Finished refactoring

numass-control/cryotemp/src/main/java/inr/numass/cryotemp/PKT8Device.java

@@ -15,7 +15,7 @@
  */
 package inr.numass.cryotemp;
 
-import hep.dataforge.content.Named;
+import hep.dataforge.names.Named;
 import hep.dataforge.context.Context;
 import hep.dataforge.control.collectors.RegularPointCollector;
 import hep.dataforge.control.measurements.DataDevice;

numass-control/vac/src/main/java/inr/numass/readvac/fx/VacuumeterView.java

@@ -5,7 +5,7 @@
  */
 package inr.numass.readvac.fx;
 
-import hep.dataforge.content.Named;
+import hep.dataforge.names.Named;
 import hep.dataforge.control.connections.DeviceViewController;
 import hep.dataforge.control.devices.Device;
 import hep.dataforge.control.measurements.Measurement;

numass-main/src/main/java/hep/dataforge/plotfit/PlotFitResultAction.java

@@ -47,7 +47,7 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
     }
 
     @Override
-    protected FitState execute(Logable log, Meta metaData, FitState input) {
+    protected FitState execute(Logable log, String name, Meta metaData, FitState input) {
 
         PointSet data = input.getDataSet();
         if (!(input.getModel() instanceof XYModel)) {
@@ -68,12 +68,11 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
         UnivariateFunction function = (double x) -> model.getSpectrum().value(x, input.getParameters());
 
         XYPlotFrame frame = (XYPlotFrame) PlotsPlugin
-                .buildFrom(getContext()).buildPlotFrame(getName(), input.getName(),
+                .buildFrom(getContext()).buildPlotFrame(getName(), name,
                 metaData.getNode("plot", null));
         //JFreeChartFrame.drawFrame(reader.getString("plotTitle", "Fit result plot for "+input.getName()), null);
 
 //        double[] x = new double[data.size()];
-
 //        double[] y = new double[data.size()];
 //        double xMin = Double.POSITIVE_INFINITY;
 //
@@ -94,7 +93,6 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
 //                xMax = x[i];
 //            }
 //        }
-
         frame.add(new PlottableFunction("fit", function, data, adapter));//FIXME replace by helper
 
         frame.add(PlottableData.plot("data", adapter, data));

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

@@ -15,19 +15,20 @@
  */
 package inr.numass;
 
-import hep.dataforge.actions.ActionResult;
+import hep.dataforge.actions.RunManager;
-import static hep.dataforge.actions.RunManager.executeXML;
 import hep.dataforge.context.Context;
 import static hep.dataforge.context.GlobalContext.out;
-import hep.dataforge.data.DataManager;
+import hep.dataforge.data.DataNode;
+import hep.dataforge.data.FileDataFactory;
 import hep.dataforge.datafitter.MINUITPlugin;
 import hep.dataforge.io.IOManager;
+import hep.dataforge.io.MetaFileReader;
+import hep.dataforge.meta.Meta;
 import static inr.numass.NumassContext.printDescription;
 import inr.numass.workbench.Workbench;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.Locale;
-import static java.util.Locale.setDefault;
 import javax.swing.JFileChooser;
 import javax.swing.JFrame;
 import javax.swing.filechooser.FileFilter;
@@ -40,6 +41,7 @@ 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;
 
 /**
  *
@@ -55,7 +57,7 @@ public class Main {
     }
 
     @SuppressWarnings("deprecation")
-    public static ActionResult run(NumassContext context, String[] args) throws Exception {
+    public static DataNode run(NumassContext context, String[] args) throws Exception {
         Logger logger = LoggerFactory.getLogger("numass-main");
 
         Options options = prepareOptions();
@@ -67,15 +69,15 @@ public class Main {
         } catch (ParseException exp) {
             // oops, something went wrong
             logger.error("Command line error.  Reason: " + exp.getMessage());
-            return ActionResult.empty();
+            return DataNode.empty();
         }
 
         if (line.hasOption("lc")) {
             printDescription(context, true);
-            return ActionResult.empty();
+            return DataNode.empty();
         } else if (line.hasOption("l")) {
             printDescription(context, false);
-            return ActionResult.empty();
+            return DataNode.empty();
         }
 
         String cfgPath;
@@ -90,20 +92,22 @@ public class Main {
             cfgPath = line.getOptionValue("c");
             if (cfgPath == null) {
                 logger.info("Configutation path not provided.");
-                return ActionResult.empty();
+                return DataNode.empty();
             }
 
-            File config = context.io().getFile(cfgPath);
+            File configFile = context.io().getFile(cfgPath);
 
-            if (!config.exists()) {
+            if (!configFile.exists()) {
                 throw new FileNotFoundException("Configuration file not found");
             }
             
-            context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, config.getParentFile().toString());
+            Meta config = MetaFileReader.read(configFile).build();
+
+            context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, configFile.getParentFile().toString());
 
             applyCLItoContext(line, context);
 
-            return executeXML(context, config);
+            return RunManager.executeAction(context, config);
         } else {
             Workbench.main(args);
             return null;
@@ -125,7 +129,7 @@ public class Main {
                 dataDir = new File(workDir, dataPath);
             }
             if (dataDir.exists() && dataDir.isDirectory()) {
-                context.putValue(DataManager.DATA_DIR, dataDir.getAbsolutePath());
+                context.putValue(FileDataFactory.DATA_DIR_KEY, dataDir.getAbsolutePath());
             } else {
                 throw new FileNotFoundException("Data directory not found");
             }

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

@@ -15,6 +15,7 @@
  */
 package inr.numass;
 
+import hep.dataforge.data.FileData;
 import hep.dataforge.io.BasicIOManager;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.names.Name;
@@ -29,6 +30,7 @@ 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;
 
 /**
@@ -96,7 +98,7 @@ public class NumassIO extends BasicIOManager {
         }
     }
 
-    public static RawNMFile readAsDat(BinaryData source, Meta config) {
+    public static RawNMFile readAsDat(FileData source, Meta config) {
         try {
             return new NumassDataReader(source, config).read();
         } catch (IOException ex) {
@@ -104,17 +106,14 @@ public class NumassIO extends BasicIOManager {
         }
     }
 
-    public static RawNMFile readAsPaw(BinaryData source) {
+    public static RawNMFile readAsPaw(FileData source) {
-        try {
+        return new NumassPawReader().readPaw(source.get(), source.fileName());
-            return new NumassPawReader().readPaw(source.getInputStream(), source.getName());
-        } catch (IOException ex) {
-            throw new RuntimeException(ex);
-        }
     }
 
     public static RawNMFile getNumassData(FileData source, Meta config) {
         RawNMFile dataFile;
-        switch (source.getExtension()) {
+        String extension = FilenameUtils.getExtension(source.fileName());
+        switch (extension) {
             case "paw":
                 dataFile = readAsPaw(source);
                 break;

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

@@ -30,13 +30,13 @@ public class AdjustErrorsAction extends OneToOneAction<PointSet, PointSet> {
     }
 
     @Override
-    protected PointSet execute(Logable log, Meta meta, PointSet input) {
+    protected PointSet execute(Logable log, String name,Meta meta, PointSet input) {
         List<DataPoint> points = new ArrayList<>();
         for (DataPoint dp : input) {
             points.add(evalPoint(meta, dp));
         }
 
-        return new ListPointSet(input.getName(), input.meta(), points, input.getDataFormat());
+        return new ListPointSet(points, input.getDataFormat());
     }
 
     private DataPoint evalPoint(Meta meta, DataPoint dp) {

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

@@ -40,13 +40,12 @@ import java.io.PrintWriter;
 @ValueDef(name = "maxcr", type = "NUMBER", def = "100", info = "Maximum count rate for debunching")
 public class DebunchAction extends OneToOneAction<RawNMFile, RawNMFile> {
 
-
     public DebunchAction(Context context, Meta an) {
         super(context, an);
     }
 
     @Override
-    protected RawNMFile execute(Logable log, Meta reader, RawNMFile source) throws ContentException {
+    protected RawNMFile execute(Logable log, String name, Meta reader, RawNMFile source) throws ContentException {
         log.log("File {} started", source.getName());
 
         int upper = source.meta().getInt("upperchanel", this.meta().getInt("upperchanel", RawNMPoint.MAX_CHANEL));
@@ -72,7 +71,7 @@ public class DebunchAction extends OneToOneAction<RawNMFile,RawNMFile> {
         });
         log.log("File {} completed", source.getName());
 
-        log.getLog().print(new PrintWriter(buildActionOutput(source)));
+        log.getLog().print(new PrintWriter(buildActionOutput(name)));
 
 //        res.configure(source.meta());
         return res;

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

@@ -33,13 +33,12 @@ import java.io.OutputStream;
 @TypedActionDef(name = "findBorder", inputType = NMFile.class, outputType = NMFile.class)
 public class FindBorderAction extends OneToOneAction<NMFile, NMFile> {
 
-
     public FindBorderAction(Context context, Meta an) {
         super(context, an);
     }
 
     @Override
-    protected NMFile execute(Logable log, Meta reader, NMFile source) throws ContentException {
+    protected NMFile execute(Logable log, String name, Meta reader, NMFile source) throws ContentException {
         log.log("File {} started", source.getName());
 
         int upperBorder = meta().getInt("upper", 4096);
@@ -56,7 +55,7 @@ public class FindBorderAction extends OneToOneAction<NMFile, NMFile> {
 
         BorderData bData = new BorderData(source, upperBorder, lowerBorder, referencePoint);
 
-        OutputStream stream = buildActionOutput(source);
+        OutputStream stream = buildActionOutput(name);
 
         ColumnedDataWriter.writeDataSet(stream, bData, String.format("%s : lower = %d upper = %d", source.getName(), lowerBorder, upperBorder));
 

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

@@ -17,8 +17,8 @@ package inr.numass.actions;
 
 import hep.dataforge.actions.ManyToOneAction;
 import hep.dataforge.actions.GroupBuilder;
-import hep.dataforge.content.NamedGroup;
 import hep.dataforge.context.Context;
+import hep.dataforge.data.DataNode;
 import hep.dataforge.points.DataPoint;
 import hep.dataforge.points.ListPointSet;
 import hep.dataforge.points.MapPoint;
@@ -27,12 +27,15 @@ import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.io.log.Logable;
 import hep.dataforge.meta.Meta;
+import hep.dataforge.meta.MetaBuilder;
 import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import hep.dataforge.points.PointSet;
+import java.util.Collection;
+import java.util.stream.Collectors;
 
 /**
  *
@@ -40,7 +43,6 @@ import hep.dataforge.points.PointSet;
  */
 @TypedActionDef(name = "merge", inputType = PointSet.class, outputType = PointSet.class, description = "Merge different numass data files into one.")
 @NodeDef(name = "grouping", info = "The defenition of grouping rule for this merge", target = "method::hep.dataforge.content.GroupBuilder.byAnnotation")
-//@Parameter(name = "groupBy", def = "mergeTag", info = "Defines the name of the value by which grouping is made. The value is supposed to be a String, but in practice could be any type which could be converted to String.")
 public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
 
     public static final String MERGE_NAME = "mergeName";
@@ -51,80 +53,61 @@ public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
     }
 
     @Override
-    protected List<NamedGroup<PointSet>> buildGroups(Meta reader, List<PointSet> input) {
+    @SuppressWarnings("unchecked")
-        List<NamedGroup<PointSet>> groups;
+    protected List<DataNode<PointSet>> buildGroups(DataNode input) {
-        if (reader.hasValue("grouping.byValue")) {
+        Meta meta = inputMeta(input.meta());
-            groups = super.buildGroups(reader, input);
+        List<DataNode<PointSet>> groups;
+        if (meta.hasValue("grouping.byValue")) {
+            groups = super.buildGroups(input);
         } else {
-            groups = GroupBuilder.byValue(MERGE_NAME, reader.getString(MERGE_NAME, "merge")).group(input);
+            groups = GroupBuilder.byValue(MERGE_NAME, meta.getString(MERGE_NAME, "merge")).group(input);
         }
         return groups;
     }
 
     @Override
-    protected PointSet execute(Logable log, Meta reader, NamedGroup<PointSet> input) {
+    protected PointSet execute(Logable log, DataNode<PointSet> input) {
-        return mergeOne(log, input.getName(), input.asList());
+        return mergeOne(log, input);
-//        List<DataSet> res = new ArrayList<>();
-//        for (NamedGroup<DataSet> buildGroups : groups) {
-//            res.add(mergeOne(log, buildGroups.getName(), buildGroups.asList()));
-//        }
-//        return new ContentList<>(input.getName(), PointSet.class, res);
     }
 
-    private PointSet mergeOne(Logable log, String fileName, List<PointSet> files) {
+    private PointSet mergeOne(Logable log, DataNode<PointSet> input) {
-        PointSet[] data = new PointSet[files.size()];
+        List<PointSet> data = input.stream().<PointSet>map(item -> item.getValue().get()).collect(Collectors.toList());
-        String head = "Numass data merge\n";
+        PointSet res = mergeDataSets(input.getName(), data);
+        return res.sort("Uset", true);
+    }
 
-        String numassPath = "";
+    @Override
+    protected void afterGroup(Logable log, String groupName, Meta outputMeta, PointSet output) {
+        OutputStream stream = buildActionOutput(groupName);
+        ColumnedDataWriter.writeDataSet(stream, output, outputMeta.toString());
+    }
 
-        /*
+    @Override
-         * Проверяем являются ли пути одинаковыми у всех файлов 
+    protected MetaBuilder outputMeta(DataNode<PointSet> input) {
-         * TODO не изящное решение
+
-         */
+        String numassPath = input.stream().<String>map(item -> item.getValue().meta().getString("numass.path", null))
-        for (int i = 0; i < files.size(); i++) {
+                .reduce("", (String path, String newPath) -> {
-            data[i] = files.get(i);
+                    if (path == null) {
-            head += "\t" + data[i].getName() + "\n";
+                        return null;
-            if (numassPath != null) {
+                    } else if (path.isEmpty()) {
-                String newPath = data[i].meta().getString("numass.path", null);
+                        return newPath;
-                if (numassPath.isEmpty()) {
+                    } else if (!path.equals(newPath)) {
-                    numassPath = newPath;
+                        return null;
                     } else {
-                    if (!numassPath.equals(newPath)) {
+                        return newPath;
-                        numassPath = null;
-                    }
-                }
-            }
                     }
+        });
 
-        PointSet res = mergeDataSets(fileName, data);
+        MetaBuilder builder = super.outputMeta(input);
-
         /*
-         * Указываем путь только если он одинаковый для всех входных файлов
+         * Указываем путь только есл0и он одинаковый для всех входных файлов
          */
         if (numassPath != null) {
-            res.setMeta(res.meta().getBuilder().putValue("numass.path", numassPath).build());
+            builder.putValue("numass.path", numassPath);
+        }
+        return builder;
     }
 
-        res = res.sort("Uset", true);
-
-        OutputStream stream = buildActionOutput(res);
-
-        ColumnedDataWriter.writeDataSet(stream, res, head);
-
-        return res;
-    }
-
-//    private Map<String, List<DataSet>> buildMergeGroups(String mergeBy, NamedGroup<DataSet> input) {
-//        Map<String, List<DataSet>> map = new HashMap<>();
-//        for (PointSet ds : input) {
-//            String tag = ds.meta().getString(mergeBy, meta().getString(mergeBy, "merge"));
-//            if (!map.containsKey(tag)) {
-//                map.put(tag, new ArrayList<>());
-//            }
-//            map.get(tag).add(ds);
-//        }
-//        return map;
-//    }
     private DataPoint mergeDataPoints(DataPoint dp1, DataPoint dp2) {
         if (dp1 == null) {
             return dp2;
@@ -167,7 +150,7 @@ public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
         return map;
     }
 
-    private PointSet mergeDataSets(String name, PointSet... ds) {
+    private PointSet mergeDataSets(String name, Collection<PointSet> ds) {
         //Сливаем все точки в один набор данных
         Map<Double, List<DataPoint>> points = new LinkedHashMap<>();
         for (PointSet d : ds) {
@@ -185,15 +168,17 @@ public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
 
         List<DataPoint> res = new ArrayList<>();
 
-        for (Map.Entry<Double, List<DataPoint>> entry : points.entrySet()) {
+        points.entrySet().stream().map((entry) -> {
             DataPoint curPoint = null;
             for (DataPoint newPoint : entry.getValue()) {
                 curPoint = mergeDataPoints(curPoint, newPoint);
             }
+            return curPoint;
+        }).forEach((curPoint) -> {
             res.add(curPoint);
-        }
+        });
 
-        return new ListPointSet(name, null, res);
+        return new ListPointSet(res);
 
     }
 

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

@@ -57,7 +57,7 @@ public class MonitorCorrectAction extends OneToOneAction<PointSet, PointSet> {
     }
 
     @Override
-    protected PointSet execute(Logable log, Meta reader, PointSet sourceData) throws ContentException {
+    protected PointSet execute(Logable log, String name, Meta reader, PointSet sourceData) throws ContentException {
 
         double monitor = reader.getDouble("monitorPoint", Double.NaN);
 
@@ -131,9 +131,9 @@ public class MonitorCorrectAction extends OneToOneAction<PointSet, PointSet> {
 //        } else {
 //            format = DataFormat.of(parnames);
 //        }
-        PointSet data = new ListPointSet(sourceData.getName(), sourceData.meta(), dataList);
+        PointSet data = new ListPointSet(dataList);
 
-        OutputStream stream = buildActionOutput(data);
+        OutputStream stream = buildActionOutput(name);
 
         ColumnedDataWriter.writeDataSet(stream, data, head);
 
@@ -141,15 +141,15 @@ public class MonitorCorrectAction extends OneToOneAction<PointSet, PointSet> {
     }
 
     @Override
-    protected void afterAction(ActionResult<PointSet> pack) throws ContentException {
+    protected void afterAction(String name, PointSet res) {
         printMonitorData();
-        super.afterAction(pack);
+        super.afterAction(name, res); //To change body of generated methods, choose Tools | Templates.
     }
 
     private void printMonitorData() {
         String monitorFileName = meta().getString("monitorFile", "monitor");
         OutputStream stream = buildActionOutput(monitorFileName);
-        ListPointSet data = new ListPointSet("monitor", null, monitorPoints);
+        ListPointSet data = new ListPointSet(monitorPoints);
         ColumnedDataWriter.writeDataSet(stream, data.sort("Timestamp", true), "Monitor points", monitorNames);
     }
 

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

@@ -62,7 +62,7 @@ public class PrepareDataAction extends OneToOneAction<NMFile, PointSet> {
     }
 
     @Override
-    protected ListPointSet execute(Logable log, Meta reader, NMFile dataFile) throws ContentException {
+    protected ListPointSet execute(Logable log, String name, Meta reader, NMFile dataFile) {
 //        log.logString("File %s started", dataFile.getName());
 
         int upper = dataFile.meta().getInt("upperWindow", this.meta().getInt("upperWindow", RawNMPoint.MAX_CHANEL - 1));
@@ -112,9 +112,9 @@ public class PrepareDataAction extends OneToOneAction<NMFile, PointSet> {
         }
         head = head + "\n" + new XMLMetaWriter().writeString(meta(), null) + "\n";
 
-        ListPointSet data = new ListPointSet(dataFile.getName(), dataFile.meta(), dataList, format);
+        ListPointSet data = new ListPointSet(dataList, format);
 
-        OutputStream stream = buildActionOutput(data);
+        OutputStream stream = buildActionOutput(name);
 
         ColumnedDataWriter.writeDataSet(stream, data, head);
 //        log.logString("File %s completed", dataFile.getName());

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

@@ -17,7 +17,7 @@ package inr.numass.actions;
 
 import hep.dataforge.actions.OneToOneAction;
 import hep.dataforge.context.Context;
-import hep.dataforge.points.FileData;
+import hep.dataforge.data.FileData;
 import hep.dataforge.description.NodeDef;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.description.ValueDef;
@@ -46,16 +46,16 @@ public class ReadNumassDataAction extends OneToOneAction<FileData, NMFile> {
     }
 
     @Override
-    protected NMFile execute(Logable log, Meta reader, FileData source) throws ContentException {
+    protected NMFile execute(Logable log, String name, Meta reader, FileData source) throws ContentException {
 //        log.logString("File '%s' started", source.getName());
         RawNMFile raw = getNumassData(source, meta());
         if (meta().getBoolean("paw", false)) {
-            raw.generatePAW(buildActionOutput(source.getName() + ".paw"));
+            raw.generatePAW(buildActionOutput(name + ".paw"));
         }
 
         if (meta().hasNode("debunch")) {
             DebunchAction debunch = new DebunchAction(getContext(), meta().getNode("debunch"));
-            raw = debunch.execute(log, null, raw);
+            raw = debunch.execute(log, name, null, raw);
         }
 
         NMFile result = new NMFile(raw);

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

@@ -70,7 +70,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
     }
 
     @Override
-    protected FitState execute(Logable log, Meta reader, FitState input) {
+    protected FitState execute(Logable log, String name, Meta reader, FitState input) {
         ParamSet pars = input.getParameters();
         if (!pars.names().contains(names)) {
             LoggerFactory.getLogger(getClass()).error("Wrong input FitState. Must be loss spectrum fit.");
@@ -80,9 +80,9 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
         UnivariateFunction scatterFunction;
         boolean calculateRatio = false;
         XYPlotFrame frame = (XYPlotFrame) PlotsPlugin.buildFrom(getContext())
-                .buildPlotFrame(getName(), input.getName()+".loss",
+                .buildPlotFrame(getName(), name + ".loss",
                         new MetaBuilder("plot")
-                        .setValue("plotTitle", "Differential scattering crossection for " + input.getName())
+                        .setValue("plotTitle", "Differential scattering crossection for " + name)
                 );
         switch (input.getModel().getName()) {
             case "scatter-variable":
@@ -107,12 +107,12 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
             threshold = reader.getDouble("ionThreshold", 17);
             ionRatio = calcultateIonRatio(pars, threshold);
             log.log("The ionization ratio (using threshold {}) is {}", threshold, ionRatio);
-            ionRatioError = calultateIonRatioError(input, threshold);
+            ionRatioError = calultateIonRatioError(name, input, threshold);
             log.log("the ionization ration standard deviation (using threshold {}) is {}", threshold, ionRatioError);
         }
 
         if (reader.getBoolean("printResult", false)) {
-            PrintWriter writer = new PrintWriter(new OutputStreamWriter(buildActionOutput(input), Charset.forName("UTF-8")));
+            PrintWriter writer = new PrintWriter(new OutputStreamWriter(buildActionOutput(name), Charset.forName("UTF-8")));
 //            writer.println("*** FIT PARAMETERS ***");
             input.print(writer);
 //            for (Param param : pars.getSubSet(names).getParams()) {
@@ -150,7 +150,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
             }
             writer.printf("%s%n", "chi2");
 
-            writer.printf("%s\t", input.getName());
+            writer.printf("%s\t", name);
 
             for (Param param : pars.getSubSet(names).getParams()) {
                 writer.printf("%f\t%f\t", param.value(), param.getErr());
@@ -174,7 +174,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
 
                 ParamSet parameters = input.getParameters().getSubSet(new String[]{"exPos", "ionPos", "exW", "ionW", "exIonRatio"});
                 NamedMatrix covariance = input.getCovariance();
-                PointSet spreadData = generateSpread(writer, input.getName(), parameters, covariance);
+                PointSet spreadData = generateSpread(writer, name, parameters, covariance);
                 ColumnedDataWriter.writeDataSet(System.out, spreadData, "", spreadData.getDataFormat().asArray());
             }
         }
@@ -208,10 +208,10 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
         return exProb / ionProb;
     }
 
-    public double calultateIonRatioError(FitState state, double threshold) {
+    public double calultateIonRatioError(String dataNeme, FitState state, double threshold) {
         ParamSet parameters = state.getParameters().getSubSet(new String[]{"exPos", "ionPos", "exW", "ionW", "exIonRatio"});
         NamedMatrix covariance = state.getCovariance();
-        return calultateIonRatioError(state.getName(), parameters, covariance, threshold);
+        return calultateIonRatioError(dataNeme, parameters, covariance, threshold);
     }
 
     @SuppressWarnings("Unchecked")
@@ -225,14 +225,14 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
                 .filter(d -> !Double.isNaN(d))
                 .toArray();
 
-        Histogram hist = new Histogram("ionRatio", 0.3, 0.5, 0.002);
+        Histogram hist = new Histogram(0.3, 0.5, 0.002);
         hist.fill(res);
         XYPlotFrame frame = (XYPlotFrame) PlotsPlugin.buildFrom(getContext())
                 .buildPlotFrame(getName(), name + ".ionRatio",
                         new MetaBuilder("plot").setValue("plotTitle", "Ion ratio Distribution for " + name)
                 );
 //        XYPlotFrame frame = JFreeChartFrame.drawFrame("Ion ratio Distribution for " + name, null);
-        frame.add(PlottableData.plot(hist, new XYAdapter("binCenter", "count")));
+        frame.add(PlottableData.plot("ionRatio", hist, new XYAdapter("binCenter", "count")));
 
         return new DescriptiveStatistics(res).getStandardDeviation();
     }
@@ -272,7 +272,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
             }
         }
         String[] pointNames = {"e", "central", "lower", "upper", "dispersion"};
-        ListPointSet res = new ListPointSet("spread", pointNames);
+        ListPointSet res = new ListPointSet(pointNames);
         for (int i = 0; i < gridPoints; i++) {
             res.add(new MapPoint(pointNames, grid[i], central[i], lower[i], upper[i], dispersion[i]));
 

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

@@ -50,7 +50,7 @@ public class ShowSpectrumAction extends OneToOneAction<NMFile, NMFile> {
     }
 
     @Override
-    protected NMFile execute(Logable log, Meta reader, NMFile source) throws ContentException {
+    protected NMFile execute(Logable log, String name, Meta reader, NMFile source) throws ContentException {
         log.log("File {} started", source.getName());
 
         List<NMPoint> printPoints = new ArrayList<>();
@@ -73,9 +73,9 @@ public class ShowSpectrumAction extends OneToOneAction<NMFile, NMFile> {
         }
 
         if (printPoints.size() > 0) {
-            ESpectrum data = new ESpectrum(source.getName(), printPoints, chanelsPerBin, normalize);
+            ESpectrum data = new ESpectrum(printPoints, chanelsPerBin, normalize);
 
-            OutputStream stream = buildActionOutput(data);
+            OutputStream stream = buildActionOutput(name);
 
             ColumnedDataWriter.writeDataSet(stream, data, source.getName());
 

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

@@ -49,7 +49,7 @@ public class SlicingAction extends OneToOneAction<NMFile, NMFile> {
     }
 
     @Override
-    protected NMFile execute(Logable log, Meta reader, NMFile source) throws ContentException {
+    protected NMFile execute(Logable log, String name, Meta reader, NMFile source) throws ContentException {
         boolean normalize;
         Map<String, Pair<Integer, Integer>> slicingConfig;
 
@@ -73,7 +73,7 @@ public class SlicingAction extends OneToOneAction<NMFile, NMFile> {
 
         SlicedData sData = new SlicedData(source, slicingConfig, normalize);
 
-        OutputStream stream = buildActionOutput(source);
+        OutputStream stream = buildActionOutput(name);
 
         ColumnedDataWriter.writeDataSet(stream, sData, null);
 

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

@@ -17,8 +17,9 @@ package inr.numass.actions;
 
 import hep.dataforge.actions.ManyToOneAction;
 import hep.dataforge.actions.GroupBuilder;
-import hep.dataforge.content.NamedGroup;
 import hep.dataforge.context.Context;
+import hep.dataforge.data.Data;
+import hep.dataforge.data.DataNode;
 import hep.dataforge.points.Format;
 import hep.dataforge.points.DataPoint;
 import hep.dataforge.points.ListPointSet;
@@ -33,6 +34,8 @@ import java.io.OutputStream;
 import java.util.Arrays;
 import java.util.List;
 import hep.dataforge.points.PointSet;
+import java.util.function.Consumer;
+import javafx.util.Pair;
 
 /**
  *
@@ -48,18 +51,20 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
     }
 
     @Override
-    protected List<NamedGroup<FitState>> buildGroups(Meta reader, List<FitState> input) {
+    @SuppressWarnings("unchecked")    
-        List<NamedGroup<FitState>> groups;
+    protected List<DataNode<PointSet>> buildGroups(DataNode input) {
-        if (reader.hasNode("grouping")) {
+        Meta meta = inputMeta(input.meta());
-            groups = super.buildGroups(reader, input);
+        List<DataNode<PointSet>> groups;
+        if (meta.hasValue("grouping.byValue")) {
+            groups = super.buildGroups(input);
         } else {
-            groups = GroupBuilder.byValue(SUMMARY_NAME, reader.getString(SUMMARY_NAME, "summary")).group(input);
+            groups = GroupBuilder.byValue(SUMMARY_NAME, meta.getString(SUMMARY_NAME, "summary")).group(input);
         }
         return groups;
     }
 
     @Override
-    protected PointSet execute(Logable log, Meta reader, NamedGroup<FitState> input){
+    protected PointSet execute(Logable log, DataNode<FitState> input) {
         String[] parNames = meta().getStringArray("parnames");
         String[] names = new String[2 * parNames.length + 2];
         names[0] = "file";
@@ -69,19 +74,19 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
         }
         names[names.length - 1] = "chi2";
 
-//        boolean calculateWAV = meta().getBoolean("wav", true);
+        ListPointSet res = new ListPointSet(Format.forNames(8, names));
-        String fileName = reader.getString(SUMMARY_NAME, "summary");
-
-        ListPointSet res = new ListPointSet(fileName, Format.forNames(8, names));
 
         double[] weights = new double[parNames.length];
         Arrays.fill(weights, 0);
         double[] av = new double[parNames.length];
         Arrays.fill(av, 0);
 
-        for (FitState state : input) {
+        input.stream().forEach(new Consumer<Pair<String, Data<? extends FitState>>>() {
+            @Override
+            public void accept(Pair<String, Data<? extends FitState>> item) {
+                FitState state = item.getValue().get();
                 Value[] values = new Value[names.length];
-            values[0] = Value.of(state.getName());
+                values[0] = Value.of(item.getKey());
                 for (int i = 0; i < parNames.length; i++) {
                     Value val = Value.of(state.getParameters().getValue(parNames[i]));
                     values[2 * i + 1] = val;
@@ -95,6 +100,7 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
                 DataPoint point = new MapPoint(names, values);
                 res.add(point);
             }
+        });
 
         Value[] averageValues = new Value[names.length];
         averageValues[0] = Value.of("average");
@@ -107,11 +113,15 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
 
         res.add(new MapPoint(names, averageValues));
 
-        OutputStream stream = buildActionOutput(res);
-
-        ColumnedDataWriter.writeDataSet(stream, res, fileName);
-
         return res;
     }
 
+    @Override
+    protected void afterGroup(Logable log, String groupName, Meta outputMeta, PointSet output) {
+        OutputStream stream = buildActionOutput(groupName);
+        ColumnedDataWriter.writeDataSet(stream, output, groupName);
+
+        super.afterGroup(log, groupName, outputMeta, output);
+    }
+
 }

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

@@ -24,19 +24,12 @@ import hep.dataforge.values.ValueFormat;
 import hep.dataforge.values.ValueFormatFactory;
 import hep.dataforge.values.ValueType;
 import java.io.OutputStream;
-import static java.lang.String.format;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import static java.lang.String.format;
-import static java.lang.String.format;
-import static java.lang.String.format;
-import static java.lang.String.format;
-import static java.lang.String.format;
-import static java.lang.String.format;
-import static java.lang.String.format;
 
 /**
  *
@@ -61,8 +54,8 @@ public class ESpectrum extends ListPointSet {
     
     int binning = 1;
 
-    public ESpectrum(String name, List<NMPoint> points, int binning, boolean normalize) {
+    public ESpectrum(List<NMPoint> points, int binning, boolean normalize) {
-        super(name, prepareFormat(points));
+        super(prepareFormat(points));
         this.binning = binning;
         fill(points, normalize);
     }

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

@@ -15,7 +15,7 @@
  */
 package inr.numass.data;
 
-import hep.dataforge.content.NamedMetaHolder;
+import hep.dataforge.names.NamedMetaHolder;
 import hep.dataforge.description.ValueDef;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;

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

@@ -5,7 +5,7 @@
  */
 package inr.numass.data;
 
-import hep.dataforge.content.Named;
+import hep.dataforge.names.Named;
 import hep.dataforge.meta.Meta;
 import java.time.Instant;
 import java.util.List;

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

@@ -15,7 +15,7 @@
  */
 package inr.numass.data;
 
-import hep.dataforge.points.BinaryData;
+import hep.dataforge.data.FileData;
 import hep.dataforge.meta.MergeRule;
 import hep.dataforge.meta.Meta;
 import java.io.BufferedInputStream;
@@ -39,9 +39,9 @@ public class NumassDataReader {
     private Meta config;
     private double HVdev;
 
-    public NumassDataReader(BinaryData data, Meta config) throws IOException {
+    public NumassDataReader(FileData data, Meta config) throws IOException {
-        this(data.getInputStream(), data.meta()
+        this(data.get(), data.meta()
-                .getString("filename", data.getName()), MergeRule.replace(config, data.meta()));
+                .getString("filename", data.fileName()), MergeRule.replace(config, data.meta()));
     }
 
     public NumassDataReader(String file, String fname, Meta config) throws FileNotFoundException {

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

@@ -15,8 +15,7 @@
  */
 package inr.numass.data;
 
-import hep.dataforge.content.Content;
+import hep.dataforge.names.NamedMetaHolder;
-import hep.dataforge.content.NamedMetaHolder;
 import java.io.BufferedOutputStream;
 import java.io.OutputStream;
 import java.io.PrintWriter;
@@ -27,7 +26,7 @@ import java.util.List;
  * Contains the whole data but requires a lot of memory
  * @author Darksnake
  */
-public class RawNMFile extends NamedMetaHolder implements Content {
+public class RawNMFile extends NamedMetaHolder {
 
 //    public static String TYPE = ":data:numassdatafile";
 

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

@@ -21,6 +21,7 @@ import hep.dataforge.functions.ParametricFunction;
 import static hep.dataforge.maths.MatrixOperations.inverse;
 import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.NamedMatrix;
+import inr.numass.utils.TritiumUtils;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
 import org.apache.commons.math3.linear.RealMatrix;
@@ -56,7 +57,7 @@ public class SpectrumInformation {
      * @return
      */
     public NamedMatrix getInformationMatrix(NamedDoubleSet set, ListPointSet data, String... parNames) {
-        SpectrumDataAdapter reader = new SpectrumDataAdapter(data.meta().getNode("aliases"));
+        SpectrumDataAdapter reader = TritiumUtils.adapter();
 
         String[] names = parNames;
         if (names.length == 0) {

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

@@ -18,6 +18,7 @@ package inr.numass.models;
 import hep.dataforge.actions.ActionResult;
 import hep.dataforge.actions.RunManager;
 import hep.dataforge.context.Context;
+import hep.dataforge.data.DataNode;
 import hep.dataforge.points.DataPoint;
 import hep.dataforge.io.ColumnedDataReader;
 import hep.dataforge.meta.Meta;
@@ -47,8 +48,8 @@ public class TransmissionInterpolator implements UnivariateFunction {
 
     @SuppressWarnings("unchecked")
     public static TransmissionInterpolator fromAction(Context context, Meta actionAnnotation, String xName, String yName, int nSmooth, double w, double border) throws InterruptedException {
-        ActionResult<PointSet> pack = RunManager.executeAction(context, actionAnnotation);
+        DataNode<PointSet> node = RunManager.executeAction(context, actionAnnotation);
-        PointSet data = pack.iterator().next().get();
+        PointSet data = node.iterator().next().get();
         return new TransmissionInterpolator(data, xName, yName, nSmooth, w, border);
     }
 

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

@@ -18,17 +18,10 @@ package inr.numass.utils;
 import hep.dataforge.points.DataPoint;
 import hep.dataforge.points.ListPointSet;
 import inr.numass.data.SpectrumDataAdapter;
-import static java.lang.Math.abs;
 import static java.lang.Math.exp;
 import static java.lang.Math.sqrt;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import static java.lang.Math.abs;
-import static java.lang.Math.abs;
-import static java.lang.Math.abs;
-import static java.lang.Math.abs;
-import static java.lang.Math.abs;
-import static java.lang.Math.abs;
-import static java.lang.Math.abs;
 
 /**
  *
@@ -68,7 +61,7 @@ public class TritiumUtils {
      * @return
      */
     public static ListPointSet correctForDeadTime(ListPointSet data, double dtime) {
-        SpectrumDataAdapter reader = new SpectrumDataAdapter(data.meta().getNode("aliases"));            
+        SpectrumDataAdapter reader = adapter();
         ListPointSet res = new ListPointSet(data.getDataFormat());
         for (DataPoint dp : data) {
             double corrFactor = 1 / (1 - dtime * reader.getCount(dp) /reader.getTime(dp));
@@ -86,7 +79,7 @@ public class TritiumUtils {
      * @return
      */
     public static ListPointSet setHVScale(ListPointSet data, double beta) {
-        SpectrumDataAdapter reader = new SpectrumDataAdapter(data.meta().getNode("aliases"));        
+        SpectrumDataAdapter reader = adapter();
         ListPointSet res = new ListPointSet(data.getDataFormat());
         for (DataPoint dp : data) {
             double corrFactor = 1 + beta;
@@ -95,6 +88,10 @@ public class TritiumUtils {
         return res;
     }
     
+    public static SpectrumDataAdapter adapter(){
+        return new SpectrumDataAdapter("Uset", "CR", "CRerr", "Time");
+    }
+    
     /**
      * Integral beta spectrum background with given amplitude (total count rate
      * from)

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

@@ -14,7 +14,9 @@ import hep.dataforge.actions.ActionStateListener;
 import hep.dataforge.actions.RunManager;
 import hep.dataforge.context.Context;
 import hep.dataforge.context.GlobalContext;
-import hep.dataforge.data.DataManager;
+import hep.dataforge.data.DataFactory;
+import hep.dataforge.data.DataNode;
+import hep.dataforge.data.FileDataFactory;
 import hep.dataforge.description.ActionDescriptor;
 import hep.dataforge.description.DescriptorUtils;
 import hep.dataforge.exceptions.NameNotFoundException;
@@ -296,9 +298,9 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
     public void runActions() {
         clearAllStages();
         new Thread(() -> {
-            ActionResult data = new DataManager(getContext()).readFromConfig(getDataConfiguration());
+            DataNode data = new FileDataFactory().build(getContext(), getDataConfiguration());
             Action action = RunManager.readAction(getContext(), getActionConfiguration());
-            action.addListener(this);
+//            action.addListener(this);
             action.run(data);
             Platform.runLater(() -> statusBar.setText("Execution complete"));
         }, "actions").start();

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

@@ -5,7 +5,7 @@
  */
 package inr.numass.workbench;
 
-import hep.dataforge.content.Named;
+import hep.dataforge.names.Named;
 import javafx.scene.control.Tab;
 
 /**

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

@@ -5,7 +5,7 @@
  */
 package inr.numass.workbench;
 
-import hep.dataforge.content.Named;
+import hep.dataforge.names.Named;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.plots.PlotFrame;
 import java.util.HashMap;

numass-prop/src/main/java/inr/numass/prop/ar/JNAEpisode.java

@@ -15,7 +15,7 @@
  */
 package inr.numass.prop.ar;
 
-import hep.dataforge.content.NamedMetaHolder;
+import hep.dataforge.names.NamedMetaHolder;
 import hep.dataforge.meta.Meta;
 import java.util.Iterator;
 import java.util.List;

numass-prop/src/main/java/inr/numass/prop/ar/JNASpectrum.java

@@ -15,7 +15,7 @@
  */
 package inr.numass.prop.ar;
 
-import hep.dataforge.content.NamedMetaHolder;
+import hep.dataforge.names.NamedMetaHolder;
 import hep.dataforge.points.DataPoint;
 import hep.dataforge.points.ListPointSet;
 import hep.dataforge.points.MapPoint;