Revising numass scripts

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

@@ -2,12 +2,19 @@ package inr.numass.data;
 
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
+import hep.dataforge.tables.ListTable;
+import hep.dataforge.tables.Table;
+import hep.dataforge.tables.TableFormat;
+import hep.dataforge.tables.TableFormatBuilder;
 import inr.numass.data.api.NumassPoint;
 import inr.numass.data.api.NumassSet;
 
 import java.util.Collection;
 import java.util.stream.Stream;
 
+import static hep.dataforge.tables.XYAdapter.*;
+import static inr.numass.data.api.NumassAnalyzer.*;
+
 /**
  * Created by darksnake on 30-Jan-17.
  */
@@ -34,7 +41,29 @@ public class NumassDataUtils {
         };
     }
 
-//    public static Collection<NumassPoint> joinSpectra(Stream<NumassSet> spectra) {
+    /**
+     * Subtract reference spectrum.
+     *
+     * @param sp1
+     * @param sp2
+     * @return
+     */
+    public static Table subtractSpectrum(Table sp1, Table sp2) {
+        TableFormat format = new TableFormatBuilder()
+                .addNumber(CHANNEL_KEY, X_VALUE_KEY)
+                .addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
+                .addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
+                .build();
+        ListTable.Builder builder = new ListTable.Builder(format);
+        for (int i = 0; i < sp1.size(); i++) {
+            double value = sp1.getDouble(COUNT_RATE_KEY, i) - sp2.getDouble(COUNT_RATE_KEY, i);
+            double error = Math.sqrt(Math.pow(sp1.getDouble(COUNT_RATE_ERROR_KEY, i), 2d) + Math.pow(sp2.getDouble(COUNT_RATE_ERROR_KEY, i), 2d));
+            builder.row(sp1.get(CHANNEL_KEY, i).intValue(), value, error);
+        }
+        return builder.build();
+    }
+
+    //    public static Collection<NumassPoint> joinSpectra(Stream<NumassSet> spectra) {
 //        Map<Double, NumassPoint> map = new LinkedHashMap<>();
 //        spectra.forEach(datum -> {
 //            datum.forEach(point -> {

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

@@ -6,34 +6,64 @@
 
 package inr.numass.scripts
 
-import hep.dataforge.io.ColumnedDataWriter
+import hep.dataforge.grind.Grind
+import hep.dataforge.meta.Meta
 import hep.dataforge.storage.commons.StorageUtils
 import hep.dataforge.tables.Table
 import inr.numass.data.NumassDataUtils
+import inr.numass.data.analyzers.TimeAnalyzer
+import inr.numass.data.api.NumassAnalyzer
 import inr.numass.data.api.NumassPoint
-import inr.numass.data.api.NumassSet
+import inr.numass.data.api.SimpleNumassPoint
 import inr.numass.data.storage.NumassStorage
 import inr.numass.data.storage.NumassStorageFactory
-import inr.numass.utils.UnderflowCorrection
+
+import java.util.stream.Collectors
+
+import static inr.numass.data.api.NumassAnalyzer.CHANNEL_KEY
+import static inr.numass.data.api.NumassAnalyzer.COUNT_RATE_KEY
+
+//Defining root directory
 
 //File rootDir = new File("D:\\Work\\Numass\\data\\2016_10\\Fill_1")
 //File rootDir = new File("D:\\Work\\Numass\\data\\2016_10\\Fill_2_wide")
 //File rootDir = new File("D:\\Work\\Numass\\data\\2017_01\\Fill_2_wide")
-File rootDir = new File("D:\\Work\\Numass\\data\\2017_05\\Fill_1")
+File rootDir = new File("D:\\Work\\Numass\\data\\2017_05\\Fill_2")
+
+//creating storage instance
 
 NumassStorage storage = NumassStorageFactory.buildLocal(rootDir);
 
-NumassSet data = NumassDataUtils.join(
+//Reading points
-        "data",
+Map<Double, List<NumassPoint>> allPoints = StorageUtils
-        StorageUtils.loaderStream(storage)
+        .loaderStream(storage)
         .filter { it.key.matches("set_.{1,3}") }
         .map {
     println "loading ${it.key}"
     it.value
-                }.collect { (NumassSet) it }
+}.flatMap { it.points }
-)
+        .collect(Collectors.groupingBy { it.voltage })
 
-data = NumassDataUtils.substractReferencePoint(data, 18600d);
+Meta analyzerMeta = Grind.buildMeta(t0: 3e4)
+NumassAnalyzer analyzer = new TimeAnalyzer()
+
+//creating spectra
+Map spectra = allPoints.collectEntries {
+    def point = new SimpleNumassPoint(it.key, it.value)
+    println "generating spectrum for ${point.voltage}"
+    return [(point.voltage): analyzer.getSpectrum(point, analyzerMeta)]
+}
+
+//subtracting reference point
+
+def refereceVoltage = 18600
+def referencePoint = spectra[refereceVoltage]
+
+if (referencePoint) {
+    spectra = spectra.findAll { it.key != refereceVoltage }.collectEntries {
+        return [(it.key): NumassDataUtils.subtractSpectrum(it.getValue() as Table, referencePoint as Table)]
+    }
+}
 
 //println "Empty files:"
 //Collection<NMPoint> emptySpectra = NumassDataUtils.joinSpectra(
@@ -56,39 +86,30 @@ data = NumassDataUtils.substractReferencePoint(data, 18600d);
 //    }
 //}
 
-def printPoint(Iterable<NumassPoint> data, List<Double> us, int binning = 20, normalize = true) {
+//printing selected points
-    List<NumassPoint> points = data.findAll { it.voltage in us }.sort { it.voltage }
+def printPoint = { Map<Double, Table> points, int binning = 20, normalize = true ->
-
-    Map spectra = points.first().getMap(binning, normalize).collectEntries { key, value ->
-        [key, [value]]
-    };
-
     print "channel"
-    points.eachWithIndex { it, index ->
+    points.each { print "\t${it.key}" }
-        print "\t${it.voltage}"
-        it.getMap(binning, normalize).each { k, v ->
-            spectra[k].add(v)
-        }
-    }
-
     println()
 
-    spectra.each { key, value ->
+    def firstPoint = points.values().first()
-        print key
+    (0..firstPoint.size()).each { i ->
-        value.each {
+        print firstPoint.get(CHANNEL_KEY, i).intValue()
-            print "\t${it}"
+        points.values().each {
+            print "\t${it.get(COUNT_RATE_KEY, i).doubleValue()}"
         }
         println()
     }
+    println()
 }
 
 println "\n# spectra\n"
 
 //printPoint(data, [16200d, 16400d, 16800d, 17000d, 17200d, 17700d])
-printPoint(data, [14000d, 14500d, 15000d, 15500d, 16500d])
+printPoint(spectra.findAll { it.key in [16200d, 16400d, 16800d, 17000d, 17200d, 17700d] })
 
 println()
 
-Table t = new UnderflowCorrection().fitAllPoints(data, 350, 550, 3100, 20);
+//Table t = new UnderflowCorrection().fitAllPoints(data, 350, 550, 3100, 20);
-ColumnedDataWriter.writeTable(System.out, t, "underflow parameters")
+//ColumnedDataWriter.writeTable(System.out, t, "underflow parameters")
 

numass-main/src/main/java/inr/numass/utils/NumassUtils.java

@@ -15,8 +15,8 @@
  */
 package inr.numass.utils;
 
-import hep.dataforge.io.envelopes.DefaultEnvelopeWriter;
 import hep.dataforge.io.envelopes.EnvelopeBuilder;
+import hep.dataforge.io.envelopes.TaglessEnvelopeType;
 import hep.dataforge.io.markup.Markedup;
 import hep.dataforge.io.markup.SimpleMarkupRenderer;
 import hep.dataforge.meta.Meta;
@@ -99,7 +99,7 @@ public class NumassUtils {
     public static void writeEnvelope(OutputStream stream, Meta meta, Consumer<OutputStream> dataWriter) {
         //TODO replace by text envelope when it is ready
         try {
-            new DefaultEnvelopeWriter().write(
+            TaglessEnvelopeType.instance.getWriter().write(
                     stream,
                     new EnvelopeBuilder()
                             .setMeta(meta)