(pointNames, voltage, a, sigma, a * sigma * Math.exp(xLow / sigma as double) / norm + 1d);
|
||||
}
|
||||
|
||||
static Table fitAllPoints(Map<Double, Table> data, int xLow, int xHigh, int upper, int binning) {
|
||||
ListTable.Builder builder = new ListTable.Builder(pointNames);
|
||||
data.each { voltage, spectrum -> builder.row(fitPoint(voltage, spectrum, xLow, xHigh, upper, binning)) }
|
||||
return builder.build();
|
||||
}
|
||||
|
||||
/**
|
||||
* Calculate underflow exponent parameters using (xLow, xHigh) window for
|
||||
* extrapolation
|
||||
*
|
||||
* @param xLow
|
||||
* @param xHigh
|
||||
* @return
|
||||
*/
|
||||
private static double[] getUnderflowExpParameters(Table spectrum, int xLow, int xHigh, int binning) {
|
||||
try {
|
||||
if (xHigh <= xLow) {
|
||||
throw new IllegalArgumentException("Wrong borders for underflow calculation");
|
||||
}
|
||||
Table binned = TableTransform.filter(
|
||||
NumassAnalyzerKt.spectrumWithBinning(spectrum, binning),
|
||||
CHANNEL_KEY,
|
||||
xLow,
|
||||
xHigh
|
||||
);
|
||||
|
||||
List<WeightedObservedPoint> points = binned.getRows()
|
||||
.map {
|
||||
new WeightedObservedPoint(
|
||||
1d,//1d / p.getValue() , //weight
|
||||
it.getDouble(CHANNEL_KEY) as double, // x
|
||||
it.getDouble(COUNT_RATE_KEY) / binning as double) //y
|
||||
}
|
||||
.collect(Collectors.toList());
|
||||
SimpleCurveFitter fitter = SimpleCurveFitter.create(new ExponentFunction(), [1d, 200d] as double[])
|
||||
return fitter.fit(points);
|
||||
} catch (Exception ex) {
|
||||
return [0, 0] as double[];
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Exponential function for fitting
|
||||
*/
|
||||
private static class ExponentFunction implements ParametricUnivariateFunction {
|
||||
@Override
|
||||
public double value(double x, double ... parameters) {
|
||||
if (parameters.length != 2) {
|
||||
throw new DimensionMismatchException(parameters.length, 2);
|
||||
}
|
||||
double a = parameters[0];
|
||||
double sigma = parameters[1];
|
||||
//return a * (Math.exp(x / sigma) - 1);
|
||||
return a * Math.exp(x / sigma as double);
|
||||
}
|
||||
|
||||
@Override
|
||||
public double[] gradient(double x, double ... parameters) {
|
||||
if (parameters.length != 2) {
|
||||
throw new DimensionMismatchException(parameters.length, 2);
|
||||
}
|
||||
double a = parameters[0];
|
||||
double sigma = parameters[1];
|
||||
return [Math.exp(x / sigma as double), -a * x / sigma / sigma * Math.exp(x / sigma as double)] as double[]
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
@ -1,73 +0,0 @@
|
||||
package inr.numass.scripts.underflow
|
||||
|
||||
import hep.dataforge.cache.CachePlugin
|
||||
import hep.dataforge.data.DataNode
|
||||
import hep.dataforge.data.DataSet
|
||||
import hep.dataforge.grind.GrindShell
|
||||
import hep.dataforge.grind.actions.GrindPipe
|
||||
import hep.dataforge.meta.Meta
|
||||
import hep.dataforge.storage.commons.StorageUtils
|
||||
import hep.dataforge.tables.Table
|
||||
import inr.numass.data.analyzers.NumassAnalyzer
|
||||
import inr.numass.data.analyzers.TimeAnalyzer
|
||||
import inr.numass.data.api.NumassPoint
|
||||
import inr.numass.data.api.NumassSet
|
||||
import inr.numass.data.api.SimpleNumassPoint
|
||||
import inr.numass.data.storage.NumassStorage
|
||||
import inr.numass.data.storage.NumassStorageFactory
|
||||
|
||||
import java.util.stream.Collectors
|
||||
|
||||
import static hep.dataforge.grind.Grind.buildMeta
|
||||
|
||||
class UnderflowUtils {
|
||||
|
||||
static DataNode<Table> getSpectraMap(GrindShell shell, Meta meta) {
|
||||
return shell.eval {
|
||||
//Defining root directory
|
||||
File dataDirectory = new File(meta.getString("data.dir"))
|
||||
|
||||
//creating storage instance
|
||||
|
||||
NumassStorage storage = NumassStorageFactory.buildLocal(dataDirectory);
|
||||
|
||||
//Reading points
|
||||
//Free operation. No reading done
|
||||
List<NumassSet> sets = StorageUtils
|
||||
.loaderStream(storage)
|
||||
.filter { it.key.matches(meta.getString("data.mask")) }
|
||||
.map {
|
||||
println "loading ${it.key}"
|
||||
return it.value
|
||||
}.collect(Collectors.toList());
|
||||
|
||||
NumassAnalyzer analyzer = new TimeAnalyzer();
|
||||
|
||||
def dataBuilder = DataSet.builder(NumassPoint);
|
||||
|
||||
sets.sort { it.startTime }
|
||||
.collectMany { NumassSet set -> set.points.collect() }
|
||||
.groupBy { NumassPoint point -> point.voltage }
|
||||
.each { key, value ->
|
||||
def point = new SimpleNumassPoint(key as double, value as List<NumassPoint>)
|
||||
String name = (key as Integer).toString()
|
||||
dataBuilder.putStatic(name, point, buildMeta(voltage: key));
|
||||
}
|
||||
|
||||
DataNode<NumassPoint> data = dataBuilder.build()
|
||||
|
||||
def generate = GrindPipe.build("generate") {
|
||||
result { input ->
|
||||
return analyzer.getAmplitudeSpectrum(input as NumassPoint, delegate.meta)
|
||||
}
|
||||
}
|
||||
|
||||
DataNode<Table> spectra = generate.run(shell.context, data, meta.getMeta("generate"));
|
||||
Meta id = buildMeta {
|
||||
put meta.getMeta("data")
|
||||
put meta.getMeta("generate")
|
||||
}
|
||||
return shell.context.getFeature(CachePlugin).cacheNode("underflow", id, spectra)
|
||||
} as DataNode<Table>
|
||||
}
|
||||
}
|
||||
@ -26,6 +26,7 @@ import inr.numass.NumassPlugin
|
||||
import inr.numass.data.NumassDataUtils
|
||||
import inr.numass.data.analyzers.NumassAnalyzer
|
||||
import inr.numass.data.analyzers.SmartAnalyzer
|
||||
import inr.numass.data.analyzers.subtractAmplitudeSpectrum
|
||||
import inr.numass.data.api.NumassSet
|
||||
import inr.numass.data.storage.NumassStorageFactory
|
||||
|
||||
|
||||
149
numass-main/src/main/kotlin/inr/numass/subthreshold/SubFit.kt
Normal file
149
numass-main/src/main/kotlin/inr/numass/subthreshold/SubFit.kt
Normal file
@ -0,0 +1,149 @@
|
||||
package inr.numass.subthreshold
|
||||
|
||||
import hep.dataforge.context.Context
|
||||
import hep.dataforge.data.DataNode
|
||||
import hep.dataforge.data.DataSet
|
||||
import hep.dataforge.kodex.buildMeta
|
||||
import hep.dataforge.kodex.pipe
|
||||
import hep.dataforge.kodex.toList
|
||||
import hep.dataforge.meta.Meta
|
||||
import hep.dataforge.storage.commons.StorageUtils
|
||||
import hep.dataforge.tables.ListTable
|
||||
import hep.dataforge.tables.Table
|
||||
import hep.dataforge.tables.TableTransform
|
||||
import hep.dataforge.tables.ValueMap
|
||||
import hep.dataforge.values.Values
|
||||
import inr.numass.data.analyzers.NumassAnalyzer.Companion.CHANNEL_KEY
|
||||
import inr.numass.data.analyzers.NumassAnalyzer.Companion.COUNT_RATE_KEY
|
||||
import inr.numass.data.analyzers.TimeAnalyzer
|
||||
import inr.numass.data.analyzers.spectrumWithBinning
|
||||
import inr.numass.data.api.NumassPoint
|
||||
import inr.numass.data.api.NumassSet
|
||||
import inr.numass.data.api.SimpleNumassPoint
|
||||
import inr.numass.data.storage.NumassStorageFactory
|
||||
import org.apache.commons.math3.analysis.ParametricUnivariateFunction
|
||||
import org.apache.commons.math3.exception.DimensionMismatchException
|
||||
import org.apache.commons.math3.fitting.SimpleCurveFitter
|
||||
import org.apache.commons.math3.fitting.WeightedObservedPoint
|
||||
import java.util.stream.Collectors
|
||||
|
||||
internal fun getSpectraMap(context: Context, meta: Meta): DataNode<Table> {
|
||||
|
||||
//creating storage instance
|
||||
val storage = NumassStorageFactory.buildLocal(context, meta.getString("data.dir"), true, false);
|
||||
|
||||
//Reading points
|
||||
//Free operation. No reading done
|
||||
val sets = StorageUtils
|
||||
.loaderStream(storage)
|
||||
.filter { it.fullName.toString().matches(meta.getString("data.mask").toRegex()) }
|
||||
.map {
|
||||
println("loading ${it.fullName}")
|
||||
it as NumassSet
|
||||
}.collect(Collectors.toList());
|
||||
|
||||
val analyzer = TimeAnalyzer();
|
||||
|
||||
val data = DataSet.builder(NumassPoint::class.java).also { dataBuilder ->
|
||||
sets.sortedBy { it.startTime }
|
||||
.flatMap { set -> set.points.toList() }
|
||||
.groupBy { it.voltage }
|
||||
.forEach { key, value ->
|
||||
val point = SimpleNumassPoint(key, value)
|
||||
val name = key.toInt().toString()
|
||||
dataBuilder.putStatic(name, point, buildMeta("meta", "voltage" to key));
|
||||
}
|
||||
}.build()
|
||||
|
||||
return data.pipe(context, meta) {
|
||||
result { input ->
|
||||
analyzer.getAmplitudeSpectrum(input, this.meta)
|
||||
}
|
||||
}
|
||||
// val id = buildMeta {
|
||||
// +meta.getMeta("data")
|
||||
// +meta.getMeta("analyze")
|
||||
// }
|
||||
// return context.getFeature(CachePlugin::class.java).cacheNode("subThreshold", id, spectra)
|
||||
}
|
||||
|
||||
private val pointNames = arrayOf("U", "amp", "expConst", "correction");
|
||||
|
||||
/**
|
||||
* Exponential function for fitting
|
||||
*/
|
||||
private class ExponentFunction : ParametricUnivariateFunction {
|
||||
override fun value(x: Double, vararg parameters: Double): Double {
|
||||
if (parameters.size != 2) {
|
||||
throw DimensionMismatchException(parameters.size, 2);
|
||||
}
|
||||
val a = parameters[0];
|
||||
val sigma = parameters[1];
|
||||
//return a * (Math.exp(x / sigma) - 1);
|
||||
return a * Math.exp(x / sigma);
|
||||
}
|
||||
|
||||
override fun gradient(x: Double, vararg parameters: Double): DoubleArray {
|
||||
if (parameters.size != 2) {
|
||||
throw DimensionMismatchException(parameters.size, 2);
|
||||
}
|
||||
val a = parameters[0];
|
||||
val sigma = parameters[1];
|
||||
return doubleArrayOf(Math.exp(x / sigma), -a * x / sigma / sigma * Math.exp(x / sigma))
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Calculate underflow exponent parameters using (xLow, xHigh) window for
|
||||
* extrapolation
|
||||
*
|
||||
* @param xLow
|
||||
* @param xHigh
|
||||
* @return
|
||||
*/
|
||||
private fun getUnderflowExpParameters(spectrum: Table, xLow: Int, xHigh: Int, binning: Int): Pair<Double, Double> {
|
||||
try {
|
||||
if (xHigh <= xLow) {
|
||||
throw IllegalArgumentException("Wrong borders for underflow calculation");
|
||||
}
|
||||
val binned = TableTransform.filter(
|
||||
spectrumWithBinning(spectrum, binning),
|
||||
CHANNEL_KEY,
|
||||
xLow,
|
||||
xHigh
|
||||
);
|
||||
|
||||
val points = binned.rows
|
||||
.map {
|
||||
WeightedObservedPoint(
|
||||
1.0,//1d / p.getValue() , //weight
|
||||
it.getDouble(CHANNEL_KEY), // x
|
||||
it.getDouble(COUNT_RATE_KEY) / binning) //y
|
||||
}
|
||||
.collect(Collectors.toList());
|
||||
val fitter = SimpleCurveFitter.create(ExponentFunction(), doubleArrayOf(1.0, 200.0))
|
||||
val res = fitter.fit(points)
|
||||
return Pair(res[0], res[1])
|
||||
} catch (ex: Exception) {
|
||||
return Pair(0.0, 0.0);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
internal fun fitPoint(voltage: Double, spectrum: Table, xLow: Int, xHigh: Int, upper: Int, binning: Int): Values {
|
||||
val norm = spectrum.rows.filter { row ->
|
||||
row.getInt(CHANNEL_KEY) in (xLow + 1)..(upper - 1);
|
||||
}.mapToDouble { it.getValue(COUNT_RATE_KEY).doubleValue() }.sum();
|
||||
|
||||
val (a, sigma) = getUnderflowExpParameters(spectrum, xLow, xHigh, binning);
|
||||
|
||||
return ValueMap.of(pointNames, voltage, a, sigma, a * sigma * Math.exp(xLow / sigma) / norm + 1.0);
|
||||
}
|
||||
|
||||
internal fun fitAllPoints(data: Map<Double, Table>, xLow: Int, xHigh: Int, upper: Int, binning: Int): Table {
|
||||
return ListTable.Builder(*pointNames).apply {
|
||||
data.forEach { voltage, spectrum -> row(fitPoint(voltage, spectrum, xLow, xHigh, upper, binning)) }
|
||||
}.build()
|
||||
}
|
||||
@ -272,17 +272,21 @@ class StorageView(private val context: Context = Global.instance()) : View(title
|
||||
// }
|
||||
|
||||
private fun loadDirectory(path: URI) {
|
||||
statusBar.text = "Loading storage: $path"
|
||||
statusBar.progress = -1.0;
|
||||
runGoal("loadDirectory[$path]") {
|
||||
title = "Load storage ($path)"
|
||||
progress = -1.0
|
||||
message = "Building numass storage tree..."
|
||||
(StorageManager.buildStorage(context, NumassStorageFactory.buildStorageMeta(path, true, true)) as NumassStorage).also {
|
||||
(StorageManager.buildStorage(context, NumassStorageFactory.buildStorageMeta(path, true, false)) as NumassStorage).also {
|
||||
progress = 1.0
|
||||
}
|
||||
} ui {
|
||||
storage = it
|
||||
storageName = "Storage: " + path
|
||||
|
||||
statusBar.text = "OK"
|
||||
statusBar.progress = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user