numass update

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

@@ -19,9 +19,10 @@ import static inr.numass.data.api.NumassPoint.HV_KEY;
  */
 public abstract class AbstractAnalyzer implements NumassAnalyzer {
     public static String WINDOW_KEY = "window";
+    public static String TIME_KEY = "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 = {LENGTH_KEY, COUNT_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, WINDOW_KEY, TIME_KEY};
-    public static String[] NAME_LIST_WITH_HV = {HV_KEY, 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, TIME_KEY};
     @Nullable
     private final SignalProcessor processor;
 
@@ -64,10 +65,13 @@ public abstract class AbstractAnalyzer implements NumassAnalyzer {
         }
     }
 
-
+    /**
-    @Override
+     * Get table format for summary table
-    public Table analyze(NumassSet set, Meta config) {
+     * @param config
-        TableFormat format = new TableFormatBuilder()
+     * @return
+     */
+    protected TableFormat getTableFormat(Meta config){
+        return new TableFormatBuilder()
                 .addNumber(HV_KEY, X_VALUE_KEY)
                 .addNumber(LENGTH_KEY)
                 .addNumber(COUNT_KEY)
@@ -76,6 +80,12 @@ public abstract class AbstractAnalyzer implements NumassAnalyzer {
                 .addColumn(WINDOW_KEY)
                 .addTime()
                 .build();
+    }
+
+
+    @Override
+    public Table analyze(NumassSet set, Meta config) {
+        TableFormat format = getTableFormat(config);
 
         return new ListTable.Builder(format)
                 .rows(set.getPoints().map(point -> analyze(point, config)))

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

@@ -27,13 +27,14 @@ public class SimpleAnalyzer extends AbstractAnalyzer {
         int loChannel = config.getInt("window.lo", 0);
         int upChannel = config.getInt("window.up", Integer.MAX_VALUE);
         long count = getEvents(block, config).count();
-        double countRate = (double) count / block.getLength().toMillis() * 1000;
+        double length = (double) block.getLength().toNanos()/1e9;
-        double countRateError = Math.sqrt((double) count) / block.getLength().toMillis() * 1000;
+        double countRate = (double) count / length;
+        double countRateError = Math.sqrt((double) count) / length;
 
         if (block instanceof NumassPoint) {
             return ValueMap.of(NAME_LIST_WITH_HV,
                     ((NumassPoint) block).getVoltage(),
-                    block.getLength().toNanos(),
+                    length,
                     count,
                     countRate,
                     countRateError,
@@ -41,7 +42,7 @@ public class SimpleAnalyzer extends AbstractAnalyzer {
                     block.getStartTime());
         } else {
             return ValueMap.of(NAME_LIST,
-                    block.getLength().toNanos(),
+                    length,
                     count,
                     countRate,
                     countRateError,

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

@@ -1,11 +1,18 @@
 package inr.numass.data.analyzers;
 
+import hep.dataforge.description.ValueDef;
 import hep.dataforge.meta.Meta;
+import hep.dataforge.tables.TableFormat;
+import hep.dataforge.tables.ValueMap;
+import hep.dataforge.values.Value;
+import hep.dataforge.values.ValueType;
 import hep.dataforge.values.Values;
 import inr.numass.data.api.NumassBlock;
 import inr.numass.data.api.SignalProcessor;
 import org.jetbrains.annotations.Nullable;
 
+import java.util.Map;
+
 /**
  * An analyzer dispatcher which uses different analyzer for different meta
  * Created by darksnake on 11.07.2017.
@@ -27,7 +34,6 @@ public class SmartAnalyzer extends AbstractAnalyzer {
 
     @Override
     public Values analyze(NumassBlock block, Meta config) {
-        //TODO add result caching
         if (config.hasValue("type")) {
             switch (config.getString("type")) {
                 case "simple":
@@ -40,11 +46,46 @@ public class SmartAnalyzer extends AbstractAnalyzer {
                     throw new IllegalArgumentException("Analyzer not found");
             }
         } else {
-            if(config.hasValue("t0")){
+            int t0 = getT0(block, config);
-                return timeAnalyzer.analyze(block,config);
+            if (t0 == 0) {
+                Map<String, Value> map = simpleAnalyzer.analyze(block, config).asMap();
+                map.putIfAbsent(TimeAnalyzer.T0_KEY, Value.of(0d));
+                return new ValueMap(map);
             } else {
-                return simpleAnalyzer.analyze(block,config);
+                return timeAnalyzer.analyze(block, config.getBuilder().putValue(TimeAnalyzer.T0_KEY, t0));
             }
         }
     }
+
+    private double estimateCountRate(NumassBlock block) {
+        return (double) block.getEvents().count() / block.getLength().toMillis() * 1000;
+    }
+
+    @ValueDef(name = "t0", type = ValueType.NUMBER, info = "Constant t0 cut")
+    @ValueDef(name = "t0.crFraction", type = ValueType.NUMBER, info = "The relative fraction of events that should be removed by time cut")
+    @ValueDef(name = "t0.min", type = ValueType.NUMBER, def = "0", info = "Minimal t0")
+    private int getT0(NumassBlock block, Meta meta) {
+        if (meta.hasValue("t0")) {
+            return meta.getInt("t0");
+        } else if (meta.hasMeta("t0")) {
+            double fraction = meta.getDouble("t0.crFraction");
+            double cr = estimateCountRate(block);
+            if (cr < meta.getDouble("t0.minCR", 0)) {
+                return 0;
+            } else {
+                return (int) Math.max(-1e9 / cr * Math.log(1d - fraction), meta.getDouble("t0.min", 0));
+            }
+        } else {
+            return 0;
+        }
+
+    }
+
+    @Override
+    protected TableFormat getTableFormat(Meta config) {
+        if (config.hasValue(TimeAnalyzer.T0_KEY) || config.hasMeta(TimeAnalyzer.T0_KEY)) {
+            return timeAnalyzer.getTableFormat(config);
+        }
+        return super.getTableFormat(config);
+    }
 }

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

@@ -1,6 +1,8 @@
 package inr.numass.data.analyzers;
 
 import hep.dataforge.meta.Meta;
+import hep.dataforge.tables.TableFormat;
+import hep.dataforge.tables.TableFormatBuilder;
 import hep.dataforge.tables.ValueMap;
 import hep.dataforge.values.Values;
 import inr.numass.data.api.NumassBlock;
@@ -14,11 +16,18 @@ import java.util.concurrent.atomic.AtomicLong;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.stream.Stream;
 
+import static hep.dataforge.tables.XYAdapter.*;
+import static inr.numass.data.api.NumassPoint.HV_KEY;
+
 /**
  * An analyzer which uses time information from events
  * Created by darksnake on 11.07.2017.
  */
 public class TimeAnalyzer extends AbstractAnalyzer {
+    public static String T0_KEY = "t0";
+
+    public static String[] NAME_LIST = {LENGTH_KEY, COUNT_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, WINDOW_KEY, TIME_KEY, T0_KEY};
+    public static String[] NAME_LIST_WITH_HV = {HV_KEY, LENGTH_KEY, COUNT_KEY, COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, WINDOW_KEY, TIME_KEY, T0_KEY};
 
     public TimeAnalyzer(@Nullable SignalProcessor processor) {
         super(processor);
@@ -37,6 +46,7 @@ public class TimeAnalyzer extends AbstractAnalyzer {
         AtomicLong totalT = new AtomicLong(0);
 
         getEventsWithDelay(block, config)
+                .filter(pair -> pair.getValue() >= t0)
                 .forEach(pair -> {
                     totalN.incrementAndGet();
                     //TODO add progress listener here
@@ -45,8 +55,9 @@ public class TimeAnalyzer extends AbstractAnalyzer {
 
         double countRate = 1e6 * totalN.get() / (totalT.get() / 1000 - t0 * totalN.get() / 1000);//1e9 / (totalT.get() / totalN.get() - t0);
         double countRateError = countRate / Math.sqrt(totalN.get());
-        long count = (long) (totalT.get() * (countRate / 1e9));
+        double length = totalT.get() / 1e9;
-        double length = totalT.get();
+        long count = (long) (length * countRate);
+
 
         if (block instanceof NumassPoint) {
             return ValueMap.of(NAME_LIST_WITH_HV,
@@ -56,7 +67,9 @@ public class TimeAnalyzer extends AbstractAnalyzer {
                     countRate,
                     countRateError,
                     new Integer[]{loChannel, upChannel},
-                    block.getStartTime());
+                    block.getStartTime(),
+                    (double)t0 / 1000d
+            );
         } else {
             return ValueMap.of(NAME_LIST,
                     length,
@@ -64,7 +77,8 @@ public class TimeAnalyzer extends AbstractAnalyzer {
                     countRate,
                     countRateError,
                     new Integer[]{loChannel, upChannel},
-                    block.getStartTime()
+                    block.getStartTime(),
+                    (double)t0 / 1000d
             );
         }
     }
@@ -81,37 +95,46 @@ public class TimeAnalyzer extends AbstractAnalyzer {
      * @return
      */
     public Stream<Pair<NumassEvent, Long>> getEventsWithDelay(NumassBlock block, Meta config) {
-        long t0 = getT0(block, config);
-
         AtomicReference<NumassEvent> lastEvent = new AtomicReference<>(null);
 
         Stream<NumassEvent> eventStream = super.getEvents(block, config);//using super implementation
 
         return eventStream.map(event -> {
-            if (lastEvent.get() == null) {
+            long res = lastEvent.get() == null ? -1L : event.getTimeOffset() - lastEvent.get().getTimeOffset();
-                lastEvent.set(event);
+
-                return new Pair<>(event, 0L);
+            if (res < 0) {
-            } else {
+                res = 0L;
-                long res = event.getTimeOffset() - lastEvent.get().getTimeOffset();
+            }
-                if (res >= 0) {
+
             lastEvent.set(event);
             return new Pair<>(event, res);
-                } else {
+        });
-                    lastEvent.set(null);
-                    return new Pair<>(event, 0L);
-                }
-            }
-        }).filter(pair -> pair.getValue() >= t0);
     }
 
     /**
      * The filtered stream of events
+     *
      * @param block
      * @param config
      * @return
      */
     @Override
     public Stream<NumassEvent> getEvents(NumassBlock block, Meta config) {
-        return getEventsWithDelay(block, config).map(Pair::getKey);
+        long t0 = getT0(block, config);
+        return getEventsWithDelay(block, config).filter(pair -> pair.getValue() >= t0).map(Pair::getKey);
+    }
+
+    @Override
+    protected TableFormat getTableFormat(Meta config) {
+        return new TableFormatBuilder()
+                .addNumber(HV_KEY, X_VALUE_KEY)
+                .addNumber(LENGTH_KEY)
+                .addNumber(COUNT_KEY)
+                .addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
+                .addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
+                .addColumn(WINDOW_KEY)
+                .addTime()
+                .addNumber(T0_KEY)
+                .build();
     }
 }

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

@@ -25,20 +25,20 @@ ctx.pluginManager().load(NumassPlugin.class)
 
 new GrindShell(ctx).eval {
     PlotHelper plot = plots
-    File rootDir = new File("D:\\Work\\Numass\\data\\2017_05\\Fill_3")
+    File rootDir = new File("D:\\Work\\Numass\\data\\2017_05\\Fill_2")
 
     NumassStorage storage = NumassStorageFactory.buildLocal(rootDir);
 
 
-    def set = "set_43"
+    def set = "set_2"
-    def hv = 16000;
+    def hv = 18300;
     def loader = storage.provide("loader::$set", NumassSet.class).get();
     def point = loader.provide("$hv", NumassPoint.class).get()
 
-    def loChannel = 500;
+    def loChannel = 450;
-    def upChannel = 2000;
+    def upChannel = 3100;
 
-    def histogram = PointAnalyzer.histogram(point, loChannel, upChannel, 0.7, 1000).asTable();
+    def histogram = PointAnalyzer.histogram(point, loChannel, upChannel, 1, 500).asTable();
 
     println "finished histogram calculation..."
 

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

@@ -99,16 +99,16 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
             return dp1;
         }
 
-        double Uset = dp1.getValue(parnames[0]).doubleValue();
+        double voltage = dp1.getValue(NumassPoint.HV_KEY).doubleValue();
         //усредняем измеренное напряжение
-        double Uread = (dp1.getValue(parnames[1]).doubleValue() + dp2.getValue(parnames[1]).doubleValue()) / 2;
+//        double Uread = (dp1.getValue(parnames[1]).doubleValue() + dp2.getValue(parnames[1]).doubleValue()) / 2;
 
         double t1 = dp1.getValue(NumassPoint.LENGTH_KEY).doubleValue();
         double t2 = dp2.getValue(NumassPoint.LENGTH_KEY).doubleValue();
         double time = t1 + t2;
 
-        long total = dp1.getValue(parnames[3]).intValue() + dp2.getValue(parnames[3]).intValue();
+        long total = dp1.getValue(NumassAnalyzer.COUNT_KEY).intValue() + dp2.getValue(NumassAnalyzer.COUNT_KEY).intValue();
-        long wind = dp1.getValue(parnames[4]).intValue() + dp2.getValue(parnames[4]).intValue();
+//        long wind = dp1.getValue(parnames[4]).intValue() + dp2.getValue(parnames[4]).intValue();
 //        double corr = dp1.getValue(parnames[5]).doubleValue() + dp2.getValue(parnames[5]).doubleValue();
 
         double cr1 = dp1.getValue(NumassAnalyzer.COUNT_RATE_KEY).doubleValue();
@@ -122,7 +122,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
         // абсолютные ошибки складываются квадратично
         double crErr = Math.sqrt(err1 * err1 * t1 * t1 + err2 * err2 * t2 * t2) / time;
 
-        ValueMap.Builder map = ValueMap.of(parnames, Uset, time, total, cr, crErr).builder();
+        ValueMap.Builder map = ValueMap.of(parnames, voltage, time, total, cr, crErr).builder();
 
 //        if (dp1.getNames().contains("relCR") && dp2.getNames().contains("relCR")) {
 //            double relCR = (dp1.getDouble("relCR") + dp2.getDouble("relCR")) / 2;
@@ -141,7 +141,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
                 throw new IllegalArgumentException();
             }
             for (Values dp : d) {
-                double uset = dp.getValue(parnames[0]).doubleValue();
+                double uset = dp.getValue(NumassPoint.HV_KEY).doubleValue();
                 if (!points.containsKey(uset)) {
                     points.put(uset, new ArrayList<>());
                 }

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

@@ -53,6 +53,8 @@ public class LossCalculator {
     private final Map<Integer, UnivariateFunction> cache = new HashMap<>();
 
 
+
+
     private LossCalculator() {
         cache.put(1, getSingleScatterFunction());
 //        cache.put(2, getDoubleScatterFunction());
@@ -386,7 +388,7 @@ public class LossCalculator {
             return integrator.integrate(integrand, 5d, margin);
         };
 
-        return FunctionCaching.cacheUnivariateFunction(res, 0, margin, 200);
+        return FunctionCaching.cacheUnivariateFunction(0, margin, 200, res);
 
     }
 

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

@@ -13,13 +13,13 @@ import hep.dataforge.values.Values;
 import inr.numass.models.LossCalculator;
 import inr.numass.utils.ExpressionUtils;
 import org.apache.commons.math3.analysis.BivariateFunction;
+import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.slf4j.LoggerFactory;
 
 import java.util.HashMap;
 import java.util.Map;
 
 /**
- *
  * @author <a href="mailto:altavir@gmail.com">Alexander Nozik</a>
  */
 public class NumassTransmission extends AbstractParametricBiFunction {
@@ -28,6 +28,7 @@ public class NumassTransmission extends AbstractParametricBiFunction {
     private static final double ION_POTENTIAL = 15.4;//eV
     private final LossCalculator calculator;
     private final BivariateFunction trapFunc;
+    private Map<Double, UnivariateFunction> lossCache = new HashMap<>();
 
     private final boolean adjustX;
 
@@ -93,6 +94,18 @@ public class NumassTransmission extends AbstractParametricBiFunction {
         double X = getX(eIn, set);
         // loss part
         double loss = calculator.getTotalLossValue(X, eIn, eOut);
+//        double loss;
+//
+//        if(eIn-eOut >= 300){
+//            loss = 0;
+//        } else {
+//            UnivariateFunction lossFunction = this.lossCache.computeIfAbsent(X, theX ->
+//                    FunctionCaching.cacheUnivariateFunction(0, 300, 400, x -> calculator.getTotalLossValue(theX, eIn, eIn - x))
+//            );
+//
+//            loss = lossFunction.value(eIn - eOut);
+//        }
+
         //trapping part
         double trap = getParameter("trap", set) * trapFunc.value(eIn, eOut);
         return loss + trap;