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minor fixes

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This commit is contained in:
Alexander Nozik 2016-08-26 19:21:43 +03:00
parent 6a184dddda
commit a5c485a2c1
19 changed files with 466 additions and 463 deletions
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2
numass-main/build.gradle
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@ -36,7 +36,7 @@ task listActions(dependsOn: classes, type: JavaExec) {
task workspace(dependsOn: classes, type: JavaExec) { task workspace(dependsOn: classes, type: JavaExec) {
main 'inr.numass.workspace.NumassGrindLauncher' main 'inr.numass.workspace.NumassGrindLauncher'
classpath = sourceSets.main.runtimeClasspath classpath = sourceSets.main.runtimeClasspath
args "-c \"D:\\Work\\Numass\\sterile2016\\workspace.groovy\" numass.fitsum sum".split() args "-c \"D:\\Work\\Numass\\sterile2016\\workspace.groovy\" numass.fitsum sum_down".split()
description "Run workspace task" description "Run workspace task"
group "numass" group "numass"

8
numass-main/src/main/groovy/inr/numass/NumassWorkspaceSpec.groovy
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@ -31,10 +31,10 @@ class NumassWorkspaceSpec extends WorkspaceSpec {
NumassWorkspaceSpec() { NumassWorkspaceSpec() {
//load tasks //load tasks
super.loadTask(NumassPrepareTask) super.task(NumassPrepareTask)
super.loadTask(NumassTableFilterTask) super.task(NumassTableFilterTask)
super.loadTask(NumassFitScanTask) super.task(NumassFitScanTask)
super.loadTask(NumassFitScanSummaryTask) super.task(NumassFitScanSummaryTask)
} }

87
numass-main/src/main/java/inr/numass/NumassPlugin.java
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@ -19,43 +19,20 @@ import hep.dataforge.actions.ActionManager;
import hep.dataforge.context.BasicPlugin; import hep.dataforge.context.BasicPlugin;
import hep.dataforge.context.Context; import hep.dataforge.context.Context;
import hep.dataforge.context.PluginDef; import hep.dataforge.context.PluginDef;
import hep.dataforge.maths.MathPlugin;
import hep.dataforge.meta.Meta;
import hep.dataforge.plotfit.PlotFitResultAction;
import hep.dataforge.plots.PlotDataAction;
import hep.dataforge.stat.fit.FitManager; import hep.dataforge.stat.fit.FitManager;
import hep.dataforge.stat.fit.FitPlugin; import hep.dataforge.stat.fit.FitPlugin;
import hep.dataforge.stat.models.ModelManager; import hep.dataforge.stat.models.ModelManager;
import hep.dataforge.stat.models.WeightedXYModel; import hep.dataforge.stat.models.WeightedXYModel;
import hep.dataforge.stat.models.XYModel; import hep.dataforge.stat.models.XYModel;
import hep.dataforge.maths.MathPlugin;
import hep.dataforge.meta.Meta;
import hep.dataforge.plotfit.PlotFitResultAction;
import hep.dataforge.plots.PlotDataAction;
import hep.dataforge.tables.PointAdapter; import hep.dataforge.tables.PointAdapter;
import hep.dataforge.tables.XYAdapter; import hep.dataforge.tables.XYAdapter;
import inr.numass.actions.AdjustErrorsAction; import inr.numass.actions.*;
import inr.numass.actions.FindBorderAction; import inr.numass.models.*;
import inr.numass.actions.MergeDataAction;
import inr.numass.actions.MonitorCorrectAction;
import inr.numass.actions.PrepareDataAction;
import inr.numass.actions.ReadNumassDataAction;
import inr.numass.actions.ReadNumassStorageAction;
import inr.numass.actions.ShowEnergySpectrumAction;
import inr.numass.actions.ShowLossSpectrumAction;
import inr.numass.actions.SlicingAction;
import inr.numass.actions.SubstractSpectrumAction;
import inr.numass.actions.SummaryAction;
import inr.numass.models.BetaSpectrum;
import inr.numass.models.CustomNBkgSpectrum;
import inr.numass.models.EmpiricalLossSpectrum;
import inr.numass.models.ExperimentalVariableLossSpectrum;
import inr.numass.models.GaussSourceSpectrum;
import inr.numass.models.GunSpectrum;
import inr.numass.models.ModularSpectrum;
import inr.numass.models.NBkgSpectrum;
import inr.numass.models.RangedNamedSetSpectrum;
import inr.numass.models.ResolutionFunction;
import inr.numass.models.TransmissionInterpolator;
import inr.numass.models.VariableLossSpectrum;
import inr.numass.models.sterile.SterileNeutrinoSpectrum; import inr.numass.models.sterile.SterileNeutrinoSpectrum;
import org.apache.commons.math3.analysis.BivariateFunction;
import org.apache.commons.math3.analysis.UnivariateFunction; import org.apache.commons.math3.analysis.UnivariateFunction;
import org.apache.commons.math3.util.FastMath; import org.apache.commons.math3.util.FastMath;
@ -88,7 +65,6 @@ public class NumassPlugin extends BasicPlugin {
actions.registerAction(PlotFitResultAction.class); actions.registerAction(PlotFitResultAction.class);
actions.registerAction(ShowLossSpectrumAction.class); actions.registerAction(ShowLossSpectrumAction.class);
actions.registerAction(AdjustErrorsAction.class); actions.registerAction(AdjustErrorsAction.class);
actions.registerAction(ReadNumassStorageAction.class);
actions.registerAction(ShowEnergySpectrumAction.class); actions.registerAction(ShowEnergySpectrumAction.class);
actions.registerAction(SubstractSpectrumAction.class); actions.registerAction(SubstractSpectrumAction.class);
} }
@ -121,7 +97,7 @@ public class NumassPlugin extends BasicPlugin {
double A = an.getDouble("resolution", 8.3e-5);//8.3e-5 double A = an.getDouble("resolution", 8.3e-5);//8.3e-5
double from = an.getDouble("from", 14400d); double from = an.getDouble("from", 14400d);
double to = an.getDouble("to", 19010d); double to = an.getDouble("to", 19010d);
RangedNamedSetSpectrum beta = new BetaSpectrum(context.io().getFile("FS.txt")); RangedNamedSetSpectrum beta = new BetaSpectrum(getClass().getResourceAsStream("/data/FS.txt"));
ModularSpectrum sp = new ModularSpectrum(beta, A, from, to); ModularSpectrum sp = new ModularSpectrum(beta, A, from, to);
NBkgSpectrum spectrum = new NBkgSpectrum(sp); NBkgSpectrum spectrum = new NBkgSpectrum(sp);
@ -226,55 +202,6 @@ public class NumassPlugin extends BasicPlugin {
return new XYModel(spectrum, getAdapter(meta)); return new XYModel(spectrum, getAdapter(meta));
}); });
manager.addModel("sterile-old", (context, meta) -> {
double A = meta.getDouble("resolution", meta.getDouble("resolution.width", 8.3e-5));//8.3e-5
double from = meta.getDouble("from", 13900d);
double to = meta.getDouble("to", 18700d);
context.getReport().report("Setting up tritium model with real transmission function");
BivariateFunction resolutionTail;
if (meta.hasValue("resolution.tailAlpha")) {
resolutionTail = ResolutionFunction.getAngledTail(meta.getDouble("resolution.tailAlpha"), meta.getDouble("resolution.tailBeta", 0));
} else {
resolutionTail = ResolutionFunction.getRealTail();
}
RangedNamedSetSpectrum beta = new BetaSpectrum(context.io().getFile("FS.txt"));
ModularSpectrum sp = new ModularSpectrum(beta, new ResolutionFunction(A, resolutionTail), from, to);
if (meta.getBoolean("caching", false)) {
context.getReport().report("Caching turned on");
sp.setCaching(true);
}
//Adding trapping energy dependence
if (meta.hasValue("transmission.trapping")) {
BivariateFunction trap = MathPlugin.buildFrom(context).buildBivariateFunction(meta.getString("transmussion.trapping"));
sp.setTrappingFunction(trap);
}
NBkgSpectrum spectrum = new NBkgSpectrum(sp);
return new XYModel(spectrum, getAdapter(meta));
});
manager.addModel("modularbeta-unadeabatic", (context, an) -> {
double A = an.getDouble("resolution", 8.3e-5);//8.3e-5
double from = an.getDouble("from", 14400d);
double to = an.getDouble("to", 19010d);
BivariateFunction reolutionTail = (double E, double U) -> {
double x = E - U;
if (x > 1500) {
return 0.98;
} else //Intercept = 1.00051, Slope = -1.3552E-5
{
return 1.00051 - 1.3552E-5 * x;
}
};
RangedNamedSetSpectrum beta = new BetaSpectrum(context.io().getFile("FS.txt"));
ModularSpectrum sp = new ModularSpectrum(beta, new ResolutionFunction(A, reolutionTail), from, to);
NBkgSpectrum spectrum = new NBkgSpectrum(sp);
return new XYModel(spectrum, getAdapter(an));
});
manager.addModel("gun", (context, an) -> { manager.addModel("gun", (context, an) -> {
GunSpectrum gsp = new GunSpectrum(); GunSpectrum gsp = new GunSpectrum();

93
numass-main/src/main/java/inr/numass/actions/ReadNumassStorageAction.java
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@ -1,93 +0,0 @@
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package inr.numass.actions;
import hep.dataforge.actions.GenericAction;
import hep.dataforge.computation.WorkManager.Callback;
import hep.dataforge.data.Data;
import hep.dataforge.data.DataFilter;
import hep.dataforge.data.DataNode;
import hep.dataforge.data.DataSet;
import hep.dataforge.description.TypedActionDef;
import hep.dataforge.description.ValueDef;
import hep.dataforge.meta.Meta;
import hep.dataforge.storage.api.Loader;
import hep.dataforge.storage.commons.StorageUtils;
import inr.numass.storage.NumassData;
import inr.numass.storage.NumassDataLoader;
import inr.numass.storage.NumassStorage;
import inr.numass.storage.SetDirectionUtility;
import java.util.concurrent.CompletableFuture;
/**
*
* @author Alexander Nozik
*/
@TypedActionDef(name = "readStorage",
outputType = NumassData.class, info = "Read numass storage data")
@ValueDef(name = "uri", info = "The path to Numass storage")
//@NodeDef(name = "debunch", target = "class::inr.numass.actions.DebunchAction", info = "If given, governs debunching")
public class ReadNumassStorageAction extends GenericAction<Void, NumassData> {
@Override
public DataNode<NumassData> run(DataNode<Void> data, Meta actionMeta) {
try {
NumassStorage storage = NumassStorage.buildNumassRoot(actionMeta.getString("uri"), true, false);
DataFilter filter = new DataFilter().configure(actionMeta);
boolean forwardOnly = actionMeta.getBoolean("forwardOnly", false);
boolean reverseOnly = actionMeta.getBoolean("reverseOnly", false);
//FIXME make Work actually submitted only when calculation starts
CompletableFuture<DataSet<NumassData>> future = getContext().workManager()
.<DataSet<NumassData>>post(getName(), (Callback callback) -> {
//FIXME remove in later revisions
SetDirectionUtility.load(getContext());
DataSet.Builder<NumassData> builder = DataSet.builder(NumassData.class);
callback.setMaxProgress(StorageUtils.loaderStream(storage).count());
StorageUtils.loaderStream(storage).forEach(pair -> {
Loader loader = pair.getValue();
if (loader instanceof NumassData) {
NumassDataLoader nd = (NumassDataLoader) loader;
Data<NumassData> datum = Data.buildStatic(nd);
if (filter.acceptData(pair.getKey(), datum)) {
boolean accept = true;
if (forwardOnly || reverseOnly) {
boolean reversed = nd.isReversed();
accept = (reverseOnly && reversed) || (forwardOnly && !reversed);
}
if (accept) {
builder.putData(pair.getKey(), datum);
}
}
}
callback.increaseProgress(1d);
});
if (actionMeta.getBoolean("loadLegacy", false)) {
logger().info("Loading legacy files");
storage.legacyFiles().forEach(nd -> {
Data<NumassData> datum = Data.buildStatic(nd);
if (filter.acceptData(nd.getName(), datum)) {
builder.putData("legacy." + nd.getName(), datum);
}
});
}
//FIXME remove in later revisions
SetDirectionUtility.save(getContext());
return builder.build();
});
return future.get();
} catch (Exception ex) {
throw new RuntimeException("Failed to load storage", ex);
}
}
}

26
numass-main/src/main/java/inr/numass/models/BetaSpectrum.java
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@ -19,15 +19,18 @@ import hep.dataforge.exceptions.NotDefinedException;
import hep.dataforge.stat.parametric.AbstractParametricFunction; import hep.dataforge.stat.parametric.AbstractParametricFunction;
import hep.dataforge.values.NamedValueSet; import hep.dataforge.values.NamedValueSet;
import hep.dataforge.values.ValueProvider; import hep.dataforge.values.ValueProvider;
import java.io.File; import java.io.File;
import static java.lang.Math.abs; import java.io.FileInputStream;
import static java.lang.Math.exp; import java.io.FileNotFoundException;
import static java.lang.Math.sqrt; import java.io.InputStream;
import static java.lang.Math.*;
/** /**
*
* @author Darksnake * @author Darksnake
*/ */
@Deprecated
public class BetaSpectrum extends AbstractParametricFunction implements RangedNamedSetSpectrum { public class BetaSpectrum extends AbstractParametricFunction implements RangedNamedSetSpectrum {
static final double K = 1E-23; static final double K = 1E-23;
@ -39,10 +42,17 @@ public class BetaSpectrum extends AbstractParametricFunction implements RangedNa
super(list); super(list);
} }
public BetaSpectrum(File FSSFile) { public BetaSpectrum(InputStream FSStream) {
super(list);
if (FSStream != null) {
this.fss = new FSS(FSStream);
}
}
public BetaSpectrum(File FSSFile) throws FileNotFoundException {
super(list); super(list);
if (FSSFile != null) { if (FSSFile != null) {
this.fss = new FSS(FSSFile); this.fss = new FSS(new FileInputStream(FSSFile));
} }
} }
@ -197,11 +207,11 @@ public class BetaSpectrum extends AbstractParametricFunction implements RangedNa
// P(rootsterile)+ (1-P)root // P(rootsterile)+ (1-P)root
} }
public void setFSS(File FSSFile) { public void setFSS(File FSSFile) throws FileNotFoundException {
if (FSSFile == null) { if (FSSFile == null) {
this.fss = null; this.fss = null;
} else { } else {
this.fss = new FSS(FSSFile); this.fss = new FSS(new FileInputStream(FSSFile));
} }
} }

13
numass-main/src/main/java/inr/numass/models/FSS.java
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@ -19,12 +19,10 @@ import hep.dataforge.io.IOUtils;
import hep.dataforge.tables.DataPoint; import hep.dataforge.tables.DataPoint;
import hep.dataforge.tables.PointSource; import hep.dataforge.tables.PointSource;
import java.io.File; import java.io.InputStream;
import java.io.FileNotFoundException;
import java.util.ArrayList; import java.util.ArrayList;
/** /**
*
* @author Darksnake * @author Darksnake
*/ */
public class FSS { public class FSS {
@ -32,10 +30,8 @@ public class FSS{
private final ArrayList<Double> es = new ArrayList<>(); private final ArrayList<Double> es = new ArrayList<>();
private double norm; private double norm;
public FSS(File FSSFile) { public FSS(InputStream stream) {
try { PointSource data = IOUtils.readColumnedData(stream, "E", "P");
PointSource data = IOUtils.readColumnedData(FSSFile,"E","P");
norm = 0; norm = 0;
for (DataPoint dp : data) { for (DataPoint dp : data) {
es.add(dp.getDouble("E")); es.add(dp.getDouble("E"));
@ -46,9 +42,6 @@ public class FSS{
if (ps.isEmpty()) { if (ps.isEmpty()) {
throw new RuntimeException("Error reading FSS FILE. No points."); throw new RuntimeException("Error reading FSS FILE. No points.");
} }
} catch (FileNotFoundException ex) {
throw new RuntimeException("Error reading FSS FILE. File not found.");
}
} }
public double getE(int n) { public double getE(int n) {

7
numass-main/src/main/java/inr/numass/models/sterile/NumassBeta.java
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@ -8,9 +8,8 @@ package inr.numass.models.sterile;
import hep.dataforge.exceptions.NotDefinedException; import hep.dataforge.exceptions.NotDefinedException;
import hep.dataforge.stat.parametric.AbstractParametricBiFunction; import hep.dataforge.stat.parametric.AbstractParametricBiFunction;
import hep.dataforge.values.NamedValueSet; import hep.dataforge.values.NamedValueSet;
import static java.lang.Math.abs;
import static java.lang.Math.exp; import static java.lang.Math.*;
import static java.lang.Math.sqrt;
/** /**
* A bi-function for beta-spectrum calculation taking energy and final state as * A bi-function for beta-spectrum calculation taking energy and final state as
@ -197,9 +196,7 @@ public class NumassBeta extends AbstractParametricBiFunction {
protected double getDefaultParameter(String name) { protected double getDefaultParameter(String name) {
switch (name) { switch (name) {
case "mnu2": case "mnu2":
return 0;
case "U2": case "U2":
return 0;
case "msterile2": case "msterile2":
return 0; return 0;
default: default:

118
numass-main/src/main/java/inr/numass/models/sterile/SterileNeutrinoSpectrum.java
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@ -10,16 +10,20 @@ import hep.dataforge.context.GlobalContext;
import hep.dataforge.description.NodeDef; import hep.dataforge.description.NodeDef;
import hep.dataforge.description.ValueDef; import hep.dataforge.description.ValueDef;
import hep.dataforge.exceptions.NotDefinedException; import hep.dataforge.exceptions.NotDefinedException;
import hep.dataforge.maths.integration.UnivariateIntegrator;
import hep.dataforge.meta.Meta;
import hep.dataforge.stat.parametric.AbstractParametricBiFunction; import hep.dataforge.stat.parametric.AbstractParametricBiFunction;
import hep.dataforge.stat.parametric.AbstractParametricFunction; import hep.dataforge.stat.parametric.AbstractParametricFunction;
import hep.dataforge.stat.parametric.ParametricBiFunction; import hep.dataforge.stat.parametric.ParametricBiFunction;
import hep.dataforge.maths.integration.UnivariateIntegrator;
import hep.dataforge.meta.Meta;
import hep.dataforge.values.NamedValueSet; import hep.dataforge.values.NamedValueSet;
import inr.numass.NumassIntegrator; import inr.numass.NumassIntegrator;
import inr.numass.models.FSS; import inr.numass.models.FSS;
import org.apache.commons.math3.analysis.UnivariateFunction; import org.apache.commons.math3.analysis.UnivariateFunction;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.InputStream;
/** /**
* Compact all-in-one model for sterile neutrino spectrum * Compact all-in-one model for sterile neutrino spectrum
* *
@ -27,21 +31,15 @@ import org.apache.commons.math3.analysis.UnivariateFunction;
*/ */
@NodeDef(name = "resolution") @NodeDef(name = "resolution")
@NodeDef(name = "transmission") @NodeDef(name = "transmission")
@ValueDef(name = "fssFile") @ValueDef(name = "fssFile", info = "The name for external FSS file. By default internal FSS file is used")
@ValueDef(name = "useFSS", type = "BOOLEAN")
public class SterileNeutrinoSpectrum extends AbstractParametricFunction { public class SterileNeutrinoSpectrum extends AbstractParametricFunction {
private static final String[] list = {"X", "trap", "E0", "mnu2", "msterile2", "U2"}; private static final String[] list = {"X", "trap", "E0", "mnu2", "msterile2", "U2"};
// private final RandomGenerator rnd;
// private RealDistribution fssDistribution;
private FSS fss;
/** /**
* variables:Eo offset,Ein; parameters: "mnu2", "msterile2", "U2" * variables:Eo offset,Ein; parameters: "mnu2", "msterile2", "U2"
*/ */
private final ParametricBiFunction source = new NumassBeta(); private final ParametricBiFunction source = new NumassBeta();
/** /**
* variables:Ein,Eout; parameters: "A" * variables:Ein,Eout; parameters: "A"
*/ */
@ -50,26 +48,32 @@ public class SterileNeutrinoSpectrum extends AbstractParametricFunction {
* variables:Eout,U; parameters: "X", "trap" * variables:Eout,U; parameters: "X", "trap"
*/ */
private final ParametricBiFunction resolution; private final ParametricBiFunction resolution;
/** /**
* auxiliary function for trans-res convolution * auxiliary function for trans-res convolution
*/ */
private final ParametricBiFunction transRes; private final ParametricBiFunction transRes;
private FSS fss;
// private boolean useMC; // private boolean useMC;
private boolean fast; private boolean fast;
public SterileNeutrinoSpectrum(Context context, Meta configuration) { public SterileNeutrinoSpectrum(Context context, Meta configuration) {
super(list); super(list);
// rnd = new SynchronizedRandomGenerator(new JDKRandomGenerator()); if (configuration.getBoolean("useFSS", true)) {
InputStream fssStream;
if (configuration.hasValue("fssFile")) { if (configuration.hasValue("fssFile")) {
fss = new FSS(context.io().getFile(configuration.getString("fssFile"))); try {
// fssDistribution = new EnumeratedRealDistribution(rnd, fss.getEs(), fss.getPs()); fssStream = new FileInputStream(context.io().getFile(configuration.getString("fssFile")));
} catch (FileNotFoundException e) {
throw new RuntimeException("Could not locate FSS file");
}
} else {
fssStream = getClass().getResourceAsStream("/data/FS.txt");
}
fss = new FSS(fssStream);
} }
transmission = new NumassTransmission(context, configuration.getNodeOrEmpty("transmission")); transmission = new NumassTransmission(context, configuration.getNodeOrEmpty("transmission"));
resolution = new NumassResolution(configuration.getNode("resolution", Meta.empty())); resolution = new NumassResolution(configuration.getNode("resolution", Meta.empty()));
// this.useMC = configuration.getBoolean("useMC", false);
this.fast = configuration.getBoolean("fast", true); this.fast = configuration.getBoolean("fast", true);
transRes = new TransRes(); transRes = new TransRes();
} }
@ -103,96 +107,18 @@ public class SterileNeutrinoSpectrum extends AbstractParametricFunction {
return integrate(u, source, transRes, set); return integrate(u, source, transRes, set);
} }
// private int numCalls(double u) {
// return 100000;
// }
//
// private boolean useDirect() {
// return !useMC;
// }
@Override @Override
public boolean providesDeriv(String name) { public boolean providesDeriv(String name) {
return source.providesDeriv(name) && transmission.providesDeriv(name) && resolution.providesDeriv(name); return source.providesDeriv(name) && transmission.providesDeriv(name) && resolution.providesDeriv(name);
} }
// /**
// * Random E generator
// *
// * @param a
// * @param b
// * @return
// */
// private double rndE(double a, double b) {
// return rnd.nextDouble() * (b - a) + a;
// }
//
// private double integrate(
// double u,
// ParametricBiFunction sourceFunction,
// ParametricBiFunction transmissionFunction,
// ParametricBiFunction resolutionFunction,
// NamedValueSet set) {
// if (useDirect()) {
// return integrateDirect(u, sourceFunction, transmissionFunction, resolutionFunction, set);
// } else {
// return integrateRandom(u, sourceFunction, transmissionFunction, resolutionFunction, set);
// }
// }
// /**
// * Monte-Carlo integration of spectrum
// *
// * @param u
// * @param sourceFunction
// * @param transmissionFunction
// * @param resolutionFunction
// * @param set
// * @return
// */
// private double integrateRandom(
// double u,
// ParametricBiFunction sourceFunction,
// ParametricBiFunction transmissionFunction,
// ParametricBiFunction resolutionFunction,
// NamedValueSet set) {
//
// int num = numCalls(u);
// double eMax = set.getDouble("E0") + 5d;
// if (u > eMax) {
// return 0;
// }
//
// double sum = DoubleStream.generate(() -> {
// // generate final state
// double fs;
// if (fssDistribution != null) {
// fs = fssDistribution.sample();
// } else {
// fs = 0;
// }
//
// double eIn = rndE(u, eMax);
//
// double eOut = rndE(u, eIn);
//
// double res = sourceFunction.value(fs, eIn, set)
// * transmissionFunction.value(eIn, eOut, set)
// * resolutionFunction.value(eOut, u, set);
//
// if (Double.isNaN(res)) {
// throw new Error();
// }
// return res;
// }).parallel().limit(num).sum();
// //triangle surface
// return Math.pow(eMax - u, 2d) / 2d * sum / num;
// }
/** /**
* Direct Gauss-Legandre integration * Direct Gauss-Legandre integration
* *
* @param u * @param u
* @param sourceFunction * @param sourceFunction
* @param transmissionFunction * @param transResFunction
* @param resolutionFunction
* @param set * @param set
* @return * @return
*/ */

15
numass-main/src/main/java/inr/numass/utils/PileUpSimulator.java
View File

@ -8,24 +8,24 @@ package inr.numass.utils;
import inr.numass.storage.NMEvent; import inr.numass.storage.NMEvent;
import inr.numass.storage.NMPoint; import inr.numass.storage.NMPoint;
import inr.numass.storage.RawNMPoint; import inr.numass.storage.RawNMPoint;
import static java.lang.Math.max;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import static java.lang.Math.max;
/** /**
*
* @author Alexander Nozik <altavir@gmail.com> * @author Alexander Nozik <altavir@gmail.com>
*/ */
public class PileUpSimulator { public class PileUpSimulator {
private final static double us = 1e-6;//microsecond private final static double us = 1e-6;//microsecond
private double uSet = 0;
private final double pointLength; private final double pointLength;
private final NMEventGenerator generator; private final NMEventGenerator generator;
private final List<NMEvent> generated = new ArrayList<>(); private final List<NMEvent> generated = new ArrayList<>();
private final List<NMEvent> pileup = new ArrayList<>(); private final List<NMEvent> pileup = new ArrayList<>();
private final List<NMEvent> registred = new ArrayList<>(); private final List<NMEvent> registred = new ArrayList<>();
private double uSet = 0;
public PileUpSimulator(double countRate, double length) { public PileUpSimulator(double countRate, double length) {
generator = new NMEventGenerator(countRate); generator = new NMEventGenerator(countRate);
@ -96,8 +96,9 @@ public class PileUpSimulator {
* @param delay * @param delay
* @return * @return
*/ */
private boolean nextEventRegistered(double delay) { private boolean nextEventRegistered(short prevChanel, double delay) {
double prob = 1d - 1d / (1d + Math.pow(delay / 6.2, 75.91)); double average = 6.76102 - 4.31897E-4 * prevChanel + 7.88429E-8 * prevChanel * prevChanel;
double prob = 1d - 1d / (1d + Math.pow(delay / average, 75.91));
return random(prob); return random(prob);
} }
@ -120,7 +121,7 @@ public class PileUpSimulator {
//not counting double pileups //not counting double pileups
if (last != null) { if (last != null) {
double delay = (next.getTime() - lastRegisteredTime) / us; //time between events in microseconds double delay = (next.getTime() - lastRegisteredTime) / us; //time between events in microseconds
if (nextEventRegistered(delay)) { if (nextEventRegistered(last.getChanel(), delay)) {
//just register new event //just register new event
registred.add(next); registred.add(next);
lastRegisteredTime = next.getTime(); lastRegisteredTime = next.getTime();

20
numass-main/src/main/java/inr/numass/workspace/NumassFitScanSummaryTask.java
View File

@ -7,8 +7,7 @@ package inr.numass.workspace;
import hep.dataforge.actions.Action; import hep.dataforge.actions.Action;
import hep.dataforge.actions.ManyToOneAction; import hep.dataforge.actions.ManyToOneAction;
import hep.dataforge.computation.WorkManager; import hep.dataforge.computation.ProgressCallback;
import hep.dataforge.context.Context;
import hep.dataforge.data.DataNode; import hep.dataforge.data.DataNode;
import hep.dataforge.data.DataSet; import hep.dataforge.data.DataSet;
import hep.dataforge.description.TypedActionDef; import hep.dataforge.description.TypedActionDef;
@ -19,9 +18,8 @@ import hep.dataforge.stat.fit.ParamSet;
import hep.dataforge.stat.fit.UpperLimitGenerator; import hep.dataforge.stat.fit.UpperLimitGenerator;
import hep.dataforge.tables.ListTable; import hep.dataforge.tables.ListTable;
import hep.dataforge.tables.Table; import hep.dataforge.tables.Table;
import hep.dataforge.workspace.GenericTask; import hep.dataforge.workspace.AbstractTask;
import hep.dataforge.workspace.TaskModel; import hep.dataforge.workspace.TaskModel;
import hep.dataforge.workspace.TaskState;
import java.io.OutputStream; import java.io.OutputStream;
import java.util.Map; import java.util.Map;
@ -29,21 +27,21 @@ import java.util.Map;
/** /**
* @author Alexander Nozik * @author Alexander Nozik
*/ */
public class NumassFitScanSummaryTask extends GenericTask { public class NumassFitScanSummaryTask extends AbstractTask<Table> {
@Override @Override
protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { protected DataNode<Table> run(TaskModel model, ProgressCallback callback, DataNode<?> data) {
DataSet.Builder<Table> builder = DataSet.builder(Table.class); DataSet.Builder<Table> builder = DataSet.builder(Table.class);
Action<FitState, Table> action = new FitSummaryAction().withContext(context); Action<FitState, Table> action = new FitSummaryAction().withContext(model.getWorkspace().getContext());
DataNode<FitState> data = state.getData().getCheckedNode("fitscan", FitState.class); DataNode<FitState> input = data.getCheckedNode("fitscan", FitState.class);
data.nodeStream().forEach(node -> input.nodeStream().forEach(node ->
builder.putData(node.getName(), action.run((DataNode<FitState>) node, config).getData())); builder.putData(node.getName(), action.run((DataNode<FitState>) node, model.meta()).getData()));
// if (data.nodeStream().count() > 1) { // if (data.nodeStream().count() > 1) {
//merge tables if there is more than one //merge tables if there is more than one
// } // }
state.finish(builder.build()); return builder.build();
} }
@Override @Override

26
numass-main/src/main/java/inr/numass/workspace/NumassFitScanTask.java
View File

@ -6,8 +6,7 @@
package inr.numass.workspace; package inr.numass.workspace;
import hep.dataforge.actions.Action; import hep.dataforge.actions.Action;
import hep.dataforge.computation.WorkManager; import hep.dataforge.computation.ProgressCallback;
import hep.dataforge.context.Context;
import hep.dataforge.data.DataNode; import hep.dataforge.data.DataNode;
import hep.dataforge.data.DataTree; import hep.dataforge.data.DataTree;
import hep.dataforge.meta.Meta; import hep.dataforge.meta.Meta;
@ -16,22 +15,23 @@ import hep.dataforge.stat.fit.FitAction;
import hep.dataforge.stat.fit.FitState; import hep.dataforge.stat.fit.FitState;
import hep.dataforge.tables.Table; import hep.dataforge.tables.Table;
import hep.dataforge.values.Value; import hep.dataforge.values.Value;
import hep.dataforge.workspace.GenericTask; import hep.dataforge.workspace.AbstractTask;
import hep.dataforge.workspace.TaskModel; import hep.dataforge.workspace.TaskModel;
import hep.dataforge.workspace.TaskState;
/** /**
* @author Alexander Nozik * @author Alexander Nozik
*/ */
public class NumassFitScanTask extends GenericTask { public class NumassFitScanTask extends AbstractTask<FitState> {
@Override @Override
protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { protected DataNode<FitState> run(TaskModel model, ProgressCallback callback, DataNode<?> data) {
Meta config = model.meta();
String scanParameter = config.getString("scanPar", "msterile2"); String scanParameter = config.getString("scanPar", "msterile2");
Value scanValues = config.getValue("scanValues", Value.of("[2.5e5, 1e6, 2.25e6, 4e6, 6.25e6, 9e6]")); Value scanValues = config.getValue("scanValues", Value.of("[2.5e5, 1e6, 2.25e6, 4e6, 6.25e6, 9e6]"));
Action<Table, FitState> action = new FitAction().withContext(context).withParentProcess(callback.workName()); Action<Table, FitState> action = new FitAction().withContext(model.getContext()).withParentProcess(callback.workName());
DataTree.Builder<FitState> resultBuilder = DataTree.builder(FitState.class); DataTree.Builder<FitState> resultBuilder = DataTree.builder(FitState.class);
DataNode<?> sourceNode = state.getData().getNode("prepare").get(); DataNode<?> sourceNode = data.getNode("prepare").get();
if (config.hasNode("merge")) { if (config.hasNode("merge")) {
//use merged data and ignore raw data //use merged data and ignore raw data
@ -41,11 +41,11 @@ public class NumassFitScanTask extends GenericTask {
//do fit //do fit
Meta fitConfig = config.getMeta("fit"); Meta fitConfig = config.getMeta("fit");
sourceNode.forEachDataWithType(Table.class, data -> { sourceNode.forEachDataWithType(Table.class, d -> {
for (int i = 0; i < scanValues.listValue().size(); i++) { for (int i = 0; i < scanValues.listValue().size(); i++) {
Value val = scanValues.listValue().get(i); Value val = scanValues.listValue().get(i);
MetaBuilder overrideMeta = new MetaBuilder(fitConfig); MetaBuilder overrideMeta = new MetaBuilder(fitConfig);
overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", data.getName(), scanParameter, val.stringValue())); overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", d.getName(), scanParameter, val.stringValue()));
if (overrideMeta.hasNode("params." + scanParameter)) { if (overrideMeta.hasNode("params." + scanParameter)) {
overrideMeta.setValue("params." + scanParameter + ".value", val); overrideMeta.setValue("params." + scanParameter + ".value", val);
@ -54,13 +54,13 @@ public class NumassFitScanTask extends GenericTask {
.filter(par -> par.getString("name") == scanParameter).forEach(par -> par.setValue("value", val)); .filter(par -> par.getString("name") == scanParameter).forEach(par -> par.setValue("value", val));
} }
// Data<Table> newData = new Data<Table>(data.getGoal(),data.type(),overrideMeta); // Data<Table> newData = new Data<Table>(data.getGoal(),data.type(),overrideMeta);
DataNode node = action.run(DataNode.of("fit_" + i, data, Meta.empty()), overrideMeta); DataNode node = action.run(DataNode.of("fit_" + i, d, Meta.empty()), overrideMeta);
resultBuilder.putData(data.getName() + ".fit_" + i, node.getData()); resultBuilder.putData(d.getName() + ".fit_" + i, node.getData());
} }
}); });
state.finish(resultBuilder.build()); return resultBuilder.build();
} }
@Override @Override

91
numass-main/src/main/java/inr/numass/workspace/NumassPrepareTask.java
View File

@ -6,29 +6,32 @@
package inr.numass.workspace; package inr.numass.workspace;
import hep.dataforge.actions.Action; import hep.dataforge.actions.Action;
import hep.dataforge.computation.WorkManager; import hep.dataforge.computation.ProgressCallback;
import hep.dataforge.context.Context; import hep.dataforge.context.Context;
import hep.dataforge.data.DataNode; import hep.dataforge.data.*;
import hep.dataforge.data.DataTree;
import hep.dataforge.meta.Meta; import hep.dataforge.meta.Meta;
import hep.dataforge.meta.Template; import hep.dataforge.meta.Template;
import hep.dataforge.storage.api.Loader;
import hep.dataforge.storage.commons.StorageUtils;
import hep.dataforge.tables.Table; import hep.dataforge.tables.Table;
import hep.dataforge.tables.TransformTableAction; import hep.dataforge.workspace.AbstractTask;
import hep.dataforge.workspace.GenericTask;
import hep.dataforge.workspace.TaskModel; import hep.dataforge.workspace.TaskModel;
import hep.dataforge.workspace.TaskState;
import inr.numass.actions.MergeDataAction; import inr.numass.actions.MergeDataAction;
import inr.numass.actions.MonitorCorrectAction; import inr.numass.actions.MonitorCorrectAction;
import inr.numass.actions.PrepareDataAction; import inr.numass.actions.PrepareDataAction;
import inr.numass.actions.ReadNumassStorageAction;
import inr.numass.storage.NumassData; import inr.numass.storage.NumassData;
import inr.numass.storage.NumassDataLoader;
import inr.numass.storage.NumassStorage;
import inr.numass.storage.SetDirectionUtility;
import java.net.URI;
/** /**
* Prepare data task * Prepare data task
* *
* @author Alexander Nozik * @author Alexander Nozik
*/ */
public class NumassPrepareTask extends GenericTask { public class NumassPrepareTask extends AbstractTask<Table> {
/* /*
<action type="readStorage" uri="file://D:\Work\Numass\data\2016_04\T2_data\"> <action type="readStorage" uri="file://D:\Work\Numass\data\2016_04\T2_data\">
@ -46,27 +49,27 @@ public class NumassPrepareTask extends GenericTask {
<action type="merge" mergeName="${numass.setName}"/> <action type="merge" mergeName="${numass.setName}"/>
*/ */
@Override @Override
@SuppressWarnings("unchecked") protected DataNode<Table> run(TaskModel model, ProgressCallback callback, DataNode<?> input) {
protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { Meta config = model.meta();
Context context = model.getContext();
//acquiring initial data. Data node could not be empty //acquiring initial data. Data node could not be empty
Meta dataMeta = config.getNode("data"); Meta dataMeta = config.getNode("data");
DataNode<NumassData> data = runAction(new ReadNumassStorageAction(), callback, context, DataNode.empty(), dataMeta); URI storageUri = input.getCheckedData("dataRoot", URI.class).get();
state.setData("data", data); DataNode<NumassData> data = readData(callback, context, storageUri, dataMeta);
//preparing table data //preparing table data
Meta prepareMeta = config.getNode("prepare"); Meta prepareMeta = config.getNode("prepare");
DataNode<Table> tables = runAction(new PrepareDataAction(), callback, context, data, prepareMeta); DataNode<Table> tables = runAction(new PrepareDataAction(), callback, context, data, prepareMeta);
state.setData("prepare", tables);
if (config.hasNode("monitor")) { if (config.hasNode("monitor")) {
Meta monitorMeta = config.getNode("monitor"); Meta monitorMeta = config.getNode("monitor");
tables = runAction(new MonitorCorrectAction(), callback, context, tables, monitorMeta); tables = runAction(new MonitorCorrectAction(), callback, context, tables, monitorMeta);
state.setData("monitor", tables);
} }
//merging if needed //merging if needed
if (config.hasNode("merge")) { if (config.hasNode("merge")) {
DataTree.Builder resultBuilder = DataTree.builder(Table.class); DataTree.Builder<Table> resultBuilder = DataTree.builder(Table.class);
// tables.dataStream().forEach(d -> resultBuilder.putData(d));
DataNode<Table> finalTables = tables; DataNode<Table> finalTables = tables;
config.getNodes("merge").forEach(mergeNode -> { config.getNodes("merge").forEach(mergeNode -> {
Meta mergeMeta = Template.compileTemplate(mergeNode, config); Meta mergeMeta = Template.compileTemplate(mergeNode, config);
@ -78,15 +81,61 @@ public class NumassPrepareTask extends GenericTask {
tables = resultBuilder.build(); tables = resultBuilder.build();
} }
if (config.hasNode("transform")) { return tables;
Meta filterMeta = config.getNode("transform");
tables = runAction(new TransformTableAction(), callback, context, tables, filterMeta);
} }
state.finish(tables); @Override
protected TaskModel transformModel(TaskModel model) {
String rootName = model.meta().getString("data.root", "dataRoot");
model.data(rootName, "dataRoot");
return super.transformModel(model);
} }
private <T, R> DataNode<R> runAction(Action<T, R> action, WorkManager.Callback callback, Context context, DataNode<T> data, Meta meta) { private DataNode<NumassData> readData(ProgressCallback callback, Context context, URI numassRoot, Meta meta) {
NumassStorage storage = NumassStorage.buildNumassRoot(numassRoot, true, false);
DataFilter filter = new DataFilter().configure(meta);
boolean forwardOnly = meta.getBoolean("forwardOnly", false);
boolean reverseOnly = meta.getBoolean("reverseOnly", false);
SetDirectionUtility.load(context);
DataSet.Builder<NumassData> builder = DataSet.builder(NumassData.class);
callback.setMaxProgress(StorageUtils.loaderStream(storage).count());
StorageUtils.loaderStream(storage).forEach(pair -> {
Loader loader = pair.getValue();
if (loader instanceof NumassData) {
NumassDataLoader nd = (NumassDataLoader) loader;
Data<NumassData> datum = Data.buildStatic(nd);
if (filter.acceptData(pair.getKey(), datum)) {
boolean accept = true;
if (forwardOnly || reverseOnly) {
boolean reversed = nd.isReversed();
accept = (reverseOnly && reversed) || (forwardOnly && !reversed);
}
if (accept) {
builder.putData(pair.getKey(), datum);
}
}
}
callback.increaseProgress(1d);
});
if (meta.getBoolean("loadLegacy", false)) {
storage.legacyFiles().forEach(nd -> {
Data<NumassData> datum = Data.buildStatic(nd);
if (filter.acceptData(nd.getName(), datum)) {
builder.putData("legacy." + nd.getName(), datum);
}
});
}
//FIXME remove in later revisions
SetDirectionUtility.save(context);
return builder.build();
}
private <T, R> DataNode<R> runAction(Action<T, R> action, ProgressCallback callback, Context context, DataNode<T> data, Meta meta) {
return action.withContext(context).withParentProcess(callback.workName()).run(data, meta); return action.withContext(context).withParentProcess(callback.workName()).run(data, meta);
} }

20
numass-main/src/main/java/inr/numass/workspace/NumassTableFilterTask.java
View File

@ -1,22 +1,19 @@
package inr.numass.workspace; package inr.numass.workspace;
import hep.dataforge.actions.Action;
import hep.dataforge.actions.OneToOneAction; import hep.dataforge.actions.OneToOneAction;
import hep.dataforge.computation.WorkManager;
import hep.dataforge.context.Context;
import hep.dataforge.data.DataNode; import hep.dataforge.data.DataNode;
import hep.dataforge.description.TypedActionDef; import hep.dataforge.description.TypedActionDef;
import hep.dataforge.meta.Laminate; import hep.dataforge.meta.Laminate;
import hep.dataforge.meta.Meta;
import hep.dataforge.meta.MetaBuilder; import hep.dataforge.meta.MetaBuilder;
import hep.dataforge.tables.Table; import hep.dataforge.tables.Table;
import hep.dataforge.workspace.GenericTask; import hep.dataforge.workspace.SingleActionTask;
import hep.dataforge.workspace.TaskModel; import hep.dataforge.workspace.TaskModel;
import hep.dataforge.workspace.TaskState;
/** /**
* Created by darksnake on 13-Aug-16. * Created by darksnake on 13-Aug-16.
*/ */
public class NumassTableFilterTask extends GenericTask<Table> { public class NumassTableFilterTask extends SingleActionTask<Table, Table> {
@Override @Override
public String getName() { public String getName() {
@ -24,9 +21,8 @@ public class NumassTableFilterTask extends GenericTask<Table> {
} }
@Override @Override
protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { protected DataNode<Table> gatherNode(DataNode<?> data) {
DataNode<Table> sourceNode = (DataNode<Table>) state.getData().getNode("prepare").get(); return data.getCheckedNode("prepare", Table.class);
state.finish(new FilterTableAction().withContext(context).run(sourceNode, config));
} }
@Override @Override
@ -37,12 +33,18 @@ public class NumassTableFilterTask extends GenericTask<Table> {
return model; return model;
} }
@Override
protected Action<Table, Table> getAction(TaskModel model) {
return new FilterTableAction();
}
@TypedActionDef(name = "filterTable", inputType = Table.class, outputType = Table.class) @TypedActionDef(name = "filterTable", inputType = Table.class, outputType = Table.class)
private class FilterTableAction extends OneToOneAction<Table, Table> { private class FilterTableAction extends OneToOneAction<Table, Table> {
@Override @Override
protected Table execute(String name, Laminate inputMeta, Table input) { protected Table execute(String name, Laminate inputMeta, Table input) {
double uLo = inputMeta.getDouble("filter.from", 0); double uLo = inputMeta.getDouble("filter.from", 0);
double uHi = inputMeta.getDouble("filter.to", Double.POSITIVE_INFINITY); double uHi = inputMeta.getDouble("filter.to", Double.POSITIVE_INFINITY);
getLogger().debug("Filtering finished");
return input.filter("Uset", uLo, uHi); return input.filter("Uset", uLo, uHi);
} }
} }

193
numass-main/src/main/resources/data/FS.txt Normal file
View File

@ -0,0 +1,193 @@
0.000 0.008
0.097 0.005
0.197 0.028
0.297 0.055
0.397 0.056
0.497 0.218
0.597 0.191
0.697 0.434
0.797 0.429
0.897 0.688
0.997 1.300
1.097 1.078
1.197 2.793
1.297 3.715
1.397 4.480
1.497 7.176
1.597 6.825
1.697 5.171
1.797 6.187
1.897 5.023
1.997 3.334
2.097 2.239
2.197 1.493
2.297 1.008
2.397 1.562
2.647 0.940
2.897 0.518
3.147 0.249
3.397 0.116
3.647 0.055
3.897 0.036
4.397 0.007
4.897 0.001
20.881 0.003
21.881 0.021
22.881 0.109
23.881 0.385
24.881 0.973
25.881 1.833
26.881 2.671
27.881 3.093
28.881 2.913
29.881 2.276
30.881 1.503
31.881 0.882
32.881 0.727
33.881 1.389
34.881 2.175
35.881 2.086
36.881 1.310
37.881 0.676
38.725 0.010
38.881 0.416
39.881 0.370
40.881 0.350
41.881 0.269
42.732 0.965
42.881 0.166
43.405 0.029
43.881 0.091
43.963 0.372
44.147 0.128
44.881 0.043
45.881 0.016
46.881 0.004
47.913 0.129
50.599 1.216
52.553 0.440
55.109 0.065
55.852 0.154
57.004 0.159
58.092 0.000
58.592 0.001
59.092 0.003
59.592 0.010
60.092 0.026
60.592 0.058
61.092 0.126
61.592 0.206
62.092 0.301
62.592 0.377
63.092 0.418
63.592 0.377
64.092 0.301
64.386 0.003
64.592 0.206
64.886 0.007
65.092 0.126
65.386 0.023
65.592 0.058
65.886 0.060
66.092 0.026
66.386 0.133
66.592 0.010
66.886 0.288
67.092 0.003
67.386 0.471
67.592 0.001
67.886 0.688
68.092 0.000
68.386 0.863
68.886 0.956
69.386 0.863
69.886 0.688
70.386 0.471
70.886 0.288
71.386 0.133
71.725 0.306
71.886 0.060
72.386 0.023
72.886 0.007
73.386 0.003
74.820 0.245
76.169 0.088
76.868 0.100
77.221 0.273
79.427 0.020
80.865 0.238
81.965 0.137
83.429 0.151
84.170 0.212
84.218 0.112
86.123 0.014
87.374 0.010
88.259 0.009
88.876 0.013
89.871 0.026
90.690 0.023
91.784 0.052
93.247 0.178
94.333 0.133
96.192 0.026
96.701 0.054
97.543 0.023
98.514 0.005
98.840 0.010
100.263 0.014
100.784 0.003
101.620 0.003
102.426 0.005
102.842 0.001
103.170 0.001
103.594 0.006
104.236 0.002
105.008 0.001
105.799 0.002
106.990 0.006
108.711 0.010
109.189 0.008
109.975 0.007
111.148 0.005
112.339 0.013
113.145 0.010
113.882 0.005
114.892 0.002
115.612 0.002
116.455 0.001
117.594 0.005
118.481 0.023
119.245 0.023
120.360 0.009
121.764 0.013
123.594 0.009
124.247 0.005
125.709 0.012
127.715 0.003
129.373 0.002
130.271 0.004
132.887 0.060
133.402 0.025
134.813 0.082
135.371 0.006
136.379 0.005
136.916 0.003
138.243 0.008
139.737 0.010
141.093 0.006
142.461 0.047
144.001 0.004
144.391 0.007
147.073 0.021
148.311 0.015
148.895 0.001
150.849 0.004
151.442 0.001
152.854 0.000
154.169 0.002
156.093 0.001
157.003 0.003
158.134 0.003
159.271 0.002
162.054 0.007
164.173 0.002

63
numass-storage/src/main/java/inr/numass/storage/NumassStorage.java
View File

@ -22,18 +22,21 @@ import hep.dataforge.meta.Meta;
import hep.dataforge.meta.MetaBuilder; import hep.dataforge.meta.MetaBuilder;
import hep.dataforge.storage.filestorage.FileStorage; import hep.dataforge.storage.filestorage.FileStorage;
import hep.dataforge.storage.filestorage.VFSUtils; import hep.dataforge.storage.filestorage.VFSUtils;
import org.apache.commons.vfs2.FileObject;
import org.apache.commons.vfs2.FileSystemException;
import org.apache.commons.vfs2.FileType;
import org.slf4j.LoggerFactory;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.io.OutputStream; import java.io.OutputStream;
import java.net.URI;
import java.nio.ByteBuffer; import java.nio.ByteBuffer;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import org.apache.commons.vfs2.FileObject;
import org.apache.commons.vfs2.FileSystemException;
import org.apache.commons.vfs2.FileType;
import static org.apache.commons.vfs2.FileType.FOLDER; import static org.apache.commons.vfs2.FileType.FOLDER;
import org.slf4j.LoggerFactory;
/** /**
* The file storage containing numass data directories or zips. * The file storage containing numass data directories or zips.
@ -51,6 +54,17 @@ public class NumassStorage extends FileStorage {
public static final String NUMASS_DATA_LOADER_TYPE = "numassData"; public static final String NUMASS_DATA_LOADER_TYPE = "numassData";
public static final String GROUP_META_FILE = "numass_group_meta"; public static final String GROUP_META_FILE = "numass_group_meta";
protected NumassStorage(FileStorage parent, String path, Meta config) throws StorageException {
super(parent, path, config);
super.refresh();
//TODO read meta from numass_group_meta to .numass element
}
protected NumassStorage(FileObject dir, Meta config) throws StorageException {
super(dir, config);
super.refresh();
}
/** /**
* Create root numass storage * Create root numass storage
* *
@ -91,34 +105,30 @@ public class NumassStorage extends FileStorage {
return new NumassStorage(parent, path, meta); return new NumassStorage(parent, path, meta);
} }
public static NumassStorage buildNumassRoot(String uri, boolean readOnly, boolean monitor) throws StorageException { public static NumassStorage buildNumassRoot(String uri, boolean readOnly, boolean monitor) {
try { try {
Meta meta = new MetaBuilder("storage") Meta meta = new MetaBuilder("storage")
.setValue("type", "file.numass") .setValue("type", "file.numass")
.setValue("readOnly", readOnly) .setValue("readOnly", readOnly)
.setValue("monitor", monitor); .setValue("monitor", monitor);
return new NumassStorage(VFSUtils.getRemoteFile(uri), meta); return new NumassStorage(VFSUtils.getFile(uri), meta);
} catch (FileSystemException ex) { } catch (Exception ex) {
throw new RuntimeException(ex); throw new RuntimeException(ex);
} }
} }
protected NumassStorage(FileStorage parent, String path, Meta config) throws StorageException { public static NumassStorage buildNumassRoot(URI uri, boolean readOnly, boolean monitor) {
super(parent, path, config); try {
super.refresh(); Meta meta = new MetaBuilder("storage")
//TODO read meta from numass_group_meta to .numass element .setValue("type", "file.numass")
.setValue("readOnly", readOnly)
.setValue("monitor", monitor);
return new NumassStorage(VFSUtils.getFile(uri), meta);
} catch (Exception ex) {
throw new RuntimeException(ex);
}
} }
protected NumassStorage(FileObject dir, Meta config) throws StorageException {
super(dir, config);
super.refresh();
}
// protected NumassStorage(FileObject dir, boolean readOnly) throws StorageException {
// super(dir, null);
// super.setReadOnly(readOnly);
// super.refresh();
// }
@Override @Override
protected void updateDirectoryLoaders() { protected void updateDirectoryLoaders() {
try { try {
@ -163,10 +173,7 @@ public class NumassStorage extends FileStorage {
/** /**
* Read nm.zip content and write it as a new nm.zip file * Read nm.zip content and write it as a new nm.zip file
* *
* @param path
* @param fileName * @param fileName
* @param stream
* @param size
*/ */
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
public void pushNumassData(String fileName, ByteBuffer data) throws StorageException { public void pushNumassData(String fileName, ByteBuffer data) throws StorageException {
@ -229,6 +236,10 @@ public class NumassStorage extends FileStorage {
public static final String FILE_NAME_KEY = "fileName"; public static final String FILE_NAME_KEY = "fileName";
public static final String FILE_SIZE_KEY = "fileSize"; public static final String FILE_SIZE_KEY = "fileSize";
public NumassDataPointEvent(Meta meta) {
super(meta);
}
public static NumassDataPointEvent build(String source, String fileName, int fileSize) { public static NumassDataPointEvent build(String source, String fileName, int fileSize) {
return new NumassDataPointEvent(builder(source, fileName, fileSize).buildEventMeta()); return new NumassDataPointEvent(builder(source, fileName, fileSize).buildEventMeta());
} }
@ -240,10 +251,6 @@ public class NumassStorage extends FileStorage {
.setMetaValue(FILE_SIZE_KEY, fileSize); .setMetaValue(FILE_SIZE_KEY, fileSize);
} }
public NumassDataPointEvent(Meta meta) {
super(meta);
}
public int getFileSize() { public int getFileSize() {
return meta().getInt(FILE_SIZE_KEY, 0); return meta().getInt(FILE_SIZE_KEY, 0);
} }

46
numass-viewer/src/main/java/inr/numass/viewer/MainViewerController.java
View File

@ -15,43 +15,36 @@
*/ */
package inr.numass.viewer; package inr.numass.viewer;
import hep.dataforge.computation.ProgressCallback;
import hep.dataforge.context.Context; import hep.dataforge.context.Context;
import hep.dataforge.context.GlobalContext; import hep.dataforge.context.GlobalContext;
import hep.dataforge.computation.WorkManager;
import hep.dataforge.exceptions.StorageException; import hep.dataforge.exceptions.StorageException;
import hep.dataforge.fx.ConsoleFragment; import hep.dataforge.fx.ConsoleFragment;
import hep.dataforge.fx.work.WorkManagerFragment; import hep.dataforge.fx.work.WorkManagerFragment;
import inr.numass.NumassProperties; import inr.numass.NumassProperties;
import inr.numass.storage.NumassData; import inr.numass.storage.NumassData;
import inr.numass.storage.NumassStorage; import inr.numass.storage.NumassStorage;
import java.io.File;
import java.net.URL;
import java.util.Optional;
import java.util.ResourceBundle;
import java.util.logging.Level;
import java.util.logging.Logger;
import javafx.application.Platform; import javafx.application.Platform;
import javafx.event.ActionEvent; import javafx.event.ActionEvent;
import javafx.fxml.FXML; import javafx.fxml.FXML;
import javafx.fxml.Initializable; import javafx.fxml.Initializable;
import javafx.geometry.Insets; import javafx.geometry.Insets;
import javafx.scene.Node; import javafx.scene.Node;
import javafx.scene.control.Button; import javafx.scene.control.*;
import javafx.scene.control.ButtonBar.ButtonData; import javafx.scene.control.ButtonBar.ButtonData;
import javafx.scene.control.ButtonType;
import javafx.scene.control.Dialog;
import javafx.scene.control.Label;
import javafx.scene.control.Tab;
import javafx.scene.control.TabPane;
import javafx.scene.control.TextField;
import javafx.scene.control.ToggleButton;
import javafx.scene.control.TreeTableView;
import javafx.scene.layout.AnchorPane; import javafx.scene.layout.AnchorPane;
import javafx.scene.layout.GridPane; import javafx.scene.layout.GridPane;
import javafx.stage.DirectoryChooser; import javafx.stage.DirectoryChooser;
import javafx.util.Pair; import javafx.util.Pair;
import org.controlsfx.control.StatusBar; import org.controlsfx.control.StatusBar;
import java.io.File;
import java.net.URL;
import java.util.Optional;
import java.util.ResourceBundle;
import java.util.logging.Level;
import java.util.logging.Logger;
/** /**
* FXML Controller class * FXML Controller class
* *
@ -59,24 +52,15 @@ import org.controlsfx.control.StatusBar;
*/ */
public class MainViewerController implements Initializable { public class MainViewerController implements Initializable {
public static MainViewerController build(NumassStorage root) {
MainViewerController res = new MainViewerController();
res.setRootStorage(root);
return res;
}
// private ConsoleFragment consoleFragment; // private ConsoleFragment consoleFragment;
// private WorkManagerFragment processFragment = WorkManagerFragment.attachToContext(GlobalContext.instance()); // private WorkManagerFragment processFragment = WorkManagerFragment.attachToContext(GlobalContext.instance());
@FXML @FXML
private ToggleButton consoleButton; private ToggleButton consoleButton;
@FXML @FXML
private Button loadDirectoryButton; private Button loadDirectoryButton;
private MspViewController mspController; private MspViewController mspController;
@FXML @FXML
private AnchorPane mspPlotPane; private AnchorPane mspPlotPane;
//main pane views //main pane views
@FXML @FXML
private AnchorPane numassLoaderViewContainer; private AnchorPane numassLoaderViewContainer;
@ -84,7 +68,6 @@ public class MainViewerController implements Initializable {
private TreeTableView<NumassLoaderTreeBuilder.TreeItemValue> numassLoaderDataTree; private TreeTableView<NumassLoaderTreeBuilder.TreeItemValue> numassLoaderDataTree;
@FXML @FXML
private StatusBar statusBar; private StatusBar statusBar;
//tabs //tabs
@FXML @FXML
private TabPane tabPane; private TabPane tabPane;
@ -103,7 +86,14 @@ public class MainViewerController implements Initializable {
@FXML @FXML
private ToggleButton processManagerButton; private ToggleButton processManagerButton;
public static MainViewerController build(NumassStorage root) {
MainViewerController res = new MainViewerController();
res.setRootStorage(root);
return res;
}
// private Popup progressPopup; // private Popup progressPopup;
/** /**
* Initializes the controller class. * Initializes the controller class.
* *
@ -139,7 +129,7 @@ public class MainViewerController implements Initializable {
} }
private void loadDirectory(String path) { private void loadDirectory(String path) {
getContext().workManager().submit("viewer.loadDirectory", (WorkManager.Callback callback) -> { getContext().workManager().submit("viewer.loadDirectory", (ProgressCallback callback) -> {
callback.updateTitle("Load storage (" + path + ")"); callback.updateTitle("Load storage (" + path + ")");
callback.setProgress(-1); callback.setProgress(-1);
callback.updateMessage("Building numass storage tree..."); callback.updateMessage("Building numass storage tree...");
@ -162,7 +152,7 @@ public class MainViewerController implements Initializable {
public void setRootStorage(NumassStorage root) { public void setRootStorage(NumassStorage root) {
getContext().workManager().cleanup(); getContext().workManager().cleanup();
getContext().workManager().submit("viewer.storage.load", (WorkManager.Callback callback) -> { getContext().workManager().submit("viewer.storage.load", (ProgressCallback callback) -> {
callback.updateTitle("Fill data to UI (" + root.getName() + ")"); callback.updateTitle("Fill data to UI (" + root.getName() + ")");
callback.setProgress(-1); callback.setProgress(-1);
Platform.runLater(() -> statusBar.setProgress(-1)); Platform.runLater(() -> statusBar.setProgress(-1));

12
numass-viewer/src/main/java/inr/numass/viewer/MspViewController.java
View File

@ -20,8 +20,9 @@ package inr.numass.viewer;
* To change this template file, choose Tools | Templates * To change this template file, choose Tools | Templates
* and open the template in the editor. * and open the template in the editor.
*/ */
import hep.dataforge.computation.ProgressCallback;
import hep.dataforge.context.Context; import hep.dataforge.context.Context;
import hep.dataforge.computation.WorkManager;
import hep.dataforge.exceptions.StorageException; import hep.dataforge.exceptions.StorageException;
import hep.dataforge.plots.PlotUtils; import hep.dataforge.plots.PlotUtils;
import hep.dataforge.plots.data.DynamicPlottable; import hep.dataforge.plots.data.DynamicPlottable;
@ -33,13 +34,14 @@ import hep.dataforge.storage.api.Storage;
import hep.dataforge.tables.DataPoint; import hep.dataforge.tables.DataPoint;
import hep.dataforge.tables.MapPoint; import hep.dataforge.tables.MapPoint;
import hep.dataforge.values.Value; import hep.dataforge.values.Value;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.StreamSupport;
import javafx.application.Platform; import javafx.application.Platform;
import javafx.scene.layout.AnchorPane; import javafx.scene.layout.AnchorPane;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.StreamSupport;
/** /**
* FXML Controller class * FXML Controller class
* *
@ -85,7 +87,7 @@ public class MspViewController {
public void fillMspData(Storage rootStorage) { public void fillMspData(Storage rootStorage) {
if (rootStorage != null) { if (rootStorage != null) {
context.workManager().submit("viewer.msp.fill", (WorkManager.Callback callback) -> { context.workManager().submit("viewer.msp.fill", (ProgressCallback callback) -> {
try { try {
// callback.updateTitle("Fill msp data (" + rootStorage.getName() + ")"); // callback.updateTitle("Fill msp data (" + rootStorage.getName() + ")");

17
numass-viewer/src/main/java/inr/numass/viewer/NumassLoaderTreeBuilder.java
View File

@ -15,14 +15,10 @@
*/ */
package inr.numass.viewer; package inr.numass.viewer;
import hep.dataforge.computation.WorkManager; import hep.dataforge.computation.ProgressCallback;
import hep.dataforge.exceptions.StorageException; import hep.dataforge.exceptions.StorageException;
import inr.numass.storage.NumassData; import inr.numass.storage.NumassData;
import inr.numass.storage.NumassStorage; import inr.numass.storage.NumassStorage;
import java.time.Instant;
import java.util.ArrayList;
import java.util.List;
import java.util.function.Consumer;
import javafx.application.Platform; import javafx.application.Platform;
import javafx.beans.property.SimpleStringProperty; import javafx.beans.property.SimpleStringProperty;
import javafx.scene.control.TreeItem; import javafx.scene.control.TreeItem;
@ -32,13 +28,18 @@ import javafx.scene.input.MouseEvent;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.time.Instant;
import java.util.ArrayList;
import java.util.List;
import java.util.function.Consumer;
/** /**
* *
* @author darksnake * @author darksnake
*/ */
public class NumassLoaderTreeBuilder { public class NumassLoaderTreeBuilder {
public void build(WorkManager.Callback callback, public void build(ProgressCallback callback,
TreeTableView<TreeItemValue> numassLoaderDataTree, TreeTableView<TreeItemValue> numassLoaderDataTree,
NumassStorage rootStorage, NumassStorage rootStorage,
Consumer<NumassData> numassViewBuilder) throws StorageException { Consumer<NumassData> numassViewBuilder) throws StorageException {
@ -81,7 +82,7 @@ public class NumassLoaderTreeBuilder {
} }
private TreeItem<TreeItemValue> buildNode(NumassStorage storage, private TreeItem<TreeItemValue> buildNode(NumassStorage storage,
Consumer<NumassData> numassViewBuilder, WorkManager.Callback callback) throws StorageException { Consumer<NumassData> numassViewBuilder, ProgressCallback callback) throws StorageException {
TreeItem<TreeItemValue> node = new TreeItem<>(buildValue(storage)); TreeItem<TreeItemValue> node = new TreeItem<>(buildValue(storage));
node.getChildren().setAll(buildChildren(storage, numassViewBuilder, callback)); node.getChildren().setAll(buildChildren(storage, numassViewBuilder, callback));
return node; return node;
@ -92,7 +93,7 @@ public class NumassLoaderTreeBuilder {
} }
private List<TreeItem<TreeItemValue>> buildChildren(NumassStorage storage, private List<TreeItem<TreeItemValue>> buildChildren(NumassStorage storage,
Consumer<NumassData> numassViewBuilder, WorkManager.Callback callback) throws StorageException { Consumer<NumassData> numassViewBuilder, ProgressCallback callback) throws StorageException {
List<TreeItem<TreeItemValue>> list = new ArrayList<>(); List<TreeItem<TreeItemValue>> list = new ArrayList<>();
storage.shelves().values().stream().forEach(subStorage -> { storage.shelves().values().stream().forEach(subStorage -> {

8
numass-viewer/src/main/java/inr/numass/viewer/NumassLoaderViewComponent.java
View File

@ -21,7 +21,7 @@ package inr.numass.viewer;
* and open the template in the editor. * and open the template in the editor.
*/ */
import hep.dataforge.computation.WorkManager; import hep.dataforge.computation.ProgressCallback;
import hep.dataforge.context.Context; import hep.dataforge.context.Context;
import hep.dataforge.io.ColumnedDataWriter; import hep.dataforge.io.ColumnedDataWriter;
import hep.dataforge.meta.Meta; import hep.dataforge.meta.Meta;
@ -214,7 +214,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
public void loadData(NumassData data) { public void loadData(NumassData data) {
this.data = data; this.data = data;
if (data != null) { if (data != null) {
context.workManager().<List<NMPoint>>submit("viewer.numass.load", (WorkManager.Callback callback) -> { context.workManager().<List<NMPoint>>submit("viewer.numass.load", (ProgressCallback callback) -> {
callback.updateTitle("Load numass data (" + data.getName() + ")"); callback.updateTitle("Load numass data (" + data.getName() + ")");
points = data.getNMPoints(); points = data.getNMPoints();
@ -239,7 +239,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
} }
private void setupHVPane(Supplier<Table> hvData) { private void setupHVPane(Supplier<Table> hvData) {
context.workManager().submit("viewer.numass.hv", (WorkManager.Callback callback) -> { context.workManager().submit("viewer.numass.hv", (ProgressCallback callback) -> {
Table t = hvData.get(); Table t = hvData.get();
Platform.runLater(() -> { Platform.runLater(() -> {
if (t != null) { if (t != null) {
@ -343,7 +343,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
detectorPlot.removePlot(); detectorPlot.removePlot();
} }
context.workManager().submit("viewer.numass.load.detector", (WorkManager.Callback callback) -> { context.workManager().submit("viewer.numass.load.detector", (ProgressCallback callback) -> {
Meta plottableConfig = new MetaBuilder("plot") Meta plottableConfig = new MetaBuilder("plot")
.setValue("connectionType", "step") .setValue("connectionType", "step")
.setValue("thickness", 2) .setValue("thickness", 2)