working on grind multi threading and dsl

numass-main/private/cache/retriever/catalog.xml

@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="system">
-    <system systemId="http://javafx.com/javafx/8.0.65" uri="www.oracle.com/technetwork/java/javase/overview/index.html"/>
-</catalog>

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

@@ -87,18 +87,18 @@ res = fm.runDefaultTask(res, "E0", "N", "bkg", "mnu2");
 
 res.print(out);
 
-//spectrum.counter.print(out);
+//spectrum.counter.print(onComplete);
 //
 ////        fm.setPriorProb(new GaussianPrior("X", 0.47, 0.47*0.03));
 ////        fm.setPriorProb(new MultivariateGaussianPrior(allPars.getSubSet("X","trap")));
 //res = fm.runTask(res, "MINUIT", "run", "E0", "N", "bkg", "mnu2");
 ////
-//res.print(out);
+//res.print(onComplete);
 
 //sp.setCaching(true);
 //sp.setSuppressWarnings(true);
 //
 //BayesianManager bm = new BayesianManager();
-//bm.printMarginalLikelihood(out, "U2", res, ["E0", "N", "bkg", "U2", "X"], 10000);
+//bm.printMarginalLikelihood(onComplete, "U2", res, ["E0", "N", "bkg", "U2", "X"], 10000);
 
-//        PrintNamed.printLike2D(Out.out, "like", res, "N", "E0", 30, 60, 2);
+//        PrintNamed.printLike2D(Out.onComplete, "like", res, "N", "E0", 30, 60, 2);

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

@@ -72,8 +72,8 @@ allPars.setParValue("trap", 0);
 allPars.setParError("trap", 0.01d);
 allPars.setParDomain("trap", 0d, Double.POSITIVE_INFINITY);
 
-//        PrintNamed.printSpectrum(GlobalContext.out(), spectrum, allPars, 0.0, 18700.0, 600);
+//        PrintNamed.printSpectrum(GlobalContext.onComplete(), spectrum, allPars, 0.0, 18700.0, 600);
-//String fileName = "d:\\PlayGround\\merge\\scans.out";
+//String fileName = "d:\\PlayGround\\merge\\scans.onComplete";
 //        String configName = "d:\\PlayGround\\SCAN.CFG";
 //        ListTable config = OldDataReader.readConfig(configName);
 SpectrumGenerator generator = new SpectrumGenerator(model, allPars, 12316);

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

@@ -15,9 +15,10 @@
  */
 package inr.numass.scripts
 
-import static groovy.io.FileType.*
 import org.apache.commons.io.FilenameUtils
 
+import static groovy.io.FileType.FILES
+
 
 File dir = new File("D:\\loss-2014\\");
 File resultDir = new File(dir, ".dataforge\\showLoss\\");
@@ -33,7 +34,7 @@ resultFile.setText("name\tX\tX_err\texPos\texPos_err\tionPos\tionPos_err\texW\te
 dir.eachFileMatch FILES, {it ==~ /[dh]2_\d\d_\d(?:_bkg)?\.xml/}, {
     try{
         inr.numass.Main.main("-c", it.getAbsolutePath())
-        File outFile = new File(resultDir, FilenameUtils.getBaseName(it.getName())+"_loss.out")
+        File outFile = new File(resultDir, FilenameUtils.getBaseName(it.getName()) + "_loss.onComplete")
         resultFile.append(outFile.readLines().get(50));
         resultFile.append("\r\n");
     } catch(Exception ex){

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

@@ -13,22 +13,19 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.scripts;
+package inr.numass.scripts
 
-import hep.dataforge.meta.MetaBuilder;
+import hep.dataforge.context.GlobalContext
-import hep.dataforge.context.GlobalContext;
+import hep.dataforge.meta.MetaBuilder
-import hep.dataforge.stat.fit.ParamSet;
+import hep.dataforge.stat.fit.ParamSet
-import inr.numass.data.SpectrumInformation;
+import inr.numass.data.SpectrumInformation
-import inr.numass.models.ModularSpectrum;
+import inr.numass.models.BetaSpectrum
-import inr.numass.models.BetaSpectrum;
+import inr.numass.models.ModularSpectrum
-import inr.numass.models.NBkgSpectrum;
+import inr.numass.models.NBkgSpectrum
-import inr.numass.models.ResolutionFunction;
+import inr.numass.models.ResolutionFunction
-import java.util.HashMap;
+import org.apache.commons.math3.analysis.UnivariateFunction
-import java.util.Locale;
-import static java.util.Locale.setDefault;
-import java.util.Map;
-import org.apache.commons.math3.analysis.UnivariateFunction;
 
+import static java.util.Locale.setDefault
 
 setDefault(Locale.US);
 GlobalContext global = GlobalContext.instance();
@@ -86,7 +83,7 @@ SpectrumInformation sign = new SpectrumInformation(spectrum);
 //        PrintNamed.printNamedMatrix(Out.out, infoMatrix);
 //        NamedMatrix cov = sign.getExpetedCovariance(allPars, config,"U2","E0","N");
 //
-//        PrintWriter out = GlobalContext.out();
+//        PrintWriter onComplete = GlobalContext.onComplete();
 //
 //        printNamedMatrix(out, cov);
 //

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

@@ -15,7 +15,10 @@
  */
 package inr.numass.scripts
 
-import hep.dataforge.stat.fit.*
+import hep.dataforge.stat.fit.FitManager
+import hep.dataforge.stat.fit.FitState
+import hep.dataforge.stat.fit.MINUITPlugin
+import hep.dataforge.stat.fit.ParamSet
 import hep.dataforge.stat.models.XYModel
 import hep.dataforge.tables.ListTable
 import inr.numass.data.SpectrumDataAdapter
@@ -70,8 +73,8 @@ allPars.setParValue("trap", 1d);
 allPars.setParError("trap", 0.01d);
 allPars.setParDomain("trap", 0d, Double.POSITIVE_INFINITY);
 
-//        PrintNamed.printSpectrum(GlobalContext.out(), spectrum, allPars, 0.0, 18700.0, 600);
+//        PrintNamed.printSpectrum(GlobalContext.onComplete(), spectrum, allPars, 0.0, 18700.0, 600);
-//String fileName = "d:\\PlayGround\\merge\\scans.out";
+//String fileName = "d:\\PlayGround\\merge\\scans.onComplete";
 //        String configName = "d:\\PlayGround\\SCAN.CFG";
 //        ListTable config = OldDataReader.readConfig(configName);
 SpectrumGenerator generator = new SpectrumGenerator(model, allPars, 12316);

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

@@ -16,10 +16,10 @@
 package inr.numass.scripts
 
 import hep.dataforge.context.GlobalContext
+import hep.dataforge.io.FittingIOUtils
 import hep.dataforge.stat.fit.FitManager
 import hep.dataforge.stat.fit.ParamSet
 import hep.dataforge.stat.models.XYModel
-import hep.dataforge.io.FittingIOUtils
 import inr.numass.data.SpectrumDataAdapter
 import inr.numass.models.GunSpectrum
 import inr.numass.models.NBkgSpectrum
@@ -50,7 +50,7 @@ allPars.setParValue("sigma", 0.6);
 
 FittingIOUtils.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 18495, 18505, 100);
 
-//        //String fileName = "d:\\PlayGround\\merge\\scans.out";
+//        //String fileName = "d:\\PlayGround\\merge\\scans.onComplete";
 ////        String configName = "d:\\PlayGround\\SCAN.CFG";
 ////        ListTable config = OldDataReader.readConfig(configName);
 //        SpectrumGenerator generator = new SpectrumGenerator(model, allPars, 12316);
@@ -63,5 +63,5 @@ FittingIOUtils.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 184
 //
 //        FitState res = fm.runTask(state, "QOW", FitTask.TASK_RUN, "N", "bkg", "pos", "sigma");
 //
-//        res.print(out());
+//        res.print(onComplete());
 

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

@@ -77,5 +77,5 @@ FittingIOUtils.printSpectrum(GlobalContext.out(), spectrum, allPars, 14000, 1860
 //
 //        
 //
-//res.print(out());
+//res.print(onComplete());
 //

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

@@ -1,10 +0,0 @@
-package inr.numass.scripts
-
-import hep.dataforge.grind.GrindLauncher
-
-/**
- * Created by darksnake on 11-Aug-16.
- */
-
-
-new GrindLauncher().from { new File("D:\\Work\\Numass\\sterile2016\\workspace.groovy") }.runTask("numass.prepare", "fill_2")

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

@@ -69,10 +69,10 @@ allPars.setParDomain("trap", 0d, Double.POSITIVE_INFINITY);
 //        PlotManager pm = new PlotManager();
 //        String plotTitle = "Tritium spectrum";
 //        pm.plotFunction(FunctionUtils.getSpectrumFunction(spectrum, allPars), 14000, 18600, 500,plotTitle, null);
-//        PrintNamed.printSpectrum(Out.out, beta.trapping, allPars, 14000d, 18600d, 500);
+//        PrintNamed.printSpectrum(Out.onComplete, beta.trapping, allPars, 14000d, 18600d, 500);
 //        double e = 18570d;
 //        trans.alpha = 1e-4;
-//        trans.plotTransmission(System.out, allPars, e, e-1000d, e+100d, 200);
+//        trans.plotTransmission(System.onComplete, allPars, e, e-1000d, e+100d, 200);
 SpectrumGenerator generator = new SpectrumGenerator(model, allPars);
 
 //        ColumnedDataFile file = new ColumnedDataFile("d:\\PlayGround\\RUN36.cfg");
@@ -93,7 +93,7 @@ ListTable data = generator.generateData(config);
 FitState state = fm.buildState(data, model, allPars);
 
 //       fm.checkDerivs();
-//        res.print(Out.out);        
+//        res.print(Out.onComplete);
 //        fm.checkFitDerivatives();
 FitState res = fm.runDefaultTask(state, "U2", "N", "trap");
 
@@ -107,14 +107,14 @@ beta.setSuppressWarnings(true);
 BayesianManager bm = new BayesianManager();
 //        bm.setPriorProb(new OneSidedUniformPrior("trap", 0, true));
 //        bm.setPriorProb(new GaussianPrior("trap", 1d, 0.002));
-//        bm.printMarginalLikelihood(Out.out,"U2", res);
+//        bm.printMarginalLikelihood(Out.onComplete,"U2", res);
 
 FitState conf = bm.getConfidenceInterval("U2", res, ["U2", "N", "trap"]);
 //        plotTitle = String.format("Marginal likelihood for parameter \'%s\'", "U2");
 //        pm.plotFunction(bm.getMarginalLikelihood("U2", res), 0, 2e-3, 40,plotTitle, null);
 
 conf.print(out);
-//        PrintNamed.printLogProbRandom(Out.out, res, 5000,0.5d, "E0","N");
+//        PrintNamed.printLogProbRandom(Out.onComplete, res, 5000,0.5d, "E0","N");
 
 spectrum.counter.print(out);
 

numass-main/src/main/groovy/inr/numass/scripts/workspace/TestActions.groovy

@@ -0,0 +1,16 @@
+package inr.numass.scripts.workspace
+
+import hep.dataforge.actions.ActionUtils
+import hep.dataforge.context.Context
+import hep.dataforge.io.IOManager
+import inr.numass.NumassPlugin
+
+/**
+ * Created by darksnake on 12-Aug-16.
+ */
+
+
+Context context = new Context("numass");
+context.loadPlugin(new NumassPlugin());
+context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, "D:\\Work\\Numass\\sterile2016");
+ActionUtils.runConfig(context, "test.xml").computeAll()

numass-main/src/main/groovy/inr/numass/scripts/workspace/TestWorkspace.groovy

@@ -0,0 +1,13 @@
+package inr.numass.scripts.workspace
+
+import hep.dataforge.grind.GrindLauncher
+
+/**
+ * Created by darksnake on 11-Aug-16.
+ */
+
+
+new GrindLauncher().from {
+    new File("D:\\Work\\Numass\\sterile2016\\workspace.groovy")
+}.runTask("numass.prepare", "fill_2").computeAll()
+

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

@@ -17,29 +17,24 @@ package inr.numass;
 
 import hep.dataforge.actions.ActionUtils;
 import hep.dataforge.context.Context;
-import hep.dataforge.context.GlobalContext;
-import static hep.dataforge.context.GlobalContext.out;
 import hep.dataforge.data.FileDataFactory;
-import hep.dataforge.stat.fit.MINUITPlugin;
 import hep.dataforge.io.IOManager;
 import hep.dataforge.io.MetaFileReader;
 import hep.dataforge.meta.Meta;
-import static inr.numass.Numass.printDescription;
+import hep.dataforge.stat.fit.MINUITPlugin;
+import org.apache.commons.cli.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.swing.*;
+import javax.swing.filechooser.FileFilter;
+import javax.swing.filechooser.FileNameExtensionFilter;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.Locale;
-import javax.swing.JFileChooser;
+
-import javax.swing.JFrame;
+import static hep.dataforge.context.GlobalContext.out;
-import javax.swing.filechooser.FileFilter;
+import static inr.numass.Numass.printDescription;
-import javax.swing.filechooser.FileNameExtensionFilter;
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.DefaultParser;
-import org.apache.commons.cli.HelpFormatter;
-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;
 
 /**
@@ -152,7 +147,7 @@ public class Main {
         options.addOption("h", "home", true,
                 "Working directory (by default the working directory is the directory where config file is placed)");
         options.addOption("d", "data", true, "Data directory (absolute or relative to working directory)");
-        options.addOption("o", "out", true, "Output directory (absolute or relative to working directory)");
+        options.addOption("o", "onComplete", true, "Output directory (absolute or relative to working directory)");
         options.addOption("l", "list", false, "List of available actions");
         options.addOption("lc", "list-color", false, "List of available actions with ANSI coloring");
 

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

@@ -20,19 +20,16 @@ import hep.dataforge.data.binary.Binary;
 import hep.dataforge.io.BasicIOManager;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.names.Name;
-import inr.numass.storage.NumassDataReader;
 import inr.numass.data.NumassPawReader;
+import inr.numass.storage.NumassDataReader;
 import inr.numass.storage.RawNMFile;
-import java.io.File;
+import org.apache.commons.io.FilenameUtils;
-import java.io.FileNotFoundException;
+import org.apache.commons.io.output.TeeOutputStream;
-import java.io.FileOutputStream;
+
-import java.io.IOException;
+import java.io.*;
-import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.output.TeeOutputStream;
 
 /**
  *
@@ -42,25 +39,8 @@ public class NumassIO extends BasicIOManager {
 
     public static final String NUMASS_OUTPUT_CONTEXT_KEY = "numass.outputDir";
 
-    @Override
+    public static RawNMFile readAsDat(Binary source, Meta config) throws IOException {
-    public OutputStream out(Name stage, Name name) {
+        return new NumassDataReader(source, config).read();
-        List<String> tokens = new ArrayList<>();
-        if (getContext().hasValue("numass.path")) {
-            String path = getContext().getString("numass.path");
-            if (path.contains(".")) {
-                tokens.addAll(Arrays.asList(path.split(".")));
-            } else {
-                tokens.add(path);
-            }
-        }
-
-        if (stage != null) {
-            tokens.addAll(Arrays.asList(stage.asArray()));
-        }
-
-        String dirName = String.join(File.separator, tokens);
-        String fileName = name.removeNameSpace().toString() + ".out";
-        return buildOut(getWorkDirectory(), dirName, fileName);
     }
 
 //    private File getOutputDir() {
@@ -73,36 +53,6 @@ public class NumassIO extends BasicIOManager {
 //
 //    }
 
-    protected OutputStream buildOut(File parentDir, String dirName, String fileName) {
-        File outputFile;
-
-        if (!parentDir.exists()) {
-            throw new RuntimeException("Working directory does not exist");
-        }
-        if (dirName != null && !dirName.isEmpty()) {
-            parentDir = new File(parentDir, dirName);
-            if (!parentDir.exists()) {
-                parentDir.mkdirs();
-            }
-        }
-
-//        String output = source.meta().getString("output", this.meta().getString("output", fileName + ".out"));
-        outputFile = new File(parentDir, fileName);
-        try {
-            if (getContext().getBoolean("numass.consoleOutput", false)) {
-                return new TeeOutputStream(new FileOutputStream(outputFile), System.out);
-            } else {
-                return new FileOutputStream(outputFile);
-            }
-        } catch (FileNotFoundException ex) {
-            throw new RuntimeException(ex);
-        }
-    }
-
-    public static RawNMFile readAsDat(Binary source, Meta config) throws IOException {
-        return new NumassDataReader(source, config).read();
-    }
-
     public static RawNMFile readAsPaw(Binary source, Meta config) throws IOException {
         return new NumassPawReader().readPaw(source, config.getString(FileDataFactory.FILE_NAME_KEY));
     }
@@ -126,4 +76,51 @@ public class NumassIO extends BasicIOManager {
             throw new RuntimeException(ex);
         }
     }
+
+    @Override
+    public OutputStream out(Name stage, Name name) {
+        List<String> tokens = new ArrayList<>();
+        if (getContext().hasValue("numass.path")) {
+            String path = getContext().getString("numass.path");
+            if (path.contains(".")) {
+                tokens.addAll(Arrays.asList(path.split(".")));
+            } else {
+                tokens.add(path);
+            }
+        }
+
+        if (stage != null) {
+            tokens.addAll(Arrays.asList(stage.asArray()));
+        }
+
+        String dirName = String.join(File.separator, tokens);
+        String fileName = name.removeNameSpace().toString() + ".out";
+        return buildOut(getWorkDirectory(), dirName, fileName);
+    }
+
+    protected OutputStream buildOut(File parentDir, String dirName, String fileName) {
+        File outputFile;
+
+        if (!parentDir.exists()) {
+            throw new RuntimeException("Working directory does not exist");
+        }
+        if (dirName != null && !dirName.isEmpty()) {
+            parentDir = new File(parentDir, dirName);
+            if (!parentDir.exists()) {
+                parentDir.mkdirs();
+            }
+        }
+
+//        String output = source.meta().getString("output", this.meta().getString("output", fileName + ".onComplete"));
+        outputFile = new File(parentDir, fileName);
+        try {
+            if (getContext().getBoolean("numass.consoleOutput", false)) {
+                return new TeeOutputStream(new FileOutputStream(outputFile), System.out);
+            } else {
+                return new FileOutputStream(outputFile);
+            }
+        } catch (FileNotFoundException ex) {
+            throw new RuntimeException(ex);
+        }
+    }
 }

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

@@ -24,21 +24,12 @@ import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.io.reports.Reportable;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
-import hep.dataforge.tables.DataPoint;
+import hep.dataforge.tables.*;
-import hep.dataforge.tables.ListTable;
+
-import hep.dataforge.tables.MapPoint;
-import hep.dataforge.tables.PointSource;
-import hep.dataforge.tables.Table;
-import hep.dataforge.tables.TableFormat;
 import java.io.OutputStream;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
 
 /**
- *
  * @author Darksnake
  */
 @TypedActionDef(name = "merge", inputType = Table.class, outputType = Table.class, info = "Merge different numass data files into one.")
@@ -64,7 +55,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
     @Override
     protected Table execute(Reportable log, String nodeName, Map<String, Table> data, Meta meta) {
         Table res = mergeDataSets(nodeName, data.values());
-        return new ListTable(res.getFormat(),res.sort("Uset", true));
+        return new ListTable(res.getFormat(), res.sort("Uset", true));
     }
 
     @Override
@@ -76,7 +67,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
     @Override
     protected MetaBuilder outputMeta(DataNode<Table> input) {
 
-        String numassPath = input.dataStream().<String>map(item -> item.getValue().meta().getString("numass.path", null))
+        String numassPath = input.dataStream().<String>map(data -> data.meta().getString("numass.path", null))
                 .reduce("", (String path, String newPath) -> {
                     if (path == null) {
                         return null;
@@ -169,7 +160,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
             res.add(curPoint);
         });
 
-        return new ListTable(TableFormat.forNames(parnames),res);
+        return new ListTable(TableFormat.forNames(parnames), res);
 
     }
 

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

@@ -28,6 +28,10 @@ import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.MapPoint;
 import hep.dataforge.tables.Table;
 import hep.dataforge.values.Value;
+import javafx.util.Pair;
+import org.apache.commons.math3.analysis.interpolation.SplineInterpolator;
+import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
+
 import java.io.OutputStream;
 import java.time.Instant;
 import java.util.ArrayList;
@@ -35,9 +39,6 @@ import java.util.List;
 import java.util.Map.Entry;
 import java.util.TreeMap;
 import java.util.concurrent.CopyOnWriteArrayList;
-import javafx.util.Pair;
-import org.apache.commons.math3.analysis.interpolation.SplineInterpolator;
-import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
 
 /**
  *
@@ -45,7 +46,7 @@ import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
  */
 @TypedActionDef(name = "monitor", inputType = Table.class, outputType = Table.class)
 @ValueDef(name = "monitorPoint", type = "NUMBER", required = true, info = "The Uset for monitor point")
-@ValueDef(name = "monitorFile", info = "The outputfile for monitor points", def = "monitor.out")
+@ValueDef(name = "monitorFile", info = "The outputfile for monitor points", def = "monitor.onComplete")
 @ValueDef(name = "calculateRelative", info = "Calculate count rate relative to average monitor point", def = "false")
 public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
 

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

@@ -24,23 +24,21 @@ import hep.dataforge.io.XMLMetaWriter;
 import hep.dataforge.io.reports.Reportable;
 import hep.dataforge.meta.Laminate;
 import hep.dataforge.meta.Meta;
-import hep.dataforge.tables.DataPoint;
+import hep.dataforge.tables.*;
-import hep.dataforge.tables.ListTable;
-import hep.dataforge.tables.MapPoint;
-import hep.dataforge.tables.Table;
-import hep.dataforge.tables.TableFormat;
 import inr.numass.storage.NMPoint;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.RawNMPoint;
 import inr.numass.utils.TritiumUtils;
-import static inr.numass.utils.TritiumUtils.evaluateExpression;
 import inr.numass.utils.UnderflowCorrection;
+
 import java.io.OutputStream;
 import java.time.Instant;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.function.Function;
 
+import static inr.numass.utils.TritiumUtils.evaluateExpression;
+
 /**
  *
  * @author Darksnake
@@ -143,7 +141,6 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
      * @param log
      * @param point
      * @param meta
-     * @param countRate precalculated count rate in main window
      * @return
      */
     private double correction(Reportable log, NMPoint point, Laminate meta) {

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

@@ -16,11 +16,6 @@
 package inr.numass.actions;
 
 import hep.dataforge.actions.OneToOneAction;
-import hep.dataforge.stat.fit.FitState;
-import hep.dataforge.stat.fit.FitTaskResult;
-import hep.dataforge.stat.fit.Param;
-import hep.dataforge.stat.fit.ParamSet;
-import hep.dataforge.stat.models.Histogram;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.io.PrintFunction;
@@ -34,6 +29,11 @@ import hep.dataforge.plots.PlotsPlugin;
 import hep.dataforge.plots.XYPlotFrame;
 import hep.dataforge.plots.data.PlottableData;
 import hep.dataforge.plots.data.PlottableXYFunction;
+import hep.dataforge.stat.fit.FitState;
+import hep.dataforge.stat.fit.FitTaskResult;
+import hep.dataforge.stat.fit.Param;
+import hep.dataforge.stat.fit.ParamSet;
+import hep.dataforge.stat.models.Histogram;
 import hep.dataforge.stat.simulation.GaussianParameterGenerator;
 import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.MapPoint;
@@ -41,13 +41,8 @@ import hep.dataforge.tables.Table;
 import hep.dataforge.tables.XYAdapter;
 import hep.dataforge.values.NamedValueSet;
 import inr.numass.NumassIntegrator;
-import inr.numass.Numass;
 import inr.numass.models.ExperimentalVariableLossSpectrum;
 import inr.numass.models.LossCalculator;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.nio.charset.Charset;
-import java.util.Arrays;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
 import org.apache.commons.math3.analysis.interpolation.UnivariateInterpolator;
@@ -55,6 +50,11 @@ import org.apache.commons.math3.stat.StatUtils;
 import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
 import org.slf4j.LoggerFactory;
 
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.nio.charset.Charset;
+import java.util.Arrays;
+
 /**
  *
  * @author darksnake
@@ -65,6 +65,55 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
 
     private static final String[] names = {"X", "exPos", "ionPos", "exW", "ionW", "exIonRatio"};
 
+    public static double calcultateIonRatio(NamedValueSet set, double threshold) {
+        UnivariateIntegrator integrator = NumassIntegrator.getHighDensityIntegrator();
+        UnivariateFunction integrand = LossCalculator.getSingleScatterFunction(set);
+        return 1d - integrator.integrate(integrand, 5d, threshold);
+    }
+
+    public static Table generateSpread(PrintWriter writer, String name, NamedValueSet parameters, NamedMatrix covariance) {
+        int numCalls = 1000;
+        int gridPoints = 200;
+        double a = 8;
+        double b = 32;
+
+        double[] grid = GridCalculator.getUniformUnivariateGrid(a, b, gridPoints);
+
+        double[] upper = new double[gridPoints];
+        double[] lower = new double[gridPoints];
+        double[] dispersion = new double[gridPoints];
+
+        double[] central = new double[gridPoints];
+
+        UnivariateFunction func = LossCalculator.getSingleScatterFunction(parameters);
+        for (int j = 0; j < gridPoints; j++) {
+            central[j] = func.value(grid[j]);
+        }
+
+        Arrays.fill(upper, Double.NEGATIVE_INFINITY);
+        Arrays.fill(lower, Double.POSITIVE_INFINITY);
+        Arrays.fill(dispersion, 0);
+
+        GaussianParameterGenerator generator = new GaussianParameterGenerator(parameters, covariance);
+
+        for (int i = 0; i < numCalls; i++) {
+            func = LossCalculator.getSingleScatterFunction(generator.generate());
+            for (int j = 0; j < gridPoints; j++) {
+                double val = func.value(grid[j]);
+                upper[j] = Math.max(upper[j], val);
+                lower[j] = Math.min(lower[j], val);
+                dispersion[j] += (val - central[j]) * (val - central[j]) / numCalls;
+            }
+        }
+        String[] pointNames = {"e", "central", "lower", "upper", "dispersion"};
+        ListTable.Builder res = new ListTable.Builder(pointNames);
+        for (int i = 0; i < gridPoints; i++) {
+            res.row(new MapPoint(pointNames, grid[i], central[i], lower[i], upper[i], dispersion[i]));
+
+        }
+        return res.build();
+    }
+
     @Override
     protected FitState execute(Reportable log, String name, Laminate meta, FitState input) {
         ParamSet pars = input.getParameters();
@@ -115,7 +164,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
 //                writer.println(param.toString());
 //            }
 //            writer.println();
-//            out.printf("Chi squared over degrees of freedom: %g/%d = %g", input.getChi2(), input.ndf(), chi2 / this.ndf());
+//            onComplete.printf("Chi squared over degrees of freedom: %g/%d = %g", input.getChi2(), input.ndf(), chi2 / this.ndf());
 
             writer.println();
 
@@ -178,12 +227,6 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
         return input;
     }
 
-    public static double calcultateIonRatio(NamedValueSet set, double threshold) {
-        UnivariateIntegrator integrator = NumassIntegrator.getHighDensityIntegrator();
-        UnivariateFunction integrand = LossCalculator.getSingleScatterFunction(set);
-        return 1d - integrator.integrate(integrand, 5d, threshold);
-    }
-
     private double calculateIntegralExIonRatio(Table data, double X, double integralThreshold) {
         double scatterProb = 1 - Math.exp(-X);
 
@@ -233,47 +276,4 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
         return new DescriptiveStatistics(res).getStandardDeviation();
     }
 
-    public static Table generateSpread(PrintWriter writer, String name, NamedValueSet parameters, NamedMatrix covariance) {
-        int numCalls = 1000;
-        int gridPoints = 200;
-        double a = 8;
-        double b = 32;
-
-        double[] grid = GridCalculator.getUniformUnivariateGrid(a, b, gridPoints);
-
-        double[] upper = new double[gridPoints];
-        double[] lower = new double[gridPoints];
-        double[] dispersion = new double[gridPoints];
-
-        double[] central = new double[gridPoints];
-
-        UnivariateFunction func = LossCalculator.getSingleScatterFunction(parameters);
-        for (int j = 0; j < gridPoints; j++) {
-            central[j] = func.value(grid[j]);
-        }
-
-        Arrays.fill(upper, Double.NEGATIVE_INFINITY);
-        Arrays.fill(lower, Double.POSITIVE_INFINITY);
-        Arrays.fill(dispersion, 0);
-
-        GaussianParameterGenerator generator = new GaussianParameterGenerator(parameters, covariance);
-
-        for (int i = 0; i < numCalls; i++) {
-            func = LossCalculator.getSingleScatterFunction(generator.generate());
-            for (int j = 0; j < gridPoints; j++) {
-                double val = func.value(grid[j]);
-                upper[j] = Math.max(upper[j], val);
-                lower[j] = Math.min(lower[j], val);
-                dispersion[j] += (val - central[j]) * (val - central[j]) / numCalls;
-            }
-        }
-        String[] pointNames = {"e", "central", "lower", "upper", "dispersion"};
-        ListTable.Builder res = new ListTable.Builder(pointNames);
-        for (int i = 0; i < gridPoints; i++) {
-            res.row(new MapPoint(pointNames, grid[i], central[i], lower[i], upper[i], dispersion[i]));
-
-        }
-        return res.build();
-    }
-
 }

numass-main/src/main/java/inr/numass/tasks/GrindCaller.java

@@ -0,0 +1,16 @@
+package inr.numass.tasks;
+
+import hep.dataforge.grind.JavaGrindLauncher;
+
+import java.io.File;
+
+/**
+ * Created by darksnake on 12-Aug-16.
+ */
+public class GrindCaller {
+
+    public static void main(String[] args) throws Exception {
+        JavaGrindLauncher.buildWorkspace(new File("D:\\Work\\Numass\\sterile2016\\workspace.groovy")).runTask("numass.prepare", "fill_2").computeAll();
+    }
+
+}

numass-main/src/main/java/inr/numass/tasks/NumassFitScanSummaryTask.java

@@ -8,7 +8,6 @@ package inr.numass.tasks;
 import hep.dataforge.actions.ManyToOneAction;
 import hep.dataforge.computation.WorkManager;
 import hep.dataforge.context.Context;
-import hep.dataforge.data.Data;
 import hep.dataforge.data.DataNode;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.io.reports.Reportable;
@@ -20,6 +19,7 @@ import hep.dataforge.tables.Table;
 import hep.dataforge.workspace.GenericTask;
 import hep.dataforge.workspace.TaskModel;
 import hep.dataforge.workspace.TaskState;
+
 import java.util.Map;
 
 /**
@@ -29,8 +29,8 @@ import java.util.Map;
 public class NumassFitScanSummaryTask extends GenericTask {
 
     @Override
-    protected TaskState transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) {
+    protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) {
-        return state.finish(new FitSummaryAction().withContext(context).run((DataNode<FitState>) state.getData(), config));
+        state.finish(new FitSummaryAction().withContext(context).run((DataNode<FitState>) state.getData(), config));
     }
 
     @Override

numass-main/src/main/java/inr/numass/tasks/NumassFitScanTask.java

@@ -23,13 +23,12 @@ import hep.dataforge.workspace.TaskModel;
 import hep.dataforge.workspace.TaskState;
 
 /**
- *
  * @author Alexander Nozik
  */
 public class NumassFitScanTask extends GenericTask {
 
     @Override
-    protected TaskState transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) {
+    protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) {
         String scanParameter = config.getString("scanPar", "msterile2");
         Value scanValues = config.getValue("scanValues", Value.of(new String[]{"0.5, 1, 1.5, 2, 2.5, 3"}));
         Action action = new FitAction().withContext(context).withParentProcess(callback.workName());
@@ -42,25 +41,24 @@ public class NumassFitScanTask extends GenericTask {
         }
 
         //do fit
-        sourceNode.forEachDataWithType(Table.class, (name, data) -> {
+        sourceNode.forEachDataWithType(Table.class, data -> {
             DataNode res = scanValues.listValue().stream().parallel().map(val -> {
                 MetaBuilder overrideMeta = new MetaBuilder("override");
-                overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", name, scanParameter, val.stringValue()));
+                overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", data.getName(), scanParameter, val.stringValue()));
-                MetaBuilder paramMeta = MetaUtils.findNodeByValue(config, "params.param", name, scanParameter).getBuilder()
+                MetaBuilder paramMeta = MetaUtils.findNodeByValue(config, "params.param", data.getName(), scanParameter).getBuilder()
                         .setValue("value", val);
                 overrideMeta.setNode("params.param", paramMeta);
-                return action.run(DataNode.of(name, data, overrideMeta), config);
+                return action.run(DataNode.of(data.getName(), data, overrideMeta), config);
             }).collect(
                     () -> DataSet.builder(FitState.class),
                     (DataSet.Builder builder, DataNode node) -> builder.putData(node.getName(), node.getData()),
                     (DataSet.Builder builder1, DataSet.Builder builder2) -> builder1.putAll(builder2.getDataMap())
             ).build();
-            resultBuilder.putData(name, res.getData());
+            resultBuilder.putData(data.getName(), res.getData());
         });
 
 
         state.finish(resultBuilder.build());
-        return state;
     }
 
     @Override

numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java

@@ -6,8 +6,8 @@
 package inr.numass.tasks;
 
 import hep.dataforge.actions.Action;
-import hep.dataforge.context.Context;
 import hep.dataforge.computation.WorkManager;
+import hep.dataforge.context.Context;
 import hep.dataforge.data.DataNode;
 import hep.dataforge.data.DataTree;
 import hep.dataforge.meta.Meta;
@@ -47,7 +47,7 @@ public class NumassPrepareTask extends GenericTask {
      */
     @Override
     @SuppressWarnings("unchecked")
-    protected TaskState transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) {
+    protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) {
         //acquiring initial data. Data node could not be empty
         Meta dataMeta = Template.compileTemplate(config.getNode("data"), config);
         DataNode<NumassData> data = runAction(new ReadNumassStorageAction(), callback, context, DataNode.empty(), dataMeta);
@@ -66,13 +66,13 @@ public class NumassPrepareTask extends GenericTask {
         //merging if needed
         if (config.hasNode("merge")) {
             DataTree.Builder resultBuilder = DataTree.builder(Table.class);
-            tables.dataStream().forEach(pair -> resultBuilder.putData(pair.getKey(), pair.getValue()));
+//            tables.dataStream().forEach(d -> resultBuilder.putData(d));
             DataNode<Table> finalTables = tables;
             config.getNodes("merge").forEach(mergeNode -> {
                 Meta mergeMeta = Template.compileTemplate(mergeNode, config);
                 DataNode<Table> mergeData = runAction(new MergeDataAction(), callback, context, finalTables, mergeMeta);
-                mergeData.dataStream().forEach(pair -> {
+                mergeData.dataStream().forEach(d -> {
-                    resultBuilder.putData("merge." + pair.getKey(), pair.getValue());
+                    resultBuilder.putData("merge." + d.getName(), d.anonymize());
                 });
             });
             tables = resultBuilder.build();
@@ -84,7 +84,6 @@ public class NumassPrepareTask extends GenericTask {
         }
 
         state.finish(tables);
-        return state;
     }
 
     private <T, R> DataNode<R> runAction(Action<T, R> action, WorkManager.Callback callback, Context context, DataNode<T> data, Meta meta) {

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

@@ -6,11 +6,12 @@
 package inr.numass.workbench;
 
 import hep.dataforge.fx.FXDataOutputPane;
-import java.io.OutputStream;
 import javafx.event.Event;
 
+import java.io.OutputStream;
+
 /**
- * A text output tab. Basically it is attached to IOManager::out
+ * A text output tab. Basically it is attached to IOManager::onComplete
  *
  * @author Alexander Nozik <altavir@gmail.com>
  */
@@ -27,7 +28,7 @@ public class TextOutputTab extends OutputTab {
      */
     public TextOutputTab(String name) {
         super(name);
-//        out = new DataOutputPane();
+//        onComplete = new DataOutputPane();
         out = new FXDataOutputPane();
         setContent(out.getRoot());
         setOnClosed((Event event) -> close());

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

@@ -8,10 +8,11 @@ package inr.numass.workbench;
 import hep.dataforge.context.Context;
 import hep.dataforge.io.IOManager;
 import hep.dataforge.names.Name;
+import org.apache.commons.io.output.TeeOutputStream;
+
 import java.io.File;
 import java.io.InputStream;
 import java.io.OutputStream;
-import org.apache.commons.io.output.TeeOutputStream;
 
 /**
  * An IOManager wrapper that redirects output to appropriate FX components
@@ -32,6 +33,11 @@ public class WorkbenchIOManager implements IOManager {
         return manager.getContext();
     }
 
+    @Override
+    public void setContext(Context context) {
+        manager.setContext(context);
+    }
+
     @Override
     public File getFile(String path) {
         return manager.getFile(path);
@@ -63,12 +69,7 @@ public class WorkbenchIOManager implements IOManager {
     @Override
     public OutputStream out() {
         return manager.out();
-//        return new ConsoleStream(holder.getLogArea(), new PrintStream(manager.out()));
+//        return new ConsoleStream(holder.getLogArea(), new PrintStream(manager.onComplete()));
-    }
-
-    @Override
-    public void setContext(Context context) {
-        manager.setContext(context);
     }
     
 }

numass-main/src/test/java/inr/numass/models/TransmissionInterpolatorTest.java

@@ -31,11 +31,11 @@ public class TransmissionInterpolatorTest {
         JFreeChartFrame frame = FXPlotUtils.displayJFreeChart("TransmissionInterpolatorTest", null);
 //JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null);
         TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(GlobalContext.instance(),
-                "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.out", "Uset", "CR", 15, 0.8, 19002d);
+                "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.onComplete", "Uset", "CR", 15, 0.8, 19002d);
         frame.add(PlottableData.plot("data", interpolator.getX(), interpolator.getY()));
         frame.add(PlottableXYFunction.plotFunction("interpolated", x->interpolator.value(x), interpolator.getXmin(), interpolator.getXmax(), 2000));
 
-//        PrintFunction.printFuntionSimple(new PrintWriter(System.out), interpolator, interpolator.getXmin(), interpolator.getXmax(), 500);
+//        PrintFunction.printFuntionSimple(new PrintWriter(System.onComplete), interpolator, interpolator.getXmin(), interpolator.getXmax(), 500);
     }
 
 }

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

@@ -20,37 +20,22 @@ package inr.numass.viewer;
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-import hep.dataforge.context.Context;
+
 import hep.dataforge.computation.WorkManager;
+import hep.dataforge.context.Context;
 import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
 import hep.dataforge.plots.PlotFrame;
 import hep.dataforge.plots.XYPlotFrame;
-import hep.dataforge.plots.data.ChangeablePlottableData;
+import hep.dataforge.plots.data.*;
-import hep.dataforge.plots.data.DynamicPlottable;
-import hep.dataforge.plots.data.DynamicPlottableSet;
-import hep.dataforge.plots.data.PlotDataUtils;
-import hep.dataforge.plots.data.PlottableData;
 import hep.dataforge.plots.fx.PlotContainer;
 import hep.dataforge.plots.jfreechart.JFreeChartFrame;
 import hep.dataforge.storage.commons.JSONMetaWriter;
-import hep.dataforge.tables.DataPoint;
+import hep.dataforge.tables.*;
-import hep.dataforge.tables.ListTable;
-import hep.dataforge.tables.MapPoint;
-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;
-import java.util.List;
-import java.util.ResourceBundle;
-import java.util.function.Predicate;
-import java.util.function.Supplier;
-import java.util.stream.Collectors;
 import javafx.application.Platform;
 import javafx.beans.value.ChangeListener;
 import javafx.beans.value.ObservableValue;
@@ -61,14 +46,7 @@ import javafx.fxml.FXMLLoader;
 import javafx.fxml.Initializable;
 import javafx.geometry.Insets;
 import javafx.geometry.Orientation;
-import javafx.scene.control.Button;
+import javafx.scene.control.*;
-import javafx.scene.control.CheckBox;
-import javafx.scene.control.ChoiceBox;
-import javafx.scene.control.Label;
-import javafx.scene.control.Separator;
-import javafx.scene.control.Tab;
-import javafx.scene.control.TextArea;
-import javafx.scene.control.TextField;
 import javafx.scene.layout.AnchorPane;
 import javafx.scene.layout.VBox;
 import javafx.stage.FileChooser;
@@ -80,6 +58,15 @@ import org.controlsfx.validation.Validator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.List;
+import java.util.ResourceBundle;
+import java.util.function.Predicate;
+import java.util.function.Supplier;
+import java.util.stream.Collectors;
+
 /**
  * FXML Controller class
  *
@@ -387,7 +374,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
         if (points != null && !points.isEmpty()) {
             FileChooser fileChooser = new FileChooser();
             fileChooser.setTitle("Choose text export destination");
-            fileChooser.setInitialFileName(data.getName() + "_spectrum.out");
+            fileChooser.setInitialFileName(data.getName() + "_spectrum.onComplete");
             File destination = fileChooser.showSaveDialog(spectrumPlotPane.getScene().getWindow());
             if (destination != null) {
                 String[] names = new String[]{"Uset", "Uread", "Length", "Total", "Window", "CR", "CRerr", "Timestamp"};
@@ -428,7 +415,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
     private void onExportButtonClick(ActionEvent event) {
         FileChooser fileChooser = new FileChooser();
         fileChooser.setTitle("Choose text export destination");
-        fileChooser.setInitialFileName(data.getName() + "_detector.out");
+        fileChooser.setInitialFileName(data.getName() + "_detector.onComplete");
         File destination = fileChooser.showSaveDialog(detectorPlotPane.getScene().getWindow());
         if (destination != null) {
             Table detectorData = PlotDataUtils.collectXYDataFromPlot((XYPlotFrame) detectorPlot.getPlot(), true);