Revising numass scripts
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c7369b6b34
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@ -6,10 +6,12 @@ import hep.dataforge.tables.ListTable;
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import hep.dataforge.tables.Table;
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import hep.dataforge.tables.TableFormat;
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import hep.dataforge.tables.TableFormatBuilder;
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import hep.dataforge.values.Values;
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import inr.numass.data.api.NumassPoint;
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import inr.numass.data.api.NumassSet;
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import java.util.Collection;
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import java.util.Optional;
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import java.util.stream.Stream;
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import static hep.dataforge.tables.XYAdapter.*;
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@ -56,8 +58,17 @@ public class NumassDataUtils {
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.build();
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ListTable.Builder builder = new ListTable.Builder(format);
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for (int i = 0; i < sp1.size(); i++) {
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double value = sp1.getDouble(COUNT_RATE_KEY, i) - sp2.getDouble(COUNT_RATE_KEY, i);
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double error = Math.sqrt(Math.pow(sp1.getDouble(COUNT_RATE_ERROR_KEY, i), 2d) + Math.pow(sp2.getDouble(COUNT_RATE_ERROR_KEY, i), 2d));
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Values row1 = sp1.getRow(i);
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Optional<Values> row2 = sp2.getRows().filter(row -> row.getDouble(CHANNEL_KEY) == row1.getDouble(CHANNEL_KEY)).findFirst();
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double value1 = row1.getDouble(COUNT_RATE_KEY);
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double value2 = row2.map(it -> it.getDouble(COUNT_RATE_KEY)).orElse(0d);
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double error1 = row1.getDouble(COUNT_RATE_ERROR_KEY);
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double error2 = row2.map(it-> it.getDouble(COUNT_RATE_ERROR_KEY)).orElse(0d);
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double value = value1 - value2;
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double error = Math.sqrt(error1*error1 + error2*error2);
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builder.row(sp1.get(CHANNEL_KEY, i).intValue(), value, error);
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}
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return builder.build();
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@ -2,12 +2,12 @@ package inr.numass.data.api;
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import hep.dataforge.meta.Meta;
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import hep.dataforge.tables.*;
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import hep.dataforge.values.Value;
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import hep.dataforge.values.Values;
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import java.util.NavigableMap;
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import java.util.TreeMap;
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import java.util.concurrent.atomic.AtomicLong;
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import java.util.concurrent.atomic.AtomicReference;
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import java.util.stream.IntStream;
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import java.util.stream.Stream;
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import static hep.dataforge.tables.XYAdapter.*;
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@ -17,9 +17,11 @@ import static hep.dataforge.tables.XYAdapter.*;
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* Created by darksnake on 06-Jul-17.
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*/
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public interface NumassAnalyzer {
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short MAX_CHANNEL = 10000;
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/**
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* Calculate number of counts in the given channel
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*
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* @param spectrum
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* @param loChannel
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* @param upChannel
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@ -35,19 +37,20 @@ public interface NumassAnalyzer {
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/**
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* Apply window and binning to a spectrum
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*
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* @param lo
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* @param up
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* @param binSize
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* @return
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*/
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static Table spectrumWithBinning(Table spectrum, int lo, int up, int binSize) {
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static Table spectrumWithBinning(Table spectrum, int binSize) {
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TableFormat format = new TableFormatBuilder()
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.addNumber(CHANNEL_KEY, X_VALUE_KEY)
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.addNumber(COUNT_KEY, Y_VALUE_KEY)
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.addNumber(COUNT_RATE_KEY)
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.addNumber("binSize");
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ListTable.Builder builder = new ListTable.Builder(format);
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for (int chan = lo; chan < up - binSize; chan += binSize) {
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int loChannel = spectrum.getColumn(CHANNEL_KEY).stream().mapToInt(Value::intValue).min().orElse(0);
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int upChannel = spectrum.getColumn(CHANNEL_KEY).stream().mapToInt(Value::intValue).max().orElse(1);
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for (int chan = loChannel; chan < upChannel - binSize; chan += binSize) {
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AtomicLong count = new AtomicLong(0);
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AtomicReference<Double> countRate = new AtomicReference<>(0d);
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@ -61,7 +64,7 @@ public interface NumassAnalyzer {
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count.addAndGet(row.getValue(COUNT_KEY).numberValue().longValue());
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countRate.accumulateAndGet(row.getDouble(COUNT_RATE_KEY), (d1, d2) -> d1 + d2);
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});
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int bin = Math.min(binSize, up - chan);
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int bin = Math.min(binSize, upChannel - chan);
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builder.row((double) chan + (double) bin / 2d, count.get(), countRate.get(), bin);
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}
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return builder.build();
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@ -114,24 +117,32 @@ public interface NumassAnalyzer {
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.addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
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.updateMeta(metaBuilder -> metaBuilder.setNode("config", config))
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.build();
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NavigableMap<Short, AtomicLong> map = new TreeMap<>();
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//optimized for fastest computation
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//TODO requires additional performance optimization
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AtomicLong[] spectrum = new AtomicLong[MAX_CHANNEL];
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getEventStream(block, config).forEach(event -> {
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if (map.containsKey(event.getChanel())) {
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map.get(event.getChanel()).incrementAndGet();
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if (spectrum[event.getChanel()] == null) {
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spectrum[event.getChanel()] = new AtomicLong(1);
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} else {
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map.put(event.getChanel(), new AtomicLong(1));
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spectrum[event.getChanel()].incrementAndGet();
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}
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});
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double seconds = (double) block.getLength().toMillis() / 1000d;
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return new ListTable.Builder(format)
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.rows(map.entrySet().stream()
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.map(entry ->
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new ValueMap(format.namesAsArray(),
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entry.getKey(),
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entry.getValue(),
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(double) entry.getValue().get() / block.getLength().toMillis() * 1000d,
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Math.sqrt(entry.getValue().get()) / block.getLength().toMillis() * 1000d
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)
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)
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.rows(IntStream.range(0, MAX_CHANNEL)
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.filter(i -> spectrum[i] != null)
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.mapToObj(i -> {
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long value = spectrum[i].get();
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return new ValueMap(
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format.namesAsArray(),
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i,
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value,
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(double) value / seconds,
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Math.sqrt(value) / seconds
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);
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})
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).build();
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}
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@ -156,6 +167,4 @@ public interface NumassAnalyzer {
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default long getLength(NumassBlock block, Meta config) {
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return analyze(block, config).getValue(LENGTH_KEY).numberValue().longValue();
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}
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}
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@ -54,40 +54,28 @@ Map spectra = allPoints.collectEntries {
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return [(point.voltage): analyzer.getSpectrum(point, analyzerMeta)]
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}
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def refereceVoltage = 18600d
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int binning = 20
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//subtracting reference point
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def refereceVoltage = 18600
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def referencePoint = spectra[refereceVoltage]
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if (referencePoint) {
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if (refereceVoltage) {
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def referencePoint = spectra[refereceVoltage]
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spectra = spectra.findAll { it.key != refereceVoltage }.collectEntries {
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return [(it.key): NumassDataUtils.subtractSpectrum(it.getValue() as Table, referencePoint as Table)]
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}
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}
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//println "Empty files:"
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//Collection<NMPoint> emptySpectra = NumassDataUtils.joinSpectra(
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// StorageUtils.loaderStream(storage).filter{ it.key.matches("Empty.*")}.map {
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// println it.key
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// it.value
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// }
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//)
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//emptySpectra = NumassDataUtils.substractReferencePoint(emptySpectra,18600);
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//
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//data = data.collect { point ->
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// NMPoint ref = emptySpectra.find { it.u == point.u }
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// if (ref) {
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// println "substracting tritium background for point ${point.u}"
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// NumassDataUtils.substractPoint(point, ref)
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// } else {
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// println "point ${point.u} skipped"
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// point
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// }
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//}
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//Apply binning
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if (binning) {
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spectra = spectra.collectEntries {
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[(it.key): NumassAnalyzer.spectrumWithBinning(it.value as Table, binning)];
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}
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}
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//printing selected points
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def printPoint = { Map<Double, Table> points, int binning = 20, normalize = true ->
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def printPoint = { Map<Double, Table> points ->
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print "channel"
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points.each { print "\t${it.key}" }
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println()
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@ -113,3 +101,23 @@ println()
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//Table t = new UnderflowCorrection().fitAllPoints(data, 350, 550, 3100, 20);
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//ColumnedDataWriter.writeTable(System.out, t, "underflow parameters")
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//println "Empty files:"
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//Collection<NMPoint> emptySpectra = NumassDataUtils.joinSpectra(
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// StorageUtils.loaderStream(storage).filter{ it.key.matches("Empty.*")}.map {
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// println it.key
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// it.value
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// }
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//)
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//emptySpectra = NumassDataUtils.substractReferencePoint(emptySpectra,18600);
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//
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//data = data.collect { point ->
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// NMPoint ref = emptySpectra.find { it.u == point.u }
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// if (ref) {
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// println "substracting tritium background for point ${point.u}"
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// NumassDataUtils.substractPoint(point, ref)
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// } else {
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// println "point ${point.u} skipped"
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// point
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// }
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//}
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@ -8,6 +8,7 @@ package inr.numass.utils;
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import hep.dataforge.meta.Meta;
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import hep.dataforge.tables.ListTable;
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import hep.dataforge.tables.Table;
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import hep.dataforge.tables.TableTransform;
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import hep.dataforge.tables.ValueMap;
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import hep.dataforge.values.Values;
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import inr.numass.data.api.NumassAnalyzer;
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@ -106,13 +107,18 @@ public class UnderflowCorrection {
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if (xHigh <= xLow) {
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throw new IllegalArgumentException("Wrong borders for underflow calculation");
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}
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Table binned = NumassAnalyzer.spectrumWithBinning(spectrum, xLow, xHigh, binning);
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Table binned = TableTransform.filter(
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NumassAnalyzer.spectrumWithBinning(spectrum, binning),
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CHANNEL_KEY,
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xLow,
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xHigh
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);
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List<WeightedObservedPoint> points = binned.getRows()
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.map(p -> new WeightedObservedPoint(
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1d,//1d / p.getValue() , //weight
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p.getDouble(CHANNEL_KEY), // x
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p.getDouble(COUNT_RATE_KEY) / binning ) //y
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p.getDouble(COUNT_RATE_KEY) / binning) //y
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)
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.collect(Collectors.toList());
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SimpleCurveFitter fitter = SimpleCurveFitter.create(new ExponentFunction(), new double[]{1d, 200d});
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@ -324,7 +324,7 @@ class NumassLoaderView : View() {
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PlottableData.plot(
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seriesName,
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XYAdapter(NumassAnalyzer.CHANNEL_KEY, valueAxis),
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NumassAnalyzer.spectrumWithBinning(getSpectrum(point), 0, 4000, binning)
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NumassAnalyzer.spectrumWithBinning(getSpectrum(point), binning)
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).apply {
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configure(plottableConfig)
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}.also {
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