Corrections redesign

numass-core/src/main/java/inr/numass/data/analyzers/AbstractAnalyzer.java

@@ -18,8 +18,10 @@ import static inr.numass.data.api.NumassPoint.HV_KEY;
  * Created by darksnake on 11.07.2017.
  */
 public abstract class AbstractAnalyzer implements NumassAnalyzer {
-    public static String[] NAME_LIST = {LENGTH_KEY, COUNT_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, "window", "timestamp"};
+    public static String WINDOW_KEY = "window";
-    public static String[] NAME_LIST_WITH_HV = {HV_KEY, LENGTH_KEY, COUNT_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, "window", "timestamp"};
+
+    public static String[] NAME_LIST = {LENGTH_KEY, COUNT_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, WINDOW_KEY, "timestamp"};
+    public static String[] NAME_LIST_WITH_HV = {HV_KEY, LENGTH_KEY, COUNT_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, WINDOW_KEY, "timestamp"};
     @Nullable
     private final SignalProcessor processor;
 
@@ -40,17 +42,25 @@ public abstract class AbstractAnalyzer implements NumassAnalyzer {
      * @return
      */
     public Stream<NumassEvent> getEvents(NumassBlock block, Meta config) {
+        int loChannel = config.getInt("window.lo", 0);
+        int upChannel = config.getInt("window.up", Integer.MAX_VALUE);
+        Stream<NumassEvent> res = getAllEvents(block).filter(event -> {
+            short channel = event.getChanel();
+            return channel >= loChannel && channel < upChannel;
+        });
+        if (config.getBoolean("sort", false)) {
+            res = res.sorted(Comparator.comparing(NumassEvent::getTimeOffset));
+        }
+        return res;
+    }
+
+    protected Stream<NumassEvent> getAllEvents(NumassBlock block){
         if (block.getFrames().count() == 0) {
             return block.getEvents();
         } else if (getProcessor() == null) {
             throw new IllegalArgumentException("Signal processor needed to analyze frames");
         } else {
-            //TODO
+            return Stream.concat(block.getEvents(), block.getFrames().flatMap(getProcessor()::analyze));
-            Stream<NumassEvent> res = Stream.concat(block.getEvents(), block.getFrames().flatMap(getProcessor()::analyze));
-            if (config.getBoolean("sort", false)) {
-                res = res.sorted(Comparator.comparing(NumassEvent::getTimeOffset));
-            }
-            return res;
         }
     }
 
@@ -63,7 +73,7 @@ public abstract class AbstractAnalyzer implements NumassAnalyzer {
                 .addNumber(COUNT_KEY)
                 .addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
                 .addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
-                .addColumn("window")
+                .addColumn(WINDOW_KEY)
                 .addTime()
                 .build();
 

numass-core/src/main/java/inr/numass/data/analyzers/SimpleAnalyzer.java

@@ -4,13 +4,10 @@ import hep.dataforge.meta.Meta;
 import hep.dataforge.tables.ValueMap;
 import hep.dataforge.values.Values;
 import inr.numass.data.api.NumassBlock;
-import inr.numass.data.api.NumassEvent;
 import inr.numass.data.api.NumassPoint;
 import inr.numass.data.api.SignalProcessor;
 import org.jetbrains.annotations.Nullable;
 
-import java.util.stream.Stream;
-
 /**
  * A simple event counter
  * Created by darksnake on 07.07.2017.
@@ -24,15 +21,12 @@ public class SimpleAnalyzer extends AbstractAnalyzer {
     public SimpleAnalyzer() {
     }
 
-    public Stream<NumassEvent> getEventStream(NumassBlock block, int loChannel, int upChannel) {
-        return getEvents(block, Meta.empty()).filter(it -> it.getChanel() >= loChannel && it.getChanel() < upChannel);
-    }
 
     @Override
     public Values analyze(NumassBlock block, Meta config) {
         int loChannel = config.getInt("window.lo", 0);
         int upChannel = config.getInt("window.up", Integer.MAX_VALUE);
-        long count = getEventStream(block, loChannel, upChannel).count();
+        long count = getEvents(block, config).count();
         double countRate = (double) count / block.getLength().toMillis() * 1000;
         double countRateError = Math.sqrt((double) count) / block.getLength().toMillis() * 1000;
 
@@ -43,7 +37,7 @@ public class SimpleAnalyzer extends AbstractAnalyzer {
                     count,
                     countRate,
                     countRateError,
-                    new int[]{loChannel, upChannel},
+                    new Integer[]{loChannel, upChannel},
                     block.getStartTime());
         } else {
             return ValueMap.of(NAME_LIST,
@@ -51,7 +45,7 @@ public class SimpleAnalyzer extends AbstractAnalyzer {
                     count,
                     countRate,
                     countRateError,
-                    new int[]{loChannel, upChannel},
+                    new Integer[]{loChannel, upChannel},
                     block.getStartTime());
         }
     }

numass-core/src/main/java/inr/numass/data/analyzers/TimeAnalyzer.java

@@ -37,10 +37,6 @@ public class TimeAnalyzer extends AbstractAnalyzer {
         AtomicLong totalT = new AtomicLong(0);
 
         getEventsWithDelay(block, config)
-                .filter(pair -> {
-                    short channel = pair.getKey().getChanel();
-                    return channel >= loChannel && channel < upChannel;
-                })
                 .forEach(pair -> {
                     totalN.incrementAndGet();
                     //TODO add progress listener here
@@ -59,7 +55,7 @@ public class TimeAnalyzer extends AbstractAnalyzer {
                     count,
                     countRate,
                     countRateError,
-                    new int[]{loChannel, upChannel},
+                    new Integer[]{loChannel, upChannel},
                     block.getStartTime());
         } else {
             return ValueMap.of(NAME_LIST,
@@ -67,7 +63,7 @@ public class TimeAnalyzer extends AbstractAnalyzer {
                     count,
                     countRate,
                     countRateError,
-                    new int[]{loChannel, upChannel},
+                    new Integer[]{loChannel, upChannel},
                     block.getStartTime()
             );
         }

numass-core/src/main/java/inr/numass/data/api/NumassAnalyzer.java

@@ -55,7 +55,7 @@ public interface NumassAnalyzer {
      * @param block
      * @return
      */
-    Stream<NumassEvent> getEvents(NumassBlock block, Meta config);
+    Stream<NumassEvent> getEvents(NumassBlock block, Meta meta);
 
     /**
      * Analyze the whole set. And return results as a table

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

@@ -33,6 +33,8 @@ import hep.dataforge.stat.models.XYModel;
 import hep.dataforge.tables.PointAdapter;
 import hep.dataforge.tables.XYAdapter;
 import inr.numass.actions.*;
+import inr.numass.data.api.NumassAnalyzer;
+import inr.numass.data.api.NumassPoint;
 import inr.numass.models.*;
 import inr.numass.models.sterile.SterileNeutrinoSpectrum;
 import inr.numass.tasks.*;
@@ -296,7 +298,7 @@ public class NumassPlugin extends BasicPlugin {
         if (an.hasMeta(PointAdapter.DATA_ADAPTER_KEY)) {
             return new XYAdapter(an.getMeta(PointAdapter.DATA_ADAPTER_KEY));
         } else {
-            return new XYAdapter("Uread", "CR", "CRerr");
+            return new XYAdapter(NumassPoint.HV_KEY, NumassAnalyzer.COUNT_RATE_KEY, NumassAnalyzer.COUNT_RATE_ERROR_KEY);
         }
     }
 }

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

@@ -34,8 +34,8 @@ import java.util.*;
 /**
  * @author Darksnake
  */
-@TypedActionDef(name = "merge", inputType = Table.class, outputType = Table.class, info = "Merge different numass data files into one.")
+@TypedActionDef(name = "numass.merge", inputType = Table.class, outputType = Table.class, info = "Merge different numass data files into one.")
-@NodeDef(name = "grouping", info = "The defenition of grouping rule for this merge", target = "method::hep.dataforge.actions.GroupBuilder.byMeta")
+@NodeDef(name = "grouping", info = "The definition of grouping rule for this merge", target = "method::hep.dataforge.actions.GroupBuilder.byMeta")
 public class MergeDataAction extends ManyToOneAction<Table, Table> {
 
     public static final String MERGE_NAME = "mergeName";

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

@@ -7,6 +7,7 @@ import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.description.ValueDef;
 import hep.dataforge.meta.Laminate;
 import hep.dataforge.meta.Meta;
+import hep.dataforge.meta.MetaUtils;
 import hep.dataforge.names.Named;
 import hep.dataforge.tables.ColumnFormat;
 import hep.dataforge.tables.ColumnTable;
@@ -14,11 +15,10 @@ import hep.dataforge.tables.ListColumn;
 import hep.dataforge.tables.Table;
 import hep.dataforge.values.Values;
 import inr.numass.utils.NumassUtils;
+import javafx.util.Pair;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.function.Function;
-import java.util.stream.Collectors;
 
 import static hep.dataforge.values.ValueType.NUMBER;
 import static hep.dataforge.values.ValueType.STRING;
@@ -36,15 +36,18 @@ import static inr.numass.utils.NumassUtils.pointExpression;
 @ValueDef(name = "utransform", info = "Expression for voltage transformation. Uses U as input")
 @NodeDef(name = "correction", multiple = true, target = "method::inr.numass.actions.TransformDataAction.makeCorrection")
 public class TransformDataAction extends OneToOneAction<Table, Table> {
+
     @Override
     protected Table execute(Context context, String name, Table input, Laminate meta) {
 
         List<Correction> corrections = new ArrayList<>();
-        if (meta.optMeta("correction").isPresent()) {
+
-            corrections.addAll(meta.getMetaList("correction").stream()
+        meta.optMeta("corrections").ifPresent(corrs ->
-                    .map((Function<Meta, Correction>) this::makeCorrection)
+                MetaUtils.nodeStream(corrs)
-                    .collect(Collectors.toList()));
+                        .map(Pair::getValue)
-        }
+                        .map(this::makeCorrection)
+                        .forEach(corrections::add)
+        );
 
         if (meta.hasValue("correction")) {
             final String correction = meta.getString("correction");
@@ -112,7 +115,7 @@ public class TransformDataAction extends OneToOneAction<Table, Table> {
         return new Correction() {
             @Override
             public String getName() {
-                return corrMeta.getString("name", "");
+                return corrMeta.getString("name", corrMeta.getName());
             }
 
             @Override

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

@@ -287,7 +287,7 @@ public class LossCalculator {
      * @return
      */
     public List<Double> getLossProbabilities(double X) {
-        return lossProbCache.computeIfAbsent(X, (x) -> {
+        return lossProbCache.computeIfAbsent(X, x -> {
             List<Double> res = new ArrayList<>();
             double prob;
             if (x > 0) {

numass-main/src/main/java/inr/numass/models/sterile/NumassTransmission.java

@@ -29,9 +29,12 @@ public class NumassTransmission extends AbstractParametricBiFunction {
     private final LossCalculator calculator;
     private final BivariateFunction trapFunc;
 
+    private final boolean adjustX;
+
     public NumassTransmission(Context context, Meta meta) {
         super(list);
         this.calculator = LossCalculator.instance();
+        adjustX = meta.getBoolean("adjustX",false);
         if (meta.hasValue("trapping")) {
             String trapFuncStr = meta.getString("trapping");
             if (trapFuncStr.startsWith("function::")) {
@@ -50,12 +53,16 @@ public class NumassTransmission extends AbstractParametricBiFunction {
         }
     }
 
-    public static double getX(double eIn, Values set) {
+    public double getX(double eIn, Values set) {
+        if(adjustX){
             //From our article
             return set.getDouble("X") * Math.log(eIn / ION_POTENTIAL) * eIn * ION_POTENTIAL / 1.9580741410115568e6;
+        } else {
+            return set.getDouble("X");
+        }
     }
 
-    public static double p0(double eIn, Values set) {
+    public double p0(double eIn, Values set) {
         return LossCalculator.instance().getLossProbability(0, getX(eIn, set));
     }
 

numass-main/src/main/java/inr/numass/models/sterile/SterileNeutrinoSpectrum.java

@@ -45,7 +45,7 @@ public class SterileNeutrinoSpectrum extends AbstractParametricFunction {
     /**
      * variables:Ein,Eout; parameters: "A"
      */
-    private final ParametricBiFunction transmission;
+    private final NumassTransmission transmission;
     /**
      * variables:Eout,U; parameters: "X", "trap"
      */
@@ -193,7 +193,7 @@ public class SterileNeutrinoSpectrum extends AbstractParametricFunction {
         @Override
         public double value(double eIn, double u, Values set) {
 
-            double p0 = NumassTransmission.p0(eIn, set);
+            double p0 = transmission.p0(eIn, set);
             return p0 * resolution.value(eIn, u, set) + lossRes(transmission, eIn, u, set);
         }
 

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

@@ -38,7 +38,7 @@ public class NumassTableFilterTask extends SingleActionTask<Table, Table> {
     protected TaskModel transformModel(TaskModel model) {
         MetaBuilder metaBuilder = new MetaBuilder(model.meta()).removeNode("filter");
         if (model.meta().hasMeta("empty")) {
-            model.dependsOn("substractEmpty", metaBuilder.build(), "prepare");
+            model.dependsOn("subtractEmpty", metaBuilder.build(), "prepare");
         } else {
             model.dependsOn("prepare", metaBuilder.build(), "prepare");
         }

numass-viewer/src/main/kotlin/inr/numass/viewer/NumassLoaderView.kt

@@ -17,6 +17,7 @@ import hep.dataforge.storage.commons.JSONMetaWriter
 import hep.dataforge.tables.Table
 import hep.dataforge.tables.ValueMap
 import hep.dataforge.tables.XYAdapter
+import inr.numass.data.NumassDataUtils
 import inr.numass.data.analyzers.SimpleAnalyzer
 import inr.numass.data.api.NumassAnalyzer
 import inr.numass.data.api.NumassPoint
@@ -324,7 +325,7 @@ class NumassLoaderView : View() {
                 PlottableData.plot(
                         seriesName,
                         XYAdapter(NumassAnalyzer.CHANNEL_KEY, valueAxis),
-                        NumassAnalyzer.spectrumWithBinning(getSpectrum(point), binning)
+                        NumassDataUtils.spectrumWithBinning(getSpectrum(point), binning)
                 ).apply {
                     configure(plottableConfig)
                 }.also {