bugfixes

numass-control/msp/src/main/java/inr/numass/control/msp/fx/MspViewController.java

@@ -244,7 +244,7 @@ public class MspViewController implements Initializable, MspListener {
                 )
                 .setValue("xAxis.type", "time");
 
-        this.plot = new JFreeChartFrame(mspName, plotConfig);
+        this.plot = new JFreeChartFrame(plotConfig);
         PlotContainer container = PlotContainer.anchorTo(plotPane);
         container.setPlot(plot);
         updatePlot();

numass-control/vac/src/main/java/inr/numass/readvac/VACFrame.java

@@ -433,7 +433,7 @@ public class VACFrame extends javax.swing.JFrame {
                             .setValue("axisUnits", "mbar")
                     )
                     .setValue("xAxis.timeAxis", true);
-            this.plotFrame = new JFreeChartFrame("pressures", plotConfig).display(chartPannel);
+            this.plotFrame = new JFreeChartFrame(plotConfig).display(chartPannel);
             XYPlot xyPlot = plotFrame.getChart().getXYPlot();
 
             LogarithmicAxis logAxis = new LogarithmicAxis("Pressure (mbar)");

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

@@ -171,7 +171,7 @@ public class VacCollectorController implements Initializable, DeviceListener, Me
                         .setValue("axisUnits", "mbar")
                 )
                 .setValue("xAxis.type", "time");
-        JFreeChartFrame frame = new JFreeChartFrame("pressure", plotConfig);
+        JFreeChartFrame frame = new JFreeChartFrame(plotConfig);
         frame.addAll(plottables);
         return frame;
     }

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

@@ -0,0 +1,23 @@
+/*
+ * 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.scripts
+
+import inr.numass.storage.NMFile
+import inr.numass.storage.NumassData
+import inr.numass.storage.NumassDataLoader
+import hep.dataforge.meta.Meta
+import inr.numass.actions.FindBorderAction
+import hep.dataforge.grind.GrindMetaBuilder
+
+File dataDir = new File("D:\\Work\\Numass\\data\\2016_04\\T2_data\\Fill_1_7\\set_2_3b127e3254010000")
+if(!dataDir.exists()){
+    println "dataDir directory does not exist"
+}
+Meta config = new GrindMetaBuilder().config(lower: 500, upper: 1600)
+println config
+NumassData data = NumassDataLoader.fromLocalDir(null, dataDir)
+new FindBorderAction().eval(data, config)

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

@@ -27,6 +27,7 @@ import hep.dataforge.datafitter.models.XYModel;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.plotfit.PlotFitResultAction;
 import hep.dataforge.plots.PlotDataAction;
+import hep.dataforge.storage.commons.StorageManager;
 import hep.dataforge.tables.PointAdapter;
 import hep.dataforge.tables.XYAdapter;
 import inr.numass.actions.AdjustErrorsAction;
@@ -35,6 +36,7 @@ import inr.numass.actions.MergeDataAction;
 import inr.numass.actions.MonitorCorrectAction;
 import inr.numass.actions.PrepareDataAction;
 import inr.numass.actions.ReadNumassDataAction;
+import inr.numass.actions.ReadNumassStorageAction;
 import inr.numass.actions.ShowLossSpectrumAction;
 import inr.numass.actions.ShowSpectrumAction;
 import inr.numass.actions.SlicingAction;
@@ -65,6 +67,7 @@ public class NumassPlugin extends BasicPlugin {
 
     @Override
     public void attach(Context context) {
+//        StorageManager.buildFrom(context);
         FitManager fm = context.provide("fitting", FitPlugin.class).getFitManager();
         ModelManager mm = fm.getModelManager();
         loadModels(mm);
@@ -82,6 +85,7 @@ public class NumassPlugin extends BasicPlugin {
         actions.registerAction(PlotFitResultAction.class);
         actions.registerAction(ShowLossSpectrumAction.class);
         actions.registerAction(AdjustErrorsAction.class);
+        actions.registerAction(ReadNumassStorageAction.class);
     }
 
     @Override

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

@@ -20,6 +20,7 @@ import hep.dataforge.tables.SimplePointSource;
 import hep.dataforge.values.Value;
 import inr.numass.storage.NMFile;
 import inr.numass.storage.NMPoint;
+import inr.numass.storage.NumassData;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -43,7 +44,7 @@ public class BorderData extends SimplePointSource {
         return res;
     }
 
-    public BorderData(NMFile file, int upper, int lower, NMPoint reference) {
+    public BorderData(NumassData file, int upper, int lower, NMPoint reference) {
         super(names);
         if (upper <= lower) {
             throw new IllegalArgumentException();
@@ -51,7 +52,7 @@ public class BorderData extends SimplePointSource {
         fill(file, lower, upper, reference);
     }
 
-    private void fill(NMFile file, int lower, int upper, NMPoint reference) {
+    private void fill(NumassData file, int lower, int upper, NMPoint reference) {
         for (NMPoint point : file.getNMPoints()) {
             if ((reference != null) && (point.getUset() == reference.getUset())) {
                 continue;

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

@@ -24,6 +24,7 @@ import hep.dataforge.io.reports.Reportable;
 import hep.dataforge.meta.Laminate;
 import inr.numass.storage.NMFile;
 import inr.numass.storage.NMPoint;
+import inr.numass.storage.NumassData;
 import java.io.OutputStream;
 
 /**
@@ -31,13 +32,13 @@ import java.io.OutputStream;
  * @author Darksnake
  */
 @TypedActionDef(name = "findBorder", inputType = NMFile.class, outputType = NMFile.class)
-public class FindBorderAction extends OneToOneAction<NMFile, NMFile> {
+public class FindBorderAction extends OneToOneAction<NumassData, NumassData> {
 
     @Override
-    protected NMFile execute(Context context, Reportable log, String name, Laminate meta, NMFile source) throws ContentException {
+    protected NumassData execute(Context context, Reportable log, String name, Laminate meta, NumassData source) throws ContentException {
         log.report("File {} started", source.getName());
 
-        int upperBorder = meta.getInt("upper", 4096);
+        int upperBorder = meta.getInt("upper", 4094);
         int lowerBorder = meta.getInt("lower", 0);
         double substractReference = meta.getDouble("reference", 0);
 

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

@@ -30,6 +30,7 @@ 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.Collection;

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

@@ -144,10 +144,12 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
     }
 
     private void printMonitorData(Context context, Meta meta) {
-        String monitorFileName = meta.getString("monitorFile", "monitor");
+        if (!monitorPoints.isEmpty()) {
-        OutputStream stream = buildActionOutput(context, monitorFileName);
+            String monitorFileName = meta.getString("monitorFile", "monitor");
-        ListTable data = new ListTable(monitorPoints);
+            OutputStream stream = buildActionOutput(context, monitorFileName);
-        ColumnedDataWriter.writeDataSet(stream, data.sort("Timestamp", true), "Monitor points", monitorNames);
+            ListTable data = new ListTable(monitorPoints);
+            ColumnedDataWriter.writeDataSet(stream, data.sort("Timestamp", true), "Monitor points", monitorNames);
+        }
     }
 
     private boolean isMonitorPoint(double monitor, DataPoint point) {
@@ -155,7 +157,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
     }
 
     private LocalDateTime getTime(DataPoint point) {
-        return LocalDateTime.ofInstant(point.getValue("Timestamp").timeValue(), ZoneId.of("GMT+3"));
+        return LocalDateTime.ofInstant(point.getValue("Timestamp").timeValue(), ZoneId.systemDefault());
     }
 
     private int getTotal(DataPoint point) {

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

@@ -30,8 +30,8 @@ import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.MapPoint;
 import hep.dataforge.tables.Table;
 import hep.dataforge.tables.TableFormat;
-import inr.numass.storage.NMFile;
 import inr.numass.storage.NMPoint;
+import inr.numass.storage.NumassData;
 import inr.numass.storage.RawNMPoint;
 import java.io.OutputStream;
 import java.time.Instant;
@@ -42,12 +42,12 @@ import java.util.List;
  *
  * @author Darksnake
  */
-@TypedActionDef(name = "prepareData", inputType = NMFile.class, outputType = Table.class)
+@TypedActionDef(name = "prepareData", inputType = NumassData.class, outputType = Table.class)
 @ValueDef(name = "lowerWindow", type = "NUMBER", def = "0", info = "Base for the window lowerWindow bound")
 @ValueDef(name = "lowerWindowSlope", type = "NUMBER", def = "0", info = "Slope for the window lowerWindow bound")
 @ValueDef(name = "upperWindow", type = "NUMBER", info = "Upper bound for window")
 @ValueDef(name = "deadTime", type = "NUMBER", def = "0", info = "Dead time in us")
-public class PrepareDataAction extends OneToOneAction<NMFile, Table> {
+public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
 
     public static String[] parnames = {"Uset", "Uread", "Length", "Total", "Window", "Corrected", "CR", "CRerr", "Timestamp"};
 
@@ -59,8 +59,8 @@ public class PrepareDataAction extends OneToOneAction<NMFile, Table> {
     }
 
     @Override
-    protected ListTable execute(Context context, Reportable log, String name, Laminate meta, NMFile dataFile) {
+    protected ListTable execute(Context context, Reportable log, String name, Laminate meta, NumassData dataFile) {
-//        log.logString("File %s started", dataFile.getName());
+//        log.report("File %s started", dataFile.getName());
 
         int upper = meta.getInt("upperWindow", RawNMPoint.MAX_CHANEL - 1);
 
@@ -99,11 +99,9 @@ public class PrepareDataAction extends OneToOneAction<NMFile, Table> {
             format = TableFormat.fixedWidth(8, parnames);
         }
 
-//        AnnotationBuilder builder = dataFile.meta().getBuilder();
         String head;
-        if (dataFile.getHead() != null) {
+        if (dataFile.getInfo() != null) {
-            head = dataFile.getHead();
+            head = dataFile.getInfo().toString();
-//            builder.putValue("datafilehead",head);            
         } else {
             head = dataFile.getName();
         }

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

@@ -0,0 +1,64 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package inr.numass.actions;
+
+import hep.dataforge.actions.GenericAction;
+import hep.dataforge.context.Context;
+import hep.dataforge.data.Data;
+import hep.dataforge.data.DataFilter;
+import hep.dataforge.data.DataNode;
+import hep.dataforge.data.DataSet;
+import hep.dataforge.data.StaticData;
+import hep.dataforge.description.TypedActionDef;
+import hep.dataforge.description.ValueDef;
+import hep.dataforge.exceptions.StorageException;
+import hep.dataforge.meta.Meta;
+import hep.dataforge.storage.api.Loader;
+import hep.dataforge.storage.commons.StorageUtils;
+import inr.numass.storage.NumassData;
+import inr.numass.storage.NumassStorage;
+
+/**
+ *
+ * @author Alexander Nozik
+ */
+@TypedActionDef(name = "readStorage",
+        outputType = NumassData.class, info = "Read numass storage data")
+@ValueDef(name = "uri", info = "The path to Numass storage")
+//@NodeDef(name = "debunch", target = "class::inr.numass.actions.DebunchAction", info = "If given, governs debunching")
+public class ReadNumassStorageAction extends GenericAction<Void, NumassData> {
+
+    @Override
+    public DataNode<NumassData> run(Context context, DataNode<Void> data, Meta actionMeta) {
+        try {
+            NumassStorage storage = NumassStorage.buildNumassRoot(actionMeta.getString("uri"), true, false);
+            DataFilter filter = new DataFilter().configure(actionMeta);
+            DataSet.Builder<NumassData> builder = DataSet.builder(NumassData.class);
+
+            StorageUtils.loaderStream(storage).forEach(pair -> {
+                Loader loader = pair.getValue();
+                if (loader instanceof NumassData) {
+                    Data<NumassData> datum = new StaticData<>((NumassData) loader);
+                    if (filter.acceptData(pair.getKey(), datum)) {
+                        builder.putData(pair.getKey(), datum);
+                    }
+                }
+            });
+
+            storage.legacyFiles().forEach(nd -> {
+                Data<NumassData> datum = new StaticData<>(nd);
+                if (filter.acceptData(nd.getName(), datum)) {
+                    builder.putData("legacy." + nd.getName(), datum);
+                }
+            });
+
+            return builder.build();
+        } catch (StorageException ex) {
+            throw new RuntimeException("Failed to load storage", ex);
+        }
+    }
+
+}

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

@@ -5,8 +5,6 @@
  */
 package inr.numass.workbench;
 
-import ch.qos.logback.classic.Level;
-import de.jensd.shichimifx.utils.ConsoleDude;
 import hep.dataforge.actions.Action;
 import hep.dataforge.actions.ActionManager;
 import hep.dataforge.actions.ActionStateListener;
@@ -18,6 +16,7 @@ import hep.dataforge.data.FileDataFactory;
 import hep.dataforge.description.ActionDescriptor;
 import hep.dataforge.description.DescriptorUtils;
 import hep.dataforge.exceptions.NameNotFoundException;
+import hep.dataforge.fx.ConsoleFragment;
 import hep.dataforge.fx.FXProcessManager;
 import hep.dataforge.fx.LogOutputPane;
 import hep.dataforge.fx.MetaEditor;
@@ -51,11 +50,13 @@ import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
 import javafx.scene.Node;
 import javafx.scene.control.Accordion;
+import javafx.scene.control.Alert;
 import javafx.scene.control.Button;
 import javafx.scene.control.Tab;
 import javafx.scene.control.TabPane;
 import javafx.scene.control.TextArea;
 import javafx.scene.control.TitledPane;
+import javafx.scene.control.ToggleButton;
 import javafx.stage.FileChooser;
 import org.controlsfx.control.StatusBar;
 
@@ -79,6 +80,7 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
     Map<String, StagePane> stages = new ConcurrentHashMap<>();
 
     ProcessManagerFragment processWindow = new ProcessManagerFragment(new FXProcessManager());
+    ConsoleFragment consoleWindow = new ConsoleFragment();
 
     @FXML
     private StatusBar statusBar;
@@ -97,7 +99,7 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
     @FXML
     private Button runButton;
     @FXML
-    private TextArea consoleArea;
+    private ToggleButton consoleButton;
 
     @Override
     public void clearStage(String stageName) {
@@ -117,7 +119,9 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
     public void initialize(URL url, ResourceBundle rb) {
         logPane = new LogOutputPane();
         logTab.setContent(logPane);
-        ConsoleDude.hookStdStreams(consoleArea);
+        consoleWindow.bindTo(consoleButton);
+        consoleWindow.addRootLogHandler();
+        consoleWindow.hookStd();
     }
 
     public Context getContext() {
@@ -132,17 +136,15 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
         this.context = this.contextFactory.build(parentContext, config);
         context.setIO(new WorkbenchIOManager(new NumassIO(), this));
         processWindow = ProcessManagerFragment.attachToContext(context);
+        processWindow.setOwner(this.logPane.getScene().getWindow());
         buildContextPane();
-        this.logPane.attachLog(context);
+        this.logPane.listenTo(context);
-        context.getLogger().addAppender(logPane.getLoggerAppender());
+//        this.logPane.listenTo(context);
-        context.getLogger().setLevel(Level.ALL);
+//        this.logPane.listenTo(GlobalContext.instance().getLogger());
-        GlobalContext.instance().getLogger().addAppender(logPane.getLoggerAppender());
 
         ((PlotsPlugin) context.provide("plots")).setPlotHolderDelegate(this);
     }
 
-
-
     private Tab findTabWithName(TabPane pane, String name) {
         return pane.getTabs().stream().filter((t) -> t.getText().equals(name)).findFirst().orElse(null);
     }
@@ -254,9 +256,9 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
 
     private void clearAllStages() {
         logPane.clear();
-        for (String stageName : stages.keySet()) {
+        stages.keySet().stream().forEach((stageName) -> {
             clearStage(stageName);
-        }
+        });
     }
 
     /**
@@ -264,6 +266,7 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
      */
     private synchronized void cleanUp() {
         //clear previus action panes
+        processWindow.getManager().cleanup();
         metaContainer.getPanes().removeIf((ap) -> ap.getText().startsWith("action"));
         clearAllStages();
         actionsConfig = null;
@@ -294,7 +297,7 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
 
     @FXML
     private void onRunButtonClick(ActionEvent event) {
-        if (getContext() != null && !dataConfig.isEmpty() && !actionsConfig.isEmpty()) {
+        if (getContext() != null && !actionsConfig.isEmpty()) {
             statusBar.setText("Starting action execution");
             runActions();
         }
@@ -314,12 +317,26 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
         processWindow.show();
         new Thread(() -> {
             DataNode data = new FileDataFactory().build(getContext(), getDataConfiguration());
-            if (data.isEmpty()) {
+            Platform.runLater(() -> statusBar.setProgress(-1));
-                //FIXME evaluate error here
+            try {
-                throw new Error("Empty data");
+                ActionUtils.runAction(getContext(), data, getActionConfiguration()).compute();
+                Platform.runLater(() -> statusBar.setText("Execution complete"));
+            } catch (Exception ex) {
+                GlobalContext.instance().getLogger().error("Exception while executing action chain", ex);
+                Platform.runLater(() -> {
+//                    ex.printStackTrace();
+                    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(() -> statusBar.setProgress(0));
             }
-            ActionUtils.runAction(getContext(), data, getActionConfiguration()).compute();
+
-            Platform.runLater(() -> statusBar.setText("Execution complete"));
         }, "actions").start();
     }
 

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

@@ -16,7 +16,7 @@ public class PlotOutputTab extends OutputTab {
     public PlotOutputTab(String name, Meta meta) {
         super(name);
         PlotContainer container = new PlotContainer();
-        frame = new JFreeChartFrame(name, meta);
+        frame = new JFreeChartFrame(meta);
         container.setPlot(frame);
 //        AnchorPane pane = new AnchorPane();
 //        frame = new JFreeChartFrame(name, meta).display(pane);
@@ -26,7 +26,7 @@ public class PlotOutputTab extends OutputTab {
     public PlotOutputTab(String name, String title, Meta meta) {
         super(name, title);
         PlotContainer container = new PlotContainer();
-        frame = new JFreeChartFrame(name, meta);
+        frame = new JFreeChartFrame(meta);
         container.setPlot(frame);        
         setContent(container);
     }

numass-main/src/main/resources/fxml/NumassWorkbench.fxml

@@ -1,16 +1,22 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<?import javafx.geometry.*?>
+<?import javafx.scene.control.Accordion?>
-<?import javafx.scene.text.*?>
+<?import javafx.scene.control.Button?>
-<?import org.controlsfx.control.*?>
+<?import javafx.scene.control.ScrollPane?>
-<?import java.lang.*?>
+<?import javafx.scene.control.SplitPane?>
-<?import java.net.*?>
+<?import javafx.scene.control.Tab?>
-<?import java.util.*?>
+<?import javafx.scene.control.TabPane?>
-<?import javafx.scene.*?>
+<?import javafx.scene.control.TitledPane?>
-<?import javafx.scene.control.*?>
+<?import javafx.scene.control.ToggleButton?>
-<?import javafx.scene.layout.*?>
+<?import javafx.scene.control.ToolBar?>
+<?import javafx.scene.layout.AnchorPane?>
+<?import javafx.scene.layout.BorderPane?>
+<?import javafx.scene.layout.Pane?>
+<?import javafx.scene.layout.VBox?>
+<?import javafx.scene.text.Font?>
+<?import org.controlsfx.control.StatusBar?>
 
-<AnchorPane id="AnchorPane" prefHeight="600.0" prefWidth="800.0" xmlns:fx="http://javafx.com/fxml/1" xmlns="http://javafx.com/javafx/8.0.40" fx:controller="inr.numass.workbench.NumassWorkbenchController">
+<AnchorPane id="AnchorPane" prefHeight="600.0" prefWidth="800.0" xmlns="http://javafx.com/javafx/8.0.65" xmlns:fx="http://javafx.com/fxml/1" fx:controller="inr.numass.workbench.NumassWorkbenchController">
     <children>
         <BorderPane layoutX="-165.0" layoutY="100.0" prefHeight="200.0" prefWidth="765.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
             <bottom>
@@ -21,12 +27,7 @@
                     <items>
                         <TabPane fx:id="stagesPane" prefHeight="200.0" prefWidth="200.0" side="LEFT" tabClosingPolicy="UNAVAILABLE">
                             <tabs>
-                                <Tab fx:id="LogTab" closable="false" text="Log" />
+                                <Tab fx:id="logTab" closable="false" text="Log" />
-                        <Tab text="System">
-                           <content>
-                              <TextArea fx:id="consoleArea" editable="false" prefHeight="200.0" prefWidth="200.0" wrapText="true" />
-                           </content>
-                        </Tab>
                             </tabs>
                         </TabPane>
                         <VBox alignment="TOP_CENTER" style="-fx-border-color: blue;">
@@ -39,6 +40,8 @@
                                                 <Font name="System Bold" size="12.0" />
                                             </font>
                                         </Button>
+                              <Pane />
+                              <ToggleButton fx:id="consoleButton" mnemonicParsing="false" text="Console" />
                                     </items>
                                 </ToolBar>
                                 <ScrollPane fitToHeight="true" fitToWidth="true">

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

@@ -82,36 +82,6 @@ public class NMFile extends NamedMetaHolder implements NumassData {
         return points;
     }
 
-    /**
-     * merge of all point with given Uset
-     *
-     * @param U
-     * @return
-     */
-    public NMPoint getByUset(double U) {
-        for (NMPoint point : points) {
-            if (point.getUset() == U) {
-                return point;
-            }
-        }
-        return null;
-    }
-
-    /**
-     * merge of all point with given Uread
-     *
-     * @param U
-     * @return
-     */
-    public NMPoint getByUread(double U) {
-        for (NMPoint point : points) {
-            if (point.getUread() == U) {
-                return point;
-            }
-        }
-        return null;
-    }
-
     @Override
     public boolean isEmpty() {
         return false;

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

@@ -5,7 +5,6 @@
  */
 package inr.numass.storage;
 
-import inr.numass.storage.NMPoint;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.names.Named;
 import java.time.Instant;
@@ -15,7 +14,7 @@ import java.util.List;
  *
  * @author Alexander Nozik <altavir@gmail.com>
  */
-public interface NumassData extends Named{
+public interface NumassData extends Named {
 
     String getDescription();
 
@@ -27,4 +26,34 @@ public interface NumassData extends Named{
 
     Instant startTime();
 
+    /**
+     * Find first point with given Uset
+     *
+     * @param U
+     * @return
+     */
+    default NMPoint getByUset(double U) {
+        for (NMPoint point : getNMPoints()) {
+            if (point.getUset() == U) {
+                return point;
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Find first point with given Uread
+     *
+     * @param U
+     * @return
+     */
+    default NMPoint getByUread(double U) {
+        for (NMPoint point : getNMPoints()) {
+            if (point.getUread() == U) {
+                return point;
+            }
+        }
+        return null;
+    }
+
 }

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

@@ -15,6 +15,7 @@
  */
 package inr.numass.storage;
 
+import hep.dataforge.context.GlobalContext;
 import hep.dataforge.data.binary.Binary;
 import hep.dataforge.exceptions.StorageException;
 import hep.dataforge.io.envelopes.DefaultEnvelopeReader;
@@ -31,24 +32,19 @@ import java.net.URL;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.time.Instant;
-import java.time.LocalDate;
-import java.time.LocalDateTime;
-import java.time.LocalTime;
-import java.time.ZoneOffset;
-import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.function.Function;
 import java.util.function.Supplier;
+import java.util.stream.Collectors;
 import org.apache.commons.vfs2.FileObject;
 import org.apache.commons.vfs2.FileSystemException;
 import static org.apache.commons.vfs2.FileType.FOLDER;
 import org.apache.commons.vfs2.VFS;
-import org.apache.commons.vfs2.provider.local.DefaultLocalFileProvider;
 import org.slf4j.LoggerFactory;
 
 /**
@@ -75,7 +71,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
     public static final String HV_FRAGMENT_NAME = "voltage";
 
     public static NumassDataLoader fromLocalDir(Storage storage, File directory) throws IOException {
-        return fromDir(storage, new DefaultLocalFileProvider().findLocalFile(directory), null);
+        return fromDir(storage, VFS.getManager().toFileObject(directory), null);
     }
 
     public static NumassDataLoader fromZip(Storage storage, FileObject zipFile) throws IOException {
@@ -98,6 +94,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
         Meta annotation = new MetaBuilder("loader")
                 .putValue("type", "numass")
                 .putValue("numass.loaderFormat", "dir")
+                .putValue("file.timeCreated", Instant.ofEpochMilli(directory.getContent().getLastModifiedTime()))
                 .build();
 
         if (name == null || name.isEmpty()) {
@@ -106,44 +103,50 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
 
         URL url = directory.getURL();
 
-        return new NumassDataLoader(storage, name, annotation, () -> {
+        Map<String, Supplier<Envelope>> items = new LinkedHashMap<>();
-            FileObject dir = null;
-            try {
-                dir = VFS.getManager().resolveFile(url.toString());
 
-                Map<String, Envelope> items = new HashMap<>();
+        FileObject dir = null;
-                for (FileObject it : dir.getChildren()) {
+        try {
-                    Envelope envelope = readFile(it);
+            dir = VFS.getManager().resolveFile(url.toString());
-                    if (envelope != null) {
+
-                        items.put(it.getName().getBaseName(), envelope);
+            for (FileObject it : dir.getChildren()) {
-                    }
+                items.put(it.getName().getBaseName(), () -> readFile(it));
-                }
+            }
-                return items;
+
-            } catch (Exception ex) {
+        } catch (Exception ex) {
-                LoggerFactory.getLogger(NumassDataLoader.class)
+            LoggerFactory.getLogger(NumassDataLoader.class)
-                        .error("Can't load numass data directory " + directory.getName().getBaseName(), ex);
+                    .error("Can't load numass data directory " + directory.getName().getBaseName(), ex);
-                return null;
+            return null;
-            } finally {
+        } finally {
-                if (dir != null) {
+            if (dir != null) {
-                    try {
+                try {
-                        dir.close();
+                    dir.close();
-                    } catch (FileSystemException ex) {
+                } catch (FileSystemException ex) {
-                        LoggerFactory.getLogger(NumassDataLoader.class)
+                    LoggerFactory.getLogger(NumassDataLoader.class)
-                                .error("Can't close remote directory", ex);
+                            .error("Can't close remote directory", ex);
-                    }
                 }
             }
-        });
+        }
+
+        return new NumassDataLoader(storage, name, annotation, items);
     }
 
-    private static Envelope readFile(FileObject file) throws FileSystemException {
+    private static Envelope readFile(FileObject file) {
-        String fileName = file.getName().getBaseName();
+        //VFS file reading seems to work basly in parallel
-        if (fileName.equals(META_FRAGMENT_NAME)
+        synchronized (GlobalContext.instance()) {
-                || fileName.equals(HV_FRAGMENT_NAME)
+            String fileName = file.getName().getBaseName();
-                || fileName.startsWith(POINT_FRAGMENT_NAME)) {
+            if (fileName.equals(META_FRAGMENT_NAME)
-            return readStream(file.getContent().getInputStream());
+                    || fileName.equals(HV_FRAGMENT_NAME)
-        } else {
+                    || fileName.startsWith(POINT_FRAGMENT_NAME)) {
-            return null;
+                try {
+                    return readStream(file.getContent().getInputStream());
+                } catch (FileSystemException ex) {
+                    LoggerFactory.getLogger(NumassDataLoader.class).error("Can't read file envelope", ex);
+                    return null;
+                }
+            } else {
+                return null;
+            }
         }
     }
 
@@ -154,7 +157,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
      * @param transformation
      * @return
      */
-    public static NMPoint readPoint(Envelope envelope, Function<RawNMPoint, NMPoint> transformation) {
+    public NMPoint readPoint(Envelope envelope, Function<RawNMPoint, NMPoint> transformation) {
         List<NMEvent> events = new ArrayList<>();
         ByteBuffer buffer;
         try {
@@ -181,7 +184,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
 //        LocalDateTime startTime = envelope.meta().get
         double u = envelope.meta().getDouble("external_meta.HV1_value", 0);
         double pointTime;
-        if(envelope.meta().hasValue("external_meta.acquisition_time")){
+        if (envelope.meta().hasValue("external_meta.acquisition_time")) {
             pointTime = envelope.meta().getValue("external_meta.acquisition_time").doubleValue();
         } else {
             pointTime = envelope.meta().getValue("acquisition_time").doubleValue();
@@ -194,12 +197,15 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
         return transformation.apply(raw);
     }
 
+    /**
+     * "start_time": "2016-04-20T04:08:50",
+     *
+     * @param meta
+     * @return
+     */
     private static Instant readTime(Meta meta) {
-        if (meta.hasValue("date") && meta.hasValue("start_time")) {
+        if (meta.hasValue("start_time")) {
-            LocalDate date = LocalDate.parse(meta.getString("date"), DateTimeFormatter.ofPattern("uuuu.MM.dd"));
+            return meta.getValue("start_time").timeValue();
-            LocalTime time = LocalTime.parse(meta.getString("start_time"));
-            LocalDateTime dateTime = LocalDateTime.of(date, time);
-            return dateTime.toInstant(ZoneOffset.UTC);
         } else {
             return Instant.EPOCH;
         }
@@ -211,7 +217,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
      * @param envelope
      * @return
      */
-    public static NMPoint readPoint(Envelope envelope) {
+    public NMPoint readPoint(Envelope envelope) {
         return readPoint(envelope, (p) -> new NMPoint(p));
     }
 
@@ -226,27 +232,22 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
         }
     }
 
-    private final Supplier<Map<String, Envelope>> items;
+    private final Map<String, Supplier<Envelope>> itemsProvider;
 
     private NumassDataLoader(Storage storage, String name, Meta annotation) {
         super(storage, name, annotation);
-        items = () -> new HashMap<>();
+        itemsProvider = new HashMap<>();
         readOnly = true;
     }
 
-    private NumassDataLoader(Storage storage, String name, Meta annotation, Supplier<Map<String, Envelope>> items) {
+    private NumassDataLoader(Storage storage, String name, Meta annotation, Map<String, Supplier<Envelope>> items) {
         super(storage, name, annotation);
-        this.items = items;
+        this.itemsProvider = items;
         readOnly = true;
     }
 
-    private Map<String, Envelope> getItems() {
+    private Map<String, Supplier<Envelope>> getItems() {
-        Map<String, Envelope> map = items.get();
+        return itemsProvider;
-        if (map == null) {
-            return Collections.emptyMap();
-        } else {
-            return map;
-        }
     }
 
     @Override
@@ -258,6 +259,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
     public Meta getInfo() {
         return getItems()
                 .get(META_FRAGMENT_NAME)
+                .get()
                 .meta();
     }
 
@@ -266,28 +268,16 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
 //    }
     @Override
     public List<NMPoint> getNMPoints() {
-        List<NMPoint> res = new ArrayList<>();
+        return this.getPoints().stream().parallel().map(env -> readPoint(env)).collect(Collectors.toList());
-        this.getPoints().stream().forEachOrdered((point) -> {
-            res.add(readPoint(point));
-        });
-//        res.sort((NMPoint o1, NMPoint o2) -> o1.getStartTime().compareTo(o2.getStartTime()));
-        return res;
     }
 
-    protected List<Envelope> getPoints() {
+    private List<Envelope> getPoints() {
-        List<Envelope> res = new ArrayList<>();
+        return getItems().entrySet().stream()
-        getItems().forEach((k, v) -> {
+                .filter(entry -> entry.getKey().startsWith(POINT_FRAGMENT_NAME) && entry.getValue() != null)
-            if (k.startsWith(POINT_FRAGMENT_NAME)) {
+                .map(entry -> entry.getValue().get())//TODO check for nulls?
-                if (v != null) {
+                .sorted((Envelope t, Envelope t1)
-                    res.add(v);
+                        -> t.meta().getInt("external_meta.point_index", -1).compareTo(t1.meta().getInt("external_meta.point_index", -1)))
-                }
+                .collect(Collectors.toList());
-            }
-        });
-
-        res.sort((Envelope t, Envelope t1) -> t.meta().getInt("external_meta.point_index", -1)
-                .compareTo(t1.meta().getInt("external_meta.point_index", -1)));
-
-        return res;
     }
 
     @Override
@@ -298,7 +288,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
     @Override
     public Envelope pull(String header) {
         //PENDING read data to memory?
-        return getItems().get(header);
+        return getItems().get(header).get();
     }
 
     @Override
@@ -313,13 +303,12 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
 
     @Override
     public Instant startTime() {
-        return null;
+        if (meta().hasValue("file.timeCreated")) {
-//        List<NMPoint> points = getNMPoints();
+            return meta().getValue("file.timeCreated").timeValue();
-//        if(!points.isEmpty()){
+        } else {
-//            return points.get(0).getStartTime();
+            return null;
-//        } else {
+        }
-//            return null;
+
-//        }
     }
 
     @Override

numass-viewer/proguard.cfg

@@ -0,0 +1,9 @@
+-injars build\libs\numass-viewer-0.3.1-all.jar
+-outjars build\libs\numass-viewer-0.3.1-min.jar
+
+-libraryjars 'c:\Program Files\Java\jdk\jre\lib\rt.jar'
+-libraryjars 'C:\Program Files\Java\jdk\jre\lib\ext\jfxrt.jar'
+-libraryjars 'C:\Users\darksnake\.posh_gvm\groovy\2.4.6\lib\groovy-2.4.6.jar'
+
+-dontobfuscate
+-dontwarn

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

@@ -68,7 +68,7 @@ public class MspViewController {
 //                        .setValue("axisUnits", "mbar")
 //                        .setValue("type", "log")
 //                );
-        JFreeChartFrame frame = new JFreeChartFrame("mspData", null);
+        JFreeChartFrame frame = new JFreeChartFrame();
         PlotUtils.setYAxis(frame, "partial pressure", "mbar", "log");
         frame.getConfig().setValue("yAxis.range.lower", 1e-10);
         frame.getConfig().setValue("yAxis.range.upper", 1e-3);

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

@@ -17,8 +17,6 @@ package inr.numass.viewer;
 
 import hep.dataforge.context.ProcessManager;
 import hep.dataforge.exceptions.StorageException;
-import hep.dataforge.storage.api.Loader;
-import hep.dataforge.storage.api.Storage;
 import inr.numass.storage.NumassData;
 import inr.numass.storage.NumassStorage;
 import java.time.Instant;
@@ -31,6 +29,8 @@ import javafx.scene.control.TreeItem;
 import javafx.scene.control.TreeTableColumn;
 import javafx.scene.control.TreeTableView;
 import javafx.scene.input.MouseEvent;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  *
@@ -108,41 +108,41 @@ public class NumassLoaderTreeBuilder {
         return node;
     }
 
+    private Logger getLogger() {
+        return LoggerFactory.getLogger(getClass());
+    }
+
     private List<TreeItem<TreeItemValue>> buildChildren(NumassStorage storage,
             Consumer<NumassData> numassViewBuilder, ProcessManager.Callback callback) throws StorageException {
         List<TreeItem<TreeItemValue>> list = new ArrayList<>();
 
-        for (Storage subStorage : storage.shelves().values()) {
+        storage.shelves().values().stream().forEach(subStorage -> {
             if (subStorage instanceof NumassStorage) {
-                NumassStorage numassSubStorage = (NumassStorage) subStorage;
+                try {
-                TreeItem<TreeItemValue> childNode = buildNode(numassSubStorage, numassViewBuilder, callback);
+                    NumassStorage numassSubStorage = (NumassStorage) subStorage;
-                if (!childNode.isLeaf()) {
+                    TreeItem<TreeItemValue> childNode = buildNode(numassSubStorage, numassViewBuilder, callback);
-                    list.add(buildNode(numassSubStorage, numassViewBuilder, callback));
+                    if (!childNode.isLeaf()) {
+                        list.add(buildNode(numassSubStorage, numassViewBuilder, callback));
+                    }
+                } catch (StorageException ex) {
+                    getLogger().error("Error while loading numass storage node", ex);
                 }
             }
-        }
+        });
 
         callback.updateMessage("Building storage " + storage.getName());
         callback.setProgress(0);
         callback.setMaxProgress(storage.loaders().size());
-        for (Loader loader : storage.loaders().values()) {
+        storage.loaders().values().stream()
-            if (loader instanceof NumassData) {
+                .forEach(loader -> {
-                callback.updateMessage("Building numass data loader " + loader.getName());
+                    if (loader instanceof NumassData) {
-                NumassData numassLoader = (NumassData) loader;
+                        callback.updateMessage("Building numass data loader " + loader.getName());
-                TreeItem<TreeItemValue> numassLoaderTreeItem = new TreeItem<>(buildValue(numassLoader));
+                        NumassData numassLoader = (NumassData) loader;
-
+                        TreeItem<TreeItemValue> numassLoaderTreeItem = new TreeItem<>(buildValue(numassLoader));
-//                numassLoaderTreeItem.addEventHandler(MouseEvent.MOUSE_CLICKED, (MouseEvent event) -> {
+                        list.add(numassLoaderTreeItem);
-//                    if (event.getClickCount() >= 2) {
+                    }
-//                        TreeItemValue value = numassLoaderTreeItem.getValue();
+                    callback.increaseProgress(1);
-//                        if (value.isLoader()) {
+                });
-//                            numassViewBuilder.accept(value.getLoader());
-//                        }
-//                    }
-//                });
-                list.add(numassLoaderTreeItem);
-            }
-            callback.increaseProgress(1);
-        }
 
         callback.updateMessage("Loading legacy DAT files");
         callback.setProgress(0);
@@ -184,7 +184,11 @@ public class NumassLoaderTreeBuilder {
 
             @Override
             public String getTime() {
-                return "";
+                if (getStorage().meta().hasValue("file.timeModified")) {
+                    return getStorage().meta().getValue("file.timeModified").stringValue();
+                } else {
+                    return null;
+                }
             }
 
             @Override

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

@@ -279,7 +279,8 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
                     .setValue("yAxis.axisUnits", "Hz")
                     .setValue("legend.show", false);
 
-            spectrumPlotFrame = new JFreeChartFrame("spectrum", plotMeta).display(spectrumPlotPane);
+            spectrumPlotFrame = new JFreeChartFrame(plotMeta).display(spectrumPlotPane);
+            
         }
 
         if (spectrumData == null) {
@@ -337,7 +338,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
                             .build())
                     .build();
 
-            detectorPlotFrame = new JFreeChartFrame("detectorSignal", frameMeta).display(detectorPlotPane);
+            detectorPlotFrame = new JFreeChartFrame(frameMeta).display(detectorPlotPane);
 
             for (XYPlottable pl : detectorData) {
                 detectorPlotFrame.add(pl);