Numass statistical count rate

numass-control/build.gradle

@@ -1,5 +1,5 @@
 buildscript {
-    ext.kotlin_version = '1.1.2-5'
+    ext.kotlin_version = '1.1.3'
 
     repositories {
         mavenCentral()
@@ -29,7 +29,7 @@ dependencies {
 
     //graphics
     compile 'org.controlsfx:controlsfx:8.40.12'
-    compile "no.tornado:tornadofx:1.7.5"
+    compile "no.tornado:tornadofx:1.7.8"
 }
 
 task installAll(type: Copy) {

numass-control/cryotemp/src/main/kotlin/inr/numass/control/cryotemp/PKT8ViewConnection.kt

@@ -65,13 +65,13 @@ class PKT8ViewConnection : DeviceViewConnection<PKT8Device>(), MeasurementListen
         private var plotButton: ToggleButton by singleAssign()
         private var logButton: ToggleButton by singleAssign()
 
-        private val logWindow = FragmentWindow(LogFragment().apply {
+//        private val logWindow = FragmentWindow(LogFragment().apply {
-            addLogHandler(device.logger)
+//            addLogHandler(device.logger)
-        })
+//        })
 
         // need those to have strong references to listeners
         private val plotView = CryoPlotView();
-        private val plotWindow = FragmentWindow(FXFragment.buildFromNode(plotView.title) { plotView.root })
+//        private val plotWindow = FragmentWindow(FXFragment.buildFromNode(plotView.title) { plotView.root })
 
         override val root = borderpane {
             top {
@@ -92,12 +92,16 @@ class PKT8ViewConnection : DeviceViewConnection<PKT8Device>(), MeasurementListen
 
                     plotButton = togglebutton("Plot") {
                         isSelected = false
-                        plotWindow.bindTo(this)
+                        FragmentWindow.build(this) { FXFragment.buildFromNode(plotView.title) { plotView.root } }
                     }
 
                     logButton = togglebutton("Log") {
                         isSelected = false
-                        logWindow.bindTo(this)
+                        FragmentWindow.build(this) {
+                            LogFragment().apply {
+                                addLogHandler(device.logger)
+                            }
+                        }
                     }
                 }
             }

numass-control/msp/src/main/kotlin/inr/numass/control/msp/MspViewConnection.kt

@@ -109,9 +109,9 @@ class MspViewConnection() : DeviceViewConnection<MspDevice>(), DeviceListener, N
             }
         }
 
-        private val logWindow = FragmentWindow(LogFragment().apply {
+//        private val logWindow = FragmentWindow(LogFragment().apply {
-            addLogHandler(device.logger)
+//            addLogHandler(device.logger)
-        })
+//        })
 
         val filamentProperty = SimpleObjectProperty<Int>(this, "filament", 1).apply {
             addListener { _, oldValue, newValue ->
@@ -173,7 +173,9 @@ class MspViewConnection() : DeviceViewConnection<MspDevice>(), DeviceListener, N
 
                     togglebutton("Log") {
                         isSelected = false
-                        logWindow.bindTo(this)
+                        FragmentWindow.build(this){LogFragment().apply {
+                            addLogHandler(device.logger)
+                        }}
                     }
                 }
             }

numass-control/src/main/kotlin/inr/numass/control/DeviceViewConnection.kt

@@ -141,7 +141,7 @@ abstract class DeviceViewConnection<D : Device> : Component(), Connection, Devic
             }
             togglebutton("View") {
                 isSelected = false
-                FragmentWindow(FXFragment.buildFromNode(device.name) { fxNode }).bindTo(this)
+                FragmentWindow.build(this){FXFragment.buildFromNode(device.name) { fxNode }}
             }
         }
     }

numass-control/vac/src/main/kotlin/inr/numass/control/readvac/VacCollectorViewConnection.kt

@@ -74,9 +74,9 @@ class VacCollectorViewConnection : DeviceViewConnection<VacCollectorDevice>() {
             setValue("thickness", 3)
         }
 
-        private val logWindow = FragmentWindow(LogFragment().apply {
+//        private val logWindow = FragmentWindow(LogFragment().apply {
-            addLogHandler(device.logger)
+//            addLogHandler(device.logger)
-        })
+//        })
 
         override val root = borderpane {
             top {
@@ -89,7 +89,9 @@ class VacCollectorViewConnection : DeviceViewConnection<VacCollectorDevice>() {
                     separator(Orientation.VERTICAL)
                     togglebutton("Log") {
                         isSelected = false
-                        logWindow.bindTo(this)
+                        FragmentWindow.build(this){LogFragment().apply {
+                            addLogHandler(device.logger)
+                        }}
                     }
                 }
             }

numass-core/src/main/java/inr/numass/data/LegacyDataReader.java

@@ -23,35 +23,37 @@ import java.io.*;
 import java.time.LocalDateTime;
 import java.time.ZoneOffset;
 import java.time.format.DateTimeFormatter;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Scanner;
 
 /**
  *
  * @author Darksnake, based on program by S.V.Zadorozhny, 1996
  */
-public class NumassDataReader {
+public class LegacyDataReader {
 
     private final InputStream stream;
     private String name;
     private double HVdev = 2.468555393226049;
     private boolean noUset = false;
 
-    public NumassDataReader(Binary file, Meta config) throws IOException {
+    public LegacyDataReader(Binary file, Meta config) throws IOException {
         this(file.getStream(), config.getString(FileDataFactory.FILE_NAME_KEY), config);
     }
     
-    public NumassDataReader(File file) throws IOException {
+    public LegacyDataReader(File file) throws IOException {
         this(new FileInputStream(file), file.getName(), Meta.empty());
     }    
 
-    public NumassDataReader(String file, String fname, Meta config) throws FileNotFoundException {
+    public LegacyDataReader(String file, String fname, Meta config) throws FileNotFoundException {
         this(new FileInputStream(file), fname, config);
         if ((fname == null) || (fname.isEmpty())) {
             name = file;
         }
     }
 
-    public NumassDataReader(InputStream is, String fname, Meta config) {
+    public LegacyDataReader(InputStream is, String fname, Meta config) {
         this.stream = new BufferedInputStream(is);
         this.name = fname;
         HVdev = config.getDouble("HVdev", 2.468555393226049);
@@ -204,12 +206,14 @@ public class NumassDataReader {
         }
 
         lab = readByte();
+
+        List<NMEvent> events = new ArrayList<>();
         while (lab == 0xBF) {
             skip(4);//badHV
             lab = readByte();
         }
         do {
-            point.putEvent(readEvent(lab, timeDiv));
+            events.add(readEvent(lab, timeDiv));
             lab = readByte();
         } while (lab != 0xAF);
 
@@ -226,7 +230,6 @@ public class NumassDataReader {
             absoluteTime = absoluteTime.plusDays(1);
         }
 
-        point.setStartTime(absoluteTime.toInstant(ZoneOffset.UTC));
 
         rx = readBlock(4);
         int Uread = rx[2] + 256 * rx[3];
@@ -234,15 +237,14 @@ public class NumassDataReader {
 
         skip(21);
 
-        point.setLength(time_out);
+        double uset;
-        point.setUread(Uread / 10d / HVdev);
         if (noUset) {
-            point.setUset(Uread / 10d / HVdev);
+            uset = Uread / 10d / HVdev;
         } else {
-            point.setUset(voltage / 10d);
+            uset = voltage / 10d;
         }
 
-        return point;
+        return new RawNMPoint(uset, Uread / 10d / HVdev, events, time_out, absoluteTime.toInstant(ZoneOffset.UTC));
     }
 
     private long readTime() throws IOException {

numass-core/src/main/java/inr/numass/data/NMFile.java

@@ -47,11 +47,11 @@ public class NMFile extends NamedMetaHolder implements NumassData {
     }
 
     public static NMFile readStream(InputStream is, String fname, Meta config) throws IOException {
-        return new NMFile(new NumassDataReader(is, fname, config).read());
+        return new NMFile(new LegacyDataReader(is, fname, config).read());
     }
 
     public static NMFile readFile(File file) throws IOException {
-        return new NMFile(new NumassDataReader(file).read());
+        return new NMFile(new LegacyDataReader(file).read());
     }
 
     @Override

numass-core/src/main/java/inr/numass/data/NumassData.java

@@ -10,6 +10,7 @@ import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.Metoid;
 import hep.dataforge.names.Named;
 import hep.dataforge.tables.Table;
+import org.jetbrains.annotations.NotNull;
 
 import java.time.Instant;
 import java.util.Iterator;
@@ -29,6 +30,7 @@ public interface NumassData extends Named, Metoid, Iterable<NumassPoint> {
 
     Stream<NumassPoint> stream();
 
+    @NotNull
     @Override
     default Iterator<NumassPoint> iterator() {
         return stream().iterator();

numass-core/src/main/java/inr/numass/data/NumassDataUtils.java

@@ -45,7 +45,7 @@ public class NumassDataUtils {
         }
         int[] newArray = new int[first.getSpectrum().length];
         Arrays.setAll(newArray, i -> first.getSpectrum()[i] + second.getSpectrum()[i]);
-        return new NMPoint(
+        return new NumassPointImpl(
                 first.getVoltage(),
                 Instant.EPOCH,
                 first.getLength() + second.getLength(),
@@ -56,7 +56,7 @@ public class NumassDataUtils {
     public static NumassPoint substractPoint(NumassPoint point, NumassPoint reference) {
         int[] array = new int[point.getSpectrum().length];
         Arrays.setAll(array, i -> Math.max(0, point.getSpectrum()[i] - reference.getSpectrum()[i]));
-        return new NMPoint(
+        return new NumassPointImpl(
                 point.getVoltage(),
                 point.getStartTime(),
                 point.getLength(),

numass-core/src/main/java/inr/numass/data/NumassPointImpl.java

@@ -26,7 +26,7 @@ import java.util.stream.IntStream;
 /**
  * @author Darksnake
  */
-public class NMPoint implements NumassPoint {
+public class NumassPointImpl implements NumassPoint {
     //TODO andThen to annotated and move some parameters to meta
     private final int[] spectrum;
     private Instant startTime;
@@ -34,7 +34,7 @@ public class NMPoint implements NumassPoint {
     private double pointLength;
     private double u;
 
-    public NMPoint(double u, Instant startTime, double pointLength, int[] spectrum) {
+    public NumassPointImpl(double u, Instant startTime, double pointLength, int[] spectrum) {
         this.startTime = startTime;
         this.pointLength = pointLength;
         this.spectrum = spectrum;

numass-core/src/main/java/inr/numass/data/PointBuilders.java

@@ -27,7 +27,7 @@ public class PointBuilders {
                 )),0
         );
 
-        return new NMPoint(u, startTime, pointLength, spectrum);
+        return new NumassPointImpl(u, startTime, pointLength, spectrum);
     }
 
     private static int[] calculateSpectrum(RawNMPoint point) {
@@ -37,7 +37,7 @@ public class PointBuilders {
 
     @NotNull
     public static NumassPoint readRawPoint(@NotNull RawNMPoint point) {
-        return new NMPoint(point.getUset(), point.getStartTime(), point.getLength(), calculateSpectrum(point));
+        return new NumassPointImpl(point.getUset(), point.getStartTime(), point.getLength(), calculateSpectrum(point));
     }
 
     private static int[] count(IntStream stream, int maxChannel) {

numass-core/src/main/java/inr/numass/data/RawNMFile.java

@@ -82,7 +82,7 @@ public class RawNMFile extends NamedMetaHolder {
         for (RawNMPoint point : points) {
             if (point.getUset() == U) {
                 if (res == null) {
-                    res = point.clone();
+                    res = point;
                 } else {
                     res = res.merge(point);
                 }
@@ -104,7 +104,7 @@ public class RawNMFile extends NamedMetaHolder {
         for (RawNMPoint point : points) {
             if (point.getUread() == U) {
                 if (res == null) {
-                    res = point.clone();
+                    res = point;
                 } else {
                     res = res.merge(point);
                 }
@@ -120,17 +120,17 @@ public class RawNMFile extends NamedMetaHolder {
         return points;
     }
 
-    public void putEvent(double U, short chanel, double time) {
+//    public void putEvent(double U, short chanel, double time) {
-        for (RawNMPoint point : this.getData()) {
+//        for (RawNMPoint point : this.getData()) {
-            if (U == point.getUread()) {
+//            if (U == point.getUread()) {
-                point.putEvent(new NMEvent(chanel, time));
+//                point.putEvent(new NMEvent(chanel, time));
-                return;
+//                return;
-            }
+//            }
-        }
+//        }
-        RawNMPoint newpoint = new RawNMPoint();
+//        RawNMPoint newpoint = new RawNMPoint();
-        newpoint.putEvent(new NMEvent(chanel, time));
+//        newpoint.putEvent(new NMEvent(chanel, time));
-        this.putPoint(newpoint);
+//        this.putPoint(newpoint);
-    }
+//    }
 
     public void putPoint(RawNMPoint point) {
         points.add(point);

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

@@ -21,14 +21,14 @@ import java.util.List;
 
 /**
  * Хранит информацию о спектре точки, но не об отдельных событиях.
- * 
+ *
  * @author Darksnake
  */
-public class RawNMPoint implements Cloneable {
+public class RawNMPoint {
 
     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;
@@ -65,24 +65,22 @@ public class RawNMPoint implements Cloneable {
         length = Double.NaN;
     }
 
-    @Override
+//    @Override
-    public RawNMPoint clone() {
+//    public RawNMPoint clone() {
-        ArrayList<NMEvent> newevents = new ArrayList<>();
+//        ArrayList<NMEvent> newevents = new ArrayList<>();
-        for (NMEvent event : this.getEvents()) {
+//        newevents.addAll(this.getEvents());
-            newevents.add(event);
+//        return new RawNMPoint(getUset(), getUread(), newevents, getLength());
-        }
+//    }
-        return new RawNMPoint(getUset(), getUread(), newevents, getLength());
-    }
 
     public Instant getStartTime() {
         return startTime;
     }
 
-    public double getCR() {
+    public double getCr() {
         return getEventsCount() / getLength();
     }
 
-    public double getCRError() {
+    public double getCrError() {
         return Math.sqrt(getEventsCount()) / getLength();
     }
 
@@ -99,6 +97,7 @@ public class RawNMPoint implements Cloneable {
 
     /**
      * Measurement time
+     *
      * @return the tset
      */
     public double getLength() {
@@ -131,18 +130,18 @@ public class RawNMPoint implements Cloneable {
     }
 
     public RawNMPoint merge(RawNMPoint point) {
-        RawNMPoint res = this.clone();
+        List<NMEvent> events = new ArrayList<>(this.events);
         for (NMEvent newEvent : point.getEvents()) {
-            res.putEvent(new NMEvent(newEvent.getChanel(), newEvent.getTime() + this.getLength()));
+            events.add(new NMEvent(newEvent.getChanel(), newEvent.getTime() + this.getLength()));
         }
-        res.length += point.getLength();
+        double length = this.length + point.length;
-        res.uread = (this.uread + point.uread) / 2;
+        double uread = (this.uread + point.uread) / 2;
-        return res;
+        return new RawNMPoint(this.uset, uread, events, length, this.startTime);
     }
 
-    void putEvent(NMEvent event) {
+//    void putEvent(NMEvent event) {
-        events.add(event);
+//        events.add(event);
-    }
+//    }
 
     public RawNMPoint selectChanels(int from, int to) {
         assert to > from;
@@ -156,30 +155,30 @@ public class RawNMPoint implements Cloneable {
         return new RawNMPoint(getUset(), getUread(), res, getLength());
     }
 
-    void setStartTime(Instant absouteTime) {
+//    void setStartTime(Instant absouteTime) {
-        this.startTime = absouteTime;
+//        this.startTime = absouteTime;
-    }
+//    }
+//
+//    /**
+//     * @param tset the tset to set
+//     */
+//    void setLength(double tset) {
+//        this.length = tset;
+//    }
 
-    /**
+//    /**
-     * @param tset the tset to set
+//     * @param Uread the Uread to set
-     */
+//     */
-    void setLength(double tset) {
+//    void setUread(double Uread) {
-        this.length = tset;
+//        assert Uread >= 0;
-    }
+//        this.uread = Uread;
-
+//    }
-    /**
+//
-     * @param Uread the Uread to set
+//    /**
-     */
+//     * @param Uset the Uset to set
-    void setUread(double Uread) {
+//     */
-        assert Uread >= 0;
+//    void setUset(double Uset) {
-        this.uread = Uread;
+//        this.uset = Uset;
-    }
+//    }
-
-    /**
-     * @param Uset the Uset to set
-     */
-    void setUset(double Uset) {
-        this.uset = Uset;
-    }
 
 }

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

@@ -21,6 +21,9 @@ import hep.dataforge.io.ColumnedDataReader;
 import hep.dataforge.io.envelopes.Envelope;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
+import hep.dataforge.providers.Provider;
+import hep.dataforge.providers.Provides;
+import hep.dataforge.providers.ProvidesNames;
 import hep.dataforge.storage.api.ObjectLoader;
 import hep.dataforge.storage.api.Storage;
 import hep.dataforge.storage.filestorage.FileEnvelope;
@@ -49,13 +52,11 @@ import java.util.stream.Stream;
  *
  * @author darksnake
  */
-public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Envelope>, NumassData {
+public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Envelope>, NumassData, Provider {
 
 
     public static NumassDataLoader fromFile(Storage storage, Path zipFile) throws IOException {
         throw new UnsupportedOperationException("TODO");
-//        FileObject zipRoot = VFS.getManager().createFileSystem(zipFile);
-//        return fromDir(storage, zipRoot, zipFile.getName().getBaseName());
     }
 
 
@@ -101,19 +102,6 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
         return new NumassDataLoader(storage, name, annotation, items);
     }
 
-
-//    private static Envelope readFile(Path file) {
-//        String fileName = file.getFileName().toString();
-//        if (fileName.equals(META_FRAGMENT_NAME)
-//                || fileName.equals(HV_FRAGMENT_NAME)
-//                || fileName.startsWith(POINT_FRAGMENT_NAME)) {
-//            return FileEnvelope.open(file, true);
-//        } else {
-//            return null;
-//        }
-//        //}
-//    }
-
     /**
      * "start_time": "2016-04-20T04:08:50",
      *
@@ -226,7 +214,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
      * @param envelope
      * @return
      */
-    public NumassPoint readPoint(Envelope envelope) {
+    private NumassPoint readPoint(Envelope envelope) {
         return readPoint(envelope, PointBuilders::readRawPoint);
     }
 
@@ -347,6 +335,26 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
 
     }
 
+    @Override
+    public String defaultTarget() {
+        return "nmPoint";
+    }
+
+    @Provides("nmPoint")
+    public Optional<NumassPoint> optPoint(String u) {
+        return stream().filter(it -> it.getVoltage() == Double.parseDouble(u)).findFirst();
+    }
+
+    @ProvidesNames("nmPoint")
+    public Stream<String> listHV() {
+        return stream().map(it -> Double.toString(it.getVoltage()));
+    }
+
+    @Provides("rawPoint")
+    public Optional<RawNMPoint> optRawPoint(String u) {
+        return this.getPoints().map(this::readRawPoint).filter(it -> it.getUset() == Double.parseDouble(u)).findFirst();
+    }
+
     /**
      * Return new NumassData using given transformation for each point
      *

numass-main/src/main/groovy/inr/numass/data/PointAnalyzer.groovy

@@ -0,0 +1,38 @@
+package inr.numass.data
+
+import groovy.transform.CompileStatic
+
+/**
+ * Created by darksnake on 27-Jun-17.
+ */
+@CompileStatic
+class PointAnalyzer {
+
+    static Result analyzePoint(RawNMPoint point, double t0 = 0, int loChannel = 0, int upChannel = 4000) {
+        int totalN = 0
+        double totalT = 0;
+        NMEvent lastEvent = point.events[0];
+
+        for (int i = 1; i < point.events.size(); i++) {
+            NMEvent event = point.events[i];
+            double t = event.time - lastEvent.time;
+            if (t >= t0 && event.chanel <= upChannel && event.chanel >= loChannel) {
+                totalN++
+                totalT += t
+            }
+            lastEvent = event
+        }
+        double cr = 1d/(totalT/totalN - t0);
+        return new Result(cr: cr, crErr: cr / Math.sqrt(totalN), num: totalN, t0: t0, loChannel: loChannel, upChannel: upChannel)
+
+    }
+
+    static class Result {
+        double cr;
+        double crErr;
+        long num;
+        double t0;
+        int loChannel;
+        int upChannel;
+    }
+}

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

@@ -8,7 +8,7 @@ package inr.numass.scripts
 
 import hep.dataforge.grind.Grind
 import hep.dataforge.tables.DataPoint
-import inr.numass.data.NMPoint
+import inr.numass.data.NumassPointImpl
 import inr.numass.data.RawNMPoint
 import inr.numass.storage.NumassDataLoader
 import inr.numass.utils.NMEventGeneratorWithPulser
@@ -43,18 +43,18 @@ def data = NumassDataLoader.fromLocalDir(null, dataDir).getNMPoints()
 //)
 
 //Simulation process
-Map<String, List<NMPoint>> res = [:]
+Map<String, List<NumassPointImpl>> res = [:]
 
-List<NMPoint> generated = new ArrayList<>();
+List<NumassPointImpl> generated = new ArrayList<>();
-List<NMPoint> registered = new ArrayList<>();
+List<NumassPointImpl> registered = new ArrayList<>();
-List<NMPoint> firstIteration = new ArrayList<>();
+List<NumassPointImpl> firstIteration = new ArrayList<>();
-List<NMPoint> secondIteration = new ArrayList<>();
+List<NumassPointImpl> secondIteration = new ArrayList<>();
-List<NMPoint> pileup = new ArrayList<>();
+List<NumassPointImpl> pileup = new ArrayList<>();
 
 lowerChannel = 400;
 upperChannel = 1800;
 
-PileUpSimulator buildSimulator(NMPoint point, double cr, NMPoint reference = null, boolean extrapolate = true, double scale = 1d) {
+PileUpSimulator buildSimulator(NumassPointImpl point, double cr, NumassPointImpl reference = null, boolean extrapolate = true, double scale = 1d) {
     def cfg = Grind.buildMeta(cr: cr) {
         pulser(mean: 3450, sigma: 86.45, freq: 66.43)
     }
@@ -88,7 +88,7 @@ PileUpSimulator buildSimulator(NMPoint point, double cr, NMPoint reference = nul
     return new PileUpSimulator(point.length * scale, rnd, generator).withUset(point.voltage).generate();
 }
 
-double adjustCountRate(PileUpSimulator simulator, NMPoint point) {
+double adjustCountRate(PileUpSimulator simulator, NumassPointImpl point) {
     double generatedInChannel = simulator.generated().getCountInWindow(lowerChannel, upperChannel);
     double registeredInChannel = simulator.registered().getCountInWindow(lowerChannel, upperChannel);
     return (generatedInChannel / registeredInChannel) * (point.getCountInWindow(lowerChannel, upperChannel) / point.getLength());
@@ -100,7 +100,7 @@ data.forEach { point ->
     PileUpSimulator simulator = buildSimulator(point, cr);
 
     //second iteration to exclude pileup overlap
-    NMPoint pileupPoint = simulator.pileup();
+    NumassPointImpl pileupPoint = simulator.pileup();
     firstIteration.add(simulator.registered());
 
     //updating count rate

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

@@ -0,0 +1,49 @@
+package inr.numass.scripts
+
+import hep.dataforge.context.Context
+import hep.dataforge.context.Global
+import hep.dataforge.grind.GrindShell
+import hep.dataforge.grind.helpers.PlotHelper
+import hep.dataforge.plots.fx.FXPlotManager
+import hep.dataforge.tables.MapPoint
+import inr.numass.NumassPlugin
+import inr.numass.data.PointAnalyzer
+import inr.numass.data.RawNMPoint
+import inr.numass.storage.NumassStorage
+import inr.numass.storage.NumassStorageFactory
+
+/**
+ * Created by darksnake on 27-Jun-17.
+ */
+
+
+Context ctx = Global.instance()
+ctx.pluginManager().load(FXPlotManager)
+ctx.pluginManager().load(NumassPlugin.class)
+
+GrindShell shell = new GrindShell(ctx)
+
+shell.eval {
+    PlotHelper plot = plots
+    File rootDir = new File("D:\\Work\\Numass\\data\\2017_05\\Fill_1")
+
+    NumassStorage storage = NumassStorageFactory.buildLocal(rootDir);
+
+    def hv = 15000;
+    def point = storage.provide("loader::set_2/rawPoint::$hv", RawNMPoint.class).get();
+
+    def t0 = (1..150).collect { 5.5e-6 + 2e-7 * it }
+
+    def plotPoints = t0.collect {
+        def result = PointAnalyzer.analyzePoint(point, it,500,3100)
+        MapPoint.fromMap("x.value": it, "y.value": result.cr, "y.err": result.crErr);
+    }
+    //def cr = t0.collect { PointAnalyzer.analyzePoint(point, it).cr }
+
+    plot.plot(plotPoints, ["name": hv])
+
+
+    plot.plot(title: "dead time", from: 5.5e-6, to: 2e-5) { point.cr * 1d / (1d - 6.55e-6 * point.cr) }
+
+    storage.close()
+}

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

@@ -9,9 +9,9 @@ package inr.numass.scripts
 import hep.dataforge.io.ColumnedDataWriter
 import hep.dataforge.storage.commons.StorageUtils
 import hep.dataforge.tables.Table
-import inr.numass.data.NMPoint
 import inr.numass.data.NumassData
 import inr.numass.data.NumassDataUtils
+import inr.numass.data.NumassPointImpl
 import inr.numass.storage.NumassStorage
 import inr.numass.storage.NumassStorageFactory
 import inr.numass.utils.UnderflowCorrection
@@ -23,7 +23,7 @@ File rootDir = new File("D:\\Work\\Numass\\data\\2017_05\\Fill_1")
 
 NumassStorage storage = NumassStorageFactory.buildLocal(rootDir);
 
-Collection<NMPoint> data = NumassDataUtils.joinSpectra(
+Collection<NumassPointImpl> data = NumassDataUtils.joinSpectra(
         StorageUtils.loaderStream(storage)
                 .filter { it.key.matches("set_.{1,3}") }
                 .map {
@@ -55,8 +55,8 @@ data = NumassDataUtils.substractReferencePoint(data, 18600d);
 //    }
 //}
 
-def printPoint(Iterable<NMPoint> data, List<Double> us, int binning = 20, normalize = true) {
+def printPoint(Iterable<NumassPointImpl> data, List<Double> us, int binning = 20, normalize = true) {
-    List<NMPoint> points = data.findAll { it.voltage in us }.sort { it.voltage }
+    List<NumassPointImpl> points = data.findAll { it.voltage in us }.sort { it.voltage }
 
     Map spectra = points.first().getMap(binning, normalize).collectEntries { key, value ->
         [key, [value]]

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

@@ -20,8 +20,7 @@ import hep.dataforge.data.binary.Binary;
 import hep.dataforge.io.BasicIOManager;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.names.Name;
-import inr.numass.data.NumassDataReader;
+import inr.numass.data.LegacyDataReader;
-import inr.numass.data.NumassPawReader;
 import inr.numass.data.RawNMFile;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.output.TeeOutputStream;
@@ -40,7 +39,7 @@ public class NumassIO extends BasicIOManager {
     public static final String NUMASS_OUTPUT_CONTEXT_KEY = "numass.outputDir";
 
     public static RawNMFile readAsDat(Binary source, Meta config) throws IOException {
-        return new NumassDataReader(source, config).read();
+        return new LegacyDataReader(source, config).read();
     }
 
 //    private File getOutputDir() {
@@ -53,18 +52,15 @@ public class NumassIO extends BasicIOManager {
 //
 //    }
 
-    public static RawNMFile readAsPaw(Binary source, Meta config) throws IOException {
+//    public static RawNMFile readAsPaw(Binary source, Meta config) throws IOException {
-        return new NumassPawReader().readPaw(source, config.getString(FileDataFactory.FILE_NAME_KEY));
+//        return new NumassPawReader().readPaw(source, config.getString(FileDataFactory.FILE_NAME_KEY));
-    }
+//    }
 
     public static RawNMFile getNumassData(Binary binary, Meta config) {
         try {
             RawNMFile dataFile;
             String extension = FilenameUtils.getExtension(config.getString(FileDataFactory.FILE_NAME_KEY)).toLowerCase();
             switch (extension) {
-                case "paw":
-                    dataFile = readAsPaw(binary, config);
-                    break;
                 case "dat":
                     dataFile = readAsDat(binary, config);
                     break;

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

@@ -53,7 +53,7 @@ public class DebunchAction extends OneToOneAction<RawNMFile, RawNMFile> {
 
         RawNMFile res = new RawNMFile(source.getName(), source.getHead());
         source.getData().stream().map((point) -> {
-            double cr = point.selectChanels(lower, upper).getCR();
+            double cr = point.selectChanels(lower, upper).getCr();
             if (cr < maxCR) {
                 DebunchReport report = new FrameAnalizer(rejectionprob, framelength, lower, upper).debunchPoint(point);
 

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

@@ -4,9 +4,9 @@ import hep.dataforge.actions.ManyToOneAction;
 import hep.dataforge.context.Context;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.meta.Laminate;
-import inr.numass.data.NMPoint;
 import inr.numass.data.NumassData;
 import inr.numass.data.NumassPoint;
+import inr.numass.data.NumassPointImpl;
 
 import java.util.Collection;
 import java.util.Map;
@@ -29,7 +29,7 @@ public class JoinNumassDataAction extends ManyToOneAction<NumassData, NumassData
             if (p1.getVoltage() != p2.getVoltage()) {
                 throw new RuntimeException("Can't sum points with different Uset");
             }
-            return new NMPoint(
+            return new NumassPointImpl(
                     (p1.getVoltage() + p2.getVoltage()) / 2,
                     p1.getStartTime(),
                     p1.getLength() + p2.getLength(),

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

@@ -204,7 +204,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
         double framelength = meta.getDouble("framelength", 1);
         double maxCR = meta.getDouble("maxcr", 500d);
 
-        double cr = point.selectChanels(lower, upper).getCR();
+        double cr = point.selectChanels(lower, upper).getCr();
         if (cr < maxCR) {
             DebunchReport report = new FrameAnalizer(rejectionprob, framelength, lower, upper).debunchPoint(point);
             return PointBuilders.readRawPoint(report.getPoint());

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

@@ -1,60 +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.data;
-
-import hep.dataforge.data.binary.Binary;
-
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Locale;
-import java.util.Scanner;
-
-/**
- *
- * @author Darksnake
- */
-public class NumassPawReader {
-
-    public RawNMFile readPaw(Binary file, String name) throws IOException{
-        Locale.setDefault(Locale.US);
-        return readPaw(file.getStream(), name);
-    }
-    
-    public RawNMFile readPaw(String filePath) throws FileNotFoundException{
-        return readPaw(new FileInputStream(filePath), filePath);
-    }
-    
-
-    private RawNMFile readPaw(InputStream stream, String fileName) {
-        Scanner s = new Scanner(stream);
-        RawNMFile result = new RawNMFile(fileName);
-
-        while (s.hasNext()) {
-            long eventNum = s.nextLong();
-            double time = s.nextDouble();
-            short chanel = s.nextShort();
-            short timeTotal = s.nextShort();
-            double U = s.nextDouble();
-
-//            NumassEvent event = new NumassEvent(chanel, time);
-            result.putEvent(U, chanel, time);
-        }
-        return result;
-
-    }
-}

numass-main/src/main/java/inr/numass/debunch/FrameAnalizer.java

@@ -87,7 +87,7 @@ public class FrameAnalizer implements Debuncher {
     }
 
     private DebunchReport debunch(RawNMPoint point, double prob, double frameShift, double frameLength) {
-        double cr = point.selectChanels(lowerChanel, upperChanel).getCR();
+        double cr = point.selectChanels(lowerChanel, upperChanel).getCr();
         return debunch(point, cr, prob, frameShift, frameLength);
     }
 

numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java

@@ -145,7 +145,7 @@ public class NumassPrepareTask extends AbstractTask<Table> {
 //        double framelength = meta.getDouble("framelength", 1);
 //        double maxCR = meta.getDouble("maxcr", 500d);
 //
-//        double cr = point.selectChanels(lower, upper).getCR();
+//        double cr = point.selectChanels(lower, upper).getCr();
 //        if (cr < maxCR) {
 //            DebunchReport report = new FrameAnalizer(rejectionprob, framelength, lower, upper).debunchPoint(point);
 //            return new NMPoint(report.getPoint());

numass-server/src/main/java/inr/numass/server/TestServer.java

@@ -14,6 +14,7 @@ import hep.dataforge.storage.filestorage.FileStorageFactory;
 import inr.numass.storage.NumassStorage;
 
 import java.io.BufferedReader;
+import java.io.File;
 import java.io.InputStreamReader;
 
 /**
@@ -32,7 +33,7 @@ public class TestServer {
 
         ServerManager serverManager = context.pluginManager().load(ServerManager.class);
 
-        String path = "D:/temp/test";
+        File path = new File("/D:/temp/test");
         context.getLogger().info("Starting test numass storage servlet in '{}'", path);
 
         NumassStorage storage = new NumassStorage(context, FileStorageFactory.buildStorageMeta(path, true, true));

numass-viewer/build.gradle

@@ -1,5 +1,5 @@
 plugins{
-    id "org.jetbrains.kotlin.jvm" version '1.1.2-5'
+    id "org.jetbrains.kotlin.jvm" version '1.1.3'
     id "application"
 }
 
@@ -27,7 +27,7 @@ dependencies {
     compile 'com.jcraft:jsch:0.1.54'
 
     compile 'org.controlsfx:controlsfx:8.40.12'
-    compile "no.tornado:tornadofx:1.7.5"
+    compile "no.tornado:tornadofx:1.7.8"
 }
 
 apply plugin: 'kotlin'