Moved WorkManager to fx

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

@@ -7,12 +7,15 @@
 package inr.numass.scripts
 
 import hep.dataforge.grind.Grind
+import hep.dataforge.tables.DataPoint
 import inr.numass.storage.NMPoint
 import inr.numass.storage.NumassData
 import inr.numass.storage.NumassDataLoader
+import inr.numass.storage.RawNMPoint
 import inr.numass.utils.NMEventGeneratorWithPulser
 import inr.numass.utils.PileUpSimulator
 import inr.numass.utils.TritiumUtils
+import inr.numass.utils.UnderflowCorrection
 import org.apache.commons.math3.random.JDKRandomGenerator
 
 rnd = new JDKRandomGenerator();
@@ -37,12 +40,37 @@ List<NMPoint> pileup = new ArrayList<>();
 lowerChannel = 400;
 upperChannel = 1800;
 
-PileUpSimulator buildSimulator(NMPoint point, double cr, NMPoint reference = null, double scale = 1d) {
+PileUpSimulator buildSimulator(NMPoint point, double cr, NMPoint reference = null, boolean extrapolate = true, double scale = 1d) {
     def cfg = Grind.buildMeta(cr: cr) {
         pulser(mean: 3450, sigma: 86.45, freq: 66.43)
     }
     NMEventGeneratorWithPulser generator = new NMEventGeneratorWithPulser(rnd, cfg)
-    generator.loadSpectrum(point, reference, lowerChannel, upperChannel);
+
+    if (extrapolate) {
+        double[] chanels = new double[RawNMPoint.MAX_CHANEL];
+        double[] values = new double[RawNMPoint.MAX_CHANEL];
+        DataPoint fitResult = new UnderflowCorrection().fitPoint(point, 400, 600, 1800, 20);
+
+        def amp = fitResult.getDouble("amp")
+        def sigma = fitResult.getDouble("expConst")
+        if (sigma > 0) {
+
+        for (int i = 0; i < upperChannel; i++) {
+            chanels[i] = i;
+            if (i < lowerChannel) {
+                values[i] = point.getLength()*amp * Math.exp((i as double) / sigma)
+            } else {
+                values[i] = Math.max(0, point.getCountInChanel(i) - (reference == null ? 0 : reference.getCountInChanel(i)));
+            }
+        }
+        generator.loadSpectrum(chanels, values)
+        } else {
+            generator.loadSpectrum(point, reference, lowerChannel, upperChannel);
+        }
+    } else {
+        generator.loadSpectrum(point, reference, lowerChannel, upperChannel);
+    }
+
     return new PileUpSimulator(point.length * scale, rnd, generator).withUset(point.uset).generate();
 }
 
@@ -53,7 +81,7 @@ double adjustCountRate(PileUpSimulator simulator, NMPoint point) {
 }
 
 data.NMPoints.forEach { point ->
-    double cr = TritiumUtils.countRateWithDeadTime(point, lowerChannel, upperChannel, 6.2e-6);
+    double cr = TritiumUtils.countRateWithDeadTime(point, lowerChannel, upperChannel, 6.55e-6);
 
     PileUpSimulator simulator = buildSimulator(point, cr);
 

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

@@ -45,6 +45,7 @@ public class Numass {
 
     public static void printDescription(Context context, boolean allowANSI) throws DescriptorException {
         PrintWriter writer = new PrintWriter(context.io().out());
+
         DescriptorFormatter formatter = new TextDescriptorFormatter(writer, allowANSI);
         writer.println("***Data description***");
         writer.print("  ");

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

@@ -60,6 +60,7 @@ import java.util.Arrays;
  */
 @TypedActionDef(name = "showLoss", inputType = FitState.class, outputType = FitState.class,
         info = "Show loss spectrum for fit with loss model. Calculate excitation to ionisation ratio.")
+@Deprecated
 public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
 
     private static final String[] names = {"X", "exPos", "ionPos", "exW", "ionW", "exIonRatio"};

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

@@ -68,10 +68,7 @@ public class NMEventGenerator implements Supplier<NMEvent> {
         distribution = d;
     }
 
-    public void loadSpectrum(Map<Double, Double> spectrum, int minChanel, int maxChanel) {
+    public void loadSpectrum(Map<Double, Double> spectrum) {
-        assert minChanel >= 0;
-        assert maxChanel <= RawNMPoint.MAX_CHANEL;
-
         double[] chanels = new double[spectrum.size()];
         double[] values = new double[spectrum.size()];
         int i = 0;
@@ -82,6 +79,10 @@ public class NMEventGenerator implements Supplier<NMEvent> {
         distribution = new EnumeratedRealDistribution(chanels, values);
     }
 
+    public void loadSpectrum(double[] channels, double[] values) {
+        distribution = new EnumeratedRealDistribution(channels, values);
+    }
+
     public void loadSpectrum(NMPoint point) {
         double[] chanels = new double[RawNMPoint.MAX_CHANEL];
         double[] values = new double[RawNMPoint.MAX_CHANEL];
@@ -118,6 +119,7 @@ public class NMEventGenerator implements Supplier<NMEvent> {
         distribution = new EnumeratedRealDistribution(chanels, values);
     }
 
+
     protected NMEvent nextEvent(NMEvent prev) {
         short chanel;
 

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

@@ -5,7 +5,9 @@
  */
 package inr.numass.utils;
 
+import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.ListTable;
+import hep.dataforge.tables.MapPoint;
 import hep.dataforge.tables.Table;
 import inr.numass.storage.NMPoint;
 import org.apache.commons.math3.analysis.ParametricUnivariateFunction;
@@ -23,6 +25,8 @@ import java.util.stream.Collectors;
  */
 public class UnderflowCorrection {
 
+    private static String[] pointNames = {"U", "amp", "expConst", "correction"};
+
 //    private final static int CUTOFF = -200;
 
 //    public double get(Logable log, Meta meta, NMPoint point) {
@@ -49,25 +53,28 @@ public class UnderflowCorrection {
 //        }
 //    }
 
-    public Table fitAllPoints(Iterable<NMPoint> data, int xLow, int xHigh, int binning) {
+//    public Table fitAllPoints(Iterable<NMPoint> data, int xLow, int xHigh, int binning) {
-        ListTable.Builder builder = new ListTable.Builder("U", "amp", "expConst");
+//        ListTable.Builder builder = new ListTable.Builder("U", "amp", "expConst");
-        for (NMPoint point : data) {
+//        for (NMPoint point : data) {
-            double[] fitRes = getUnderflowExpParameters(point, xLow, xHigh, binning);
+//            double[] fitRes = getUnderflowExpParameters(point, xLow, xHigh, binning);
-            builder.row(point.getUset(), fitRes[0], fitRes[1]);
+//            builder.row(point.getUset(), fitRes[0], fitRes[1]);
-        }
+//        }
-        return builder.build();
+//        return builder.build();
+//    }
+
+    public DataPoint fitPoint(NMPoint point, int xLow, int xHigh, int upper, int binning) {
+        double norm = ((double) point.getCountInWindow(xLow, upper)) / point.getLength();
+        double[] fitRes = getUnderflowExpParameters(point, xLow, xHigh, binning);
+        double a = fitRes[0];
+        double sigma = fitRes[1];
+
+        return  new MapPoint(pointNames,point.getUset(), a, sigma, a * sigma * Math.exp(xLow / sigma) / norm + 1d);
     }
 
     public Table fitAllPoints(Iterable<NMPoint> data, int xLow, int xHigh, int upper, int binning) {
-        ListTable.Builder builder = new ListTable.Builder("U", "amp", "expConst", "correction");
+        ListTable.Builder builder = new ListTable.Builder(pointNames);
         for (NMPoint point : data) {
-            double norm = ((double) point.getCountInWindow(xLow, upper)) / point.getLength();
+            builder.row(fitPoint(point,xLow,xHigh,upper,binning));
-            double[] fitRes = getUnderflowExpParameters(point, xLow, xHigh, binning);
-            double a = fitRes[0];
-            double sigma = fitRes[1];
-
-            //builder.row(point.getUset(), a, sigma, (a * sigma * (Math.exp(xLow / sigma) - 1) - a*xLow) / norm + 1d);
-            builder.row(point.getUset(), a, sigma, a * sigma * Math.exp(xLow / sigma) / norm + 1d);
         }
         return builder.build();
     }

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

@@ -1,449 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-import hep.dataforge.actions.Action;
-import hep.dataforge.actions.ActionManager;
-import hep.dataforge.actions.ActionStateListener;
-import hep.dataforge.actions.ActionUtils;
-import hep.dataforge.context.Context;
-import hep.dataforge.context.Global;
-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;
-import hep.dataforge.fx.FXDataOutputPane;
-import hep.dataforge.fx.FXReportListener;
-import hep.dataforge.fx.configuration.MetaEditor;
-import hep.dataforge.fx.fragments.FragmentWindow;
-import hep.dataforge.fx.fragments.LogFragment;
-import hep.dataforge.fx.work.WorkManagerFragment;
-import hep.dataforge.io.IOManager;
-import hep.dataforge.io.MetaFileReader;
-import hep.dataforge.meta.ConfigChangeListener;
-import hep.dataforge.meta.Configuration;
-import hep.dataforge.meta.Meta;
-import hep.dataforge.meta.MetaBuilder;
-import hep.dataforge.plots.PlotFrame;
-import hep.dataforge.plots.PlotHolder;
-import hep.dataforge.plots.PlotsPlugin;
-import hep.dataforge.utils.ContextMetaFactory;
-import hep.dataforge.values.Value;
-import inr.numass.NumassIO;
-import inr.numass.NumassProperties;
-import javafx.application.Platform;
-import javafx.beans.property.BooleanProperty;
-import javafx.beans.property.SimpleBooleanProperty;
-import javafx.beans.value.ObservableValue;
-import javafx.event.ActionEvent;
-import javafx.fxml.FXML;
-import javafx.fxml.Initializable;
-import javafx.scene.Node;
-import javafx.scene.control.*;
-import javafx.stage.FileChooser;
-import org.controlsfx.control.StatusBar;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URL;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.ResourceBundle;
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.stream.Collectors;
-
-/**
- * FXML Controller class
- *
- * @author Alexander Nozik
- */
-public class NumassWorkbenchController implements Initializable, StagePaneHolder, ActionStateListener, PlotHolder {
-
-    Context parentContext;
-    ContextMetaFactory<Context> contextFactory;
-
-    List<MetaEditor> actionEditors = new ArrayList<>();
-    MetaEditor dataEditor;
-    Context context;
-
-    Configuration dataConfig;
-    Configuration actionsConfig;
-
-    Map<String, StagePane> stages = new ConcurrentHashMap<>();
-
-    WorkManagerFragment processWindow;
-
-    FXDataOutputPane logPane;
-
-    BooleanProperty isRunning = new SimpleBooleanProperty(false);
-
-    @FXML
-    private StatusBar statusBar;
-    @FXML
-    private TabPane stagesPane;
-    @FXML
-    private Accordion metaContainer;
-    @FXML
-    private Tab logTab;
-    @FXML
-    private ToggleButton runButton;
-    @FXML
-    private ToggleButton consoleButton;
-    @FXML
-    private ToggleButton processButton;
-
-    @Override
-    public void clearStage(String stageName) {
-        StagePane sp = stages.get(stageName);
-        if (sp != null) {
-            sp.closeAll();
-            Tab t = findTabWithName(stagesPane, stageName);
-            stagesPane.getTabs().remove(t);
-            stages.remove(stageName);
-        }
-    }
-
-    /**
-     * Initializes the controller class.
-     */
-    @Override
-    public void initialize(URL url, ResourceBundle rb) {
-        logPane = new FXDataOutputPane();
-        logTab.setContent(logPane.getRoot());
-
-        LogFragment consoleWindow = new LogFragment();
-        new FragmentWindow(consoleWindow).bindTo(consoleButton);
-        consoleWindow.addRootLogHandler();
-        consoleWindow.hookStd();
-
-        processWindow = new WorkManagerFragment();
-        new FragmentWindow(processWindow).bindTo(processButton);
-
-        isRunning.addListener((ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) -> {
-            runButton.setSelected(newValue);
-            if (newValue) {
-                runButton.setText("Stop");
-            } else {
-                runButton.setText("Run");
-            }
-        });
-
-    }
-
-    public Context getContext() {
-        if (context == null) {
-            throw new RuntimeException("Context not defined");
-        } else {
-            return context;
-        }
-    }
-
-    /**
-     * Setup context for current run
-     *
-     * @param config
-     */
-    private void buildContext(Meta config) {
-        // close existing context
-        if (this.context != null) {
-            try {
-                this.context.close();
-            } catch (Exception ex) {
-                context.getLogger().error("Failed to close context", ex);
-            }
-        }
-        // building context using provided factory
-        this.context = this.contextFactory.build(parentContext, config);
-
-        // attachig visual process manager
-        processWindow.setManager(context.getWorkManager());
-
-        // setting io manager
-        context.setIO(new WorkbenchIOManager(new NumassIO(), this));
-        buildContextPane();
-        context.getLog().addListener(new FXReportListener(logPane));
-
-        // display plots iside workbench
-        PlotsPlugin.buildFrom(context).setPlotHolder(this);
-    }
-
-    private Tab findTabWithName(TabPane pane, String name) {
-        return pane.getTabs().stream().filter((t) -> t.getText().equals(name)).findFirst().orElse(null);
-    }
-
-    /**
-     * build or get tabPane for a given stage
-     *
-     * @param stage
-     * @return
-     */
-    @Override
-    public synchronized StagePane getStagePane(String stage) {
-        if (!stages.containsKey(stage)) {
-            Tab stageTab = new Tab(stage);
-            StagePane stageTabPane = new StagePane();
-            stageTab.setContent(stageTabPane);
-            stages.put(stage, stageTabPane);
-            Platform.runLater(() -> stagesPane.getTabs().add(stageTab));
-            return stageTabPane;
-        } else {
-            return stages.get(stage);
-        }
-    }
-
-    private List<ActionDescriptor> listActions() {
-        return ActionManager.buildFrom(getContext()).list();
-    }
-
-    private ActionDescriptor getDescriptorForAction(String actionType) {
-        return listActions().stream().filter((a) -> a.getName().equals(actionType)).findFirst().orElse(null);
-    }
-
-    private void buildContextPane() {
-        Configuration contextValues = new Configuration("context");
-        //TODO add asMeta method to Context and replace map here
-        context.getProperties().entrySet().stream().forEach((item) -> {
-            contextValues.setValue(item.getKey(), item.getValue());
-        });
-
-        contextValues.addObserver(new ConfigChangeListener() {
-            @Override
-            public void notifyValueChanged(String name, Value oldItem, Value newItem) {
-                context.putValue(name, newItem);
-            }
-
-            @Override
-            public void notifyElementChanged(String name, List<? extends Meta> oldItem, List<? extends Meta> newItem) {
-
-            }
-        });
-
-        MetaEditor contextEditor = MetaEditor.build(contextValues, null);
-
-        contextEditor.geTable().setShowRoot(false);
-        TitledPane contextPane = new TitledPane("Context", contextEditor);
-        metaContainer.getPanes().add(contextPane);
-    }
-
-    public void loadConfig(Meta config) {
-        cleanUp();
-        buildContext(config);
-
-        //loading data configuration
-        if (config.hasMeta("data")) {
-            dataConfig = new Configuration(config.getMeta("data"));
-            //replacing file name value with appropriate nodes
-            if (dataConfig.hasValue("file")) {
-                Value fileValue = dataConfig.getValue("file");
-                dataConfig.removeValue("file");
-                fileValue.listValue().stream().forEach((fileName) -> {
-                    dataConfig.putNode(new MetaBuilder("file")
-                            .putValue("path", fileName));
-                });
-            }
-            dataEditor = MetaEditor.build(dataConfig,
-                    DescriptorUtils.buildDescriptor(
-                            DescriptorUtils.findAnnotatedElement("class::hep.dataforge.data.FileDataFactory")
-                    ));
-            dataEditor.geTable().setShowRoot(false);
-            metaContainer.getPanes().add(new TitledPane("Data", dataEditor));
-        }
-
-        //loading actions configuration
-        actionsConfig = new Configuration("actionlist");
-
-        List<Configuration> actions = config.getMetaList("action").stream()
-                .map(m -> new Configuration(m)).collect(Collectors.toList());
-
-        actionsConfig.attachNodeItem("action", actions);
-
-        int counter = 0;
-        for (Configuration action : actions) {
-            counter++;
-            MetaEditor actionEditor = new MetaEditor();
-            //Freezing actions names
-//            rootItem.setFrozenValuePredicate((c, n) -> c.getName().equals("action") && n.equals("type"));
-            actionEditor.setRoot(action, getDescriptorForAction(action.getString("type")));
-
-            actionEditors.add(actionEditor);
-            String actionTitle = String.format("action [%d]: %s", counter, action.getString("type"));
-            TitledPane actionPane = new TitledPane(actionTitle, actionEditor);
-            metaContainer.getPanes().add(actionPane);
-        }
-        runButton.setDisable(false);
-    }
-
-    private void clearAllStages() {
-        logPane.clear();
-        stages.keySet().stream().forEach((stageName) -> {
-            clearStage(stageName);
-        });
-    }
-
-    /**
-     * Clean up results and configuration panes
-     */
-    private synchronized void cleanUp() {
-        //clear previus action panes
-        if (processWindow.getManager() != null) {
-            processWindow.getManager().cleanup();
-        }
-        metaContainer.getPanes().clear();
-        clearAllStages();
-        actionsConfig = null;
-        dataConfig = null;
-    }
-
-    @FXML
-    private void onLoadConfigClick(ActionEvent event) {
-        statusBar.setText("Loading configuration file...");
-        FileChooser fileChooser = new FileChooser();
-        fileChooser.setTitle("Open Configuration File");
-        String storageRoot = NumassProperties.getNumassProperty("numass.workbench.root");
-        if (storageRoot == null || !new File(storageRoot).exists()) {
-            fileChooser.setInitialDirectory(new File(".").getAbsoluteFile());
-        } else {
-            fileChooser.setInitialDirectory(new File(storageRoot));
-        }
-        File cfgFile = fileChooser.showOpenDialog(((Node) event.getTarget()).getScene().getWindow());
-        if (cfgFile != null) {
-            NumassProperties.setNumassProperty("numass.workbench.root", cfgFile.getParentFile().getAbsolutePath());
-            try {
-                Meta cfg = MetaFileReader.read(cfgFile).build();
-                this.loadConfig(cfg);
-                getContext().putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, cfgFile.getParentFile().toString());
-
-            } catch (IOException | ParseException ex) {
-                context.getLogger().error("Error reading configuration file", ex);
-            }
-            statusBar.setText("Configuration file loaded");
-        } else {
-            statusBar.setText("Loading configuration file canceled");
-        }
-
-    }
-
-    @FXML
-    private void onRunButtonClick(ActionEvent event) {
-        if (!isRunning.get()) {
-            if (context != null && !actionsConfig.isEmpty()) {
-                statusBar.setText("Starting action execution");
-                runActions();
-            }
-        } else {
-            this.context.getWorkManager().shutdown();
-        }
-    }
-
-    public Meta getDataConfiguration() {
-        return dataConfig == null ? Meta.empty() : new MetaBuilder(dataConfig).substituteValues(getContext()).build();
-    }
-
-    public Meta getActionConfiguration() {
-        return actionsConfig == null ? Meta.empty() : new MetaBuilder(actionsConfig).substituteValues(getContext()).build();
-    }
-
-    @SuppressWarnings("unchecked")
-    public void runActions() {
-        clearAllStages();
-//        processWindow.show();
-        new Thread(() -> {
-
-            Platform.runLater(() -> {
-                isRunning.set(true);
-                statusBar.setProgress(-1);
-            });
-
-            DataNode data = new FileDataFactory().build(getContext(), getDataConfiguration());
-            try {
-                ActionUtils.runAction(getContext(), data, getActionConfiguration()).computeAll();
-                Platform.runLater(() -> statusBar.setText("Execution complete"));
-            } catch (Exception ex) {
-                if (ex instanceof java.util.concurrent.CancellationException) {
-                    //cach cancelation exception
-                    Global.instance().getLogger().info("Interrupted by user");
-                    Platform.runLater(() -> {
-                        statusBar.setText("Execution interrupted by user");
-                    });
-                } else {
-                    //cach all other exceptions
-                    Global.instance().getLogger().error("Exception while executing action chain", ex);
-                    ex.printStackTrace(System.err);
-                    Platform.runLater(() -> {
-                        //printing stack trace to the default output
-                        statusBar.setText("Execution failed");
-                        Alert alert = new Alert(Alert.AlertType.ERROR);
-                        alert.setTitle("Exception!");
-                        alert.setHeaderText("Action execution failure");
-                        alert.setContentText(ex.getMessage());
-                        alert.show();
-                    });
-                }
-            } finally {
-                Platform.runLater(() -> {
-                    isRunning.set(false);
-                    statusBar.setProgress(0);
-                });
-            }
-
-        }, "actions").start();
-    }
-
-    public void setParentContext(Context parentContext) {
-        this.parentContext = parentContext;
-    }
-
-    public void setContextFactory(ContextMetaFactory<Context> contextFactory) {
-        this.contextFactory = contextFactory;
-    }
-
-    @Override
-    public void notifyActionStarted(Action action, Object argument) {
-        Platform.runLater(() -> statusBar.setText(String.format("Action '%s' started", action.getName())));
-    }
-
-    @Override
-    public void notifyActionFinished(Action action, Object result) {
-        Platform.runLater(() -> statusBar.setText(String.format("Action '%s' fineshed", action.getName())));
-    }
-
-    @Override
-    public void notifyAcionProgress(Action action, double progress, String message) {
-        Platform.runLater(() -> {
-            statusBar.setText(String.format("%s: %s started", action.getName(), message));
-            if (progress > 0) {
-                statusBar.setProgress(progress);
-            }
-        });
-    }
-
-    @Override
-    public PlotFrame buildPlotFrame(String stage, String name, Meta annotation) {
-        return getStagePane(stage).buildPlotOutput(name, annotation);
-    }
-
-    @Override
-    public PlotFrame getPlotFrame(String stage, String name) throws NameNotFoundException {
-        StagePane pane = getStagePane(stage);
-        Tab tab = findTabWithName(pane, "image::" + name);
-        if (tab != null && tab instanceof PlotOutputTab) {
-            return ((PlotOutputTab) tab).getFrame();
-        } else {
-            return null;
-        }
-    }
-
-    @Override
-    public boolean hasPlotFrame(String stage, String name) {
-        StagePane pane = getStagePane(stage);
-        Tab tab = findTabWithName(pane, "image::" + name);
-        return (tab != null && tab instanceof PlotOutputTab);
-    }
-
-}

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

@@ -1,37 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-import hep.dataforge.names.Named;
-import javafx.scene.control.Tab;
-
-/**
- * A tab which contains output of task or action. 
- *
- * @author <a href="mailto:altavir@gmail.com">Alexander Nozik</a>
- */
-public abstract class OutputTab extends Tab implements Named {
-
-    private String name;
-
-    public OutputTab(String name) {
-        super(name);
-    }
-
-    public OutputTab(String name, String title) {
-        super(title);
-        this.name = name;
-    }
-
-    @Override
-    public String getName() {
-        return name;
-    }
-
-    public abstract void close();
-
-    public abstract void clear();
-}

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

@@ -1,50 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-import hep.dataforge.meta.Meta;
-import hep.dataforge.plots.fx.PlotContainer;
-import hep.dataforge.plots.jfreechart.JFreeChartFrame;
-
-public class PlotOutputTab extends OutputTab {
-
-    private final JFreeChartFrame frame;
-
-    public PlotOutputTab(String name, Meta meta) {
-        super(name);
-        PlotContainer container = new PlotContainer();
-        frame = new JFreeChartFrame(meta);
-        container.setPlot(frame);
-//        AnchorPane pane = new AnchorPane();
-//        frame = new JFreeChartFrame(name, meta).display(pane);
-        setContent(container.getRoot());
-    }
-
-    public PlotOutputTab(String name, String title, Meta meta) {
-        super(name, title);
-        PlotContainer container = new PlotContainer();
-        frame = new JFreeChartFrame(meta);
-        container.setPlot(frame);        
-        setContent(container.getRoot());
-    }
-
-    @Override
-    public void close() {
-
-    }
-
-    @Override
-    public void clear() {
-
-    }
-
-    public JFreeChartFrame getFrame() {
-        return frame;
-    }
-    
-    
-
-}

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

@@ -1,75 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-import hep.dataforge.fx.FXUtils;
-import hep.dataforge.meta.Meta;
-import hep.dataforge.names.Named;
-import hep.dataforge.plots.PlotFrame;
-import javafx.application.Platform;
-import javafx.scene.control.TabPane;
-
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- *
- * @author <a href="mailto:altavir@gmail.com">Alexander Nozik</a>
- */
-public class StagePane extends TabPane implements Named {
-
-    private String name;
-    private final Map<String, OutputTab> tabs = new HashMap<>();
-
-    @Override
-    public String getName() {
-        return name;
-    }
-
-    public void closeAll() {
-        tabs.values().stream().map((tab) -> {
-            tab.close();
-            return tab;
-        }).forEach((tab) -> {
-            Platform.runLater(() -> getTabs().remove(tab));
-        });
-    }
-
-    public synchronized void closeTab(String name) {
-        FXUtils.runNow(() -> {
-            tabs.get(name).close();
-            getTabs().remove(tabs.get(name));
-            tabs.remove(name);
-        });
-    }
-
-    public synchronized TextOutputTab buildTextOutput(String name) {
-        TextOutputTab out = new TextOutputTab(name);
-        FXUtils.runNow(() -> {
-            if (tabs.containsKey(name)) {
-                tabs.get(name).close();
-                getTabs().remove(tabs.get(name));
-                tabs.replace(name, out);
-            }
-            getTabs().add(out);
-        });
-        return out;
-    }
-
-    public synchronized PlotFrame buildPlotOutput(String name, Meta meta) {
-        PlotOutputTab out = new PlotOutputTab("plot::" + name, meta);
-        FXUtils.runNow(() -> {
-            if (tabs.containsKey(name)) {
-                tabs.get(name).close();
-                getTabs().remove(tabs.get(name));
-                tabs.replace(name, out);
-            }
-            getTabs().add(out);
-        });
-        return out.getFrame();
-    }
-
-}

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

@@ -1,15 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-/**
- *
- * @author <a href="mailto:altavir@gmail.com">Alexander Nozik</a>
- */
-public interface StagePaneHolder {
-    StagePane getStagePane(String stageName);
-    void clearStage(String stageName);
-}

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

@@ -1,51 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-import hep.dataforge.fx.FXDataOutputPane;
-import javafx.event.Event;
-
-import java.io.OutputStream;
-
-/**
- * A text output tab. Basically it is attached to IOManager::onComplete
- *
- * @author <a href="mailto:altavir@gmail.com">Alexander Nozik</a>
- */
-public class TextOutputTab extends OutputTab {
-
-    private final FXDataOutputPane out;
-
-    /**
-     * Create new stream output tab
-     *
-     * @param name
-     * @param stream outputStream to which output should be redirected after
-     * displaying in window
-     */
-    public TextOutputTab(String name) {
-        super(name);
-//        onComplete = new DataOutputPane();
-        out = new FXDataOutputPane();
-        setContent(out.getRoot());
-        setOnClosed((Event event) -> close());
-    }
-
-    @Override
-    public void clear() {
-        out.clear();
-    }
-
-    @Override
-    public final void close() {
-        clear();
-    }
-
-    public OutputStream getStream() {
-        return out.getStream();
-    }
-
-}

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

@@ -1,62 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-import hep.dataforge.context.Global;
-import inr.numass.Numass;
-import javafx.application.Application;
-import javafx.fxml.FXMLLoader;
-import javafx.scene.Parent;
-import javafx.scene.Scene;
-import javafx.stage.Stage;
-import javafx.stage.WindowEvent;
-
-import java.io.IOException;
-import java.text.ParseException;
-
-/**
- *
- * @author Alexander Nozik
- */
-public class Workbench extends Application {
-
-    /**
-     * @param args the command line arguments
-     */
-    public static void main(String[] args) {
-        launch(args);
-    }
-
-    @Override
-    public void start(Stage primaryStage) throws IOException, ParseException {
-        FXMLLoader loader = new FXMLLoader(getClass().getResource("/fxml/NumassWorkbench.fxml"));
-        Parent parent = loader.load();
-
-        Scene scene = new Scene(parent, 800, 600);
-
-        NumassWorkbenchController controller = loader.getController();
-        controller.setContextFactory(Numass::buildContext);
-
-        primaryStage.setTitle("Numass workbench");
-        primaryStage.setScene(scene);
-        primaryStage.show();
-
-        scene.getWindow().setOnCloseRequest((WindowEvent event) -> {
-            try {
-                controller.getContext().getWorkManager().getRoot().cancel(true);
-            } catch (Exception e) {
-
-            }
-        });
-    }
-
-    @Override
-    public void stop() throws Exception {
-        Global.instance().close();
-        super.stop();
-    }
-
-}

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

@@ -1,65 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-import hep.dataforge.io.BasicIOManager;
-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;
-
-/**
- * An IOManager wrapper that redirects output to appropriate FX components
- * @author <a href="mailto:altavir@gmail.com">Alexander Nozik</a>
- */
-public class WorkbenchIOManager extends BasicIOManager {
-    
-    private final IOManager manager;
-    private final StagePaneHolder holder;
-
-    public WorkbenchIOManager(IOManager manager, StagePaneHolder holder) {
-        this.manager = manager;
-        this.holder = holder;
-    }
-
-    @Override
-    public File getFile(String path) {
-        return manager.getFile(path);
-    }
-
-    @Override
-    public File getRootDirectory() {
-        return manager.getRootDirectory();
-    }
-
-    @Override
-    public InputStream in() {
-        return manager.in();
-    }
-
-    @Override
-    public InputStream in(String path) {
-        return manager.in(path);
-    }
-
-    @Override
-    public OutputStream out(Name stage, Name name) {
-        //split output between parent output and holder output
-        OutputStream primary = holder.getStagePane(stage.toString()).buildTextOutput(name.toString()).getStream();
-        OutputStream secondary = manager.out(stage, name);
-        return new TeeOutputStream(primary, secondary);
-    }
-
-    @Override
-    public OutputStream out() {
-        return manager.out();
-//        return new ConsoleStream(holder.getLogArea(), new PrintStream(manager.onComplete()));
-    }
-    
-}

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

@@ -1,14 +0,0 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-package inr.numass.workbench;
-
-/**
- *
- * @author <a href="mailto:altavir@gmail.com">Alexander Nozik</a>
- */
-public class WorkbenchUtils {
-    
-}

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

@@ -20,8 +20,9 @@ import hep.dataforge.context.Global;
 import hep.dataforge.exceptions.StorageException;
 import hep.dataforge.fx.fragments.FragmentWindow;
 import hep.dataforge.fx.fragments.LogFragment;
+import hep.dataforge.fx.work.Work;
+import hep.dataforge.fx.work.WorkManager;
 import hep.dataforge.fx.work.WorkManagerFragment;
-import hep.dataforge.goals.Work;
 import inr.numass.NumassProperties;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.NumassStorage;
@@ -85,6 +86,8 @@ public class MainViewerController implements Initializable {
     @FXML
     private ToggleButton processManagerButton;
 
+    private WorkManager workManager;
+
     public static MainViewerController build(NumassStorage root) {
         MainViewerController res = new MainViewerController();
         res.setRootStorage(root);
@@ -102,9 +105,10 @@ public class MainViewerController implements Initializable {
     @Override
     public void initialize(URL url, ResourceBundle rb) {
         LogFragment logFragment = new LogFragment();
-        logFragment.hookStd();
+        logFragment.addRootLogHandler();
+        //logFragment.hookStd();
         new FragmentWindow(logFragment).bindTo(consoleButton);
-        new FragmentWindow(WorkManagerFragment.attachToContext(Global.instance())).bindTo(processManagerButton);
+        new FragmentWindow(new WorkManagerFragment(getWorkManager())).bindTo(processManagerButton);
 
         mspController = new MspViewController(getContext());
         this.mspTab.setContent(mspController.getRoot());
@@ -131,7 +135,7 @@ public class MainViewerController implements Initializable {
     }
 
     private void loadDirectory(String path) {
-        getContext().getWorkManager().startWork("viewer.loadDirectory", (Work work) -> {
+        getWorkManager().startWork("viewer.loadDirectory", (Work work) -> {
             work.setTitle("Load storage (" + path + ")");
             work.setProgress(-1);
             work.setStatus("Building numass storage tree...");
@@ -151,10 +155,18 @@ public class MainViewerController implements Initializable {
         return Global.instance();
     }
 
+    private synchronized WorkManager getWorkManager() {
+        if(workManager == null) {
+            workManager = new WorkManager();
+            workManager.startGlobal();
+        }
+        return workManager;
+    }
+
     public void setRootStorage(NumassStorage root) {
 
-        getContext().getWorkManager().cleanup();
+        getWorkManager().cleanup();
-        getContext().getWorkManager().startWork("viewer.storage.load", (Work callback) -> {
+        getWorkManager().startWork("viewer.storage.load", (Work callback) -> {
             callback.setTitle("Fill data to UI (" + root.getName() + ")");
             callback.setProgress(-1);
             Platform.runLater(() -> statusBar.setProgress(-1));

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

@@ -16,7 +16,7 @@
 package inr.numass.viewer;
 
 import hep.dataforge.exceptions.StorageException;
-import hep.dataforge.goals.Work;
+import hep.dataforge.fx.work.Work;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.NumassStorage;
 import javafx.application.Platform;

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

@@ -22,7 +22,8 @@ package inr.numass.viewer;
  */
 
 import hep.dataforge.context.Context;
-import hep.dataforge.goals.Work;
+import hep.dataforge.fx.work.Work;
+import hep.dataforge.fx.work.WorkManager;
 import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
@@ -211,10 +212,14 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
         return data;
     }
 
+    private WorkManager getWorkManager(){
+        return context.getPlugin(WorkManager.class);
+    }
+
     public void loadData(NumassData data) {
         this.data = data;
         if (data != null) {
-            context.getWorkManager().<List<NMPoint>>startWork("viewer.numass.load", (Work callback) -> {
+            getWorkManager().<List<NMPoint>>startWork("viewer.numass.load", (Work callback) -> {
                 callback.setTitle("Load numass data (" + data.getName() + ")");
                 points = data.getNMPoints();
 
@@ -239,7 +244,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
     }
 
     private void setupHVPane(Supplier<Table> hvData) {
-        context.getWorkManager().startWork("viewer.numass.hv", (Work callback) -> {
+        getWorkManager().startWork("viewer.numass.hv", (Work callback) -> {
             Table t = hvData.get();
             Platform.runLater(() -> {
                 if (t != null) {
@@ -343,7 +348,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
             detectorPlot.removePlot();
         }
 
-        context.getWorkManager().startWork("viewer.numass.load.detector", (Work callback) -> {
+        getWorkManager().startWork("viewer.numass.load.detector", (Work callback) -> {
             Meta plottableConfig = new MetaBuilder("plot")
                     .setValue("connectionType", "step")
                     .setValue("thickness", 2)