minor refactoring

numass-main/src/main/groovy/inr/numass/LaunchGrindShell.groovy

@@ -1,5 +1,6 @@
 package inr.numass
 
+import hep.dataforge.context.GlobalContext
 import hep.dataforge.grind.GrindShell
 import hep.dataforge.grind.GrindWorkspaceBuilder
 
@@ -14,10 +15,15 @@ println cli.usage
 
 String cfgPath = cli.parse(args).c;
 println "Loading config file from $cfgPath"
+try {
     new GrindShell().launch {
-    context.pluginManager().loadPlugin("plots-jfc")
         GrindWorkspaceBuilder numass = new GrindWorkspaceBuilder()
                 .withSpec(NumassWorkspaceSpec)
                 .from(new File(cfgPath))
         bind("numass", numass)
     }
+} catch (Exception ex) {
+    ex.printStackTrace();
+} finally {
+    GlobalContext.instance().close();
+}

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

@@ -0,0 +1,40 @@
+package inr.numass.actions;
+
+import hep.dataforge.actions.ManyToOneAction;
+import hep.dataforge.description.TypedActionDef;
+import hep.dataforge.meta.Meta;
+import inr.numass.storage.NMPoint;
+import inr.numass.storage.NumassData;
+
+import java.util.Collection;
+import java.util.Map;
+import java.util.stream.IntStream;
+
+/**
+ * Created by darksnake on 04-Nov-16.
+ */
+@TypedActionDef(name = "joinData", inputType = NumassData.class, outputType = NumassData.class,
+        info = "Join a number of numass data files into one single file via spectrum summing")
+public class JoinNumassDataAction extends ManyToOneAction<NumassData, NumassData> {
+
+    @Override
+    protected NumassData execute(String nodeName, Map<String, NumassData> input, Meta meta) {
+        throw new  UnsupportedOperationException("not implemented");
+    }
+
+    private NMPoint joinPoint(Collection<NMPoint> points) {
+        return points.stream().reduce((p1, p2) -> {
+            if (p1.getUset() != p2.getUset()) {
+                throw new RuntimeException("Can't sum points with different Uset");
+            }
+            return new NMPoint(
+                    p1.getUset(),
+                    (p1.getUread() + p2.getUset()) / 2,
+                    p1.getStartTime(),
+                    p1.getLength() + p2.getLength(),
+                    p1.getOverflow() + p2.getOverflow(),
+                    IntStream.range(0, p1.getSpectrum().length).map(i -> p1.getSpectrum()[i] * p2.getSpectrum()[i]).toArray()
+            );
+        }).get();
+    }
+}

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

@@ -48,14 +48,8 @@ import static inr.numass.utils.TritiumUtils.evaluateExpression;
 @ValueDef(name = "lowerWindowSlope", type = "NUMBER", def = "0", info = "Slope for the window lowerWindow bound")
 @ValueDef(name = "upperWindow", type = "NUMBER", info = "Upper bound for window")
 @ValueDef(name = "deadTime", type = "[NUMBER, STRING]", def = "0", info = "Dead time in s. Could be an expression.")
-//@ValueDef(name = "underflow", type = "BOOLEAN", def = "true",
-//        info = "Enables calculation of detector threshold underflow using exponential shape of energy spectrum tail. "
-//        + "Not recomended to use with floating window.")
-//@ValueDef(name = "underflow.upperBorder", type = "NUMBER", def = "800", info = "Upper chanel for underflow calculation.")
-//@ValueDef(name = "underflow.threshold", type = "NUMBER", def = "17000", info = "The maximum U for undeflow calculation")
-//@ValueDef(name = "underflow.function", info = "An expression for underflow correction above threshold")
 @ValueDef(name = "correction",
-        info = "An expression to correct count tumber depending on potential ${U}, point length ${T} and point itself as ${point}")
+        info = "An expression to correct count number depending on potential `U`, point length `T` and point itself as `point`")
 public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
 
     public static String[] parnames = {"Uset", "Uread", "Length", "Total", "Window", "Corr", "CR", "CRerr", "Timestamp"};
@@ -135,6 +129,11 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
         return data;
     }
 
+    @Override
+    protected String getResultName(String dataName, Meta actionMeta) {
+        return super.getResultName(dataName, actionMeta);
+    }
+
     /**
      * The factor to correct for count below detector threshold
      *

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

@@ -36,9 +36,7 @@ public class SubstractSpectrumAction extends OneToOneAction<Table, Table> {
             input.stream().forEach(point -> {
                 MapPoint.Builder pointBuilder = new MapPoint.Builder(point);
                 Optional<DataPoint> referencePoint = referenceTable.stream()
-                        .filter(p -> {
+                        .filter(p -> Math.abs(p.getDouble("Uset") - point.getDouble("Uset")) < 0.1).findFirst();
-                            return Math.abs(p.getDouble("Uset") - point.getDouble("Uset")) < 0.1;
-                        }).findFirst();
                 if (referencePoint.isPresent()) {
                     pointBuilder.putValue("CR", Math.max(0, point.getDouble("CR") - referencePoint.get().getDouble("CR")));
                     pointBuilder.putValue("CRerr", Math.sqrt(Math.pow(point.getDouble("CRerr"), 2d) + Math.pow(referencePoint.get().getDouble("CRerr"), 2d)));

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

@@ -17,35 +17,39 @@ package inr.numass.storage;
 
 import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.MapPoint;
+
 import java.time.Instant;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Arrays;
+import java.util.stream.IntStream;
+
 import static java.util.Arrays.sort;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
 
 /**
- *
  * @author Darksnake
  */
 public class NMPoint {
-
+    //TODO transform to annotated and move some parameters to meta
     static final String[] dataNames = {"chanel", "count"};
     private Instant startTime;
-
-//    private MonitorCorrector corrector = null;
-//    private double deadTime;
     private long eventsCount;
 
     private int overflow;
 
     private double pointLength;
-//    private final MeasurementPoint point;
     private final int[] spectrum;
     private double uread;
     private double uset;
 
+    public NMPoint(double uset, double uread, Instant startTime, double pointLength, int overflow, int[] spectrum) {
+        this.startTime = startTime;
+        this.overflow = overflow;
+        this.pointLength = pointLength;
+        this.spectrum = spectrum;
+        this.uread = uread;
+        this.uset = uset;
+        this.eventsCount = IntStream.of(spectrum).sum() + overflow;
+    }
+
     public NMPoint(RawNMPoint point) {
         if (point == null) {
             throw new IllegalArgumentException();
@@ -56,14 +60,9 @@ public class NMPoint {
         this.uread = point.getUread();
         this.startTime = point.getStartTime();
         this.eventsCount = point.getEventsCount();
-//        this.point = point;
         spectrum = calculateSpectrum(point);
     }
 
-//    public PointSpectrum(RawPoint point, double deadTime) {
-//        this(point);
-//        this.deadTime = deadTime;
-//    }
     private int[] calculateSpectrum(RawNMPoint point) {
         assert point.getEventsCount() > 0;
 
@@ -238,4 +237,7 @@ public class NMPoint {
         return uset;
     }
 
+    public int[] getSpectrum() {
+        return spectrum;
+    }
 }