Plots and Numass update

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

@@ -41,7 +41,7 @@ public class SpectrumDataAdapter extends XYAdapter {
     }
 
     public SpectrumDataAdapter(String xName, String yName, String yErrName, String measurementTime) {
-        super(new MetaBuilder(ValuesAdapter.DATA_ADAPTER_KEY)
+        super(new MetaBuilder(ValuesAdapter.ADAPTER_KEY)
                 .setValue(X_VALUE_KEY, xName)
                 .setValue(Y_VALUE_KEY, yName)
                 .setValue(Y_ERROR_KEY, yErrName)
@@ -51,7 +51,7 @@ public class SpectrumDataAdapter extends XYAdapter {
     }
 
     public SpectrumDataAdapter(String xName, String yName, String measurementTime) {
-        super(new MetaBuilder(ValuesAdapter.DATA_ADAPTER_KEY)
+        super(new MetaBuilder(ValuesAdapter.ADAPTER_KEY)
                 .setValue(X_VALUE_KEY, xName)
                 .setValue(Y_VALUE_KEY, yName)
                 .setValue(POINT_LENGTH_NAME, measurementTime)

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

@@ -55,7 +55,7 @@ public abstract class AbstractAnalyzer implements NumassAnalyzer {
         return res;
     }
 
-    protected Stream<NumassEvent> getAllEvents(NumassBlock block){
+    protected Stream<NumassEvent> getAllEvents(NumassBlock block) {
         if (block.getFrames().count() == 0) {
             return block.getEvents();
         } else if (getProcessor() == null) {
@@ -67,10 +67,11 @@ public abstract class AbstractAnalyzer implements NumassAnalyzer {
 
     /**
      * Get table format for summary table
+     *
      * @param config
      * @return
      */
-    protected TableFormat getTableFormat(Meta config){
+    protected TableFormat getTableFormat(Meta config) {
         return new TableFormatBuilder()
                 .addNumber(HV_KEY, X_VALUE_KEY)
                 .addNumber(LENGTH_KEY)
@@ -84,11 +85,11 @@ public abstract class AbstractAnalyzer implements NumassAnalyzer {
 
 
     @Override
-    public Table analyze(NumassSet set, Meta config) {
+    public Table analyzeSet(NumassSet set, Meta config) {
         TableFormat format = getTableFormat(config);
 
         return new ListTable.Builder(format)
-                .rows(set.getPoints().map(point -> analyze(point, config)))
+                .rows(set.getPoints().map(point -> analyzePoint(point, config)))
                 .build();
     }
 

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

@@ -4,7 +4,6 @@ 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.NumassPoint;
 import inr.numass.data.api.SignalProcessor;
 import org.jetbrains.annotations.Nullable;
 
@@ -27,20 +26,10 @@ 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 length = (double) block.getLength().toNanos()/1e9;
+        double length = (double) block.getLength().toNanos() / 1e9;
         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(),
-                    length,
-                    count,
-                    countRate,
-                    countRateError,
-                    new Integer[]{loChannel, upChannel},
-                    block.getStartTime());
-        } else {
         return ValueMap.of(NAME_LIST,
                 length,
                 count,
@@ -49,7 +38,6 @@ public class SimpleAnalyzer extends AbstractAnalyzer {
                 new Integer[]{loChannel, upChannel},
                 block.getStartTime());
     }
-    }
 
 
 }

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

@@ -4,6 +4,7 @@ import hep.dataforge.meta.Meta;
 import hep.dataforge.tables.TableFormat;
 import hep.dataforge.tables.TableFormatBuilder;
 import hep.dataforge.tables.ValueMap;
+import hep.dataforge.values.Value;
 import hep.dataforge.values.Values;
 import inr.numass.data.api.NumassBlock;
 import inr.numass.data.api.NumassEvent;
@@ -12,6 +13,8 @@ import inr.numass.data.api.SignalProcessor;
 import javafx.util.Pair;
 import org.jetbrains.annotations.Nullable;
 
+import java.util.HashMap;
+import java.util.Map;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.stream.Stream;
@@ -27,7 +30,7 @@ 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 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);
@@ -38,6 +41,12 @@ public class TimeAnalyzer extends AbstractAnalyzer {
 
     @Override
     public Values analyze(NumassBlock block, Meta config) {
+        //In case points inside points
+        if (block instanceof NumassPoint) {
+            return analyzePoint((NumassPoint) block, config);
+        }
+
+
         int loChannel = config.getInt("window.lo", 0);
         int upChannel = config.getInt("window.up", Integer.MAX_VALUE);
         long t0 = getT0(block, config);
@@ -58,19 +67,6 @@ public class TimeAnalyzer extends AbstractAnalyzer {
         double length = totalT.get() / 1e9;
         long count = (long) (length * countRate);
 
-
-        if (block instanceof NumassPoint) {
-            return ValueMap.of(NAME_LIST_WITH_HV,
-                    ((NumassPoint) block).getVoltage(),
-                    length,
-                    count,
-                    countRate,
-                    countRateError,
-                    new Integer[]{loChannel, upChannel},
-                    block.getStartTime(),
-                    (double)t0 / 1000d
-            );
-        } else {
         return ValueMap.of(NAME_LIST,
                 length,
                 count,
@@ -78,9 +74,54 @@ public class TimeAnalyzer extends AbstractAnalyzer {
                 countRateError,
                 new Integer[]{loChannel, upChannel},
                 block.getStartTime(),
-                    (double)t0 / 1000d
+                (double) t0 / 1000d
         );
     }
+
+    @Override
+    public Values analyzePoint(NumassPoint point, Meta config) {
+        //Average count rates, do not sum events
+        Values res = point.getBlocks().map(it -> analyze(it, config)).reduce(null, this::combineBlockResults);
+
+        Map<String, Value> map = new HashMap<>(res.asMap());
+        map.put(HV_KEY, Value.of(point.getVoltage()));
+        return new ValueMap(map);
+    }
+
+    /**
+     * Combine two blocks from the same point into one
+     *
+     * @param v1
+     * @param v2
+     * @return
+     */
+    private Values combineBlockResults(Values v1, Values v2) {
+        if (v1 == null) {
+            return v2;
+        }
+        if (v2 == null) {
+            return v1;
+        }
+
+        double cr1 = v1.getDouble(COUNT_RATE_KEY);
+        double cr2 = v2.getDouble(COUNT_RATE_KEY);
+        double w1 = Math.pow(v1.getDouble(COUNT_RATE_ERROR_KEY), -2);
+        double w2 = Math.pow(v2.getDouble(COUNT_RATE_ERROR_KEY), -2);
+
+        double countRate = (cr1 * w1 + cr2 * w2) / (1d * w1 + 1d * w2);
+
+        double countRateErr = Math.sqrt(1d / (w1 + w2));
+
+
+        return ValueMap.of(NAME_LIST,
+                v1.getDouble(LENGTH_KEY) + v2.getDouble(LENGTH_KEY),
+                v1.getInt(COUNT_KEY) + v2.getInt(COUNT_KEY),
+                countRate,
+                countRateErr,
+                v1.getValue(WINDOW_KEY),
+                v1.getValue(TIME_KEY),
+                v1.getDouble(T0_KEY)
+        );
     }
 
     private long getT0(NumassBlock block, Meta config) {

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

@@ -2,13 +2,17 @@ package inr.numass.data.api;
 
 import hep.dataforge.meta.Meta;
 import hep.dataforge.tables.*;
+import hep.dataforge.values.Value;
 import hep.dataforge.values.Values;
 
+import java.util.HashMap;
+import java.util.Map;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.stream.IntStream;
 import java.util.stream.Stream;
 
 import static hep.dataforge.tables.XYAdapter.*;
+import static inr.numass.data.api.NumassPoint.HV_KEY;
 
 /**
  * A general raw data analysis utility. Could have different implementations
@@ -33,7 +37,6 @@ public interface NumassAnalyzer {
     }
 
 
-
     String CHANNEL_KEY = "channel";
     String COUNT_KEY = "count";
     String LENGTH_KEY = "length";
@@ -49,6 +52,18 @@ public interface NumassAnalyzer {
      */
     Values analyze(NumassBlock block, Meta config);
 
+    /**
+     * Analysis result for point including hv information
+     * @param point
+     * @param config
+     * @return
+     */
+    default Values analyzePoint(NumassPoint point, Meta config) {
+        Map<String, Value> map = new HashMap<>(analyze(point, config).asMap());
+        map.put(HV_KEY, Value.of(point.getVoltage()));
+        return new ValueMap(map);
+    }
+
     /**
      * Return unsorted stream of events including events from frames
      *
@@ -64,7 +79,7 @@ public interface NumassAnalyzer {
      * @param config
      * @return
      */
-    Table analyze(NumassSet set, Meta config);
+    Table analyzeSet(NumassSet set, Meta config);
 
     /**
      * Calculate the energy spectrum for a given block. The s

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

@@ -5,6 +5,7 @@ import hep.dataforge.context.Global
 import hep.dataforge.data.DataSet
 import hep.dataforge.grind.Grind
 import hep.dataforge.grind.GrindShell
+import hep.dataforge.kodex.fx.plots.PlotManager
 import hep.dataforge.meta.Meta
 import inr.numass.NumassPlugin
 import inr.numass.actions.TimeAnalyzedAction
@@ -21,7 +22,7 @@ import inr.numass.data.storage.NumassStorageFactory
 
 
 Context ctx = Global.instance()
-ctx.pluginManager().load(FXPlotManager)
+ctx.pluginManager().load(PlotManager)
 ctx.pluginManager().load(NumassPlugin.class)
 
 new GrindShell(ctx).eval {
@@ -29,12 +30,15 @@ new GrindShell(ctx).eval {
 
     NumassStorage storage = NumassStorageFactory.buildLocal(rootDir);
 
-    Meta meta = Grind.buildMeta(binNum: 200) {
+    Meta meta = Grind.buildMeta(binNum: 200, plotHist: false) {
         window(lo: 500, up: 1800)
         plot(showErrors: false)
     }
 
-    def sets = (20..31).collect { "set_$it" }
+    def sets = ((2..14) + (22..31)).collect { "set_$it" }
+    //def sets = (2..14).collect { "set_$it" }
+    //def sets = (16..31).collect { "set_$it" }
+    //def sets = (20..28).collect { "set_$it" }
 
     def loaders = sets.collect { set ->
         storage.provide("loader::$set", NumassSet.class).orElse(null)

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

@@ -294,8 +294,8 @@ public class NumassPlugin extends BasicPlugin {
     }
 
     private XYAdapter getAdapter(Meta an) {
-        if (an.hasMeta(ValuesAdapter.DATA_ADAPTER_KEY)) {
+        if (an.hasMeta(ValuesAdapter.ADAPTER_KEY)) {
-            return new XYAdapter(an.getMeta(ValuesAdapter.DATA_ADAPTER_KEY));
+            return new XYAdapter(an.getMeta(ValuesAdapter.ADAPTER_KEY));
         } else {
             return new XYAdapter(NumassPoint.HV_KEY, NumassAnalyzer.COUNT_RATE_KEY, NumassAnalyzer.COUNT_RATE_ERROR_KEY);
         }

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

@@ -26,7 +26,7 @@ public class AnalyzeDataAction extends OneToOneAction<NumassSet, Table> {
     protected Table execute(Context context, String name, NumassSet input, Laminate inputMeta) {
         //TODO add processor here
         NumassAnalyzer analyzer = new SmartAnalyzer();
-        Table res = analyzer.analyze(input, inputMeta);
+        Table res = analyzer.analyzeSet(input, inputMeta);
         output(context, name, stream -> NumassUtils.writeSomething(stream, inputMeta, res));
         return res;
     }

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

@@ -42,8 +42,8 @@ public class TransformDataAction extends OneToOneAction<Table, Table> {
 
         List<Correction> corrections = new ArrayList<>();
 
-        meta.optMeta("corrections").ifPresent(corrs ->
+        meta.optMeta("corrections").ifPresent(cors ->
-                MetaUtils.nodeStream(corrs)
+                MetaUtils.nodeStream(cors)
                         .map(Pair::getValue)
                         .map(this::makeCorrection)
                         .forEach(corrections::add)

numass-main/src/main/kotlin/inr/numass/actions/TimeAnalyzedAction.kt

@@ -10,7 +10,7 @@ import hep.dataforge.meta.Laminate
 import hep.dataforge.plots.PlotPlugin
 import hep.dataforge.plots.data.DataPlot
 import hep.dataforge.tables.Table
-import hep.dataforge.tables.ValueMap
+import hep.dataforge.tables.XYAdapter
 import hep.dataforge.values.ValueType
 import inr.numass.data.analyzers.TimeAnalyzer
 import inr.numass.data.api.NumassAnalyzer
@@ -51,6 +51,9 @@ class TimeAnalyzedAction : OneToOneAction<NumassPoint, Table>() {
             "window.up" to upChannel
         }).getDouble("cr")
 
+        log.report("The expected count rate for 30 us delay is $trueCR")
+
+
         val binNum = inputMeta.getInt("binNum", 1000);
         val binSize = inputMeta.getDouble("binSize", 1.0 / trueCR * 10 / binNum * 1e6)
 
@@ -63,6 +66,8 @@ class TimeAnalyzedAction : OneToOneAction<NumassPoint, Table>() {
         //.histogram(input, loChannel, upChannel, binSize, binNum).asTable();
         log.report("Finished histogram calculation...");
 
+        if (inputMeta.getBoolean("plotHist", true)) {
+
             val histPlot = pm.getPlotFrame(getName(), "histogram");
 
             histPlot.configure {
@@ -75,22 +80,22 @@ class TimeAnalyzedAction : OneToOneAction<NumassPoint, Table>() {
                 }
             }
 
-        histPlot.add(DataPlot(name)
+            val histogramPlot = DataPlot(name)
                     .configure {
                         "showLine" to true
                         "showSymbol" to false
                         "showErrors" to false
                         "connectionType" to "step"
-                    node("adapter") {
+                        node("@adapter") {
                             "y.value" to "count"
                         }
-                }.apply {
+                    }.apply { configure(inputMeta.getMetaOrEmpty("histogram")) }
-            configure(inputMeta.getMetaOrEmpty("histogram"))
-        }
                     .fillData(histogram)
-        )
 
-        log.report("The expected count rate for 30 us delay is $trueCR")
+            histPlot.add(histogramPlot)
+        }
+
+        if(inputMeta.getBoolean("plotStat",true)) {
 
             val statPlotPoints = (1..150).map { 1000 * it }.map { t ->
                 val result = analyzer.analyze(input, buildMeta {
@@ -106,24 +111,24 @@ class TimeAnalyzedAction : OneToOneAction<NumassPoint, Table>() {
                     1.0
                 }
 
-            ValueMap.ofMap(
+                XYAdapter.DEFAULT_ADAPTER.buildXYDataPoint(
-                    mapOf(
+                        t / 1000.0,
-                            "x" to t / 1000,
+                        result.getDouble("cr") / norm,
-                            "y" to result.getDouble("cr") / norm,
+                        result.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY) / norm
-                            "y.err" to result.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY) / norm
                 )
-            );
             }
 
-        pm.getPlotFrame(getName(), "stat-method").add(
+            val statPlot = DataPlot(name).configure {
-                DataPlot(name).configure {
                 "showLine" to true
                 "thickness" to 4
                 "title" to "${name}_${input.voltage}"
             }.apply {
                 configure(inputMeta.getMetaOrEmpty("plot"))
             }.fillData(statPlotPoints)
-        )
+
+            pm.getPlotFrame(getName(), "stat-method").add(statPlot)
+        }
+
         return histogram;
     }
 }

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

@@ -372,7 +372,7 @@ class NumassLoaderView : View() {
 //                                point.startTime
 //                        )
 //                    }
-                val spectrumDataSet = analyzer.analyze(data, buildMeta {
+                val spectrumDataSet = analyzer.analyzeSet(data, buildMeta {
                     "window.lo" to loChannel
                     "window.up" to upChannel
                 })