[no commit message]

numass-main/build.gradle

@@ -7,10 +7,6 @@ mainClassName = mainClass
 
 description = """The main head of all numass projects"""
 
-ext{
-    defaultNumassPath = 'D:\\loss-2011\\'
-}
-
 dependencies {
     compile group: 'commons-cli', name: 'commons-cli', version:'1.+'
     compile group: 'commons-io', name: 'commons-io', version:'2.+'
@@ -20,22 +16,12 @@ dependencies {
     compile project(':numass-storage')
 }
 
-task runNumass(dependsOn: classes, type : JavaExec){
+task workbench(dependsOn: classes, type: JavaExec){
-    main mainClass
+    main 'inr.numass.workbench.Workbench'
     classpath = sourceSets.main.runtimeClasspath
-    workingDir defaultNumassPath
+    description "start visual numass workbench"
-    description "run Main method in the current numass working directory"
     group "numass"    
-}
 
-task debugNumass(dependsOn: classes, type: JavaExec) {
-    main mainClass
-    classpath = sourceSets.main.runtimeClasspath
-    workingDir defaultNumassPath
-    ignoreExitValue = true
-    debug = true
-    description "debug Main method in the current numass working directory"
-    group "numass"    
 }
 
 task listActions(dependsOn: classes, type: JavaExec) {

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

@@ -1,94 +0,0 @@
-/* 
- * 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.datafitter.ParamSet
-import hep.dataforge.io.FittingIOUtils
-import hep.dataforge.io.PrintFunction
-import hep.dataforge.maths.NamedDoubleArray
-import hep.dataforge.maths.NamedDoubleSet
-import hep.dataforge.maths.NamedMatrix
-import hep.dataforge.plots.PlotFrame
-import hep.dataforge.plots.data.PlottableFunction
-import hep.dataforge.plots.jfreechart.JFreeChartFrame
-import inr.numass.actions.ShowLossSpectrumAction;
-import inr.numass.models.ExperimentalVariableLossSpectrum
-import inr.numass.models.LossCalculator
-import org.apache.commons.math3.analysis.UnivariateFunction
-
-
-NamedDoubleSet transformOldMeans(NamedDoubleSet old){
-    String[] names = ["exPos", "ionPos", "exW", "ionW", "exIonRatio"];
-    double[] values = new double[5];
-    values[0] = old.getValue("loss_pos1");
-    values[1] = old.getValue("loss_pos2");
-    values[2] = old.getValue("loss_w1");
-    values[3] = old.getValue("loss_w2");
-    values[4] = old.getValue("loss_A1") / old.getValue("loss_A2");    
-
-    return new NamedDoubleArray(names, values);
-
-}
-
-ParamSet transformOldParams(ParamSet old){
-    String[] names = ["exPos", "ionPos", "exW", "ionW", "exIonRatio"];
-    ParamSet res = new ParamSet(names);
-    
-    res.setPar("exPos", old.getValue("loss_pos1"), old.getError("loss_pos1"));
-    res.setPar("ionPos", old.getValue("loss_pos2"), old.getError("loss_pos2"));
-    res.setPar("exW", old.getValue("loss_w1"), old.getError("loss_w1"));
-    res.setPar("ionW", old.getValue("loss_w2"), old.getError("loss_w2"));
-    
-    double ratioValue = old.getValue("loss_A1") / old.getValue("loss_A2");
-    
-    double a1RelErr = old.getError("loss_A1") / old.getValue("loss_A1");
-    double a2RelErr = old.getError("loss_A2") / old.getValue("loss_A2");
-    double ratioErr = Math.sqrt(a1RelErr*a1RelErr + a2RelErr*a2RelErr)*ratioValue;
-    res.setPar("exIonRatio", ratioValue, ratioErr);
-    
-    return res;
-}
-
-PrintWriter out = new PrintWriter(System.out);
-
-String name = "log14_h2_new"
-//String name = "log18_long"
-//String name = "log25_long"
-
-OldFitResultReader reader = new OldFitResultReader();
-reader.readFile(new File("C:\\Users\\darksnake\\Dropbox\\Numass\\Analysis\\loss-2014_november\\old_loss\\results\\final\\${name}.txt"));
-
-double threshold = 17d;
-
-ParamSet means = transformOldParams (reader.getParamSet());
-
-double ionRatio = ShowLossSpectrumAction.calcultateIonRatio(means, threshold);
-NamedMatrix cov = NamedMatrix.diagonal(means.getParErrors());
-double ionRatioError = ShowLossSpectrumAction.calultateIonRatioError(name, means, cov, threshold);
-
-println String.format("The ionization ratio (using threshold %f) is %f%n", threshold, ionRatio);
-println String.format("The ionization ratio standard deviation (using threshold %f) is %f%n", threshold, ionRatioError);
-println "*** FIT RESULT ***"
-
-FittingIOUtils.printParamSet(out, means);
-
-println means.toString();
-  
-UnivariateFunction scatterFunction =  LossCalculator.getSingleScatterFunction(means);
-PlotFrame frame = JFreeChartFrame.drawFrame("Differential scattering crossection for "+name, null);
-frame.add(new PlottableFunction("Cross-section", null, scatterFunction, 0, 100, 1000));
-
-PrintFunction.printFunctionSimple(out, scatterFunction, 0, 100, 500);

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

@@ -1,110 +0,0 @@
-/* 
- * 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.datafitter.ParamSet
-import hep.dataforge.maths.NamedDoubleArray
-import hep.dataforge.maths.NamedDoubleSet
-import hep.dataforge.maths.NamedMatrix
-import java.util.regex.Pattern
-import org.apache.commons.math3.linear.Array2DRowRealMatrix
-import org.apache.commons.math3.linear.RealMatrix
-import java.util.Scanner
-import java.util.regex.Matcher
-
-/**
- *
- * @author darksnake
- */
-class OldFitResultReader {
-    private static Pattern meanPattern = ~/\"(?<name>.*)\"\s*:\s*(?<value>[\d.]*)\s*/;
-    
-    private NamedDoubleSet means;
-    private RealMatrix covariance;
-    
-    void readMeans(String input){
-        Scanner scan = new Scanner(input);
-        List<String> names = new ArrayList<>();
-        List<Double> values = new ArrayList<>();
-        while(scan.hasNextLine()){
-            String nextLine = scan.nextLine();
-            if(!nextLine.isEmpty()){
-                Matcher match = meanPattern.matcher(nextLine);
-                match.matches();
-                names << match.group("name");
-                values << Double.parseDouble(match.group("value"));
-            }
-        }
-        this.means = new NamedDoubleArray(names.toArray(new String[names.size()]), values.toArray(new double[values.size()]));
-    }
-    
-    void readCovariance(String input){
-        Scanner scan = new Scanner(input);
-        List<List<Double>> matrix = new ArrayList<>();
-        while(scan.hasNextLine()){
-            String nextLine = scan.nextLine();
-            if(!nextLine.isEmpty()){
-                Scanner lineScan = new Scanner(nextLine);
-                List<Double> line = new ArrayList<>();
-                while(lineScan.hasNextDouble()){
-                    line << lineScan.nextDouble();
-                }
-                matrix << line;
-            }
-        }
-        
-        Array2DRowRealMatrix result = new Array2DRowRealMatrix(matrix.size(),matrix.size());
-        for(int i = 0; i< matrix.size; i++){
-            List<Double> line = matrix.get(i);
-            for(int j = 0; j< matrix.size; j++){
-                result.setEntry(i,j,line[j]);
-            }
-        }
-        this.covariance = result;
-    }
-    
-    void readFile(File file){
-        String text = file.getText();
-        Pattern pattern = Pattern.compile(/.*The best fit values are:\s*(?<parameters>.*)Covariation marix:\s*(?<covariance>.*)Best Likelihood logarithm/, Pattern.DOTALL);
-        List results = text.findAll(pattern);
-       
-        String res = results.get(results.size()-1);
-        Matcher match = pattern.matcher(res);
-        match.matches();
-        readMeans(match.group("parameters"));
-        readCovariance(match.group("covariance"));
-    }
-    
-    
-    NamedDoubleSet getMeans(){
-        return means;
-    }
-    
-    ParamSet getParamSet(){
-        ParamSet res = new ParamSet();
-        NamedMatrix cov = getCovariance();
-        for(String name: means.names()){
-            res.setPar(name, means.getValue(name), Math.sqrt(Math.abs(cov.getElement(name, name))));
-        }
-        return res;
-    }
-    
-    NamedMatrix getCovariance(){
-        return new NamedMatrix(covariance, means.namesAsArray());
-    }
-    
-}
-

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

@@ -40,6 +40,9 @@ import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
 
 /**
  *

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

@@ -17,6 +17,7 @@ package inr.numass;
 
 import hep.dataforge.actions.ActionManager;
 import hep.dataforge.context.Context;
+import hep.dataforge.context.GlobalContext;
 import hep.dataforge.description.ActionDescriptor;
 import hep.dataforge.description.DescriptorFormatter;
 import hep.dataforge.description.DescriptorUtils;
@@ -25,6 +26,7 @@ import hep.dataforge.exceptions.DescriptorException;
 import hep.dataforge.maths.integration.GaussRuleIntegrator;
 import hep.dataforge.maths.integration.UnivariateIntegrator;
 import hep.dataforge.meta.Meta;
+import inr.numass.storage.SetDirectionUtility;
 import java.io.PrintWriter;
 
 /**
@@ -52,8 +54,11 @@ public class NumassContext extends Context {
     }
 
     private void init() {
-        setIO(new NumassIO());
+        GlobalContext.registerContext(this);
+        loadPlugin("hep.dataforge:actions");
         loadPlugin("inr.numass:numass");
+        setIO(new NumassIO());
+        SetDirectionUtility.load(this);
     }
 
     public static void printDescription(Context context, boolean allowANSI) throws DescriptorException {
@@ -75,4 +80,10 @@ public class NumassContext extends Context {
         writer.flush();
     }
 
+    @Override
+    public void close() throws Exception {
+        SetDirectionUtility.save(this);
+        super.close();
+    }
+
 }

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

@@ -60,18 +60,18 @@ public class NumassIO extends BasicIOManager {
 
         String dirName = String.join(File.separator, tokens);
         String fileName = name.removeNameSpace().toString() + ".out";
-        return buildOut(getOutputDir(), dirName, fileName);
+        return buildOut(getWorkDirectory(), dirName, fileName);
     }
 
-    private File getOutputDir() {
+//    private File getOutputDir() {
-        String outputDirPath = getContext().getString(NUMASS_OUTPUT_CONTEXT_KEY, ".dataforge");
+//        String outputDirPath = getContext().getString(NUMASS_OUTPUT_CONTEXT_KEY, ".");
-        File res = new File(getRootDirectory(), outputDirPath);
+//        File res = new File(getRootDirectory(), outputDirPath);
-        if (!res.exists()) {
+//        if (!res.exists()) {
-            res.mkdir();
+//            res.mkdir();
-        }
+//        }
-        return res;
+//        return res;
-
+//
-    }
+//    }
 
     protected OutputStream buildOut(File parentDir, String dirName, String fileName) {
         File outputFile;

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

@@ -111,15 +111,27 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
                 } else {
                     pb.putValue("Monitor", corrFactor);
                 }
+
                 pb.putValue("CR", Value.of(dp.getValue("CR").doubleValue() / corrFactor));
                 pb.putValue("Window", Value.of(dp.getValue("Window").doubleValue() / corrFactor));
                 pb.putValue("Corrected", Value.of(dp.getValue("Corrected").doubleValue() / corrFactor));
                 pb.putValue("CRerr", Value.of(err));
+            } else {
+                double corrFactor = dp.getValue("CR").doubleValue() / norm;
+                if (dp.names().contains("Monitor")) {
+                    pb.putValue("Monitor", Value.of(dp.getValue("Monitor").doubleValue() / corrFactor));
+                } else {
+                    pb.putValue("Monitor", corrFactor);
+                }
+                pb.putValue("CR", norm);
+
             }
+
             if (meta.getBoolean("calculateRelative", false)) {
                 pb.putValue("relCR", pb.build().getValue("CR").doubleValue() / norm);
                 pb.putValue("relCRerr", pb.build().getValue("CRerr").doubleValue() / norm);
             }
+
             dataList.add(pb.build());
         }
 

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

@@ -33,10 +33,13 @@ import hep.dataforge.tables.TableFormat;
 import inr.numass.storage.NMPoint;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.RawNMPoint;
+import inr.numass.utils.ExpressionUtils;
 import java.io.OutputStream;
 import java.time.Instant;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 /**
  *
@@ -46,6 +49,8 @@ import java.util.List;
 @ValueDef(name = "lowerWindow", type = "NUMBER", def = "0", info = "Base for the window lowerWindow bound")
 @ValueDef(name = "lowerWindowSlope", type = "NUMBER", def = "0", info = "Slope for the window lowerWindow bound")
 @ValueDef(name = "upperWindow", type = "NUMBER", info = "Upper bound for window")
+@ValueDef(name = "correction",
+        info = "An expression to correct coun tumber depending on potential U, count rate CR and point length T")
 @ValueDef(name = "deadTime", type = "NUMBER", def = "0", info = "Dead time in us")
 public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
 
@@ -55,7 +60,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
         double b = meta.getDouble("lowerWindow", 0);
         double a = meta.getDouble("lowerWindowSlope", 0);
 
-        return (int) (b + Uset * a);
+        return Math.max((int) (b + Uset * a), 0);
     }
 
     @Override
@@ -77,14 +82,27 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
             int a = getLowerBorder(meta, Uset);
             int b = Math.min(upper, RawNMPoint.MAX_CHANEL);
 
-//            analyzer.setMonitorCorrector(corrector);
+            // count in window
             long wind = point.getCountInWindow(a, b);
 
+            // count in window with deadTime applied
             double corr = point.getCountRate(a, b, deadTime) * point.getLength();// - bkg * (b - a);
 
+            // count rate after all corrections
             double cr = point.getCountRate(a, b, deadTime);
+            // count rate error after all corrections
             double crErr = point.getCountRateErr(a, b, deadTime);
             
+            if(meta.hasValue("correction")){
+                Map<String,Double> exprParams = new HashMap<>();
+                exprParams.put("U", point.getUread());
+                exprParams.put("CR", cr);
+                exprParams.put("T", time);
+                double correctionFactor = ExpressionUtils.evaluate(meta.getString("correction"), exprParams);
+                cr = cr*correctionFactor;
+                crErr = crErr*correctionFactor;
+            }
+
             Instant timestamp = point.getStartTime();
 
             dataList.add(new MapPoint(parnames, new Object[]{Uset, Uread, time, total, wind, corr, cr, crErr, timestamp}));

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

@@ -80,9 +80,5 @@ public class ReadNumassStorageAction extends GenericAction<Void, NumassData> {
             throw new RuntimeException("Failed to load storage", ex);
         }
     }
-    /*
-    
-
-     */
 
 }

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

@@ -27,7 +27,6 @@ import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.io.PrintFunction;
 import hep.dataforge.io.reports.Reportable;
 import hep.dataforge.maths.GridCalculator;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.NamedMatrix;
 import hep.dataforge.maths.integration.UnivariateIntegrator;
 import hep.dataforge.meta.Laminate;
@@ -41,6 +40,7 @@ import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.MapPoint;
 import hep.dataforge.tables.Table;
 import hep.dataforge.tables.XYAdapter;
+import hep.dataforge.values.NamedValueSet;
 import inr.numass.NumassContext;
 import inr.numass.models.ExperimentalVariableLossSpectrum;
 import inr.numass.models.LossCalculator;
@@ -129,7 +129,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
             }
 
 //            double integralThreshold = reader.getDouble("numass.eGun", 19005d) - reader.getDouble("integralThreshold", 14.82);
-//            double integralRatio = calculateIntegralExIonRatio(input.getDataSet(), input.getParameters().getValue("X"), integralThreshold);
+//            double integralRatio = calculateIntegralExIonRatio(input.getDataSet(), input.getParameters().getDouble("X"), integralThreshold);
 //            writer.printf("The excitation to ionization ratio from integral spectrum (using threshold %f) is %f%n", integralThreshold, integralRatio);
             writer.println();
 
@@ -178,7 +178,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
         return input;
     }
 
-    public static double calcultateIonRatio(NamedDoubleSet set, double threshold) {
+    public static double calcultateIonRatio(NamedValueSet set, double threshold) {
         UnivariateIntegrator integrator = NumassContext.highDensityIntegrator;
         UnivariateFunction integrand = LossCalculator.getSingleScatterFunction(set);
         return 1d - integrator.integrate(integrand, 5d, threshold);
@@ -211,7 +211,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
     }
 
     @SuppressWarnings("Unchecked")
-    public double calultateIonRatioError(Context context, String name, NamedDoubleSet parameters, NamedMatrix covariance, double threshold) {
+    public double calultateIonRatioError(Context context, String name, NamedValueSet parameters, NamedMatrix covariance, double threshold) {
         int number = 10000;
 
         double[] res = new GaussianParameterGenerator(parameters, covariance)
@@ -233,7 +233,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
         return new DescriptiveStatistics(res).getStandardDeviation();
     }
 
-    public static Table generateSpread(PrintWriter writer, String name, NamedDoubleSet parameters, NamedMatrix covariance) {
+    public static Table generateSpread(PrintWriter writer, String name, NamedValueSet parameters, NamedMatrix covariance) {
         int numCalls = 1000;
         int gridPoints = 200;
         double a = 8;

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

@@ -80,7 +80,7 @@ public class SummaryAction extends ManyToOneAction<FitState, Table> {
             Value[] values = new Value[names.length];
             values[0] = Value.of(key);
             for (int i = 0; i < parNames.length; i++) {
-                Value val = Value.of(state.getParameters().getValue(parNames[i]));
+                Value val = Value.of(state.getParameters().getDouble(parNames[i]));
                 values[2 * i + 1] = val;
                 Value err = Value.of(state.getParameters().getError(parNames[i]));
                 values[2 * i + 2] = err;

numass-main/src/main/java/inr/numass/data/SpectrumInformation.java

@@ -17,10 +17,10 @@ package inr.numass.data;
 
 import hep.dataforge.functions.ParametricFunction;
 import static hep.dataforge.maths.MatrixOperations.inverse;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.NamedMatrix;
 import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.ListTable;
+import hep.dataforge.values.NamedValueSet;
 import inr.numass.utils.TritiumUtils;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
@@ -38,7 +38,7 @@ public class SpectrumInformation {
         this.source = source;
     }
 
-    public NamedMatrix getExpetedCovariance(NamedDoubleSet set, ListTable data, String... parNames) {
+    public NamedMatrix getExpetedCovariance(NamedValueSet set, ListTable data, String... parNames) {
         String[] names = parNames;
         if (names.length == 0) {
             names = source.namesAsArray();
@@ -56,7 +56,7 @@ public class SpectrumInformation {
      * @param parNames
      * @return
      */
-    public NamedMatrix getInformationMatrix(NamedDoubleSet set, ListTable data, String... parNames) {
+    public NamedMatrix getInformationMatrix(NamedValueSet set, ListTable data, String... parNames) {
         SpectrumDataAdapter reader = TritiumUtils.adapter();
 
         String[] names = parNames;
@@ -80,11 +80,11 @@ public class SpectrumInformation {
     }
 
     // формула правильная!
-    public double getPoinSignificance(NamedDoubleSet set, String name1, String name2, double x) {
+    public double getPoinSignificance(NamedValueSet set, String name1, String name2, double x) {
         return source.derivValue(name1, x, set) * source.derivValue(name2, x, set) / source.value(x, set);
     }
 
-    public NamedMatrix getPointInfoMatrix(NamedDoubleSet set, double x, double t, String... parNames) {
+    public NamedMatrix getPointInfoMatrix(NamedValueSet set, double x, double t, String... parNames) {
         assert source.names().contains(set.namesAsArray());
 
         String[] names = parNames;
@@ -119,7 +119,7 @@ public class SpectrumInformation {
      * @param name2
      * @return
      */
-    public UnivariateFunction getSignificanceFunction(final NamedDoubleSet set, final String name1, final String name2) {
+    public UnivariateFunction getSignificanceFunction(final NamedValueSet set, final String name1, final String name2) {
         return (double d) -> getPoinSignificance(set, name1, name2, d);
     }
 }

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

@@ -17,7 +17,8 @@ package inr.numass.models;
 
 import hep.dataforge.exceptions.NotDefinedException;
 import hep.dataforge.functions.AbstractParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import java.io.File;
 import static java.lang.Math.abs;
 import static java.lang.Math.exp;
@@ -89,11 +90,11 @@ public class BetaSpectrum extends AbstractParametricFunction implements RangedNa
         return res;
     }
 
-    double derivRootsterile(String name, double E, NamedDoubleSet pars) throws NotDefinedException {
+    double derivRootsterile(String name, double E, ValueProvider pars) throws NotDefinedException {
-        double E0 = pars.getValue("E0");
+        double E0 = pars.getDouble("E0");
-        double mnu2 = pars.getValue("mnu2");
+        double mnu2 = pars.getDouble("mnu2");
-        double mst2 = pars.getValue("msterile2");
+        double mst2 = pars.getDouble("msterile2");
-        double u2 = pars.getValue("U2");
+        double u2 = pars.getDouble("U2");
 
         switch (name) {
             case "E0":
@@ -117,7 +118,7 @@ public class BetaSpectrum extends AbstractParametricFunction implements RangedNa
     }
 
     @Override
-    public double derivValue(String name, double E, NamedDoubleSet pars) throws NotDefinedException {
+    public double derivValue(String name, double E, NamedValueSet pars) throws NotDefinedException {
         if (this.fss == null) {
             return this.derivRootsterile(name, E, pars);
         }
@@ -137,12 +138,12 @@ public class BetaSpectrum extends AbstractParametricFunction implements RangedNa
     }
 
     @Override
-    public Double max(NamedDoubleSet set) {
+    public Double max(NamedValueSet set) {
-        return set.getValue("E0");
+        return set.getDouble("E0");
     }
 
     @Override
-    public Double min(NamedDoubleSet set) {
+    public Double min(NamedValueSet set) {
         return 0d;
     }
 
@@ -184,11 +185,11 @@ public class BetaSpectrum extends AbstractParametricFunction implements RangedNa
         return res;
     }
 
-    double rootsterile(double E, NamedDoubleSet pars) {
+    double rootsterile(double E, ValueProvider pars) {
-        double E0 = pars.getValue("E0");
+        double E0 = pars.getDouble("E0");
-        double mnu2 = pars.getValue("mnu2");
+        double mnu2 = pars.getDouble("mnu2");
-        double mst2 = pars.getValue("msterile2");
+        double mst2 = pars.getDouble("msterile2");
-        double u2 = pars.getValue("U2");
+        double u2 = pars.getDouble("U2");
 
         if (u2 == 0) {
             return root(E0, mnu2, E);
@@ -206,7 +207,7 @@ public class BetaSpectrum extends AbstractParametricFunction implements RangedNa
     }
 
     @Override
-    public double value(double E, NamedDoubleSet pars) {
+    public double value(double E, NamedValueSet pars) {
         if (this.fss == null) {
             return rootsterile(E, pars);
         }

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

@@ -6,7 +6,7 @@
 package inr.numass.models;
 
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
 import inr.numass.NumassContext;
 import inr.numass.utils.TritiumUtils;
 import org.apache.commons.math3.analysis.UnivariateFunction;
@@ -38,7 +38,7 @@ public class CustomNBkgSpectrum extends NBkgSpectrum {
     }
 
     @Override
-    public double value(double x, NamedDoubleSet set) {
+    public double value(double x, NamedValueSet set) {
         if (customBackgroundFunction == null) {
             return super.value(x, set);
         } else {

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

@@ -18,9 +18,9 @@ package inr.numass.models;
 import hep.dataforge.exceptions.NamingException;
 import hep.dataforge.exceptions.NotDefinedException;
 import hep.dataforge.functions.AbstractParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.integration.GaussRuleIntegrator;
 import hep.dataforge.maths.integration.UnivariateIntegrator;
+import hep.dataforge.values.NamedValueSet;
 import java.util.List;
 import org.apache.commons.math3.analysis.BivariateFunction;
 import org.apache.commons.math3.analysis.UnivariateFunction;
@@ -45,17 +45,17 @@ public class EmpiricalLossSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double derivValue(String parName, double x, NamedDoubleSet set) {
+    public double derivValue(String parName, double x, NamedValueSet set) {
         throw new NotDefinedException();
     }
 
     @Override
-    public double value(double U, NamedDoubleSet set) {
+    public double value(double U, NamedValueSet set) {
         if (U >= eMax) {
             return 0;
         }
-        double X = set.getValue("X");
+        double X = set.getDouble("X");
-        final double shift = set.getValue("shift");
+        final double shift = set.getDouble("shift");
 
         //FIXME тут толщины усреднены по длине источника, а надо брать чистого Пуассона
         final List<Double> probs = LossCalculator.instance().getGunLossProbabilities(X);

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

@@ -18,7 +18,8 @@ package inr.numass.models;
 import hep.dataforge.exceptions.NotDefinedException;
 import hep.dataforge.functions.AbstractParametricFunction;
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import org.apache.commons.math3.analysis.BivariateFunction;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 
@@ -37,7 +38,7 @@ public class ExperimentalVariableLossSpectrum extends VariableLossSpectrum {
         return new ExperimentalVariableLossSpectrum(new AbstractParametricFunction(new String[0]) {
 
             @Override
-            public double derivValue(String parName, double x, NamedDoubleSet set) {
+            public double derivValue(String parName, double x, NamedValueSet set) {
                 throw new NotDefinedException();
             }
 
@@ -47,7 +48,7 @@ public class ExperimentalVariableLossSpectrum extends VariableLossSpectrum {
             }
 
             @Override
-            public double value(double x, NamedDoubleSet set) {
+            public double value(double x, NamedValueSet set) {
                 return transmission.value(x);
             }
         }, eMax,smootherW);
@@ -119,12 +120,12 @@ public class ExperimentalVariableLossSpectrum extends VariableLossSpectrum {
             return (eps) -> (excitation(exPos, exW).value(eps) * exIonRatio + ionization(ionPos, ionW).value(eps)) / (1d + exIonRatio);
         }
 
-        public UnivariateFunction total(NamedDoubleSet set) {
+        public UnivariateFunction total(ValueProvider set) {
-            final double exPos = set.getValue("exPos");
+            final double exPos = set.getDouble("exPos");
-            final double ionPos = set.getValue("ionPos");
+            final double ionPos = set.getDouble("ionPos");
-            final double exW = set.getValue("exW");
+            final double exW = set.getDouble("exW");
-            final double ionW = set.getValue("ionW");
+            final double ionW = set.getDouble("ionW");
-            final double exIonRatio = set.getValue("exIonRatio");
+            final double exIonRatio = set.getDouble("exIonRatio");
             return total(exPos, ionPos, exW, ionW, exIonRatio);
         }
 

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

@@ -19,8 +19,9 @@ import hep.dataforge.context.GlobalContext;
 import hep.dataforge.exceptions.NameNotFoundException;
 import hep.dataforge.functions.AbstractParametricFunction;
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
 import static hep.dataforge.names.NamedUtils.combineNamesWithEquals;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import static java.lang.Double.isNaN;
 import static java.lang.Math.abs;
 import static java.lang.Math.exp;
@@ -28,6 +29,12 @@ import static java.lang.Math.sqrt;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.analysis.integration.SimpsonIntegrator;
 import org.apache.commons.math3.analysis.integration.UnivariateIntegrator;
+import static java.lang.Double.isNaN;
+import static java.lang.Math.abs;
+import static java.lang.Double.isNaN;
+import static java.lang.Math.abs;
+import static java.lang.Double.isNaN;
+import static java.lang.Math.abs;
 
 /**
  *
@@ -51,7 +58,7 @@ public class GaussResolution extends AbstractParametricFunction implements Trans
     }
 
     @Override
-    public double derivValue(String name, double X, NamedDoubleSet pars) {
+    public double derivValue(String name, double X, NamedValueSet pars) {
         if (abs(X - getPos(pars)) > cutoff * getW(pars)) {
             return 0;
         }
@@ -71,7 +78,7 @@ public class GaussResolution extends AbstractParametricFunction implements Trans
             int maxEval = GlobalContext.instance().getInt("INTEGR_POINTS", 500);
 
             @Override
-            public double derivValue(String parName, double x, NamedDoubleSet set) {
+            public double derivValue(String parName, double x, NamedValueSet set) {
                 double a = getLowerBound(set);
                 double b = getUpperBound(set);
                 assert b > a;
@@ -87,7 +94,7 @@ public class GaussResolution extends AbstractParametricFunction implements Trans
             }
 
             @Override
-            public double value(double x, NamedDoubleSet set) {
+            public double value(double x, NamedValueSet set) {
                 double a = getLowerBound(set);
                 double b = getUpperBound(set);
                 assert b > a;
@@ -97,11 +104,11 @@ public class GaussResolution extends AbstractParametricFunction implements Trans
     }
 
     @Override
-    public double getDeriv(String name, NamedDoubleSet set, double input, double output) {
+    public double getDeriv(String name, NamedValueSet set, double input, double output) {
         return this.derivValue(name, output - input, set);
     }
 
-    private UnivariateFunction getDerivProduct(final String name, final ParametricFunction bare, final NamedDoubleSet pars, final double x0) {
+    private UnivariateFunction getDerivProduct(final String name, final ParametricFunction bare, final NamedValueSet pars, final double x0) {
         return (double x) -> {
             double res1;
             double res2;
@@ -119,17 +126,17 @@ public class GaussResolution extends AbstractParametricFunction implements Trans
         };
     }
 
-    private double getLowerBound(final NamedDoubleSet pars) {
+    private double getLowerBound(final NamedValueSet pars) {
         return getPos(pars) - cutoff * getW(pars);
     }
 
-    private double getPos(NamedDoubleSet pars) {
+    private double getPos(ValueProvider pars) {
-//        return pars.getValue("pos");
+//        return pars.getDouble("pos");
         // вряд ли стоит ожидать, что разрешение будет сдвигать среднее, поэтому оставляем один параметр
         return 0;
     }
 
-    private UnivariateFunction getProduct(final ParametricFunction bare, final NamedDoubleSet pars, final double x0) {
+    private UnivariateFunction getProduct(final ParametricFunction bare, final NamedValueSet pars, final double x0) {
         return (double x) -> {
             double res = bare.value(x0 - x, pars) * GaussResolution.this.value(x, pars);
             assert !isNaN(res);
@@ -137,17 +144,17 @@ public class GaussResolution extends AbstractParametricFunction implements Trans
         };
     }
 
-    private double getUpperBound(final NamedDoubleSet pars) {
+    private double getUpperBound(final NamedValueSet pars) {
         return getPos(pars) + cutoff * getW(pars);
     }
 
     @Override
-    public double getValue(NamedDoubleSet set, double input, double output) {
+    public double getValue(NamedValueSet set, double input, double output) {
         return this.value(output - input, set);
     }
 
-    private double getW(NamedDoubleSet pars) {
+    private double getW(ValueProvider pars) {
-        return pars.getValue("w");
+        return pars.getDouble("w");
     }
 
     @Override
@@ -156,11 +163,11 @@ public class GaussResolution extends AbstractParametricFunction implements Trans
     }
 
     @Override
-    public double value(double X, NamedDoubleSet pars) {
+    public double value(double x, NamedValueSet pars) {
-        if (abs(X - getPos(pars)) > cutoff * getW(pars)) {
+        if (abs(x - getPos(pars)) > cutoff * getW(pars)) {
             return 0;
         }
-        double aux = (X - getPos(pars)) / getW(pars);
+        double aux = (x - getPos(pars)) / getW(pars);
         return exp(-aux * aux / 2) / getW(pars) / sqrt(2 * Math.PI);
     }
 }

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

@@ -17,7 +17,8 @@ package inr.numass.models;
 
 import hep.dataforge.exceptions.NotDefinedException;
 import hep.dataforge.functions.AbstractParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import static java.lang.Math.exp;
 import static java.lang.Math.sqrt;
 
@@ -35,7 +36,7 @@ public class GaussSourceSpectrum extends AbstractParametricFunction implements R
     }
 
     @Override
-    public double derivValue(String parName, double E, NamedDoubleSet set) {
+    public double derivValue(String parName, double E, NamedValueSet set) {
         switch (parName) {
             case "pos":
                 return getGaussPosDeriv(E, getPos(set), getSigma(set));
@@ -60,21 +61,21 @@ public class GaussSourceSpectrum extends AbstractParametricFunction implements R
     }
 
     @Override
-    public Double max(NamedDoubleSet set) {
+    public Double max(NamedValueSet set) {
         return getPos(set) + cutoff * getSigma(set);
     }
 
     @Override
-    public Double min(NamedDoubleSet set) {
+    public Double min(NamedValueSet set) {
         return getPos(set) - cutoff * getSigma(set);
     }
 
-    private double getPos(NamedDoubleSet set) {
+    private double getPos(ValueProvider set) {
-        return set.getValue("pos");
+        return set.getDouble("pos");
     }
 
-    private double getSigma(NamedDoubleSet set) {
+    private double getSigma(ValueProvider set) {
-        return set.getValue("sigma");
+        return set.getDouble("sigma");
     }
 
     @Override
@@ -83,7 +84,7 @@ public class GaussSourceSpectrum extends AbstractParametricFunction implements R
     }
 
     @Override
-    public double value(final double E, NamedDoubleSet set) {
+    public double value(final double E, NamedValueSet set) {
         return getGauss(E, getPos(set), getSigma(set));
     }
 }

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

@@ -17,8 +17,8 @@ package inr.numass.models;
 
 import hep.dataforge.exceptions.NotDefinedException;
 import hep.dataforge.functions.AbstractParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.integration.UnivariateIntegrator;
+import hep.dataforge.values.NamedValueSet;
 import inr.numass.NumassContext;
 import static java.lang.Math.abs;
 import static java.lang.Math.exp;
@@ -42,10 +42,10 @@ public class GunSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double derivValue(String parName, final double U, NamedDoubleSet set) {
+    public double derivValue(String parName, final double U, NamedValueSet set) {
-        final double pos = set.getValue("pos");
+        final double pos = set.getDouble("pos");
-        final double sigma = set.getValue("sigma");
+        final double sigma = set.getDouble("sigma");
-        final double resA = set.getValue("resA");
+        final double resA = set.getDouble("resA");
 
         if(sigma == 0) throw new NotDefinedException();
         
@@ -132,10 +132,10 @@ public class GunSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double value(final double U, NamedDoubleSet set) {
+    public double value(final double U, NamedValueSet set) {
-        final double pos = set.getValue("pos");
+        final double pos = set.getDouble("pos");
-        final double sigma = set.getValue("sigma");
+        final double sigma = set.getDouble("sigma");
-        final double resA = set.getValue("resA");
+        final double resA = set.getDouble("resA");
         
         if (sigma <1e-5 ) {
             return transmissionValueFast(U, pos, resA);

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

@@ -16,8 +16,9 @@
 package inr.numass.models;
 
 import hep.dataforge.exceptions.NotDefinedException;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.names.Names;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import static java.lang.Math.abs;
 import static java.lang.Math.exp;
 import static java.lang.Math.sqrt;
@@ -30,17 +31,17 @@ public class GunTailSpectrum implements RangedNamedSetSpectrum {
     private final String[] list = {"pos", "tailShift", "tailAmp", "sigma"};
 
     @Override
-    public double derivValue(String parName, double x, NamedDoubleSet set) {
+    public double derivValue(String parName, double x, NamedValueSet set) {
         throw new NotDefinedException();
     }
 
     @Override
-    public Double max(NamedDoubleSet set) {
+    public Double max(NamedValueSet set) {
-        return set.getValue("pos") + cutoff * set.getValue("sigma");
+        return set.getDouble("pos") + cutoff * set.getDouble("sigma");
     }
 
     @Override
-    public Double min(NamedDoubleSet set) {
+    public Double min(NamedValueSet set) {
         return 0d;
     }
 
@@ -55,10 +56,10 @@ public class GunTailSpectrum implements RangedNamedSetSpectrum {
     }
 
     @Override
-    public double value(double E, NamedDoubleSet set) {
+    public double value(double E, NamedValueSet set) {
-        double pos = set.getValue("pos");
+        double pos = set.getDouble("pos");
-        double amp = set.getValue("tailAmp");
+        double amp = set.getDouble("tailAmp");
-        double sigma = set.getValue("sigma");
+        double sigma = set.getDouble("sigma");
 
         if (E >= pos + cutoff * sigma) {
             return 0d;
@@ -75,9 +76,9 @@ public class GunTailSpectrum implements RangedNamedSetSpectrum {
         return exp(-aux * aux / 2) / sigma / sqrt(2 * Math.PI);
     }
 
-    double tail(double E, double pos, NamedDoubleSet set) {
+    double tail(double E, double pos, ValueProvider set) {
 
-        double tailShift = set.getValue("tailShift");
+        double tailShift = set.getDouble("tailShift");
 
         double delta = Math.max(pos - E - tailShift, 1d);
         UnivariateFunction func = (double d) -> 1d / d / d;

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

@@ -16,11 +16,11 @@
 package inr.numass.models;
 
 import hep.dataforge.functions.FunctionCaching;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.integration.GaussRuleIntegrator;
 import hep.dataforge.maths.integration.UnivariateIntegrator;
 import hep.dataforge.plots.XYPlotFrame;
 import hep.dataforge.plots.data.PlottableFunction;
+import hep.dataforge.values.NamedValueSet;
 import static java.lang.Math.exp;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -115,13 +115,13 @@ public class LossCalculator {
         return (e) -> func.value(e) / norm;
     }
 
-    public static UnivariateFunction getSingleScatterFunction(NamedDoubleSet set) {
+    public static UnivariateFunction getSingleScatterFunction(NamedValueSet set) {
 
-        final double exPos = set.getValue("exPos");
+        final double exPos = set.getDouble("exPos");
-        final double ionPos = set.getValue("ionPos");
+        final double ionPos = set.getDouble("ionPos");
-        final double exW = set.getValue("exW");
+        final double exW = set.getDouble("exW");
-        final double ionW = set.getValue("ionW");
+        final double ionW = set.getDouble("ionW");
-        final double exIonRatio = set.getValue("exIonRatio");
+        final double exIonRatio = set.getDouble("exIonRatio");
 
         return getSingleScatterFunction(exPos, ionPos, exW, ionW, exIonRatio);
     }
@@ -146,27 +146,27 @@ public class LossCalculator {
         return instance;
     }
 
-    public static void plotScatter(XYPlotFrame frame, NamedDoubleSet set) {
+    public static void plotScatter(XYPlotFrame frame, NamedValueSet set) {
         //"X", "shift", "exPos", "ionPos", "exW", "ionW", "exIonRatio"
 
 //        JFreeChartFrame frame = JFreeChartFrame.drawFrame("Differential scattering crosssection", null);
-        double X = set.getValue("X");
+        double X = set.getDouble("X");
 
-        final double exPos = set.getValue("exPos");
+        final double exPos = set.getDouble("exPos");
 
-        final double ionPos = set.getValue("ionPos");
+        final double ionPos = set.getDouble("ionPos");
 
-        final double exW = set.getValue("exW");
+        final double exW = set.getDouble("exW");
 
-        final double ionW = set.getValue("ionW");
+        final double ionW = set.getDouble("ionW");
 
-        final double exIonRatio = set.getValue("exIonRatio");
+        final double exIonRatio = set.getDouble("exIonRatio");
 
         UnivariateFunction scatterFunction = getSingleScatterFunction(exPos, ionPos, exW, ionW, exIonRatio);
 
         if (set.names().contains("X")) {
             final LossCalculator loss = LossCalculator.instance;
-            final List<Double> probs = loss.getGunLossProbabilities(set.getValue("X"));
+            final List<Double> probs = loss.getGunLossProbabilities(set.getDouble("X"));
             UnivariateFunction single = (double e) -> probs.get(1) * scatterFunction.value(e);
             frame.add(new PlottableFunction("Single scattering",  x->single.value(x), 0, 100, 1000));
 

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

@@ -17,8 +17,9 @@ package inr.numass.models;
 
 import hep.dataforge.functions.AbstractParametricFunction;
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.names.NamedUtils;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import java.util.ArrayList;
 import java.util.List;
 import org.apache.commons.math3.analysis.BivariateFunction;
@@ -141,7 +142,7 @@ public class ModularSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double derivValue(String parName, double U, NamedDoubleSet set) {
+    public double derivValue(String parName, double U, NamedValueSet set) {
         if (U >= sourceSpectrum.max(set)) {
             return 0;
         }
@@ -177,12 +178,12 @@ public class ModularSpectrum extends AbstractParametricFunction {
         }
     }
 
-    private double getTrap(NamedDoubleSet set) {
+    private double getTrap(ValueProvider set) {
-        return set.getValue("trap");
+        return set.getDouble("trap");
     }
 
-    private double getX(NamedDoubleSet set) {
+    private double getX(ValueProvider set) {
-        return set.getValue("X");
+        return set.getDouble("X");
     }
 
     @Override
@@ -223,7 +224,7 @@ public class ModularSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double value(double U, NamedDoubleSet set) {
+    public double value(double U, NamedValueSet set) {
         if (U >= sourceSpectrum.max(set)) {
             return 0;
         }

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

@@ -17,9 +17,10 @@ package inr.numass.models;
 
 import hep.dataforge.functions.AbstractParametricFunction;
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
 import static hep.dataforge.names.NamedUtils.combineNamesWithEquals;
 import hep.dataforge.utils.MultiCounter;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 
 /**
  *
@@ -38,7 +39,7 @@ public class NBkgSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double derivValue(String parName, double x, NamedDoubleSet set) {
+    public double derivValue(String parName, double x, NamedValueSet set) {
         this.counter.increase(parName);
         switch (parName) {
             case "N":
@@ -50,12 +51,12 @@ public class NBkgSpectrum extends AbstractParametricFunction {
         }
     }
 
-    private double getBkg(NamedDoubleSet set) {
+    private double getBkg(ValueProvider set) {
-        return set.getValue("bkg");
+        return set.getDouble("bkg");
     }
 
-    private double getN(NamedDoubleSet set) {
+    private double getN(ValueProvider set) {
-        return set.getValue("N");
+        return set.getDouble("N");
     }
 
     @Override
@@ -71,7 +72,7 @@ public class NBkgSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double value(double x, NamedDoubleSet set) {
+    public double value(double x, NamedValueSet set) {
         this.counter.increase("value");
         return getN(set) * source.value(x, set) + getBkg(set);
     }

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

@@ -19,11 +19,14 @@ import hep.dataforge.functions.AbstractParametricFunction;
 import static hep.dataforge.functions.FunctionUtils.getSpectrumDerivativeFunction;
 import static hep.dataforge.functions.FunctionUtils.getSpectrumFunction;
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleArray;
+import hep.dataforge.maths.MathUtils;
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.maths.NamedVector;
 import hep.dataforge.names.AbstractNamedSet;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Objects;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.analysis.interpolation.SplineInterpolator;
 import org.slf4j.LoggerFactory;
@@ -60,7 +63,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
     }
 
     @Override
-    public double derivValue(String parName, double x, NamedDoubleSet set) {
+    public double derivValue(String parName, double x, NamedValueSet set) {
         if (!isCachingEnabled()) {
             return source.derivValue(parName, x, set);
         }
@@ -105,7 +108,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
         return source.providesDeriv(name);
     }
 
-    protected boolean sameSet(NamedDoubleSet set1, NamedDoubleSet set2) {
+    protected boolean sameSet(ValueProvider set1, ValueProvider set2) {
 //        if((set1 instanceof NamedDoubleSet)&&(set2 instanceof NamedDoubleSet)){
 //            double[] v1 = ((NamedDoubleSet)set1).getAllValues();
 //            double[] v2 = ((NamedDoubleSet)set2).getAllValues();
@@ -113,7 +116,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
 //        }
 
         for (String name : this.names()) {
-            if (set1.getValue(name) != set2.getValue(name)) {
+            if (!Objects.equals(set1.getDouble(name), set2.getDouble(name))) {
                 return false;
             }
         }
@@ -137,8 +140,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
     /*
      * Подразумевается, что трансформация одна и та же и для спектра, и для производных.
      */
-    protected double transformation(CacheElement cache,
+    protected double transformation(CacheElement cache, NamedValueSet newSet, double x) throws TransformationNotAvailable {
-            NamedDoubleSet newSet, double x) throws TransformationNotAvailable {
 
 
         /*
@@ -150,7 +152,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
     }
 
     @Override
-    public double value(double x, NamedDoubleSet set) {
+    public double value(double x, NamedValueSet set) {
         if (!isCachingEnabled()) {
             return source.value(x, set);
         }
@@ -187,22 +189,22 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
     protected class CacheElement extends AbstractNamedSet implements UnivariateFunction {
 
         private UnivariateFunction cachedSpectrum;
-        private final NamedDoubleSet cachedParameters;
+        private final NamedValueSet cachedParameters;
         String parName;
 
-        CacheElement(NamedDoubleSet parameters, String parName) {
+        CacheElement(NamedValueSet parameters, String parName) {
             super(source);
             //на всякий случай обрезаем набор параметров до необходимого
             String[] names = source.namesAsArray();
-            this.cachedParameters = new NamedDoubleArray(names, parameters.getValues(names));
+            this.cachedParameters = new NamedVector(names, MathUtils.getDoubleArray(parameters));
             UnivariateFunction func = getSpectrumDerivativeFunction(parName, source, parameters);
             generate(func);
         }
 
-        CacheElement(NamedDoubleSet parameters) {
+        CacheElement(NamedValueSet parameters) {
             super(source);
             String[] names = source.namesAsArray();
-            this.cachedParameters = new NamedDoubleArray(names, parameters.getValues(names));
+            this.cachedParameters = new NamedVector(names, MathUtils.getDoubleArray(parameters));
             UnivariateFunction func = getSpectrumFunction(source, parameters);
             generate(func);
         }
@@ -227,7 +229,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
             return this.cachedSpectrum.value(x);
         }
 
-        public NamedDoubleSet getCachedParameters() {
+        public NamedValueSet getCachedParameters() {
             return this.cachedParameters;
         }
     }

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

@@ -15,7 +15,7 @@
  */
 package inr.numass.models;
 
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
 
 /**
  *
@@ -36,12 +36,12 @@ public class SimpleRange implements SpectrumRange{
     
     
     @Override
-    public Double max(NamedDoubleSet set) {
+    public Double max(NamedValueSet set) {
         return max;
     }
 
     @Override
-    public Double min(NamedDoubleSet set) {
+    public Double min(NamedValueSet set) {
         return min;
     }
     

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

@@ -15,7 +15,7 @@
  */
 package inr.numass.models;
 
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
 
 
 /**
@@ -23,6 +23,6 @@ import hep.dataforge.maths.NamedDoubleSet;
  * @author Darksnake
  */
 public interface SpectrumRange {
-    Double min(NamedDoubleSet set);
+    Double min(NamedValueSet set);
-    Double max(NamedDoubleSet set);
+    Double max(NamedValueSet set);
 }

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

@@ -17,8 +17,9 @@ package inr.numass.models;
 
 
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.names.NameSetContainer;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import org.apache.commons.math3.analysis.BivariateFunction;
 
 /**
@@ -27,18 +28,18 @@ import org.apache.commons.math3.analysis.BivariateFunction;
  */
 public interface Transmission extends NameSetContainer{
     
-    double getValue(NamedDoubleSet set, double input, double output);
+    double getValue(NamedValueSet set, double input, double output);
-    double getDeriv(String name, NamedDoubleSet set, double input, double output);
+    double getDeriv(String name, NamedValueSet set, double input, double output);
     boolean providesDeriv(String name);
     
     ParametricFunction getConvolutedSpectrum(RangedNamedSetSpectrum bare);
     
     
-    default BivariateFunction getBivariateFunction(final NamedDoubleSet params){
+    default BivariateFunction getBivariateFunction(final NamedValueSet params){
         return (double input, double output) -> getValue(params, input, output);
     }
     
-    default BivariateFunction getBivariateDerivFunction(final String name, final NamedDoubleSet params){
+    default BivariateFunction getBivariateDerivFunction(final String name, final NamedValueSet params){
         return (double input, double output) -> getDeriv(name, params, input, output);
     }    
 }

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

@@ -17,7 +17,7 @@ package inr.numass.models;
 
 import hep.dataforge.functions.AbstractParametricFunction;
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
 import inr.numass.NumassContext;
 import org.apache.commons.math3.analysis.BivariateFunction;
 import org.apache.commons.math3.analysis.UnivariateFunction;
@@ -45,7 +45,7 @@ class TransmissionConvolution extends AbstractParametricFunction {
     }
 
     @Override
-    public double derivValue(final String parName, final double U, NamedDoubleSet set) {
+    public double derivValue(final String parName, final double U, NamedValueSet set) {
         double min = range.min(set);
         double max = range.max(set);
 
@@ -67,7 +67,7 @@ class TransmissionConvolution extends AbstractParametricFunction {
     }
 
     @Override
-    public double value(final double U, NamedDoubleSet set) {
+    public double value(final double U, NamedValueSet set) {
         double min = range.min(set);
         double max = range.max(set);
 

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

@@ -16,8 +16,8 @@
 package inr.numass.models;
 
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleArray;
+import hep.dataforge.maths.NamedVector;
-import hep.dataforge.maths.NamedDoubleSet;
+import hep.dataforge.values.NamedValueSet;
 import static java.lang.Math.abs;
 import org.slf4j.LoggerFactory;
 
@@ -39,11 +39,11 @@ public class TritiumSpectrumCaching extends NamedSpectrumCaching {
     }
 
     @Override
-    protected double transformation(CacheElement cache, NamedDoubleSet newSet, double x) throws TransformationNotAvailable {
+    protected double transformation(CacheElement cache, NamedValueSet newSet, double x) throws TransformationNotAvailable {
         double res;
-        NamedDoubleArray curSet = new NamedDoubleArray(newSet);
+        NamedVector curSet = new NamedVector(newSet);
-        double E0new = newSet.getValue("E0");
+        double E0new = newSet.getDouble("E0");
-        double E0old = cache.getCachedParameters().getValue("E0");
+        double E0old = cache.getCachedParameters().getDouble("E0");
         double E0delta = E0new - E0old;
         if (abs(E0delta) > delta) {
             LoggerFactory.getLogger(getClass())

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

@@ -18,8 +18,9 @@ package inr.numass.models;
 import hep.dataforge.exceptions.NotDefinedException;
 import hep.dataforge.functions.AbstractParametricFunction;
 import hep.dataforge.functions.ParametricFunction;
-import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.integration.UnivariateIntegrator;
+import hep.dataforge.values.NamedValueSet;
+import hep.dataforge.values.ValueProvider;
 import inr.numass.NumassContext;
 import java.util.List;
 import org.apache.commons.math3.analysis.BivariateFunction;
@@ -41,7 +42,7 @@ public class VariableLossSpectrum extends AbstractParametricFunction {
         return new VariableLossSpectrum(new AbstractParametricFunction(new String[0]) {
 
             @Override
-            public double derivValue(String parName, double x, NamedDoubleSet set) {
+            public double derivValue(String parName, double x, NamedValueSet set) {
                 throw new NotDefinedException();
             }
 
@@ -51,7 +52,7 @@ public class VariableLossSpectrum extends AbstractParametricFunction {
             }
 
             @Override
-            public double value(double x, NamedDoubleSet set) {
+            public double value(double x, NamedValueSet set) {
                 return transmission.value(x);
             }
         }, eMax);
@@ -68,17 +69,17 @@ public class VariableLossSpectrum extends AbstractParametricFunction {
     }
 
     @Override
-    public double derivValue(String parName, double x, NamedDoubleSet set) {
+    public double derivValue(String parName, double x, NamedValueSet set) {
         throw new NotDefinedException();
     }
 
     @Override
-    public double value(double U, NamedDoubleSet set) {
+    public double value(double U, NamedValueSet set) {
         if (U >= eMax) {
             return 0;
         }
-        double X = set.getValue("X");
+        double X = set.getDouble("X");
-        final double shift = set.getValue("shift");
+        final double shift = set.getDouble("shift");
 
         final LossCalculator loss = LossCalculator.instance();
 
@@ -107,13 +108,13 @@ public class VariableLossSpectrum extends AbstractParametricFunction {
         return noLossProb * transmission.value(U - shift, set) + integrator.integrate(integrand, U, eMax);
     }
 
-    public UnivariateFunction singleScatterFunction(NamedDoubleSet set) {
+    public UnivariateFunction singleScatterFunction(ValueProvider set) {
 
-        final double exPos = set.getValue("exPos");
+        final double exPos = set.getDouble("exPos");
-        final double ionPos = set.getValue("ionPos");
+        final double ionPos = set.getDouble("ionPos");
-        final double exW = set.getValue("exW");
+        final double exW = set.getDouble("exW");
-        final double ionW = set.getValue("ionW");
+        final double ionW = set.getDouble("ionW");
-        final double exIonRatio = set.getValue("exIonRatio");
+        final double exIonRatio = set.getDouble("exIonRatio");
 
         return singleScatterFunction(exPos, ionPos, exW, ionW, exIonRatio);
     }

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

@@ -0,0 +1,33 @@
+/*
+ * 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.utils;
+
+import groovy.lang.Binding;
+import groovy.lang.GroovyShell;
+import java.util.Map;
+import org.codehaus.groovy.control.CompilerConfiguration;
+import org.codehaus.groovy.control.customizers.ImportCustomizer;
+
+/**
+ *
+ * @author Alexander Nozik
+ */
+public class ExpressionUtils {
+
+    public static Double evaluate(String expression, Map<String, Double> binding) {
+        Binding b = new Binding(binding);
+        // Add imports for script.
+        ImportCustomizer importCustomizer = new ImportCustomizer();
+        // import static com.mrhaki.blog.Type.*
+        importCustomizer.addStaticStars("java.lang.Math");
+
+        CompilerConfiguration configuration = new CompilerConfiguration();
+        configuration.addCompilationCustomizers(importCustomizer); // Create shell and execute script.
+
+        GroovyShell shell = new GroovyShell(b,configuration);
+        return (Double) shell.evaluate(expression);
+    }
+}

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

@@ -26,6 +26,9 @@ import java.io.FileNotFoundException;
 import java.util.Locale;
 import static java.util.Locale.setDefault;
 import java.util.Scanner;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
 
 /**
  *

numass-main/src/main/java/inr/numass/workbench/NumassWorkbenchController.java

@@ -132,6 +132,13 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
     }
 
     private void buildContext(Meta config) {
+        if (this.context != null) {
+            try {
+                this.context.close();
+            } catch (Exception ex) {
+                context.getLogger().error("Failed to close context", ex);
+            }
+        }
         this.context = this.contextFactory.build(parentContext, config);
         context.setIO(new WorkbenchIOManager(new NumassIO(), this));
         processWindow = ProcessManagerFragment.attachToContext(context);

numass-main/src/main/java/inr/numass/workbench/Workbench.java

@@ -5,6 +5,7 @@
  */
 package inr.numass.workbench;
 
+import hep.dataforge.context.GlobalContext;
 import inr.numass.NumassContext;
 import java.io.IOException;
 import java.text.ParseException;
@@ -40,6 +41,14 @@ public class Workbench extends Application {
         });
     }
 
+    @Override
+    public void stop() throws Exception {
+        GlobalContext.instance().close();
+        super.stop();
+    }
+    
+    
+    
     /**
      * @param args the command line arguments
      */

numass-main/src/test/java/inr/numass/NumassContextTest.java

@@ -0,0 +1,32 @@
+/*
+ * 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;
+
+import inr.numass.storage.SetDirectionUtility;
+import org.junit.Test;
+
+/**
+ *
+ * @author Alexander Nozik
+ */
+public class NumassContextTest {
+    
+    public NumassContextTest() {
+    }
+
+    /**
+     * Test of close method, of class NumassContext.
+     */
+    @Test
+    public void testClose() throws Exception {
+        System.out.println("close");
+        NumassContext instance = new NumassContext();
+        instance.close();
+        assert SetDirectionUtility.cacheFile(instance).exists();
+        
+    }
+    
+}

numass-main/src/test/java/inr/numass/actions/PrepareDataActionTest.java

@@ -0,0 +1,32 @@
+/*
+ * 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 inr.numass.utils.ExpressionUtils;
+import java.util.HashMap;
+import java.util.Map;
+import org.junit.Assert;
+
+import org.junit.Test;
+
+/**
+ *
+ * @author Alexander Nozik
+ */
+public class PrepareDataActionTest {
+
+    public PrepareDataActionTest() {
+    }
+
+    @Test
+    public void testExpression() {
+        Map<String, Double> exprParams = new HashMap<>();
+        exprParams.put("U", 18000d);
+        double correctionFactor = ExpressionUtils.evaluate("1 + 13.265 * exp(- U / 2343.4)", exprParams);
+        Assert.assertEquals("Testing expression calculation", 1.006125, correctionFactor, 1e-5);
+    }
+
+}

numass-main/src/test/java/inr/numass/run/NumassSpectrumTest.java

@@ -25,6 +25,37 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.Locale;
 import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
+import static java.util.Locale.setDefault;
 
 /**
  *

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

@@ -129,6 +129,8 @@ 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;

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

@@ -316,12 +316,14 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
 
     public boolean isReversed() {
         //TODO replace by meta tag in later revisions
-        List<Envelope> points = getPoints();
+        return SetDirectionUtility.isReversed(getFullPath(), n -> {
-        if (getPoints().size() >= 2) {
+            List<Envelope> points = getPoints();
-            return readTime(points.get(0).meta()).isAfter(readTime(points.get(1).meta()));
+            if (getPoints().size() >= 2) {
-        } else {
+                return readTime(points.get(0).meta()).isAfter(readTime(points.get(1).meta()));
-            return false;
+            } else {
-        }
+                return false;
+            }
+        });
     }
 
     @Override

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

@@ -0,0 +1,73 @@
+/*
+ * 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.storage;
+
+import hep.dataforge.context.Context;
+import hep.dataforge.context.GlobalContext;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.function.Function;
+
+/**
+ * A temporary utility to store set directions to avoid multiple file reading
+ *
+ * @author Alexander Nozik
+ */
+public class SetDirectionUtility {
+
+    private static final String FILE_NAME = "numass_set_direction.map";
+
+    private static Map<String, Boolean> directionMap = new HashMap<>();
+
+    private static boolean isLoaded = false;
+
+    static synchronized boolean isReversed(String setName, Function<String, Boolean> provider) {
+        if (!isLoaded) {
+            load(GlobalContext.instance());
+        }
+        return directionMap.computeIfAbsent(setName, provider);
+    }
+
+    public static File cacheFile(Context context) {
+        return new File(context.io().getTmpDirectory(), FILE_NAME);
+    }
+
+    public static synchronized void load(Context context) {
+        context.getLogger().info("Loading set direction utility");
+        File file = cacheFile(context);
+        if (file.exists()) {
+            try (ObjectInputStream st = new ObjectInputStream(new FileInputStream(file))) {
+                directionMap = (Map<String, Boolean>) st.readObject();
+                context.getLogger().info("Set directions successfully loaded from file");
+            } catch (ClassNotFoundException | IOException ex) {
+                context.getLogger().error("Failed to load numass direction mapping", ex);
+            }
+        }
+
+        isLoaded = true;
+    }
+
+    public static synchronized void save(Context context) {
+        try {
+            File file = cacheFile(context);
+            if (!file.exists()) {
+                file.createNewFile();
+            }
+            try (ObjectOutputStream st = new ObjectOutputStream(new FileOutputStream(file))) {
+                st.writeObject(directionMap);
+                context.getLogger().info("Set directions successfully saved to file");
+            }
+        } catch (IOException ex) {
+            context.getLogger().error("Failed to save numass direction mapping", ex);
+        }
+    }
+}