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Finished refactoring

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This commit is contained in:
Alexander Nozik 2016-03-21 15:29:31 +03:00
parent 87b70a02f7
commit cca98f4fab
29 changed files with 213 additions and 226 deletions
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2
numass-control/cryotemp/src/main/java/inr/numass/cryotemp/PKT8Device.java
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@ -15,7 +15,7 @@
*/
package inr.numass.cryotemp;
import hep.dataforge.content.Named;
import hep.dataforge.names.Named;
import hep.dataforge.context.Context;
import hep.dataforge.control.collectors.RegularPointCollector;
import hep.dataforge.control.measurements.DataDevice;

2
numass-control/vac/src/main/java/inr/numass/readvac/fx/VacuumeterView.java
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@ -5,7 +5,7 @@
*/
package inr.numass.readvac.fx;
import hep.dataforge.content.Named;
import hep.dataforge.names.Named;
import hep.dataforge.control.connections.DeviceViewController;
import hep.dataforge.control.devices.Device;
import hep.dataforge.control.measurements.Measurement;

6
numass-main/src/main/java/hep/dataforge/plotfit/PlotFitResultAction.java
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@ -47,7 +47,7 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
}
@Override
protected FitState execute(Logable log, Meta metaData, FitState input) {
protected FitState execute(Logable log, String name, Meta metaData, FitState input) {
PointSet data = input.getDataSet();
if (!(input.getModel() instanceof XYModel)) {
@ -68,12 +68,11 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
UnivariateFunction function = (double x) -> model.getSpectrum().value(x, input.getParameters());
XYPlotFrame frame = (XYPlotFrame) PlotsPlugin
.buildFrom(getContext()).buildPlotFrame(getName(), input.getName(),
.buildFrom(getContext()).buildPlotFrame(getName(), name,
metaData.getNode("plot", null));
//JFreeChartFrame.drawFrame(reader.getString("plotTitle", "Fit result plot for "+input.getName()), null);
// double[] x = new double[data.size()];
// double[] y = new double[data.size()];
// double xMin = Double.POSITIVE_INFINITY;
//
@ -94,7 +93,6 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
// xMax = x[i];
// }
// }
frame.add(new PlottableFunction("fit", function, data, adapter));//FIXME replace by helper
frame.add(PlottableData.plot("data", adapter, data));

32
numass-main/src/main/java/inr/numass/Main.java
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@ -15,19 +15,20 @@
*/
package inr.numass;
import hep.dataforge.actions.ActionResult;
import static hep.dataforge.actions.RunManager.executeXML;
import hep.dataforge.actions.RunManager;
import hep.dataforge.context.Context;
import static hep.dataforge.context.GlobalContext.out;
import hep.dataforge.data.DataManager;
import hep.dataforge.data.DataNode;
import hep.dataforge.data.FileDataFactory;
import hep.dataforge.datafitter.MINUITPlugin;
import hep.dataforge.io.IOManager;
import hep.dataforge.io.MetaFileReader;
import hep.dataforge.meta.Meta;
import static inr.numass.NumassContext.printDescription;
import inr.numass.workbench.Workbench;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Locale;
import static java.util.Locale.setDefault;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.filechooser.FileFilter;
@ -40,6 +41,7 @@ import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static java.util.Locale.setDefault;
/**
*
@ -55,7 +57,7 @@ public class Main {
}
@SuppressWarnings("deprecation")
public static ActionResult run(NumassContext context, String[] args) throws Exception {
public static DataNode run(NumassContext context, String[] args) throws Exception {
Logger logger = LoggerFactory.getLogger("numass-main");
Options options = prepareOptions();
@ -67,15 +69,15 @@ public class Main {
} catch (ParseException exp) {
// oops, something went wrong
logger.error("Command line error. Reason: " + exp.getMessage());
return ActionResult.empty();
return DataNode.empty();
}
if (line.hasOption("lc")) {
printDescription(context, true);
return ActionResult.empty();
return DataNode.empty();
} else if (line.hasOption("l")) {
printDescription(context, false);
return ActionResult.empty();
return DataNode.empty();
}
String cfgPath;
@ -90,20 +92,22 @@ public class Main {
cfgPath = line.getOptionValue("c");
if (cfgPath == null) {
logger.info("Configutation path not provided.");
return ActionResult.empty();
return DataNode.empty();
}
File config = context.io().getFile(cfgPath);
File configFile = context.io().getFile(cfgPath);
if (!config.exists()) {
if (!configFile.exists()) {
throw new FileNotFoundException("Configuration file not found");
}
context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, config.getParentFile().toString());
Meta config = MetaFileReader.read(configFile).build();
context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, configFile.getParentFile().toString());
applyCLItoContext(line, context);
return executeXML(context, config);
return RunManager.executeAction(context, config);
} else {
Workbench.main(args);
return null;
@ -125,7 +129,7 @@ public class Main {
dataDir = new File(workDir, dataPath);
}
if (dataDir.exists() && dataDir.isDirectory()) {
context.putValue(DataManager.DATA_DIR, dataDir.getAbsolutePath());
context.putValue(FileDataFactory.DATA_DIR_KEY, dataDir.getAbsolutePath());
} else {
throw new FileNotFoundException("Data directory not found");
}

15
numass-main/src/main/java/inr/numass/NumassIO.java
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@ -15,6 +15,7 @@
*/
package inr.numass;
import hep.dataforge.data.FileData;
import hep.dataforge.io.BasicIOManager;
import hep.dataforge.meta.Meta;
import hep.dataforge.names.Name;
@ -29,6 +30,7 @@ import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.output.TeeOutputStream;
/**
@ -96,7 +98,7 @@ public class NumassIO extends BasicIOManager {
}
}
public static RawNMFile readAsDat(BinaryData source, Meta config) {
public static RawNMFile readAsDat(FileData source, Meta config) {
try {
return new NumassDataReader(source, config).read();
} catch (IOException ex) {
@ -104,17 +106,14 @@ public class NumassIO extends BasicIOManager {
}
}
public static RawNMFile readAsPaw(BinaryData source) {
try {
return new NumassPawReader().readPaw(source.getInputStream(), source.getName());
} catch (IOException ex) {
throw new RuntimeException(ex);
}
public static RawNMFile readAsPaw(FileData source) {
return new NumassPawReader().readPaw(source.get(), source.fileName());
}
public static RawNMFile getNumassData(FileData source, Meta config) {
RawNMFile dataFile;
switch (source.getExtension()) {
String extension = FilenameUtils.getExtension(source.fileName());
switch (extension) {
case "paw":
dataFile = readAsPaw(source);
break;

4
numass-main/src/main/java/inr/numass/actions/AdjustErrorsAction.java
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@ -30,13 +30,13 @@ public class AdjustErrorsAction extends OneToOneAction<PointSet, PointSet> {
}
@Override
protected PointSet execute(Logable log, Meta meta, PointSet input) {
protected PointSet execute(Logable log, String name,Meta meta, PointSet input) {
List<DataPoint> points = new ArrayList<>();
for (DataPoint dp : input) {
points.add(evalPoint(meta, dp));
}
return new ListPointSet(input.getName(), input.meta(), points, input.getDataFormat());
return new ListPointSet(points, input.getDataFormat());
}
private DataPoint evalPoint(Meta meta, DataPoint dp) {

7
numass-main/src/main/java/inr/numass/actions/DebunchAction.java
View File

@ -38,15 +38,14 @@ import java.io.PrintWriter;
@ValueDef(name = "rejectprob", type = "NUMBER", def = "1e-5", info = "Rejection probability")
@ValueDef(name = "framelength", type = "NUMBER", def = "5", info = "Frame length in seconds")
@ValueDef(name = "maxcr", type = "NUMBER", def = "100", info = "Maximum count rate for debunching")
public class DebunchAction extends OneToOneAction<RawNMFile,RawNMFile> {
public class DebunchAction extends OneToOneAction<RawNMFile, RawNMFile> {
public DebunchAction(Context context, Meta an) {
super(context, an);
}
@Override
protected RawNMFile execute(Logable log, Meta reader, RawNMFile source) throws ContentException {
protected RawNMFile execute(Logable log, String name, Meta reader, RawNMFile source) throws ContentException {
log.log("File {} started", source.getName());
int upper = source.meta().getInt("upperchanel", this.meta().getInt("upperchanel", RawNMPoint.MAX_CHANEL));
@ -72,7 +71,7 @@ public class DebunchAction extends OneToOneAction<RawNMFile,RawNMFile> {
});
log.log("File {} completed", source.getName());
log.getLog().print(new PrintWriter(buildActionOutput(source)));
log.getLog().print(new PrintWriter(buildActionOutput(name)));
// res.configure(source.meta());
return res;

5
numass-main/src/main/java/inr/numass/actions/FindBorderAction.java
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@ -33,13 +33,12 @@ import java.io.OutputStream;
@TypedActionDef(name = "findBorder", inputType = NMFile.class, outputType = NMFile.class)
public class FindBorderAction extends OneToOneAction<NMFile, NMFile> {
public FindBorderAction(Context context, Meta an) {
super(context, an);
}
@Override
protected NMFile execute(Logable log, Meta reader, NMFile source) throws ContentException {
protected NMFile execute(Logable log, String name, Meta reader, NMFile source) throws ContentException {
log.log("File {} started", source.getName());
int upperBorder = meta().getInt("upper", 4096);
@ -56,7 +55,7 @@ public class FindBorderAction extends OneToOneAction<NMFile, NMFile> {
BorderData bData = new BorderData(source, upperBorder, lowerBorder, referencePoint);
OutputStream stream = buildActionOutput(source);
OutputStream stream = buildActionOutput(name);
ColumnedDataWriter.writeDataSet(stream, bData, String.format("%s : lower = %d upper = %d", source.getName(), lowerBorder, upperBorder));

109
numass-main/src/main/java/inr/numass/actions/MergeDataAction.java
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@ -17,8 +17,8 @@ package inr.numass.actions;
import hep.dataforge.actions.ManyToOneAction;
import hep.dataforge.actions.GroupBuilder;
import hep.dataforge.content.NamedGroup;
import hep.dataforge.context.Context;
import hep.dataforge.data.DataNode;
import hep.dataforge.points.DataPoint;
import hep.dataforge.points.ListPointSet;
import hep.dataforge.points.MapPoint;
@ -27,12 +27,15 @@ import hep.dataforge.description.TypedActionDef;
import hep.dataforge.io.ColumnedDataWriter;
import hep.dataforge.io.log.Logable;
import hep.dataforge.meta.Meta;
import hep.dataforge.meta.MetaBuilder;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import hep.dataforge.points.PointSet;
import java.util.Collection;
import java.util.stream.Collectors;
/**
*
@ -40,7 +43,6 @@ import hep.dataforge.points.PointSet;
*/
@TypedActionDef(name = "merge", inputType = PointSet.class, outputType = PointSet.class, description = "Merge different numass data files into one.")
@NodeDef(name = "grouping", info = "The defenition of grouping rule for this merge", target = "method::hep.dataforge.content.GroupBuilder.byAnnotation")
//@Parameter(name = "groupBy", def = "mergeTag", info = "Defines the name of the value by which grouping is made. The value is supposed to be a String, but in practice could be any type which could be converted to String.")
public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
public static final String MERGE_NAME = "mergeName";
@ -51,80 +53,61 @@ public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
}
@Override
protected List<NamedGroup<PointSet>> buildGroups(Meta reader, List<PointSet> input) {
List<NamedGroup<PointSet>> groups;
if (reader.hasValue("grouping.byValue")) {
groups = super.buildGroups(reader, input);
@SuppressWarnings("unchecked")
protected List<DataNode<PointSet>> buildGroups(DataNode input) {
Meta meta = inputMeta(input.meta());
List<DataNode<PointSet>> groups;
if (meta.hasValue("grouping.byValue")) {
groups = super.buildGroups(input);
} else {
groups = GroupBuilder.byValue(MERGE_NAME, reader.getString(MERGE_NAME, "merge")).group(input);
groups = GroupBuilder.byValue(MERGE_NAME, meta.getString(MERGE_NAME, "merge")).group(input);
}
return groups;
}
@Override
protected PointSet execute(Logable log, Meta reader, NamedGroup<PointSet> input) {
return mergeOne(log, input.getName(), input.asList());
// List<DataSet> res = new ArrayList<>();
// for (NamedGroup<DataSet> buildGroups : groups) {
// res.add(mergeOne(log, buildGroups.getName(), buildGroups.asList()));
// }
// return new ContentList<>(input.getName(), PointSet.class, res);
protected PointSet execute(Logable log, DataNode<PointSet> input) {
return mergeOne(log, input);
}
private PointSet mergeOne(Logable log, String fileName, List<PointSet> files) {
PointSet[] data = new PointSet[files.size()];
String head = "Numass data merge\n";
private PointSet mergeOne(Logable log, DataNode<PointSet> input) {
List<PointSet> data = input.stream().<PointSet>map(item -> item.getValue().get()).collect(Collectors.toList());
PointSet res = mergeDataSets(input.getName(), data);
return res.sort("Uset", true);
}
String numassPath = "";
@Override
protected void afterGroup(Logable log, String groupName, Meta outputMeta, PointSet output) {
OutputStream stream = buildActionOutput(groupName);
ColumnedDataWriter.writeDataSet(stream, output, outputMeta.toString());
}
/*
* Проверяем являются ли пути одинаковыми у всех файлов
* TODO не изящное решение
*/
for (int i = 0; i < files.size(); i++) {
data[i] = files.get(i);
head += "\t" + data[i].getName() + "\n";
if (numassPath != null) {
String newPath = data[i].meta().getString("numass.path", null);
if (numassPath.isEmpty()) {
numassPath = newPath;
@Override
protected MetaBuilder outputMeta(DataNode<PointSet> input) {
String numassPath = input.stream().<String>map(item -> item.getValue().meta().getString("numass.path", null))
.reduce("", (String path, String newPath) -> {
if (path == null) {
return null;
} else if (path.isEmpty()) {
return newPath;
} else if (!path.equals(newPath)) {
return null;
} else {
if (!numassPath.equals(newPath)) {
numassPath = null;
}
}
}
return newPath;
}
});
PointSet res = mergeDataSets(fileName, data);
MetaBuilder builder = super.outputMeta(input);
/*
* Указываем путь только если он одинаковый для всех входных файлов
* Указываем путь только есл0и он одинаковый для всех входных файлов
*/
if (numassPath != null) {
res.setMeta(res.meta().getBuilder().putValue("numass.path", numassPath).build());
builder.putValue("numass.path", numassPath);
}
return builder;
}
res = res.sort("Uset", true);
OutputStream stream = buildActionOutput(res);
ColumnedDataWriter.writeDataSet(stream, res, head);
return res;
}
// private Map<String, List<DataSet>> buildMergeGroups(String mergeBy, NamedGroup<DataSet> input) {
// Map<String, List<DataSet>> map = new HashMap<>();
// for (PointSet ds : input) {
// String tag = ds.meta().getString(mergeBy, meta().getString(mergeBy, "merge"));
// if (!map.containsKey(tag)) {
// map.put(tag, new ArrayList<>());
// }
// map.get(tag).add(ds);
// }
// return map;
// }
private DataPoint mergeDataPoints(DataPoint dp1, DataPoint dp2) {
if (dp1 == null) {
return dp2;
@ -167,7 +150,7 @@ public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
return map;
}
private PointSet mergeDataSets(String name, PointSet... ds) {
private PointSet mergeDataSets(String name, Collection<PointSet> ds) {
//Сливаем все точки в один набор данных
Map<Double, List<DataPoint>> points = new LinkedHashMap<>();
for (PointSet d : ds) {
@ -185,15 +168,17 @@ public class MergeDataAction extends ManyToOneAction<PointSet, PointSet> {
List<DataPoint> res = new ArrayList<>();
for (Map.Entry<Double, List<DataPoint>> entry : points.entrySet()) {
points.entrySet().stream().map((entry) -> {
DataPoint curPoint = null;
for (DataPoint newPoint : entry.getValue()) {
curPoint = mergeDataPoints(curPoint, newPoint);
}
return curPoint;
}).forEach((curPoint) -> {
res.add(curPoint);
}
});
return new ListPointSet(name, null, res);
return new ListPointSet(res);
}

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

@ -57,7 +57,7 @@ public class MonitorCorrectAction extends OneToOneAction<PointSet, PointSet> {
}
@Override
protected PointSet execute(Logable log, Meta reader, PointSet sourceData) throws ContentException {
protected PointSet execute(Logable log, String name, Meta reader, PointSet sourceData) throws ContentException {
double monitor = reader.getDouble("monitorPoint", Double.NaN);
@ -131,9 +131,9 @@ public class MonitorCorrectAction extends OneToOneAction<PointSet, PointSet> {
// } else {
// format = DataFormat.of(parnames);
// }
PointSet data = new ListPointSet(sourceData.getName(), sourceData.meta(), dataList);
PointSet data = new ListPointSet(dataList);
OutputStream stream = buildActionOutput(data);
OutputStream stream = buildActionOutput(name);
ColumnedDataWriter.writeDataSet(stream, data, head);
@ -141,15 +141,15 @@ public class MonitorCorrectAction extends OneToOneAction<PointSet, PointSet> {
}
@Override
protected void afterAction(ActionResult<PointSet> pack) throws ContentException {
protected void afterAction(String name, PointSet res) {
printMonitorData();
super.afterAction(pack);
super.afterAction(name, res); //To change body of generated methods, choose Tools | Templates.
}
private void printMonitorData() {
String monitorFileName = meta().getString("monitorFile", "monitor");
OutputStream stream = buildActionOutput(monitorFileName);
ListPointSet data = new ListPointSet("monitor", null, monitorPoints);
ListPointSet data = new ListPointSet(monitorPoints);
ColumnedDataWriter.writeDataSet(stream, data.sort("Timestamp", true), "Monitor points", monitorNames);
}

6
numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java
View File

@ -62,7 +62,7 @@ public class PrepareDataAction extends OneToOneAction<NMFile, PointSet> {
}
@Override
protected ListPointSet execute(Logable log, Meta reader, NMFile dataFile) throws ContentException {
protected ListPointSet execute(Logable log, String name, Meta reader, NMFile dataFile) {
// log.logString("File %s started", dataFile.getName());
int upper = dataFile.meta().getInt("upperWindow", this.meta().getInt("upperWindow", RawNMPoint.MAX_CHANEL - 1));
@ -112,9 +112,9 @@ public class PrepareDataAction extends OneToOneAction<NMFile, PointSet> {
}
head = head + "\n" + new XMLMetaWriter().writeString(meta(), null) + "\n";
ListPointSet data = new ListPointSet(dataFile.getName(), dataFile.meta(), dataList, format);
ListPointSet data = new ListPointSet(dataList, format);
OutputStream stream = buildActionOutput(data);
OutputStream stream = buildActionOutput(name);
ColumnedDataWriter.writeDataSet(stream, data, head);
// log.logString("File %s completed", dataFile.getName());

10
numass-main/src/main/java/inr/numass/actions/ReadNumassDataAction.java
View File

@ -17,7 +17,7 @@ package inr.numass.actions;
import hep.dataforge.actions.OneToOneAction;
import hep.dataforge.context.Context;
import hep.dataforge.points.FileData;
import hep.dataforge.data.FileData;
import hep.dataforge.description.NodeDef;
import hep.dataforge.description.TypedActionDef;
import hep.dataforge.description.ValueDef;
@ -46,16 +46,16 @@ public class ReadNumassDataAction extends OneToOneAction<FileData, NMFile> {
}
@Override
protected NMFile execute(Logable log, Meta reader, FileData source) throws ContentException {
protected NMFile execute(Logable log, String name, Meta reader, FileData source) throws ContentException {
// log.logString("File '%s' started", source.getName());
RawNMFile raw = getNumassData(source, meta());
if (meta().getBoolean("paw", false)) {
raw.generatePAW(buildActionOutput(source.getName() + ".paw"));
raw.generatePAW(buildActionOutput(name + ".paw"));
}
if(meta().hasNode("debunch")){
if (meta().hasNode("debunch")) {
DebunchAction debunch = new DebunchAction(getContext(), meta().getNode("debunch"));
raw = debunch.execute(log, null, raw);
raw = debunch.execute(log, name, null, raw);
}
NMFile result = new NMFile(raw);

26
numass-main/src/main/java/inr/numass/actions/ShowLossSpectrumAction.java
View File

@ -70,7 +70,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
}
@Override
protected FitState execute(Logable log, Meta reader, FitState input) {
protected FitState execute(Logable log, String name, Meta reader, FitState input) {
ParamSet pars = input.getParameters();
if (!pars.names().contains(names)) {
LoggerFactory.getLogger(getClass()).error("Wrong input FitState. Must be loss spectrum fit.");
@ -80,9 +80,9 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
UnivariateFunction scatterFunction;
boolean calculateRatio = false;
XYPlotFrame frame = (XYPlotFrame) PlotsPlugin.buildFrom(getContext())
.buildPlotFrame(getName(), input.getName()+".loss",
.buildPlotFrame(getName(), name + ".loss",
new MetaBuilder("plot")
.setValue("plotTitle", "Differential scattering crossection for " + input.getName())
.setValue("plotTitle", "Differential scattering crossection for " + name)
);
switch (input.getModel().getName()) {
case "scatter-variable":
@ -107,12 +107,12 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
threshold = reader.getDouble("ionThreshold", 17);
ionRatio = calcultateIonRatio(pars, threshold);
log.log("The ionization ratio (using threshold {}) is {}", threshold, ionRatio);
ionRatioError = calultateIonRatioError(input, threshold);
ionRatioError = calultateIonRatioError(name, input, threshold);
log.log("the ionization ration standard deviation (using threshold {}) is {}", threshold, ionRatioError);
}
if (reader.getBoolean("printResult", false)) {
PrintWriter writer = new PrintWriter(new OutputStreamWriter(buildActionOutput(input), Charset.forName("UTF-8")));
PrintWriter writer = new PrintWriter(new OutputStreamWriter(buildActionOutput(name), Charset.forName("UTF-8")));
// writer.println("*** FIT PARAMETERS ***");
input.print(writer);
// for (Param param : pars.getSubSet(names).getParams()) {
@ -150,7 +150,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
}
writer.printf("%s%n", "chi2");
writer.printf("%s\t", input.getName());
writer.printf("%s\t", name);
for (Param param : pars.getSubSet(names).getParams()) {
writer.printf("%f\t%f\t", param.value(), param.getErr());
@ -174,7 +174,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
ParamSet parameters = input.getParameters().getSubSet(new String[]{"exPos", "ionPos", "exW", "ionW", "exIonRatio"});
NamedMatrix covariance = input.getCovariance();
PointSet spreadData = generateSpread(writer, input.getName(), parameters, covariance);
PointSet spreadData = generateSpread(writer, name, parameters, covariance);
ColumnedDataWriter.writeDataSet(System.out, spreadData, "", spreadData.getDataFormat().asArray());
}
}
@ -208,10 +208,10 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
return exProb / ionProb;
}
public double calultateIonRatioError(FitState state, double threshold) {
public double calultateIonRatioError(String dataNeme, FitState state, double threshold) {
ParamSet parameters = state.getParameters().getSubSet(new String[]{"exPos", "ionPos", "exW", "ionW", "exIonRatio"});
NamedMatrix covariance = state.getCovariance();
return calultateIonRatioError(state.getName(), parameters, covariance, threshold);
return calultateIonRatioError(dataNeme, parameters, covariance, threshold);
}
@SuppressWarnings("Unchecked")
@ -225,14 +225,14 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
.filter(d -> !Double.isNaN(d))
.toArray();
Histogram hist = new Histogram("ionRatio", 0.3, 0.5, 0.002);
Histogram hist = new Histogram(0.3, 0.5, 0.002);
hist.fill(res);
XYPlotFrame frame = (XYPlotFrame) PlotsPlugin.buildFrom(getContext())
.buildPlotFrame(getName(), name+".ionRatio",
.buildPlotFrame(getName(), name + ".ionRatio",
new MetaBuilder("plot").setValue("plotTitle", "Ion ratio Distribution for " + name)
);
// XYPlotFrame frame = JFreeChartFrame.drawFrame("Ion ratio Distribution for " + name, null);
frame.add(PlottableData.plot(hist, new XYAdapter("binCenter", "count")));
frame.add(PlottableData.plot("ionRatio", hist, new XYAdapter("binCenter", "count")));
return new DescriptiveStatistics(res).getStandardDeviation();
}
@ -272,7 +272,7 @@ public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
}
}
String[] pointNames = {"e", "central", "lower", "upper", "dispersion"};
ListPointSet res = new ListPointSet("spread", pointNames);
ListPointSet res = new ListPointSet(pointNames);
for (int i = 0; i < gridPoints; i++) {
res.add(new MapPoint(pointNames, grid[i], central[i], lower[i], upper[i], dispersion[i]));

6
numass-main/src/main/java/inr/numass/actions/ShowSpectrumAction.java
View File

@ -50,7 +50,7 @@ public class ShowSpectrumAction extends OneToOneAction<NMFile, NMFile> {
}
@Override
protected NMFile execute(Logable log, Meta reader, NMFile source) throws ContentException {
protected NMFile execute(Logable log, String name, Meta reader, NMFile source) throws ContentException {
log.log("File {} started", source.getName());
List<NMPoint> printPoints = new ArrayList<>();
@ -73,9 +73,9 @@ public class ShowSpectrumAction extends OneToOneAction<NMFile, NMFile> {
}
if (printPoints.size() > 0) {
ESpectrum data = new ESpectrum(source.getName(), printPoints, chanelsPerBin, normalize);
ESpectrum data = new ESpectrum(printPoints, chanelsPerBin, normalize);
OutputStream stream = buildActionOutput(data);
OutputStream stream = buildActionOutput(name);
ColumnedDataWriter.writeDataSet(stream, data, source.getName());

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

@ -49,7 +49,7 @@ public class SlicingAction extends OneToOneAction<NMFile, NMFile> {
}
@Override
protected NMFile execute(Logable log, Meta reader, NMFile source) throws ContentException {
protected NMFile execute(Logable log, String name, Meta reader, NMFile source) throws ContentException {
boolean normalize;
Map<String, Pair<Integer, Integer>> slicingConfig;
@ -73,7 +73,7 @@ public class SlicingAction extends OneToOneAction<NMFile, NMFile> {
SlicedData sData = new SlicedData(source, slicingConfig, normalize);
OutputStream stream = buildActionOutput(source);
OutputStream stream = buildActionOutput(name);
ColumnedDataWriter.writeDataSet(stream, sData, null);

44
numass-main/src/main/java/inr/numass/actions/SummaryAction.java
View File

@ -17,8 +17,9 @@ package inr.numass.actions;
import hep.dataforge.actions.ManyToOneAction;
import hep.dataforge.actions.GroupBuilder;
import hep.dataforge.content.NamedGroup;
import hep.dataforge.context.Context;
import hep.dataforge.data.Data;
import hep.dataforge.data.DataNode;
import hep.dataforge.points.Format;
import hep.dataforge.points.DataPoint;
import hep.dataforge.points.ListPointSet;
@ -33,6 +34,8 @@ import java.io.OutputStream;
import java.util.Arrays;
import java.util.List;
import hep.dataforge.points.PointSet;
import java.util.function.Consumer;
import javafx.util.Pair;
/**
*
@ -48,18 +51,20 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
}
@Override
protected List<NamedGroup<FitState>> buildGroups(Meta reader, List<FitState> input) {
List<NamedGroup<FitState>> groups;
if (reader.hasNode("grouping")) {
groups = super.buildGroups(reader, input);
@SuppressWarnings("unchecked")
protected List<DataNode<PointSet>> buildGroups(DataNode input) {
Meta meta = inputMeta(input.meta());
List<DataNode<PointSet>> groups;
if (meta.hasValue("grouping.byValue")) {
groups = super.buildGroups(input);
} else {
groups = GroupBuilder.byValue(SUMMARY_NAME, reader.getString(SUMMARY_NAME, "summary")).group(input);
groups = GroupBuilder.byValue(SUMMARY_NAME, meta.getString(SUMMARY_NAME, "summary")).group(input);
}
return groups;
}
@Override
protected PointSet execute(Logable log, Meta reader, NamedGroup<FitState> input){
protected PointSet execute(Logable log, DataNode<FitState> input) {
String[] parNames = meta().getStringArray("parnames");
String[] names = new String[2 * parNames.length + 2];
names[0] = "file";
@ -69,19 +74,19 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
}
names[names.length - 1] = "chi2";
// boolean calculateWAV = meta().getBoolean("wav", true);
String fileName = reader.getString(SUMMARY_NAME, "summary");
ListPointSet res = new ListPointSet(fileName, Format.forNames(8, names));
ListPointSet res = new ListPointSet(Format.forNames(8, names));
double[] weights = new double[parNames.length];
Arrays.fill(weights, 0);
double[] av = new double[parNames.length];
Arrays.fill(av, 0);
for (FitState state : input) {
input.stream().forEach(new Consumer<Pair<String, Data<? extends FitState>>>() {
@Override
public void accept(Pair<String, Data<? extends FitState>> item) {
FitState state = item.getValue().get();
Value[] values = new Value[names.length];
values[0] = Value.of(state.getName());
values[0] = Value.of(item.getKey());
for (int i = 0; i < parNames.length; i++) {
Value val = Value.of(state.getParameters().getValue(parNames[i]));
values[2 * i + 1] = val;
@ -95,6 +100,7 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
DataPoint point = new MapPoint(names, values);
res.add(point);
}
});
Value[] averageValues = new Value[names.length];
averageValues[0] = Value.of("average");
@ -107,11 +113,15 @@ public class SummaryAction extends ManyToOneAction<FitState, PointSet> {
res.add(new MapPoint(names, averageValues));
OutputStream stream = buildActionOutput(res);
ColumnedDataWriter.writeDataSet(stream, res, fileName);
return res;
}
@Override
protected void afterGroup(Logable log, String groupName, Meta outputMeta, PointSet output) {
OutputStream stream = buildActionOutput(groupName);
ColumnedDataWriter.writeDataSet(stream, output, groupName);
super.afterGroup(log, groupName, outputMeta, output);
}
}

11
numass-main/src/main/java/inr/numass/data/ESpectrum.java
View File

@ -24,19 +24,12 @@ import hep.dataforge.values.ValueFormat;
import hep.dataforge.values.ValueFormatFactory;
import hep.dataforge.values.ValueType;
import java.io.OutputStream;
import static java.lang.String.format;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import static java.lang.String.format;
import static java.lang.String.format;
import static java.lang.String.format;
import static java.lang.String.format;
import static java.lang.String.format;
import static java.lang.String.format;
import static java.lang.String.format;
/**
*
@ -61,8 +54,8 @@ public class ESpectrum extends ListPointSet {
int binning = 1;
public ESpectrum(String name, List<NMPoint> points, int binning, boolean normalize) {
super(name, prepareFormat(points));
public ESpectrum(List<NMPoint> points, int binning, boolean normalize) {
super(prepareFormat(points));
this.binning = binning;
fill(points, normalize);
}

2
numass-main/src/main/java/inr/numass/data/NMFile.java
View File

@ -15,7 +15,7 @@
*/
package inr.numass.data;
import hep.dataforge.content.NamedMetaHolder;
import hep.dataforge.names.NamedMetaHolder;
import hep.dataforge.description.ValueDef;
import hep.dataforge.meta.Meta;
import hep.dataforge.meta.MetaBuilder;

2
numass-main/src/main/java/inr/numass/data/NumassData.java
View File

@ -5,7 +5,7 @@
*/
package inr.numass.data;
import hep.dataforge.content.Named;
import hep.dataforge.names.Named;
import hep.dataforge.meta.Meta;
import java.time.Instant;
import java.util.List;

8
numass-main/src/main/java/inr/numass/data/NumassDataReader.java
View File

@ -15,7 +15,7 @@
*/
package inr.numass.data;
import hep.dataforge.points.BinaryData;
import hep.dataforge.data.FileData;
import hep.dataforge.meta.MergeRule;
import hep.dataforge.meta.Meta;
import java.io.BufferedInputStream;
@ -39,9 +39,9 @@ public class NumassDataReader {
private Meta config;
private double HVdev;
public NumassDataReader(BinaryData data, Meta config) throws IOException {
this(data.getInputStream(), data.meta()
.getString("filename", data.getName()), MergeRule.replace(config, data.meta()));
public NumassDataReader(FileData data, Meta config) throws IOException {
this(data.get(), data.meta()
.getString("filename", data.fileName()), MergeRule.replace(config, data.meta()));
}
public NumassDataReader(String file, String fname, Meta config) throws FileNotFoundException {

5
numass-main/src/main/java/inr/numass/data/RawNMFile.java
View File

@ -15,8 +15,7 @@
*/
package inr.numass.data;
import hep.dataforge.content.Content;
import hep.dataforge.content.NamedMetaHolder;
import hep.dataforge.names.NamedMetaHolder;
import java.io.BufferedOutputStream;
import java.io.OutputStream;
import java.io.PrintWriter;
@ -27,7 +26,7 @@ import java.util.List;
* Contains the whole data but requires a lot of memory
* @author Darksnake
*/
public class RawNMFile extends NamedMetaHolder implements Content {
public class RawNMFile extends NamedMetaHolder {
// public static String TYPE = ":data:numassdatafile";

9
numass-main/src/main/java/inr/numass/data/SpectrumInformation.java
View File

@ -21,6 +21,7 @@ import hep.dataforge.functions.ParametricFunction;
import static hep.dataforge.maths.MatrixOperations.inverse;
import hep.dataforge.maths.NamedDoubleSet;
import hep.dataforge.maths.NamedMatrix;
import inr.numass.utils.TritiumUtils;
import org.apache.commons.math3.analysis.UnivariateFunction;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.RealMatrix;
@ -39,7 +40,7 @@ public class SpectrumInformation {
public NamedMatrix getExpetedCovariance(NamedDoubleSet set, ListPointSet data, String... parNames) {
String[] names = parNames;
if(names.length==0) {
if (names.length == 0) {
names = source.namesAsArray();
}
NamedMatrix info = this.getInformationMatrix(set, data, names);
@ -56,10 +57,10 @@ public class SpectrumInformation {
* @return
*/
public NamedMatrix getInformationMatrix(NamedDoubleSet set, ListPointSet data, String... parNames) {
SpectrumDataAdapter reader = new SpectrumDataAdapter(data.meta().getNode("aliases"));
SpectrumDataAdapter reader = TritiumUtils.adapter();
String[] names = parNames;
if(names.length==0) {
if (names.length == 0) {
names = source.namesAsArray();
}
assert source.names().contains(set.namesAsArray());
@ -97,7 +98,7 @@ public class SpectrumInformation {
for (int i = 0; i < names.length; i++) {
for (int j = i; j < names.length; j++) {
double value = getPoinSignificance(set, names[i], names[j], x)*t;
double value = getPoinSignificance(set, names[i], names[j], x) * t;
res.setEntry(i, j, value);
if (i != j) {
res.setEntry(j, i, value);

5
numass-main/src/main/java/inr/numass/models/TransmissionInterpolator.java
View File

@ -18,6 +18,7 @@ package inr.numass.models;
import hep.dataforge.actions.ActionResult;
import hep.dataforge.actions.RunManager;
import hep.dataforge.context.Context;
import hep.dataforge.data.DataNode;
import hep.dataforge.points.DataPoint;
import hep.dataforge.io.ColumnedDataReader;
import hep.dataforge.meta.Meta;
@ -47,8 +48,8 @@ public class TransmissionInterpolator implements UnivariateFunction {
@SuppressWarnings("unchecked")
public static TransmissionInterpolator fromAction(Context context, Meta actionAnnotation, String xName, String yName, int nSmooth, double w, double border) throws InterruptedException {
ActionResult<PointSet> pack = RunManager.executeAction(context, actionAnnotation);
PointSet data = pack.iterator().next().get();
DataNode<PointSet> node = RunManager.executeAction(context, actionAnnotation);
PointSet data = node.iterator().next().get();
return new TransmissionInterpolator(data, xName, yName, nSmooth, w, border);
}

15
numass-main/src/main/java/inr/numass/utils/TritiumUtils.java
View File

@ -18,17 +18,10 @@ package inr.numass.utils;
import hep.dataforge.points.DataPoint;
import hep.dataforge.points.ListPointSet;
import inr.numass.data.SpectrumDataAdapter;
import static java.lang.Math.abs;
import static java.lang.Math.exp;
import static java.lang.Math.sqrt;
import org.apache.commons.math3.analysis.UnivariateFunction;
import static java.lang.Math.abs;
import static java.lang.Math.abs;
import static java.lang.Math.abs;
import static java.lang.Math.abs;
import static java.lang.Math.abs;
import static java.lang.Math.abs;
import static java.lang.Math.abs;
/**
*
@ -68,7 +61,7 @@ public class TritiumUtils {
* @return
*/
public static ListPointSet correctForDeadTime(ListPointSet data, double dtime) {
SpectrumDataAdapter reader = new SpectrumDataAdapter(data.meta().getNode("aliases"));
SpectrumDataAdapter reader = adapter();
ListPointSet res = new ListPointSet(data.getDataFormat());
for (DataPoint dp : data) {
double corrFactor = 1 / (1 - dtime * reader.getCount(dp) /reader.getTime(dp));
@ -86,7 +79,7 @@ public class TritiumUtils {
* @return
*/
public static ListPointSet setHVScale(ListPointSet data, double beta) {
SpectrumDataAdapter reader = new SpectrumDataAdapter(data.meta().getNode("aliases"));
SpectrumDataAdapter reader = adapter();
ListPointSet res = new ListPointSet(data.getDataFormat());
for (DataPoint dp : data) {
double corrFactor = 1 + beta;
@ -95,6 +88,10 @@ public class TritiumUtils {
return res;
}
public static SpectrumDataAdapter adapter(){
return new SpectrumDataAdapter("Uset", "CR", "CRerr", "Time");
}
/**
* Integral beta spectrum background with given amplitude (total count rate
* from)

8
numass-main/src/main/java/inr/numass/workbench/NumassWorkbenchController.java
View File

@ -14,7 +14,9 @@ import hep.dataforge.actions.ActionStateListener;
import hep.dataforge.actions.RunManager;
import hep.dataforge.context.Context;
import hep.dataforge.context.GlobalContext;
import hep.dataforge.data.DataManager;
import hep.dataforge.data.DataFactory;
import hep.dataforge.data.DataNode;
import hep.dataforge.data.FileDataFactory;
import hep.dataforge.description.ActionDescriptor;
import hep.dataforge.description.DescriptorUtils;
import hep.dataforge.exceptions.NameNotFoundException;
@ -296,9 +298,9 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
public void runActions() {
clearAllStages();
new Thread(() -> {
ActionResult data = new DataManager(getContext()).readFromConfig(getDataConfiguration());
DataNode data = new FileDataFactory().build(getContext(), getDataConfiguration());
Action action = RunManager.readAction(getContext(), getActionConfiguration());
action.addListener(this);
// action.addListener(this);
action.run(data);
Platform.runLater(() -> statusBar.setText("Execution complete"));
}, "actions").start();

2
numass-main/src/main/java/inr/numass/workbench/OutputTab.java
View File

@ -5,7 +5,7 @@
*/
package inr.numass.workbench;
import hep.dataforge.content.Named;
import hep.dataforge.names.Named;
import javafx.scene.control.Tab;
/**

2
numass-main/src/main/java/inr/numass/workbench/StagePane.java
View File

@ -5,7 +5,7 @@
*/
package inr.numass.workbench;
import hep.dataforge.content.Named;
import hep.dataforge.names.Named;
import hep.dataforge.meta.Meta;
import hep.dataforge.plots.PlotFrame;
import java.util.HashMap;

2
numass-prop/src/main/java/inr/numass/prop/ar/JNAEpisode.java
View File

@ -15,7 +15,7 @@
*/
package inr.numass.prop.ar;
import hep.dataforge.content.NamedMetaHolder;
import hep.dataforge.names.NamedMetaHolder;
import hep.dataforge.meta.Meta;
import java.util.Iterator;
import java.util.List;

2
numass-prop/src/main/java/inr/numass/prop/ar/JNASpectrum.java
View File

@ -15,7 +15,7 @@
*/
package inr.numass.prop.ar;
import hep.dataforge.content.NamedMetaHolder;
import hep.dataforge.names.NamedMetaHolder;
import hep.dataforge.points.DataPoint;
import hep.dataforge.points.ListPointSet;
import hep.dataforge.points.MapPoint;