Updates in numass viewer. Minor fixes in core.

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

@@ -1,87 +0,0 @@
-/* 
- * Copyright 2015 Alexander Nozik.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package inr.numass.actions;
-
-import hep.dataforge.tables.MapPoint;
-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;
-
-/**
- *
- * @author Darksnake
- */
-public class BorderData extends SimplePointSource {
-
-    private final static String[] names = {"U", "80%", "90%", "95%", "99%"};
-    private final static double[] percents = {0.8, 0.9, 0.95, 0.99};
-
-    public static double getNorm(Map<Double, Double> spectrum, int lower, int upper) {
-        double res = 0;
-        for (Map.Entry<Double, Double> entry : spectrum.entrySet()) {
-            if ((entry.getKey() >= lower) && (entry.getKey() <= upper)) {
-                res += entry.getValue();
-            }
-        }
-
-        return res;
-    }
-
-    public BorderData(NumassData file, int upper, int lower, NMPoint reference) {
-        super(names);
-        if (upper <= lower) {
-            throw new IllegalArgumentException();
-        }
-        fill(file, lower, upper, 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;
-            }
-            //создаем основу для будущей точки
-            HashMap<String, Value> map = new HashMap<>();
-            map.put(names[0], Value.of(point.getUset()));
-            Map<Double, Double> spectrum;
-            if (reference != null) {
-                spectrum = point.getMapWithBinning(reference, 0);
-            } else {
-                spectrum = point.getMapWithBinning(0, true);
-            }
-            double norm = getNorm(spectrum, lower, upper);
-            double counter = 0;
-            int chanel = upper;
-            while (chanel > lower) {
-                chanel--;
-                counter += spectrum.get((double) chanel);
-                for (int i = 0; i < percents.length; i++) {
-                    if (counter / norm > percents[i]) {
-                        if (!map.containsKey(names[i + 1])) {
-                            map.put(names[i + 1], Value.of(chanel));
-                        }
-                    }
-                }
-            }
-            this.addRow(new MapPoint(map));
-        }
-    }
-
-}

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

@@ -22,20 +22,29 @@ import hep.dataforge.exceptions.ContentException;
 import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.io.reports.Reportable;
 import hep.dataforge.meta.Laminate;
+import hep.dataforge.tables.ListTable;
+import hep.dataforge.tables.MapPoint;
+import hep.dataforge.tables.Table;
+import hep.dataforge.values.Value;
 import inr.numass.storage.NMFile;
 import inr.numass.storage.NMPoint;
 import inr.numass.storage.NumassData;
 import java.io.OutputStream;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  *
  * @author Darksnake
  */
-@TypedActionDef(name = "findBorder", inputType = NMFile.class, outputType = NMFile.class)
+@TypedActionDef(name = "findBorder", inputType = NMFile.class, outputType = Table.class)
-public class FindBorderAction extends OneToOneAction<NumassData, NumassData> {
+public class FindBorderAction extends OneToOneAction<NumassData, Table> {
+
+    private final static String[] names = {"U", "80%", "90%", "95%", "99%"};
+    private final static double[] percents = {0.8, 0.9, 0.95, 0.99};
 
     @Override
-    protected NumassData execute(Context context, Reportable log, String name, Laminate meta, NumassData source) throws ContentException {
+    protected Table execute(Context context, Reportable log, String name, Laminate meta, NumassData source) throws ContentException {
         log.report("File {} started", source.getName());
 
         int upperBorder = meta.getInt("upper", 4094);
@@ -50,14 +59,60 @@ public class FindBorderAction extends OneToOneAction<NumassData, NumassData> {
             }
         }
 
-        BorderData bData = new BorderData(source, upperBorder, lowerBorder, referencePoint);
+        ListTable.Builder dataBuilder = new ListTable.Builder(names);
+
+        fill(dataBuilder, source, lowerBorder, upperBorder, referencePoint);
+        Table bData = dataBuilder.build();
 
         OutputStream stream = buildActionOutput(context, name);
 
-        ColumnedDataWriter.writeDataSet(stream, bData, String.format("%s : lower = %d upper = %d", source.getName(), lowerBorder, upperBorder));
+        ColumnedDataWriter.writeDataSet(stream, bData, String.format("%s : lower = %d upper = %d", name, lowerBorder, upperBorder));
 
         log.report("File {} completed", source.getName());
-        return source;
+        return bData;
+    }
+
+    private double getNorm(Map<Double, Double> spectrum, int lower, int upper) {
+        double res = 0;
+        for (Map.Entry<Double, Double> entry : spectrum.entrySet()) {
+            if ((entry.getKey() >= lower) && (entry.getKey() <= upper)) {
+                res += entry.getValue();
+            }
+        }
+
+        return res;
+    }
+
+    private void fill(ListTable.Builder dataBuilder, NumassData file, int lower, int upper, NMPoint reference) {
+        for (NMPoint point : file.getNMPoints()) {
+            if ((reference != null) && (point.getUset() == reference.getUset())) {
+                continue;
+            }
+            //создаем основу для будущей точки
+            HashMap<String, Value> map = new HashMap<>();
+            map.put(names[0], Value.of(point.getUset()));
+            Map<Double, Double> spectrum;
+            if (reference != null) {
+                spectrum = point.getMapWithBinning(reference, 0);
+            } else {
+                spectrum = point.getMapWithBinning(0, true);
+            }
+            double norm = getNorm(spectrum, lower, upper);
+            double counter = 0;
+            int chanel = upper;
+            while (chanel > lower) {
+                chanel--;
+                counter += spectrum.get((double) chanel);
+                for (int i = 0; i < percents.length; i++) {
+                    if (counter / norm > percents[i]) {
+                        if (!map.containsKey(names[i + 1])) {
+                            map.put(names[i + 1], Value.of(chanel));
+                        }
+                    }
+                }
+            }
+            dataBuilder.addRow(new MapPoint(map));
+        }
     }
 
 }

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

@@ -24,6 +24,7 @@ import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.PointSource;
 import hep.dataforge.tables.Table;
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
 import java.util.List;
@@ -39,7 +40,7 @@ public class TransmissionInterpolator implements UnivariateFunction {
     public static TransmissionInterpolator fromFile(Context context, String path, String xName, String yName, int nSmooth, double w, double border) {
         try {
             File dataFile = context.io().getFile(path);
-            ColumnedDataReader reader = new ColumnedDataReader(dataFile);
+            ColumnedDataReader reader = new ColumnedDataReader(new FileInputStream(dataFile));
             return new TransmissionInterpolator(reader, xName, yName, nSmooth, w, border);
         } catch (FileNotFoundException ex) {
             throw new RuntimeException(ex);

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

@@ -7,8 +7,10 @@ package inr.numass.storage;
 
 import hep.dataforge.meta.Meta;
 import hep.dataforge.names.Named;
+import hep.dataforge.tables.Table;
 import java.time.Instant;
 import java.util.List;
+import java.util.function.Supplier;
 
 /**
  *
@@ -26,6 +28,10 @@ public interface NumassData extends Named {
 
     Instant startTime();
 
+    default Supplier<Table> getHVData() {
+        return () -> null;
+    }
+
     /**
      * Find first point with given Uset
      *

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

@@ -18,6 +18,7 @@ package inr.numass.storage;
 import hep.dataforge.context.GlobalContext;
 import hep.dataforge.data.binary.Binary;
 import hep.dataforge.exceptions.StorageException;
+import hep.dataforge.io.ColumnedDataReader;
 import hep.dataforge.io.envelopes.DefaultEnvelopeReader;
 import hep.dataforge.io.envelopes.Envelope;
 import hep.dataforge.meta.Meta;
@@ -25,7 +26,10 @@ import hep.dataforge.meta.MetaBuilder;
 import hep.dataforge.storage.api.ObjectLoader;
 import hep.dataforge.storage.api.Storage;
 import hep.dataforge.storage.loaders.AbstractLoader;
+import hep.dataforge.tables.ListTable;
+import hep.dataforge.tables.Table;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
@@ -40,6 +44,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.function.Function;
 import java.util.function.Supplier;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 import java.util.stream.Collectors;
 import org.apache.commons.vfs2.FileObject;
 import org.apache.commons.vfs2.FileSystemException;
@@ -263,6 +269,30 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
                 .meta();
     }
 
+    @Override
+    public Supplier<Table> getHVData() {
+        Envelope hvEnvelope = getHVEnvelope();
+        if (hvEnvelope == null) {
+            return () -> null;
+        }
+        return () -> {
+            try {
+                return new ColumnedDataReader(hvEnvelope.getData().getStream(), "timestamp", "block", "value").toDataSet();
+            } catch (IOException ex) {
+                LoggerFactory.getLogger(getClass()).error("Failed to load HV data from file", ex);
+                return null;
+            }
+        };
+    }
+
+    private Envelope getHVEnvelope() {
+        if (getItems().containsKey(HV_FRAGMENT_NAME)) {
+            return getItems().get(HV_FRAGMENT_NAME).get();
+        } else {
+            return null;
+        }
+    }
+
 //    public Envelope getHvData() {
 //        return hvData;
 //    }

numass-viewer/build.gradle

@@ -5,7 +5,7 @@ if (!hasProperty('mainClass')) {
 }
 mainClassName = mainClass
 
-version = "0.3.2"
+version = "0.3.3"
 
 description = "The viewer for numass data"
 

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

@@ -28,8 +28,11 @@ import hep.dataforge.meta.MetaBuilder;
 import hep.dataforge.plots.XYPlotFrame;
 import hep.dataforge.plots.XYPlottable;
 import hep.dataforge.plots.data.ChangeablePlottableData;
+import hep.dataforge.plots.data.DynamicPlottable;
+import hep.dataforge.plots.data.DynamicPlottableSet;
 import hep.dataforge.plots.data.PlotDataUtils;
 import hep.dataforge.plots.data.PlottableData;
+import hep.dataforge.plots.data.PlottableSet;
 import hep.dataforge.plots.fx.PlotContainer;
 import hep.dataforge.plots.jfreechart.JFreeChartFrame;
 import hep.dataforge.storage.commons.JSONMetaWriter;
@@ -47,12 +50,12 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.ResourceBundle;
 import java.util.function.Predicate;
+import java.util.function.Supplier;
 import java.util.stream.Collectors;
 import javafx.application.Platform;
 import javafx.beans.value.ChangeListener;
 import javafx.beans.value.ObservableValue;
 import javafx.collections.FXCollections;
-import javafx.concurrent.Task;
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
 import javafx.fxml.FXMLLoader;
@@ -90,7 +93,8 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
     Logger logger = LoggerFactory.getLogger(NumassLoaderViewComponent.class);
     private NumassData data;
     private PlotContainer detectorPlot;
-    private XYPlotFrame spectrumPlotFrame;
+    private PlotContainer spectrumPlot;
+    private PlotContainer hvPlot;
     private ChangeablePlottableData spectrumData;
     private List<NMPoint> points;
     private ChoiceBox<Integer> detectorBinningSelector;
@@ -123,6 +127,8 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
     private Button spectrumExportButton;
     @FXML
     private TextField dTimeField;
+    @FXML
+    private AnchorPane hvPane;
 
     public NumassLoaderViewComponent(Context context) {
         this.context = context;
@@ -166,8 +172,17 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
         detectorPlot.addToSideBar(detectorDataExportButton);
 
         detectorPlot.setSideBarPosition(0.7);
-
         //setup spectrum pane
+        spectrumPlot = PlotContainer.anchorTo(spectrumPlotPane);
+
+        Meta spectrumPlotMeta = new MetaBuilder("plot")
+                .setValue("xAxis.axisTitle", "U")
+                .setValue("xAxis.axisUnits", "V")
+                .setValue("yAxis.axisTitle", "count rate")
+                .setValue("yAxis.axisUnits", "Hz")
+                .setValue("legend.show", false);
+        spectrumPlot.setPlot(new JFreeChartFrame(spectrumPlotMeta));
+
         lowChannelField.textProperty().bindBidirectional(channelSlider.lowValueProperty(), new NumberStringConverter());
         upChannelField.textProperty().bindBidirectional(channelSlider.highValueProperty(), new NumberStringConverter());
 
@@ -175,11 +190,11 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
         channelSlider.setLowValue(300d);
 
         ChangeListener<? super Number> rangeChangeListener = (ObservableValue<? extends Number> observable, Number oldValue, Number newValue) -> {
-            updateSpectrumPane(points);
+            setupSpectrumPane(points);
         };
 
         dTimeField.textProperty().addListener((ObservableValue<? extends String> observable, String oldValue, String newValue) -> {
-            updateSpectrumPane(points);
+            setupSpectrumPane(points);
         });
 
         channelSlider.lowValueProperty().addListener(rangeChangeListener);
@@ -196,6 +211,14 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
         };
 
         validationSupport.registerValidator(dTimeField, Validator.createPredicateValidator(isNumber, "Must be number"));
+
+        //setup HV plot
+        hvPlot = PlotContainer.anchorTo(hvPane);
+        Meta hvPlotMeta = new MetaBuilder("plot")
+                .setValue("xAxis.axisTitle", "time")
+                .setValue("xAxis.type", "time")
+                .setValue("yAxis.axisTitle", "HV");
+        hvPlot.setPlot(new JFreeChartFrame(hvPlotMeta));
     }
 
     public NumassData getData() {
@@ -208,43 +231,45 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
             context.processManager().<List<NMPoint>>post("viewer.numass.load", (ProcessManager.Callback callback) -> {
                 callback.updateTitle("Load numass data (" + data.getName() + ")");
                 points = data.getNMPoints();
+
                 Platform.runLater(() -> {
                     //setup detector data
                     setupDetectorPane(points);
                     //setup spectrum plot
-                    updateSpectrumPane(points);
+                    setupSpectrumPane(points);
-                    setupInfo(data);
                 });
             });
+            //setup hv plot
+            Supplier<Table> hvData = data.getHVData();
+            if (hvData != null) {
+                setupHVPane(hvData);
+            }
+            setupInfo(data);
+
         } else {
             logger.error("The data model is null");
         }
         detectorTab.getTabPane().getSelectionModel().select(detectorTab);
     }
 
-    private class LoadPointsTask extends Task<List<NMPoint>> {
+    private void setupHVPane(Supplier<Table> hvData) {
-
+        context.processManager().post("viewer.numass.hv", (ProcessManager.Callback callback) -> {
-        private final NumassData loader;
+            Table t = hvData.get();
-
-        public LoadPointsTask(NumassData loader) {
-            this.loader = loader;
-        }
-
-        @Override
-        protected List<NMPoint> call() throws Exception {
-            updateTitle("Load numass data (" + loader.getName() + ")");
-            List<NMPoint> points = loader.getNMPoints();
             Platform.runLater(() -> {
-                //setup detector data
+                if (t != null) {
-                setupDetectorPane(points);
+                    hvPlot.getPlot().plottables().clear();
-                //setup spectrum plot
+                    DynamicPlottableSet set = new DynamicPlottableSet();
-                updateSpectrumPane(points);
+                    for (DataPoint dp : t) {
-
+                        String block = dp.getString("block", "default");
-                setupInfo(data);
+                        if (!set.hasPlottable(block)) {
+                            set.addPlottable(new DynamicPlottable(block, block));
+                        }
+                        set.getPlottable(block).put(dp.getValue("timestamp").timeValue(), dp.getValue("value"));
+                    }
+                    hvPlot.getPlot().addAll(set);
+                }
             });
-            return points;
+        });
-        }
-
     }
 
     /**
@@ -274,22 +299,10 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
                 replace("\\r", "\r\t").replace("\\n", "\n\t"));
     }
 
-    private void updateSpectrumPane(List<NMPoint> points) {
+    private void setupSpectrumPane(List<NMPoint> points) {
-        if (spectrumPlotFrame == null) {
-            Meta plotMeta = new MetaBuilder("plot")
-                    .setValue("xAxis.axisTitle", "U")
-                    .setValue("xAxis.axisUnits", "V")
-                    .setValue("yAxis.axisTitle", "count rate")
-                    .setValue("yAxis.axisUnits", "Hz")
-                    .setValue("legend.show", false);
-
-            spectrumPlotFrame = new JFreeChartFrame(plotMeta).display(spectrumPlotPane);
-
-        }
-
         if (spectrumData == null) {
             spectrumData = new ChangeablePlottableData("spectrum");
-            spectrumPlotFrame.add(spectrumData);
+            spectrumPlot.getPlot().add(spectrumData);
         }
 
         int lowChannel = (int) channelSlider.getLowValue();

numass-viewer/src/main/resources/fxml/NumassLoaderView.fxml

@@ -52,7 +52,7 @@ limitations under the License.
                 </Tab>
                 <Tab fx:id="hvTab" text="HV">
                     <content>
-                        <AnchorPane minHeight="0.0" minWidth="0.0" prefHeight="180.0" prefWidth="200.0" />
+                        <AnchorPane fx:id="hvPane" minHeight="0.0" minWidth="0.0" prefHeight="180.0" prefWidth="200.0" />
                     </content>
                 </Tab>
                 <Tab fx:id="spectrumTab" text="Spectrum">