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Column table implementation

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This commit is contained in:
Alexander Nozik 2017-07-12 17:22:17 +03:00
parent acae9aae4c
commit c898422e5d
23 changed files with 414 additions and 374 deletions
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72
numass-core/src/main/java/inr/numass/data/analyzers/AbstractAnalyzer.java Normal file
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@ -0,0 +1,72 @@
package inr.numass.data.analyzers;
import hep.dataforge.meta.Meta;
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.*;
import org.jetbrains.annotations.Nullable;
import java.util.stream.Stream;
import static hep.dataforge.tables.XYAdapter.*;
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", "count", COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, "window", "timestamp"};
public static String[] NAME_LIST_WITH_HV = {HV_KEY, "length", "count", COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, "window", "timestamp"};
@Nullable
private final SignalProcessor processor;
public AbstractAnalyzer(@Nullable SignalProcessor processor) {
this.processor = processor;
}
public AbstractAnalyzer() {
this.processor = null;
}
/**
* Return unsorted stream of events including events from frames
*
* @param block
* @return
*/
public Stream<NumassEvent> getEventStream(NumassBlock block, Meta config) {
if (getProcessor() == null && block.getFrames().count() > 0) {
throw new IllegalArgumentException("Signal processor needed to analyze frames");
} else {
int loChannel = config.getInt("window.lo", 0);
int upChannel = config.getInt("window.up", Integer.MAX_VALUE);
return Stream.concat(block.getEvents(), block.getFrames().flatMap(getProcessor()::analyze))
.filter(it -> it.getChanel() >= loChannel && it.getChanel() <= upChannel);
}
}
@Override
public Table analyze(NumassSet set, Meta config) {
TableFormat format = new TableFormatBuilder()
.addNumber(HV_KEY, X_VALUE_KEY)
.addNumber("length")
.addNumber("count")
.addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
.addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
.addColumn("window")
.addTime()
.build();
return new ListTable.Builder(format)
.rows(set.getPoints().map(point -> analyze(point, config)))
.build();
}
@Nullable
public SignalProcessor getProcessor() {
return processor;
}
}

25
numass-core/src/main/java/inr/numass/data/analyzers/DebunchAnalyzer.java Normal file
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@ -0,0 +1,25 @@
package inr.numass.data.analyzers;
import hep.dataforge.meta.Meta;
import hep.dataforge.values.Values;
import inr.numass.data.api.NumassBlock;
import inr.numass.data.api.SignalProcessor;
import org.jetbrains.annotations.Nullable;
/**
* Block analyzer that can perform debunching
* Created by darksnake on 11.07.2017.
*/
public class DebunchAnalyzer extends AbstractAnalyzer {
public DebunchAnalyzer(@Nullable SignalProcessor processor) {
super(processor);
}
public DebunchAnalyzer() {
}
@Override
public Values analyze(NumassBlock block, Meta config) {
throw new UnsupportedOperationException("TODO");
}
}

92
numass-core/src/main/java/inr/numass/data/analyzers/SimpleAnalyzer.java
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@ -1,59 +1,31 @@
package inr.numass.data.analyzers;
import hep.dataforge.meta.Meta;
import hep.dataforge.tables.*;
import hep.dataforge.tables.ValueMap;
import hep.dataforge.values.Values;
import inr.numass.data.api.*;
import inr.numass.data.api.NumassBlock;
import inr.numass.data.api.NumassPoint;
import inr.numass.data.api.SignalProcessor;
import org.jetbrains.annotations.Nullable;
import java.util.NavigableMap;
import java.util.TreeMap;
import java.util.concurrent.atomic.AtomicLong;
import java.util.stream.Stream;
import static hep.dataforge.tables.XYAdapter.*;
import static inr.numass.data.api.NumassPoint.HV_KEY;
/**
* A simple event counter
* Created by darksnake on 07.07.2017.
*/
public class SimpleAnalyzer implements NumassAnalyzer {
public static String[] NAME_LIST = {"length", "count", COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, "window", "timestamp"};
public static String[] NAME_LIST_WITH_HV = {HV_KEY, "length", "count", COUNT_RATE_KEY, COUNT_RATE_ERROR_KEY, "window", "timestamp"};
@Nullable
private final SignalProcessor processor;
public class SimpleAnalyzer extends AbstractAnalyzer {
public SimpleAnalyzer(@Nullable SignalProcessor processor) {
this.processor = processor;
super(processor);
}
public SimpleAnalyzer() {
this.processor = null;
}
/**
* Return unsorted stream of events including events from frames
*
* @param block
* @return
*/
protected Stream<NumassEvent> getEventStream(NumassBlock block) {
if (processor == null && block.getFrames().count() > 0) {
throw new IllegalArgumentException("Signal processor needed to analyze frames");
} else {
return Stream.concat(block.getEvents(), block.getFrames().flatMap(processor::analyze));
}
}
@Override
public Values analyze(NumassBlock block, Meta config) {
int loChannel = config.getInt("energy.lo", 0);
int upChannel = config.getInt("energy.up", Integer.MAX_VALUE);
long count = getEventStream(block)
.filter(it -> it.getChanel() >= loChannel && it.getChanel() <= upChannel)
.count();
int loChannel = config.getInt("window.lo", 0);
int upChannel = config.getInt("window.up", Integer.MAX_VALUE);
long count = getEventStream(block, config).count();
double countRate = (double) count / block.getLength().toMillis() * 1000;
double countRateError = Math.sqrt((double) count) / block.getLength().toMillis() * 1000;
@ -84,50 +56,4 @@ public class SimpleAnalyzer implements NumassAnalyzer {
}
@Override
public Table analyze(NumassSet set, Meta config) {
TableFormat format = new TableFormatBuilder()
.addNumber(HV_KEY, X_VALUE_KEY)
.addNumber("length")
.addNumber("count")
.addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
.addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
.addColumn("window")
.addTime()
.build();
return new ListTable.Builder(format)
.rows(set.getPoints().map(point -> analyze(point, config)))
.build();
}
@Override
public Table getSpectrum(NumassBlock block, Meta config) {
TableFormat format = new TableFormatBuilder()
.addNumber("channel", X_VALUE_KEY)
.addNumber("count")
.addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
.addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
.updateMeta(metaBuilder -> metaBuilder.setNode("config", config))
.build();
NavigableMap<Short, AtomicLong> map = new TreeMap<>();
getEventStream(block).forEach(event -> {
if (map.containsKey(event.getChanel())) {
map.get(event.getChanel()).incrementAndGet();
} else {
map.put(event.getChanel(), new AtomicLong(1));
}
});
return new ListTable.Builder(format)
.rows(map.entrySet().stream()
.map(entry ->
new ValueMap(format.namesAsArray(),
entry.getKey(),
entry.getValue(),
entry.getValue().get() / block.getLength().toMillis() * 1000,
Math.sqrt(entry.getValue().get()) / block.getLength().toMillis() * 1000
)
)
).build();
}
}

42
numass-core/src/main/java/inr/numass/data/analyzers/SmartAnalyzer.java Normal file
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@ -0,0 +1,42 @@
package inr.numass.data.analyzers;
import hep.dataforge.meta.Meta;
import hep.dataforge.values.Values;
import inr.numass.data.api.NumassBlock;
import inr.numass.data.api.SignalProcessor;
import org.jetbrains.annotations.Nullable;
/**
* An analyzer dispatcher which uses different analyzer for different meta
* Created by darksnake on 11.07.2017.
*/
public class SmartAnalyzer extends AbstractAnalyzer {
private SimpleAnalyzer simpleAnalyzer = new SimpleAnalyzer();
private DebunchAnalyzer debunchAnalyzer = new DebunchAnalyzer();
private TimeAnalyzer timeAnalyzer = new TimeAnalyzer();
public SmartAnalyzer(@Nullable SignalProcessor processor) {
super(processor);
this.simpleAnalyzer = new SimpleAnalyzer(processor);
this.debunchAnalyzer = new DebunchAnalyzer(processor);
this.timeAnalyzer = new TimeAnalyzer(processor);
}
public SmartAnalyzer() {
}
@Override
public Values analyze(NumassBlock block, Meta config) {
//TODO do something more... smart... using information from point if block is point
switch (config.getString("type", "simple")) {
case "simple":
return simpleAnalyzer.analyze(block, config);
case "time":
return timeAnalyzer.analyze(block, config);
case "debunch":
return debunchAnalyzer.analyze(block, config);
default:
throw new IllegalArgumentException("Analyzer not found");
}
}
}

25
numass-core/src/main/java/inr/numass/data/analyzers/TimeAnalyzer.java Normal file
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@ -0,0 +1,25 @@
package inr.numass.data.analyzers;
import hep.dataforge.meta.Meta;
import hep.dataforge.values.Values;
import inr.numass.data.api.NumassBlock;
import inr.numass.data.api.SignalProcessor;
import org.jetbrains.annotations.Nullable;
/**
* Created by darksnake on 11.07.2017.
*/
public class TimeAnalyzer extends AbstractAnalyzer {
public TimeAnalyzer(@Nullable SignalProcessor processor) {
super(processor);
}
public TimeAnalyzer() {
}
@Override
public Values analyze(NumassBlock block, Meta config) {
throw new UnsupportedOperationException("TODO");
}
}

58
numass-core/src/main/java/inr/numass/data/api/NumassAnalyzer.java
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@ -1,14 +1,52 @@
package inr.numass.data.api;
import hep.dataforge.meta.Meta;
import hep.dataforge.tables.Table;
import hep.dataforge.tables.*;
import hep.dataforge.values.Values;
import inr.numass.data.analyzers.SmartAnalyzer;
import java.util.NavigableMap;
import java.util.TreeMap;
import java.util.concurrent.atomic.AtomicLong;
import java.util.stream.Stream;
import static hep.dataforge.tables.XYAdapter.*;
/**
* A general raw data analysis utility. Could have different implementations
* Created by darksnake on 06-Jul-17.
*/
public interface NumassAnalyzer {
static Table getSpectrum(NumassBlock block, Meta config) {
TableFormat format = new TableFormatBuilder()
.addNumber("channel", X_VALUE_KEY)
.addNumber("count")
.addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
.addNumber(COUNT_RATE_ERROR_KEY, Y_ERROR_KEY)
.updateMeta(metaBuilder -> metaBuilder.setNode("config", config))
.build();
NavigableMap<Short, AtomicLong> map = new TreeMap<>();
new SmartAnalyzer().getEventStream(block, config).forEach(event -> {
if (map.containsKey(event.getChanel())) {
map.get(event.getChanel()).incrementAndGet();
} else {
map.put(event.getChanel(), new AtomicLong(1));
}
});
return new ListTable.Builder(format)
.rows(map.entrySet().stream()
.map(entry ->
new ValueMap(format.namesAsArray(),
entry.getKey(),
entry.getValue(),
entry.getValue().get() / block.getLength().toMillis() * 1000,
Math.sqrt(entry.getValue().get()) / block.getLength().toMillis() * 1000
)
)
).build();
}
String COUNT_RATE_KEY = "cr";
String COUNT_RATE_ERROR_KEY = "crErr";
@ -21,21 +59,21 @@ public interface NumassAnalyzer {
*/
Values analyze(NumassBlock block, Meta config);
/**
* Return unsorted stream of events including events from frames
*
* @param block
* @return
*/
Stream<NumassEvent> getEventStream(NumassBlock block, Meta config);
/**
* Analyze the whole set. And return results as a table
*
* @param set
* @param config
* @return
*/
Table analyze(NumassSet set, Meta config);
/**
* Generate energy spectrum for the given block
* @param block
* @param config
* @return
*/
Table getSpectrum(NumassBlock block, Meta config);
}

12
numass-core/src/main/java/inr/numass/data/storage/ProtoNumassPoint.java
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@ -17,31 +17,27 @@ import java.util.stream.IntStream;
import java.util.stream.Stream;
/**
* Protobuf based numass point
* Created by darksnake on 09.07.2017.
*/
public class ProtoNumassPoint implements NumassPoint {
private final Envelope envelope;
NumassProto.Point point;
public ProtoNumassPoint(Envelope envelope) {
this.envelope = envelope;
}
private NumassProto.Point getPoint() {
if (point == null) {
try (InputStream stream = envelope.getData().getStream()) {
point = NumassProto.Point.parseFrom(stream);
return NumassProto.Point.parseFrom(stream);
} catch (IOException ex) {
throw new RuntimeException("Failed to read point via protbuf");
throw new RuntimeException("Failed to read point via protobuf");
}
}
return point;
}
@Override
public Stream<NumassBlock> getBlocks() {
return point.getChannelsList().stream().flatMap(channel ->
return getPoint().getChannelsList().stream().flatMap(channel ->
channel.getBlocksList().stream().map(block -> new ProtoBlock((int) channel.getNum(), block))
);
}

1
numass-main/src/main/groovy/inr/numass/scripts/FindBorder.groovy
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@ -8,7 +8,6 @@ package inr.numass.scripts
import hep.dataforge.grind.GrindMetaBuilder
import hep.dataforge.meta.Meta
import inr.numass.actions.FindBorderAction
import inr.numass.data.storage.NumassDataLoader
File dataDir = new File("D:\\Work\\Numass\\data\\2016_04\\T2_data\\Fill_2_2\\set_6_e26d123e54010000")

37
numass-main/src/main/java/inr/numass/actions/AnalyzeDataAction.java Normal file
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@ -0,0 +1,37 @@
package inr.numass.actions;
import hep.dataforge.actions.OneToOneAction;
import hep.dataforge.context.Context;
import hep.dataforge.description.TypedActionDef;
import hep.dataforge.description.ValueDef;
import hep.dataforge.io.ColumnedDataWriter;
import hep.dataforge.meta.Laminate;
import hep.dataforge.tables.Table;
import inr.numass.data.analyzers.SmartAnalyzer;
import inr.numass.data.api.NumassAnalyzer;
import inr.numass.data.api.NumassSet;
import java.io.OutputStream;
import static hep.dataforge.values.ValueType.NUMBER;
import static hep.dataforge.values.ValueType.STRING;
/**
* The action performs the readout of data and collection of count rate into a table
* Created by darksnake on 11.07.2017.
*/
@TypedActionDef(name = "numass.analyze", inputType = NumassSet.class, outputType = Table.class)
@ValueDef(name = "window.lo", type = {NUMBER, STRING}, def = "0", info = "Lower bound for window")
@ValueDef(name = "window.up", type = {NUMBER, STRING}, def = "10000", info = "Upper bound for window")
public class AnalyzeDataAction extends OneToOneAction<NumassSet, Table> {
@Override
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);
OutputStream stream = buildActionOutput(context, name);
ColumnedDataWriter.writeTable(stream, data, head);
return res;
}
}

129
numass-main/src/main/java/inr/numass/actions/FindBorderAction.java
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@ -1,129 +0,0 @@
/*
* Copyright 2015 Alexander Nozik.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package inr.numass.actions;
import hep.dataforge.actions.OneToOneAction;
import hep.dataforge.context.Context;
import hep.dataforge.description.TypedActionDef;
import hep.dataforge.exceptions.ContentException;
import hep.dataforge.io.ColumnedDataWriter;
import hep.dataforge.meta.Laminate;
import hep.dataforge.tables.ListTable;
import hep.dataforge.tables.Table;
import hep.dataforge.tables.ValueMap;
import hep.dataforge.values.Value;
import org.apache.commons.math3.analysis.UnivariateFunction;
import java.io.OutputStream;
import java.util.HashMap;
import java.util.Map;
import java.util.stream.Collectors;
/**
* @author Darksnake
*/
@TypedActionDef(name = "findBorder", inputType = NMFile.class, outputType = Table.class)
public class FindBorderAction extends OneToOneAction<NumassData, Table> {
private final static String[] names = {"U", "80%", "90%", "95%", "99%"};
private final static double[] percents = {0.8, 0.9, 0.95, 0.99};
private UnivariateFunction normCorrection = e -> 1 + 13.265 * Math.exp(-e / 2343.4);
@Override
protected Table execute(Context context, String name, NumassData source, Laminate meta) throws ContentException {
report(context, name, "File {} started", source.getName());
int upperBorder = meta.getInt("upper", 4094);
int lowerBorder = meta.getInt("lower", 0);
double substractReference = meta.getDouble("reference", 0);
NumassPoint referencePoint = null;
if (substractReference > 0) {
referencePoint = source.getByVoltage(substractReference);
if (referencePoint == null) {
report(context, name, "Reference point {} not found", substractReference);
}
}
ListTable.Builder dataBuilder = new ListTable.Builder(names);
fill(dataBuilder, source, lowerBorder, upperBorder, referencePoint);
Table bData = dataBuilder.build();
OutputStream stream = buildActionOutput(context, name);
ColumnedDataWriter.writeTable(stream, bData, String.format("%s : lower = %d upper = %d", name, lowerBorder, upperBorder));
report(context, name, "File {} completed", source.getName());
return bData;
}
private double getNorm(Map<Double, Double> spectrum, int lower, int upper) {
double res = 0;
for (Map.Entry<Double, Double> entry : spectrum.entrySet()) {
if ((entry.getKey() >= lower) && (entry.getKey() <= upper)) {
res += entry.getValue();
}
}
return res;
}
private void fill(ListTable.Builder dataBuilder, NumassData file, int lower, int upper, NumassPoint reference) {
for (NumassPoint point : file) {
if ((reference != null) && (point.getVoltage() == reference.getVoltage())) {
continue;
}
//создаем основу для будущей точки
HashMap<String, Value> map = new HashMap<>();
map.put(names[0], Value.of(point.getVoltage()));
Map<Double, Double> spectrum;
if (reference != null) {
Map<Double, Double> sp = point.getMap(0, true);
Map<Double, Double> referenceSpectrum = reference.getMap(0, true);
spectrum = sp.entrySet().stream()
.collect(Collectors.toMap(entry -> entry.getKey(), entry -> Math.max(entry.getValue() - referenceSpectrum.get(entry.getKey()), 0)));
} else {
spectrum = point.getMap(0, true);
}
double norm = getNorm(spectrum, lower, upper) * normCorrection.value(point.getVoltage());
double counter = 0;
int chanel = upper;
while (chanel > lower) {
chanel--;
counter += spectrum.get((double) chanel);
for (int i = 0; i < percents.length; i++) {
if (counter / norm > percents[i]) {
if (!map.containsKey(names[i + 1])) {
map.put(names[i + 1], Value.of(chanel));
}
}
}
}
for (String n : names) {
if (!map.containsKey(n)) {
map.put(n, Value.of(lower));
}
}
dataBuilder.row(new ValueMap(map));
}
}
}

37
numass-main/src/main/java/inr/numass/actions/JoinNumassDataAction.java
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@ -1,37 +0,0 @@
package inr.numass.actions;
import hep.dataforge.actions.ManyToOneAction;
import hep.dataforge.context.Context;
import hep.dataforge.description.TypedActionDef;
import hep.dataforge.meta.Laminate;
import java.util.Collection;
import java.util.Map;
import java.util.stream.IntStream;
/**
* Created by darksnake on 04-Nov-16.
*/
@TypedActionDef(name = "joinData", inputType = NumassData.class, outputType = NumassData.class,
info = "Join a number of numass data files into one single file via spectrum summing")
public class JoinNumassDataAction extends ManyToOneAction<NumassData, NumassData> {
@Override
protected NumassData execute(Context context, String nodeName, Map<String, NumassData> input, Laminate meta) {
throw new UnsupportedOperationException("not implemented");
}
private NumassPoint joinPoint(Collection<NumassPoint> points) {
return points.stream().reduce((p1, p2) -> {
if (p1.getVoltage() != p2.getVoltage()) {
throw new RuntimeException("Can't sum points with different Uset");
}
return new NumassPointImpl(
(p1.getVoltage() + p2.getVoltage()) / 2,
p1.getStartTime(),
p1.getLength() + p2.getLength(),
IntStream.range(0, p1.getSpectrum().length).map(i -> p1.getSpectrum()[i] * p2.getSpectrum()[i]).toArray()
);
}).get();
}
}

2
numass-main/src/main/java/inr/numass/actions/MergeDataAction.java
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@ -161,7 +161,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
res.add(curPoint);
});
return new ListTable(TableFormat.forNames(parnames), res);
return new ListTable(MetaTableFormat.forNames(parnames), res);
}

32
numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java
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@ -25,14 +25,10 @@ import hep.dataforge.io.ColumnedDataWriter;
import hep.dataforge.io.XMLMetaWriter;
import hep.dataforge.meta.Laminate;
import hep.dataforge.meta.Meta;
import hep.dataforge.tables.ListTable;
import hep.dataforge.tables.Table;
import hep.dataforge.tables.TableFormat;
import hep.dataforge.tables.ValueMap;
import hep.dataforge.tables.*;
import hep.dataforge.values.Values;
import inr.numass.data.NumassPoint;
import inr.numass.data.api.NumassPoint;
import inr.numass.data.api.NumassSet;
import inr.numass.data.storage.NumassDataLoader;
import inr.numass.debunch.DebunchReport;
import inr.numass.debunch.FrameAnalizer;
import inr.numass.utils.ExpressionUtils;
@ -77,7 +73,7 @@ public class PrepareDataAction extends OneToOneAction<NumassSet, Table> {
protected ListTable execute(Context context, String name, NumassSet dataFile, Laminate meta) {
// log.report("File %s started", dataFile.getName());
int upper = meta.getInt("upperWindow", RawNMPoint.MAX_CHANEL - 1);
int upper = meta.getInt("upperWindow", Integer.MAX_VALUE);
List<Correction> corrections = new ArrayList<>();
if (meta.hasValue("deadTime")) {
@ -107,16 +103,16 @@ public class PrepareDataAction extends OneToOneAction<NumassSet, Table> {
utransform = Function.identity();
}
if (meta.hasMeta("debunch")) {
if (dataFile instanceof NumassDataLoader) {
dataFile = ((NumassDataLoader) dataFile).applyRawTransformation(raw -> debunch(context, raw, meta.getMeta("debunch")));
} else {
throw new RuntimeException("Debunch not available");
}
}
// if (meta.hasMeta("debunch")) {
// if (dataFile instanceof NumassDataLoader) {
// dataFile = ((NumassDataLoader) dataFile).applyRawTransformation(raw -> debunch(context, raw, meta.getMeta("debunch")));
// } else {
// throw new RuntimeException("Debunch not available");
// }
// }
List<Values> dataList = new ArrayList<>();
for (NumassPoint point : dataFile) {
dataFile.getPoints().forEach( point -> {
long total = point.getTotalCount();
double uset = utransform.apply(point.getVoltage());
@ -148,15 +144,15 @@ public class PrepareDataAction extends OneToOneAction<NumassSet, Table> {
Instant timestamp = point.getStartTime();
dataList.add(new ValueMap(parnames, new Object[]{uset, uread, time, total, wind, correctionFactor, cr, crErr, timestamp}));
}
});
TableFormat format;
if (!dataList.isEmpty()) {
//Генерируем автоматический формат по первой строчке
format = TableFormat.forPoint(dataList.get(0));
format = MetaTableFormat.forPoint(dataList.get(0));
} else {
format = TableFormat.forNames(parnames);
format = MetaTableFormat.forNames(parnames);
}
String head;

63
numass-main/src/main/java/inr/numass/actions/ReadLegacyDataAction.java
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@ -1,63 +0,0 @@
/*
* Copyright 2015 Alexander Nozik.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package inr.numass.actions;
import hep.dataforge.actions.OneToOneAction;
import hep.dataforge.context.Context;
import hep.dataforge.data.binary.Binary;
import hep.dataforge.description.NodeDef;
import hep.dataforge.description.TypedActionDef;
import hep.dataforge.description.ValueDef;
import hep.dataforge.exceptions.ContentException;
import hep.dataforge.meta.Laminate;
import static hep.dataforge.values.ValueType.NUMBER;
import static inr.numass.NumassIO.getNumassData;
/**
*
* @author Darksnake
*/
@TypedActionDef(name = "readData",
inputType = Binary.class, outputType = NMFile.class, info = "Read binary numass data file")
@ValueDef(name = "fileName", info = "The name of the file. By default equals file name.")
@ValueDef(name = "HVdev", info = "Divider for HV measurements. Should be set to 1.0 for numass data 2014",
def = "2.468555393226049", type = {NUMBER})
@ValueDef(name = "noUset", info = "If 'true', then Uset = Uread")
@NodeDef(name = "debunch", target = "class::inr.numass.actions.DebunchAction", info = "If given, governs debunching")
public class ReadLegacyDataAction extends OneToOneAction<Binary, NMFile> {
@Override
protected NMFile execute(Context context, String name, Binary source, Laminate meta) throws ContentException {
// log.logString("File '%s' started", source.getName());
RawNMFile raw = getNumassData(source, meta);
// if (meta.getBoolean("paw", false)) {
// raw.generatePAW(buildActionOutput(context, name + ".paw"));
// }
if (meta.hasMeta("debunch")) {
DebunchAction debunch = new DebunchAction();
Laminate laminate = new Laminate(meta.getMeta("debunch"))
.setDescriptor(debunch.getDescriptor());
raw = debunch.execute(context, name, raw, laminate);
}
NMFile result = new NMFile(raw);
return result;
}
}

12
numass-main/src/main/java/inr/numass/actions/ShowEnergySpectrumAction.java
View File

@ -19,6 +19,7 @@ import hep.dataforge.plots.data.XYPlottable;
import hep.dataforge.tables.*;
import hep.dataforge.values.ValueType;
import hep.dataforge.values.Values;
import inr.numass.data.api.NumassSet;
import java.io.OutputStream;
import java.util.*;
@ -28,19 +29,14 @@ import java.util.stream.Collectors;
*
* @author Alexander Nozik
*/
@TypedActionDef(inputType = NumassData.class, outputType = Table.class, name = "energySpectrum", info = "Generate output table and optionally plot for detector energy spectra")
public class ShowEnergySpectrumAction extends OneToOneAction<NumassData, Table> {
@TypedActionDef(inputType = NumassSet.class, outputType = Table.class, name = "energySpectrum", info = "Generate output table and optionally plot for detector energy spectra")
public class ShowEnergySpectrumAction extends OneToOneAction<NumassSet, Table> {
@Override
protected Table execute(Context context, String name, NumassData input, Laminate inputMeta) {
protected Table execute(Context context, String name, NumassSet input, Laminate inputMeta) {
int binning = inputMeta.getInt("binning", 20);
boolean normalize = inputMeta.getBoolean("normalize", true);
List<NumassPoint> points = input.getNMPoints();
if (points.isEmpty()) {
getLogger(inputMeta).error("Empty data");
return null;
}
//build header
List<String> names = new ArrayList<>();

4
numass-main/src/main/java/inr/numass/actions/SubstractSpectrumAction.java
View File

@ -34,9 +34,9 @@ public class SubstractSpectrumAction extends OneToOneAction<Table, Table> {
File referenceFile = context.io().getFile(referencePath);
Table referenceTable = new ColumnedDataReader(referenceFile).toTable();
ListTable.Builder builder = new ListTable.Builder(input.getFormat());
input.stream().forEach(point -> {
input.getRows().forEach(point -> {
ValueMap.Builder pointBuilder = new ValueMap.Builder(point);
Optional<Values> referencePoint = referenceTable.stream()
Optional<Values> referencePoint = referenceTable.getRows()
.filter(p -> Math.abs(p.getDouble("Uset") - point.getDouble("Uset")) < 0.1).findFirst();
if (referencePoint.isPresent()) {
pointBuilder.putValue("CR", Math.max(0, point.getDouble("CR") - referencePoint.get().getDouble("CR")));

4
numass-main/src/main/java/inr/numass/actions/SummaryAction.java
View File

@ -26,8 +26,8 @@ import hep.dataforge.meta.Laminate;
import hep.dataforge.meta.Meta;
import hep.dataforge.stat.fit.FitState;
import hep.dataforge.tables.ListTable;
import hep.dataforge.tables.MetaTableFormat;
import hep.dataforge.tables.Table;
import hep.dataforge.tables.TableFormat;
import hep.dataforge.tables.ValueMap;
import hep.dataforge.values.Value;
import hep.dataforge.values.Values;
@ -75,7 +75,7 @@ public class SummaryAction extends ManyToOneAction<FitState, Table> {
}
names[names.length - 1] = "chi2";
ListTable.Builder res = new ListTable.Builder(TableFormat.forNames(names));
ListTable.Builder res = new ListTable.Builder(MetaTableFormat.forNames(names));
double[] weights = new double[parNames.length];
Arrays.fill(weights, 0);

114
numass-main/src/main/java/inr/numass/actions/TransformDataAction.java Normal file
View File

@ -0,0 +1,114 @@
package inr.numass.actions;
import hep.dataforge.actions.OneToOneAction;
import hep.dataforge.context.Context;
import hep.dataforge.description.ValueDef;
import hep.dataforge.meta.Laminate;
import hep.dataforge.meta.Meta;
import hep.dataforge.tables.Table;
import hep.dataforge.values.Values;
import inr.numass.utils.ExpressionUtils;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.function.Function;
import java.util.function.UnaryOperator;
import java.util.stream.Collectors;
import static hep.dataforge.values.ValueType.NUMBER;
import static hep.dataforge.values.ValueType.STRING;
import static inr.numass.utils.TritiumUtils.pointExpression;
/**
* Apply corrections and transformations to analyzed data
* Created by darksnake on 11.07.2017.
*/
public class TransformDataAction extends OneToOneAction<Table, Table> {
@Override
protected Table execute(Context context, String name, Table input, Laminate meta) {
UnaryOperator<Values> transformation = UnaryOperator.identity();
List<Correction> corrections = new ArrayList<>();
if (meta.optMeta("correction").isPresent()) {
corrections.addAll(meta.getMetaList("correction").stream()
.map((Function<Meta, Correction>) this::makeCorrection)
.collect(Collectors.toList()));
}
if (meta.hasValue("correction")) {
final String correction = meta.getString("correction");
corrections.add((point) -> pointExpression(correction, point));
}
Function<Double, Double> utransform;
if (meta.hasValue("utransform")) {
String func = meta.getString("utransform");
utransform = u -> {
Map<String, Object> binding = new HashMap<>();
binding.put("U", u);
return ExpressionUtils.function(func, binding);
};
} else {
utransform = Function.identity();
}
}
@ValueDef(name = "value", type = {NUMBER, STRING}, info = "Value or function to multiply count rate")
@ValueDef(name = "err", type = {NUMBER, STRING}, info = "error of the value")
private Correction makeCorrection(Meta corrMeta) {
final String expr = corrMeta.getString("value");
final String errExpr = corrMeta.getString("err", "");
return new Correction() {
@Override
public double corr(Values point) {
return pointExpression(expr, point);
}
@Override
public double corrErr(Values point) {
if (errExpr.isEmpty()) {
return 0;
} else {
return pointExpression(errExpr, point);
}
}
};
}
private interface Correction {
/**
* correction coefficient
*
* @param point
* @return
*/
double corr(Values point);
/**
* correction coefficient uncertainty
*
* @param point
* @return
*/
default double corrErr(Values point) {
return 0;
}
default double relativeErr(Values point) {
double corrErr = corrErr(point);
if (corrErr == 0) {
return 0;
} else {
return corrErr / corr(point);
}
}
}
}

2
numass-main/src/main/java/inr/numass/models/NamedSpectrumCaching.java
View File

@ -54,7 +54,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
this.a = a;
this.b = b;
this.source = spectrum;
spectrumDerivCache = new HashMap<>(source.size());
spectrumDerivCache = new HashMap<>(source.getNames().size());
// spectrumDerivCache = new CacheElement[source.getDimension()];
}

4
numass-main/src/main/java/inr/numass/tasks/NumassSubstractEmptySourceTask.java
View File

@ -83,9 +83,9 @@ public class NumassSubstractEmptySourceTask extends AbstractTask<Table> {
private Table subtract(Table merge, Table empty) {
ListTable.Builder builder = new ListTable.Builder(merge.getFormat());
merge.stream().forEach(point -> {
merge.getRows().forEach(point -> {
ValueMap.Builder pointBuilder = new ValueMap.Builder(point);
Optional<Values> referencePoint = empty.stream()
Optional<Values> referencePoint = empty.getRows()
.filter(p -> Math.abs(p.getDouble("Uset") - point.getDouble("Uset")) < 0.1).findFirst();
if (referencePoint.isPresent()) {
pointBuilder.putValue("CR", Math.max(0, point.getDouble("CR") - referencePoint.get().getDouble("CR")));

2
numass-main/src/main/java/inr/numass/tasks/NumassTableFilterTask.java
View File

@ -73,7 +73,7 @@ public class NumassTableFilterTask extends SingleActionTask<Table, Table> {
for (String field : dp.getNames()) {
Value val = dp.getValue(field);
Object obj;
switch (val.valueType()) {
switch (val.getType()) {
case BOOLEAN:
obj = val.booleanValue();
break;

13
numass-main/src/main/java/inr/numass/utils/TritiumUtils.java
View File

@ -15,6 +15,7 @@
*/
package inr.numass.utils;
import hep.dataforge.values.Values;
import org.apache.commons.math3.analysis.UnivariateFunction;
import java.util.HashMap;
@ -68,12 +69,14 @@ public class TritiumUtils {
* @param point
* @return
*/
public static double pointExpression(String expression, NumassPoint point) {
public static double pointExpression(String expression, Values point) {
Map<String, Object> exprParams = new HashMap<>();
exprParams.put("T", point.getLength());
exprParams.put("U", point.getVoltage());
exprParams.put("cr", ((double) point.getTotalCount()) / point.getLength());
exprParams.put("point", point);
//Adding all point values to expression parameters
point.getNames().forEach(name-> exprParams.put(name,point.getValue(name).value()));
//Adding aliases for commonly used parameters
exprParams.put("T", point.getDouble("length"));
exprParams.put("U", point.getDouble("voltage"));
return ExpressionUtils.function(expression, exprParams);
}
}

2
numass-server/src/main/java/inr/numass/server/HandlerUtils.java
View File

@ -20,7 +20,7 @@ public class HandlerUtils {
for (String state : states.getStateNames()) {
Value val = states.getValue(state);
String color;
switch (val.valueType()) {
switch (val.getType()) {
case NUMBER:
color = "blue";
break;