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;
@@ -52,58 +50,59 @@ 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
-                //JFreeChartFrame.drawFrame(reader.getString("plotTitle", "Fit result plot for "+input.getName()), null);
+                .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;        
+        double xMax = Double.NEGATIVE_INFINITY;
-  
+
         List<DataPoint> points = new ArrayList<>();
-        
+
         for (int i = 0; i < data.size(); i++) {
             x[i] = adapter.getX(data.get(i)).doubleValue();
 //            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];
-            }            
+            }
         }
-        
+
         frame.add(new PlottableFunction("fit", null, function, points, "x"));
-        
+
         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

@@ -13,56 +13,57 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.models;
+package inr.numass.models;
-
+
-import hep.dataforge.maths.integration.GaussRuleIntegrator;
+import hep.dataforge.plots.fx.FXPlotUtils;
-import hep.dataforge.plots.PlotFrame;
+import hep.dataforge.maths.integration.GaussRuleIntegrator;
-import hep.dataforge.plots.data.PlottableFunction;
+import hep.dataforge.plots.PlotFrame;
-import hep.dataforge.plots.jfreechart.JFreeChartFrame;
+import hep.dataforge.plots.data.PlottableFunction;
-import org.apache.commons.math3.analysis.UnivariateFunction;
+import org.apache.commons.math3.analysis.UnivariateFunction;
-
+
-/**
+/**
- *
+ *
- * @author Alexander Nozik
+ * @author Alexander Nozik
- */
+ */
-public class TestNeLossParametrisation {
+public class TestNeLossParametrisation {
-
+
-    /**
+    /**
-     * @param args the command line arguments
+     * @param args the command line arguments
-     */
+     */
-    public static void main(String[] args) {
+    public static void main(String[] args) {
-        PlotFrame frame = JFreeChartFrame.drawFrame("Loss parametrisation test", null);
+        PlotFrame frame = FXPlotUtils.displayJFreeChart("Loss parametrisation test", null);
-        UnivariateFunction oldFunction = LossCalculator.getSingleScatterFunction();
+    //JFreeChartFrame.drawFrame("Loss parametrisation test", null);
-        UnivariateFunction newFunction = getSingleScatterFunction(12.86, 16.78, 1.65, 12.38, 4.79);
+        UnivariateFunction oldFunction = LossCalculator.getSingleScatterFunction();
-        
+        UnivariateFunction newFunction = getSingleScatterFunction(12.86, 16.78, 1.65, 12.38, 4.79);
-        Double norm = new GaussRuleIntegrator(200).integrate(newFunction, 0d, 100d);
+
-        
+        Double norm = new GaussRuleIntegrator(200).integrate(newFunction, 0d, 100d);
-        System.out.println(norm);
+
-        
+        System.out.println(norm);
-        frame.add(new PlottableFunction("old", null, oldFunction, 0, 30, 300));
+
-        frame.add(new PlottableFunction("new", null, newFunction, 0, 30, 300));
+        frame.add(new PlottableFunction("old", null, oldFunction, 0, 30, 300));
-    }
+        frame.add(new PlottableFunction("new", null, newFunction, 0, 30, 300));
-
+    }
-    public static UnivariateFunction getSingleScatterFunction(
+
-            final double exPos,
+    public static UnivariateFunction getSingleScatterFunction(
-            final double ionPos,
+            final double exPos,
-            final double exW,
+            final double ionPos,
-            final double ionW,
+            final double exW,
-            final double exIonRatio) {
+            final double ionW,
-
+            final double exIonRatio) {
-        return (double eps) -> {
+
-            if (eps <= 0) {
+        return (double eps) -> {
-                return 0;
+            if (eps <= 0) {
-            }
+                return 0;
-            double z = eps - exPos;
+            }
-            // Используется полная ширина, а не полуширина.
+            double z = eps - exPos;
-            double res = exIonRatio * Math.exp(-2 * z * z / exW / exW) * Math.sqrt(2 / Math.PI) / exW;
+            // Используется полная ширина, а не полуширина.
-            
+            double res = exIonRatio * Math.exp(-2 * z * z / exW / exW) * Math.sqrt(2 / Math.PI) / exW;
-            if (eps >= ionPos) {
+
-                z = 4 * (eps - ionPos) * (eps - ionPos);
+            if (eps >= ionPos) {
-                res += 4d / (1 + z / ionW / ionW) / Math.PI / ionW;
+                z = 4 * (eps - ionPos) * (eps - ionPos);
-            }
+                res += 4d / (1 + z / ionW / ionW) / Math.PI / ionW;
-            return res / (1 + exIonRatio);
+            }
-        };
+            return res / (1 + exIonRatio);
-    }
+        };
-}
+    }
+}

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

@@ -13,28 +13,29 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.models;
+package inr.numass.models;
-
+
-import hep.dataforge.context.GlobalContext;
+import hep.dataforge.context.GlobalContext;
-import hep.dataforge.plots.data.PlottableData;
+import hep.dataforge.plots.fx.FXPlotUtils;
-import hep.dataforge.plots.data.PlottableFunction;
+import hep.dataforge.plots.data.PlottableData;
-import hep.dataforge.plots.jfreechart.JFreeChartFrame;
+import hep.dataforge.plots.data.PlottableFunction;
-
+import hep.dataforge.plots.jfreechart.JFreeChartFrame;
-/**
+
- *
+/**
- * @author darksnake
+ *
- */
+ * @author darksnake
-public class TransmissionInterpolatorTest {
+ */
-
+public class TransmissionInterpolatorTest {
-    public static void main(String[] args) {
+
-        JFreeChartFrame frame = JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null);
+    public static void main(String[] args) {
-        TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(GlobalContext.instance(),
+        JFreeChartFrame frame = FXPlotUtils.displayJFreeChart("TransmissionInterpolatorTest", null);
-                "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.out", "Uset", "CR", 15, 0.8, 19002d);
+//JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null);
-        frame.add(new PlottableData("data", interpolator.getX(), interpolator.getY()));        
+        TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(GlobalContext.instance(),
-        frame.add(new PlottableFunction("interpolated", null, interpolator, interpolator.getXmin(), interpolator.getXmax(), 2000));
+                "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()));
-//        PrintFunction.printFuntionSimple(new PrintWriter(System.out), interpolator, interpolator.getXmin(), interpolator.getXmax(), 500);
+        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>