Total plot refactoring

numass-control/cryotemp/src/main/java/inr/numass/cryotemp/PKT8MainViewController.java

@@ -166,7 +166,7 @@ public class PKT8MainViewController implements Initializable, DeviceListener, Me
             plotConfig = new MetaBuilder("plotFrame")
                     .setValue("xAxis.timeAxis", true);
         }
-        plotFrame = new JFreeChartFrame("plot", plotConfig, plotArea);
+        plotFrame = new JFreeChartFrame("plot", plotConfig).display(plotArea);
     }
 
     public void setupDevice(Meta deviceMeta) throws ControlException {

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

@@ -191,7 +191,7 @@ public class MspViewController implements Initializable, MspListener {
                         .setValue("axisUnits", "mbar")
                 )
                 .setValue("xAxis.timeAxis", true);
-        this.plotFrame = new JFreeChartFrame(mspName, plotConfig, plotPane);
+        this.plotFrame = new JFreeChartFrame(mspName, plotConfig).display(plotPane);
         updatePlot();
 //        this.plot = DynamicPlot.attachToFX(plotPane, new AnnotationBuilder("plot-config").putValue("logY", true).build());
 //        plot.setAutoRange(30 * 60);

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, chartPannel);
+            this.plotFrame = new JFreeChartFrame("pressures", plotConfig).display(chartPannel);
             XYPlot xyPlot = plotFrame.getChart().getXYPlot();
 
             LogarithmicAxis logAxis = new LogarithmicAxis("Pressure (mbar)");

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

@@ -28,12 +28,10 @@ import hep.dataforge.description.ValueDef;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.exceptions.ContentException;
 import hep.dataforge.io.log.Logable;
-import hep.dataforge.plots.PlotFrame;
 import hep.dataforge.plots.PlotsPlugin;
 import hep.dataforge.plots.XYPlotFrame;
 import hep.dataforge.plots.data.PlottableData;
 import hep.dataforge.plots.data.PlottableFunction;
-import hep.dataforge.plots.jfreechart.JFreeChartFrame;
 import java.util.ArrayList;
 import java.util.List;
 import org.apache.commons.math3.analysis.UnivariateFunction;
@@ -52,32 +50,34 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
     }
 
     @Override
-    protected FitState execute(Logable log, Meta metaData, FitState input){
+    protected FitState execute(Logable log, Meta metaData, FitState input) {
 
         DataSet data = input.getDataSet();
-        if(!(input.getModel() instanceof XYModel)){
+        if (!(input.getModel() instanceof XYModel)) {
             log.logError("The fit model should be instance of XYModel for this action. Action failed!");
             return input;
         }
-        XYModel model = (XYModel)input.getModel();
+        XYModel model = (XYModel) input.getModel();
 
         XYDataAdapter adapter;
-        if (metaData.hasNode("adapter")){
+        if (metaData.hasNode("adapter")) {
             adapter = new XYDataAdapter(metaData.getNode("adapter"));
-        } else if(input.getModel() instanceof XYModel){
+        } else if (input.getModel() instanceof XYModel) {
             adapter = model.getAdapter();
-        } else throw new ContentException("No adapter defined for data interpretation");
+        } else {
+            throw new ContentException("No adapter defined for data interpretation");
+        }
 
         UnivariateFunction function = (double x) -> model.getSpectrum().value(x, input.getParameters());
 
-        XYPlotFrame frame = (XYPlotFrame) PlotsPlugin.buildFrom(getContext()).buildPlotFrame(getName(), input.getName(), metaData);
+        XYPlotFrame frame = (XYPlotFrame) PlotsPlugin
+                .buildFrom(getContext()).buildPlotFrame(getName(), input.getName(),
+                        metaData.getNode("plot", null));
         //JFreeChartFrame.drawFrame(reader.getString("plotTitle", "Fit result plot for "+input.getName()), null);
 
         double[] x = new double[data.size()];
 
 //        double[] y = new double[data.size()];
-        
-        
         double xMin = Double.POSITIVE_INFINITY;
 
         double xMax = Double.NEGATIVE_INFINITY;
@@ -89,11 +89,11 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
 //            y[i] = adapter.getY(data.get(i)); 
 
             points.add(adapter.mapToDefault(data.get(i)));
-            if(x[i]<xMin){
+            if (x[i] < xMin) {
                 xMin = x[i];
             }
 
-            if(x[i]>xMax){
+            if (x[i] > xMax) {
                 xMax = x[i];
             }
         }
@@ -102,7 +102,6 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
 
         frame.add(new PlottableData("data", null, points));
 
-        
         return input;
     }
 

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

@@ -66,7 +66,7 @@ public class NumassPlugin extends BasicPlugin {
 
     @Override
     public void apply(Context context) {
-        FitManager fm = context.provide("hep.dataforge:fitting", FitPlugin.class).getFitManager();
+        FitManager fm = context.provide("fitting", FitPlugin.class).getFitManager();
         ModelManager mm = fm.getModelManager();
         loadModels(mm);
 

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

@@ -53,7 +53,7 @@ public class MergeDataAction extends ManyToOneAction<DataSet, DataSet> {
     @Override
     protected List<NamedGroup<DataSet>> buildGroups(Meta reader, List<DataSet> input) {
         List<NamedGroup<DataSet>> groups;
-        if (reader.hasNode("grouping")) {
+        if (reader.hasValue("grouping.byValue")) {
             groups = super.buildGroups(reader, input);
         } else {
             groups = GroupBuilder.byValue(MERGE_NAME, reader.getString(MERGE_NAME, "merge")).group(input);

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

@@ -19,6 +19,7 @@ import hep.dataforge.actions.OneToOneAction;
 import hep.dataforge.context.Context;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.exceptions.ContentException;
+import hep.dataforge.plots.fx.FXPlotUtils;
 import hep.dataforge.io.ColumnedDataWriter;
 import hep.dataforge.io.log.Logable;
 import hep.dataforge.meta.Meta;
@@ -154,7 +155,7 @@ public class ShowSpectrumAction extends OneToOneAction<NMFile, NMFile> {
             axisName += " per " + binning + " chanels";
         }
 
-        JFreeChartFrame frame = JFreeChartFrame.drawFrame(head, null);
+        JFreeChartFrame frame = FXPlotUtils.displayJFreeChart(head, null);
         
         frame.getYAxisConfig().putValue("title", axisName);
 

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

@@ -26,7 +26,9 @@ import java.util.List;
  */
 public class RawNMPoint implements Cloneable {
 
+    public static final int MAX_EVENTS_PER_POINT = 260000;
     public static int MAX_CHANEL = 4095;
+    
     private Instant startTime;
     private final List<NMEvent> events;
     private double length;
@@ -103,6 +105,9 @@ public class RawNMPoint implements Cloneable {
         if (Double.isNaN(length)) {
             throw new Error();
         }
+        if(events.size()>MAX_EVENTS_PER_POINT){
+            return events.get(events.size()-1).getTime()-events.get(0).getTime();
+        }
         return length;
     }
 

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

@@ -15,19 +15,12 @@
  */
 package inr.numass.models;
 
-import hep.dataforge.context.Context;
-import hep.dataforge.context.GlobalContext;
 import hep.dataforge.functions.FunctionCaching;
-import hep.dataforge.io.log.Logable;
 import hep.dataforge.maths.NamedDoubleSet;
 import hep.dataforge.maths.integration.GaussRuleIntegrator;
 import hep.dataforge.maths.integration.UnivariateIntegrator;
-import hep.dataforge.meta.MetaBuilder;
-import hep.dataforge.plots.PlotFrame;
-import hep.dataforge.plots.PlotsPlugin;
 import hep.dataforge.plots.XYPlotFrame;
 import hep.dataforge.plots.data.PlottableFunction;
-import hep.dataforge.plots.jfreechart.JFreeChartFrame;
 import static java.lang.Math.exp;
 import java.util.ArrayList;
 import java.util.HashMap;

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

@@ -5,26 +5,30 @@
  */
 package inr.numass.workbench;
 
+import hep.dataforge.plots.fx.PlotContainer;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.plots.jfreechart.JFreeChartFrame;
-import javafx.scene.layout.AnchorPane;
 
 public class PlotOutputTab extends OutputTab {
 
-    private JFreeChartFrame frame;
+    private final JFreeChartFrame frame;
 
     public PlotOutputTab(String name, Meta meta) {
         super(name);
-        AnchorPane pane = new AnchorPane();
+        PlotContainer container = new PlotContainer();
-        frame = new JFreeChartFrame(name, meta, pane);
+        frame = new JFreeChartFrame(name, meta);
-        setContent(pane);
+        container.setPlot(frame);
+//        AnchorPane pane = new AnchorPane();
+//        frame = new JFreeChartFrame(name, meta).display(pane);
+        setContent(container);
     }
 
     public PlotOutputTab(String name, String title, Meta meta) {
         super(name, title);
-        AnchorPane pane = new AnchorPane();
+        PlotContainer container = new PlotContainer();
-        frame = new JFreeChartFrame(name, meta, pane);
+        frame = new JFreeChartFrame(name, meta);
-        setContent(pane);
+        container.setPlot(frame);        
+        setContent(container);
     }
 
     @Override

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

@@ -16,7 +16,7 @@
 package inr.numass.models;
 
 import hep.dataforge.datafitter.ParamSet;
-import hep.dataforge.plots.jfreechart.JFreeChartFrame;
+import hep.dataforge.plots.fx.FXPlotUtils;
 
 /**
  *
@@ -36,6 +36,6 @@ public class PlotScatter {
                 + "'ionW'	= 11.33 ± 0.43\n"
                 + "'exIonRatio'	= 4.83 ± 0.36"
         );
-        LossCalculator.plotScatter(JFreeChartFrame.drawFrame("Loss function", null),pars);
+        LossCalculator.plotScatter(FXPlotUtils.displayJFreeChart("Loss function", null),pars);
     }
 }

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

@@ -15,10 +15,10 @@
  */
 package inr.numass.models;
 
+import hep.dataforge.plots.fx.FXPlotUtils;
 import hep.dataforge.maths.integration.GaussRuleIntegrator;
 import hep.dataforge.plots.PlotFrame;
 import hep.dataforge.plots.data.PlottableFunction;
-import hep.dataforge.plots.jfreechart.JFreeChartFrame;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 
 /**
@@ -31,7 +31,8 @@ public class TestNeLossParametrisation {
      * @param args the command line arguments
      */
     public static void main(String[] args) {
-        PlotFrame frame = JFreeChartFrame.drawFrame("Loss parametrisation test", null);
+        PlotFrame frame = FXPlotUtils.displayJFreeChart("Loss parametrisation test", null);
+    //JFreeChartFrame.drawFrame("Loss parametrisation test", null);
         UnivariateFunction oldFunction = LossCalculator.getSingleScatterFunction();
         UnivariateFunction newFunction = getSingleScatterFunction(12.86, 16.78, 1.65, 12.38, 4.79);
 

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

@@ -16,6 +16,7 @@
 package inr.numass.models;
 
 import hep.dataforge.context.GlobalContext;
+import hep.dataforge.plots.fx.FXPlotUtils;
 import hep.dataforge.plots.data.PlottableData;
 import hep.dataforge.plots.data.PlottableFunction;
 import hep.dataforge.plots.jfreechart.JFreeChartFrame;
@@ -27,14 +28,14 @@ import hep.dataforge.plots.jfreechart.JFreeChartFrame;
 public class TransmissionInterpolatorTest {
 
     public static void main(String[] args) {
-        JFreeChartFrame frame = JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null);
+        JFreeChartFrame frame = FXPlotUtils.displayJFreeChart("TransmissionInterpolatorTest", null);
+//JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null);
         TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(GlobalContext.instance(),
                 "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.out", "Uset", "CR", 15, 0.8, 19002d);
         frame.add(new PlottableData("data", interpolator.getX(), interpolator.getY()));
         frame.add(new PlottableFunction("interpolated", null, interpolator, interpolator.getXmin(), interpolator.getXmax(), 2000));
 
 //        PrintFunction.printFuntionSimple(new PrintWriter(System.out), interpolator, interpolator.getXmin(), interpolator.getXmax(), 500);
-
     }
 
 }

numass-prop/src/test/java/hep/dataforge/numass/prop/TestReader.java

@@ -19,6 +19,7 @@ import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
 import hep.dataforge.context.GlobalContext;
 import hep.dataforge.data.FileData;
+import hep.dataforge.plots.fx.FXPlotUtils;
 import inr.numass.prop.ar.JNAEpisode;
 import inr.numass.prop.ar.JNASpectrum;
 import inr.numass.prop.ar.ReadJNADataAction;
@@ -57,7 +58,7 @@ public class TestReader {
             System.out.printf("%g\t%d%n", entry.getKey(), entry.getValue());
         }
 
-        PlotFrame frame = JFreeChartFrame.drawFrame("JNA_Test", null);
+        PlotFrame frame = FXPlotUtils.displayJFreeChart("JNA test", null);
 
         frame.add(new PlottableData(sp.asDataSet(), "chanel", "count"));
 

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

@@ -162,12 +162,13 @@ public class NumassDataLoader extends AbstractLoader implements BinaryLoader<Env
         ByteBuffer buffer = envelope.getData();
         buffer.position(0);
         buffer.order(ByteOrder.LITTLE_ENDIAN);
+        double timeCoef = envelope.meta().getDouble("time_coeff",50);
         while (buffer.hasRemaining()) {
             try {
                 short channel = (short) Short.toUnsignedInt(buffer.getShort());
                 long time = Integer.toUnsignedLong(buffer.getInt());
                 byte status = buffer.get();
-                NMEvent event = new NMEvent(channel, time);
+                NMEvent event = new NMEvent(channel, (double)time*timeCoef*1e-9);
                 events.add(event);
             } catch (Exception ex) {
                 //LoggerFactory.getLogger(MainDataReader.class).error("Error in data format", ex);

numass-viewer/build.gradle

@@ -5,7 +5,7 @@ if (!hasProperty('mainClass')) {
 }
 mainClassName = mainClass
 
-version = "0.2.3"
+version = "0.2.4"
 
 description = "The viewer for numass data"
 

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

@@ -39,6 +39,7 @@ import javafx.scene.control.ButtonBar.ButtonData;
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.Dialog;
 import javafx.scene.control.Label;
+import javafx.scene.control.ScrollPane;
 import javafx.scene.control.SplitPane;
 import javafx.scene.control.Tab;
 import javafx.scene.control.TabPane;
@@ -103,7 +104,7 @@ public class MainViewerController implements Initializable, FXTaskManager {
     @FXML
     private Label storagePathLabel;
     @FXML
-    private AnchorPane taskPane;
+    private ScrollPane taskPane;
 
     private TaskProgressView progressView;
 
@@ -126,10 +127,10 @@ public class MainViewerController implements Initializable, FXTaskManager {
 
         consoleButton.setSelected(false);
         loadRemoteButton.setDisable(true);
-        mspController.setCallback(this);
 
         progressView = new TaskProgressView();
-        taskPane.getChildren().add(progressView);
+        taskPane.setContent(progressView);
+//        taskPane.setPrefWidth(510);
     }
 
     @FXML

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

@@ -270,7 +270,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
                     .setValue("yAxis.axisUnits", "Hz")
                     .setValue("legend.show", false);
 
-            spectrumPlotFrame = new JFreeChartFrame("spectrum", plotMeta, spectrumPlotPane);
+            spectrumPlotFrame = new JFreeChartFrame("spectrum", plotMeta).display(spectrumPlotPane);
         }
 
         if (spectrumData == null) {
@@ -328,7 +328,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab
                             .build())
                     .build();
 
-            detectorPlotFrame = new JFreeChartFrame("detectorSignal", frameMeta, detectorPlotPane);
+            detectorPlotFrame = new JFreeChartFrame("detectorSignal", frameMeta).display(detectorPlotPane);
 
             for (XYPlottable pl : detectorData) {
                 detectorPlotFrame.add(pl);

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

@@ -72,16 +72,12 @@ limitations under the License.
                               </Tab>
                           </tabs>
                       </TabPane>
-                  <SplitPane dividerPositions="0.0">
+                  <AnchorPane prefHeight="200.0" prefWidth="200.0">
-                     <items>
+                     <children>
-                        <ScrollPane minWidth="300.0" prefWidth="300.0">
+                        <ScrollPane fx:id="taskPane" hbarPolicy="NEVER" minWidth="510.0" prefWidth="510.0" vmax="510.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.topAnchor="0.0" />
-                           <content>
+                        <TextArea fx:id="consoleArea" editable="false" minHeight="0.0" wrapText="true" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="510.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0" />
-                              <AnchorPane fx:id="taskPane" minWidth="300.0" prefWidth="300.0" />
+                     </children>
-                           </content>
+                  </AnchorPane>
-                        </ScrollPane>
-                        <TextArea fx:id="consoleArea" editable="false" minHeight="0.0" wrapText="true" />
-                     </items>
-                  </SplitPane>
                </items>
             </SplitPane>
             </center>