[no commit message]

numass-main/src/main/groovy/inr/numass/scripts/SimulateGun.groovy

@@ -20,7 +20,7 @@ import hep.dataforge.datafitter.FitManager;
 import hep.dataforge.datafitter.ParamSet;
 import hep.dataforge.datafitter.models.XYModel;
 import hep.dataforge.exceptions.NamingException;
-import hep.dataforge.io.PrintNamed;
+import hep.dataforge.io.FittingIOUtils;
 import inr.numass.data.SpectrumDataAdapter;
 import inr.numass.models.GunSpectrum;
 import inr.numass.models.NBkgSpectrum;
@@ -52,7 +52,7 @@ PrintNamed.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 18495,
 
 allPars.setParValue("sigma", 0.6);
 
-PrintNamed.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 18495, 18505, 100);
+FittingIOUtils.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 18495, 18505, 100);
 
 //        //String fileName = "d:\\PlayGround\\merge\\scans.out";
 ////        String configName = "d:\\PlayGround\\SCAN.CFG";

numass-main/src/main/groovy/inr/numass/scripts/SterileDemo.groovy

@@ -0,0 +1,86 @@
+/* 
+ * Copyright 2015 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;
+
+import hep.dataforge.context.GlobalContext;
+import static hep.dataforge.context.GlobalContext.out;
+import hep.dataforge.tables.ListTable;
+import hep.dataforge.datafitter.FitManager;
+import hep.dataforge.datafitter.FitState;
+import hep.dataforge.datafitter.FitTask;
+import hep.dataforge.datafitter.MINUITPlugin
+
+import hep.dataforge.datafitter.ParamSet;
+import hep.dataforge.datafitter.models.XYModel;
+import hep.dataforge.exceptions.NamingException;
+import hep.dataforge.exceptions.PackFormatException;
+import inr.numass.data.SpectrumDataAdapter;
+import inr.numass.data.SpectrumGenerator;
+import inr.numass.models.BetaSpectrum
+import inr.numass.models.ModularSpectrum;
+import inr.numass.models.NBkgSpectrum;
+import inr.numass.utils.DataModelUtils;
+import hep.dataforge.plotfit.PlotFitResultAction;
+import java.io.FileNotFoundException;
+import java.util.Locale;
+import static java.util.Locale.setDefault;
+import inr.numass.utils.TritiumUtils;
+import inr.numass.data.SpectrumDataAdapter;
+import hep.dataforge.io.FittingIOUtils
+
+/**
+ *
+ * @author Darksnake
+ */
+
+setDefault(Locale.US);
+
+ModularSpectrum beta = new ModularSpectrum(new BetaSpectrum(), 8.3e-5, 13990d, 18600d);
+beta.setCaching(false);
+
+NBkgSpectrum spectrum = new NBkgSpectrum(beta);
+XYModel model = new XYModel(spectrum, new SpectrumDataAdapter());
+
+ParamSet allPars = new ParamSet();
+
+allPars.setPar("N", 6.6579e+05,  1.8e+03, 0d, Double.POSITIVE_INFINITY);
+allPars.setPar("bkg", 0.5387, 0.050);
+allPars.setPar("E0", 18574.94, 1.4);
+allPars.setPar("mnu2", 0d, 1d);
+allPars.setPar("msterile2", 1000d * 1000d,0);
+allPars.setPar("U2", 0.0, 1e-4, -1d, 1d);
+allPars.setPar("X", 0.04000, 0.01, 0d, Double.POSITIVE_INFINITY);
+allPars.setPar("trap", 1.634, 0.01,0d, Double.POSITIVE_INFINITY);
+
+FittingIOUtils.printSpectrum(GlobalContext.out(), spectrum, allPars, 14000.0, 18600.0, 600);
+
+//SpectrumGenerator generator = new SpectrumGenerator(model, allPars, 12316);
+//
+//ListTable data = generator.generateData(DataModelUtils.getUniformSpectrumConfiguration(14000d, 18500, 2000, 90));
+//
+//data = TritiumUtils.correctForDeadTime(data, new SpectrumDataAdapter(), 1e-8);
+////        data = data.filter("X", Value.of(15510.0), Value.of(18610.0));
+////        allPars.setParValue("X", 0.4);
+//FitState state = new FitState(data, model, allPars);
+////new PlotFitResultAction().eval(state);
+//        
+//        
+//FitState res = fm.runTask(state, "QOW", FitTask.TASK_RUN, "N", "bkg", "E0", "U2", "trap");
+//
+//        
+//
+//res.print(out());
+//

numass-main/src/main/java/inr/numass/NumassPlugin.java

@@ -106,7 +106,6 @@ public class NumassPlugin extends BasicPlugin {
             double to = an.getDouble("to", 19010d);
             RangedNamedSetSpectrum beta = new BetaSpectrum(context.io().getFile("FS.txt"));
             ModularSpectrum sp = new ModularSpectrum(beta, A, from, to);
-            sp.setCaching(false);
             NBkgSpectrum spectrum = new NBkgSpectrum(sp);
 
             return new XYModel(spectrum, getAdapter(an));
@@ -125,7 +124,6 @@ public class NumassPlugin extends BasicPlugin {
             }
 
             NBkgSpectrum spectrum = new NBkgSpectrum(sp);
-            sp.setCaching(false);
 
             return new XYModel(spectrum, getAdapter(an));
         });
@@ -212,9 +210,9 @@ public class NumassPlugin extends BasicPlugin {
             BivariateFunction resolutionTail = ResolutionFunction.getRealTail();
             RangedNamedSetSpectrum beta = new BetaSpectrum(context.io().getFile("FS.txt"));
             ModularSpectrum sp = new ModularSpectrum(beta, new ResolutionFunction(A, resolutionTail), from, to);
-            if (!an.getBoolean("caching", false)) {
+            if (an.getBoolean("caching", false)) {
-                context.getReport().report("Caching turned off");
+                context.getReport().report("Caching turned on");
-                sp.setCaching(false);
+                sp.setCaching(true);
             }
             //Adding trapping energy dependence
             //Intercept = 4.95745, B1 = -0.36879, B2 = 0.00827
@@ -244,7 +242,6 @@ public class NumassPlugin extends BasicPlugin {
             };
             RangedNamedSetSpectrum beta = new BetaSpectrum(context.io().getFile("FS.txt"));
             ModularSpectrum sp = new ModularSpectrum(beta, new ResolutionFunction(A, reolutionTail), from, to);
-            sp.setCaching(false);
             NBkgSpectrum spectrum = new NBkgSpectrum(sp);
 
             return new XYModel(spectrum, getAdapter(an));

numass-main/src/main/java/inr/numass/actions/PileupSimulationAction.java

@@ -15,6 +15,7 @@ import inr.numass.storage.NMPoint;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.RawNMPoint;
 import inr.numass.utils.PileUpSimulator;
+import inr.numass.utils.TritiumUtils;
 import java.time.Instant;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
@@ -44,7 +45,7 @@ public class PileupSimulationAction extends OneToOneAction<NumassData, Map<Strin
 
         input.getNMPoints().forEach(point -> {
             double length = point.getLength() * scale;
-            double cr = point.getCountRate(lowerChannel, upperChannel, 6.4e-6);
+            double cr = TritiumUtils.countRateWithDeadTime(point, lowerChannel, upperChannel, 6.4e-6);
 
             PileUpSimulator simulator = new PileUpSimulator(cr, length)
                     .withGenerator(point, null, lowerChannel, upperChannel)

numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java

@@ -34,6 +34,7 @@ import inr.numass.storage.NMPoint;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.RawNMPoint;
 import inr.numass.utils.ExpressionUtils;
+import inr.numass.utils.TritiumUtils;
 import java.io.OutputStream;
 import java.time.Instant;
 import java.util.ArrayList;
@@ -103,9 +104,9 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
             long wind = point.getCountInWindow(a, b);
 
             // count rate after all corrections
-            double cr = point.getCountRate(a, b, deadTimeFunction.apply(point));
+            double cr = TritiumUtils.countRateWithDeadTime(point, a, b, deadTimeFunction.apply(point));
             // count rate error after all corrections
-            double crErr = point.getCountRateErr(a, b, deadTimeFunction.apply(point));
+            double crErr = TritiumUtils.countRateWithDeadTimeErr(point, a, b, deadTimeFunction.apply(point));
 
             double correctionFactor = correction(log, point, meta);
 

numass-main/src/main/java/inr/numass/models/ModularSpectrum.java

@@ -40,7 +40,7 @@ public class ModularSpectrum extends AbstractParametricFunction {
     BivariateFunction resolution;
     RangedNamedSetSpectrum sourceSpectrum;
     BivariateFunction trappingFunction;
-    boolean caching = true;
+    boolean caching = false;
     double cacheMin;
     double cacheMax;
 
@@ -67,7 +67,6 @@ public class ModularSpectrum extends AbstractParametricFunction {
 
     public ModularSpectrum(RangedNamedSetSpectrum source, BivariateFunction resolution) {
         this(source, resolution, Double.NaN, Double.NaN);
-        setCaching(false);
     }
 
     /**

numass-main/src/main/java/inr/numass/utils/NMEventGenerator.java

@@ -122,7 +122,7 @@ public class NMEventGenerator {
             chanel = 1600;
         }
 
-        return new NMEvent(chanel, prev == null ? 0 : prev.getTime() + nextExpDecay(1 / cr));
+        return new NMEvent(chanel, prev == null ? 0 : prev.getTime() + nextExpDecay(1d / cr));
     }
 
     public double nextExpDecay(double mean) {

numass-main/src/main/java/inr/numass/utils/PileUpSimulator.java

@@ -103,44 +103,48 @@ public class PileUpSimulator {
 
     private boolean random(double prob) {
         double r = generator.nextUniform();
-        return r < prob;
+        return r <= prob;
     }
 
     public synchronized PileUpSimulator generate() {
-        NMEvent current = null;
+        NMEvent last = null;// last event
+        double lastRegisteredTime = 0; // Time of DAQ closing
+        //flag that shows that previous event was pileup
         boolean pileupFlag = false;
         while (true) {
-            NMEvent next = generator.nextEvent(current);
+            NMEvent next = generator.nextEvent(last);
             if (next.getTime() > pointLength) {
                 break;
             }
-            generated.add(next.clone());
+            generated.add(next);
-            //flag that shows that previous event was pileup
             //not counting double pileups
-            if (current != null) {
+            if (last != null) {
-                double delay = (next.getTime() - current.getTime()) / us; //time between events in microseconds
+                double delay = (next.getTime() - lastRegisteredTime) / us; //time between events in microseconds
                 if (nextEventRegistered(delay)) {
                     //just register new event
-                    registred.add(next.clone());
+                    registred.add(next);
+                    lastRegisteredTime = next.getTime();
                     pileupFlag = false;
                 } else if (pileup(delay) && !pileupFlag) {
                     //pileup event
-                    short newChannel = pileupChannel(delay, current.getChanel(), next.getChanel());
+                    short newChannel = pileupChannel(delay, last.getChanel(), next.getChanel());
-                    NMEvent newEvent = new NMEvent(newChannel, current.getTime());
+                    NMEvent newEvent = new NMEvent(newChannel, last.getTime());
                     //replace already registered event by event with new channel
                     registred.remove(registred.size() - 1);
-                    registred.add(newEvent.clone());
+                    registred.add(newEvent);
-                    pileup.add(newEvent.clone());
+                    pileup.add(newEvent);
+                    //do not change DAQ close time
                     pileupFlag = true; // up the flag to avoid secondary pileup
                 } else {
-                    // second event not registered
+                    // second event not registered, DAQ closed
                     pileupFlag = false;
                 }
             } else {
                 //register first event
-                registred.add(next.clone());
+                registred.add(next);
+                lastRegisteredTime = next.getTime();
             }
-            current = next;
+            last = next;
         }
         return this;
     }

numass-main/src/main/java/inr/numass/utils/TritiumUtils.java

@@ -19,6 +19,7 @@ import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.Table;
 import inr.numass.data.SpectrumDataAdapter;
+import inr.numass.storage.NMPoint;
 import static java.lang.Math.abs;
 import static java.lang.Math.exp;
 import static java.lang.Math.sqrt;
@@ -30,7 +31,6 @@ import org.apache.commons.math3.analysis.UnivariateFunction;
  */
 public class TritiumUtils {
 
-
     public static Table correctForDeadTime(ListTable data, double dtime) {
         return correctForDeadTime(data, adapter(), dtime);
     }
@@ -106,4 +106,21 @@ public class TritiumUtils {
         double res = Fermi * pe * Etot;
         return res * 1E-23;
     }
+
+    public static double countRateWithDeadTime(NMPoint p, int from, int to, double deadTime) {
+        double wind = p.getCountInWindow(from, to) / p.getLength();
+        double res;
+        if (deadTime > 0) {
+            double total = p.getEventsCount();
+            double time = p.getLength();
+            res = wind / (1 - total * deadTime / time);
+        } else {
+            res = wind;
+        }
+        return res;
+    }
+    
+    public static double countRateWithDeadTimeErr(NMPoint p, int from, int to, double deadTime) {
+        return Math.sqrt(countRateWithDeadTime(p,from, to, deadTime) / p.getLength());
+    }
 }

numass-storage/src/main/java/inr/numass/storage/NMEvent.java

@@ -19,7 +19,7 @@ package inr.numass.storage;
  *
  * @author Darksnake
  */
-public class NMEvent implements Cloneable{
+public class NMEvent{
     protected final short chanel;
     protected final double time;
 
@@ -28,10 +28,10 @@ public class NMEvent implements Cloneable{
         this.time = time;
     }
 
-    @Override
+//    @Override
-    public NMEvent clone() {
+//    public NMEvent clone() {
-        return new NMEvent(chanel, time);
+//        return new NMEvent(chanel, time);
-    }
+//    }
 
     /**
      * @return the chanel

numass-storage/src/main/java/inr/numass/storage/NMPoint.java

@@ -129,25 +129,6 @@ public class NMPoint {
         return res;
     }
 
-    
-    //TODO move dead time out of here!
-    public double getCountRate(int from, int to, double deadTime) {
-        double wind = getCountInWindow(from, to) / getLength();
-        double res;
-        if (deadTime > 0) {
-            double total = getEventsCount();
-            double time = getLength();
-            res = wind / (1 - total * deadTime / time);
-        } else {
-            res = wind;
-        }
-        return res;
-    }
-
-    public double getCountRateErr(int from, int to, double deadTime) {
-        return Math.sqrt(getCountRate(from, to, deadTime) / getLength());
-    }
-
     public List<DataPoint> getData() {
         List<DataPoint> data = new ArrayList<>();
         for (int i = 0; i < RawNMPoint.MAX_CHANEL; i++) {

numass-storage/src/main/java/inr/numass/storage/RawNMPoint.java

@@ -69,7 +69,7 @@ public class RawNMPoint implements Cloneable {
     public RawNMPoint clone() {
         ArrayList<NMEvent> newevents = new ArrayList<>();
         for (NMEvent event : this.getEvents()) {
-            newevents.add(event.clone());
+            newevents.add(event);
         }
         return new RawNMPoint(getUset(), getUread(), newevents, getLength());
     }

numass-viewer/src/main/java/inr/numass/viewer/NumassLoaderViewComponent.java

@@ -42,6 +42,7 @@ import hep.dataforge.tables.Table;
 import hep.dataforge.tables.XYAdapter;
 import inr.numass.storage.NMPoint;
 import inr.numass.storage.NumassData;
+import inr.numass.utils.TritiumUtils;
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
@@ -325,8 +326,8 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
     private DataPoint getSpectrumPoint(NMPoint point, int lowChannel, int upChannel, double dTime) {
         double u = point.getUread();
         return new MapPoint(new String[]{"x", "y", "yErr"}, u,
-                point.getCountRate(lowChannel, upChannel, dTime),
+                TritiumUtils.countRateWithDeadTime(point,lowChannel, upChannel, dTime),
-                point.getCountRateErr(lowChannel, upChannel, dTime));
+                TritiumUtils.countRateWithDeadTimeErr(point,lowChannel, upChannel, dTime));
     }
 
     /**
@@ -402,8 +403,8 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
                         point.getLength(),
                         point.getEventsCount(),
                         point.getCountInWindow(loChannel, upChannel),
-                        point.getCountRate(loChannel, upChannel, dTime),
+                        TritiumUtils.countRateWithDeadTime(point,loChannel, upChannel, dTime),
-                        point.getCountRateErr(loChannel, upChannel, dTime),
+                        TritiumUtils.countRateWithDeadTimeErr(point,loChannel, upChannel, dTime),
                         point.getStartTime()
                     }
                     ));