From 2cfc74dea88cb82a19adf5bf5f35b79de4b6bb33 Mon Sep 17 00:00:00 2001 From: Alexander Nozik Date: Fri, 12 Aug 2016 18:04:42 +0300 Subject: [PATCH] working on grind multi threading and dsl --- .../private/cache/retriever/catalog.xml | 4 - .../java/javase/overview/index.html | 1087 ----------------- .../groovy/inr/numass/scripts/OldTest.groovy | 8 +- .../inr/numass/scripts/ResolutionTest.groovy | 4 +- .../scripts/RunScriptsFromDirectory.groovy | 5 +- .../numass/scripts/SignificanceTest.groovy | 27 +- .../groovy/inr/numass/scripts/Simulate.groovy | 9 +- .../inr/numass/scripts/SimulateGun.groovy | 6 +- .../inr/numass/scripts/SterileDemo.groovy | 2 +- .../inr/numass/scripts/TestWorkspace.groovy | 10 - .../inr/numass/scripts/TritiumTest.groovy | 10 +- .../scripts/workspace/TestActions.groovy | 16 + .../scripts/workspace/TestWorkspace.groovy | 13 + .../src/main/java/inr/numass/Main.java | 29 +- .../src/main/java/inr/numass/NumassIO.java | 111 +- .../inr/numass/actions/MergeDataAction.java | 23 +- .../numass/actions/MonitorCorrectAction.java | 9 +- .../inr/numass/actions/PrepareDataAction.java | 11 +- .../actions/ShowLossSpectrumAction.java | 120 +- .../java/inr/numass/tasks/GrindCaller.java | 16 + .../tasks/NumassFitScanSummaryTask.java | 6 +- .../inr/numass/tasks/NumassFitScanTask.java | 14 +- .../inr/numass/tasks/NumassPrepareTask.java | 11 +- .../inr/numass/workbench/TextOutputTab.java | 7 +- .../numass/workbench/WorkbenchIOManager.java | 15 +- .../models/TransmissionInterpolatorTest.java | 4 +- .../viewer/NumassLoaderViewComponent.java | 45 +- 27 files changed, 267 insertions(+), 1355 deletions(-) delete mode 100644 numass-main/private/cache/retriever/catalog.xml delete mode 100644 numass-main/private/cache/retriever/www.oracle.com/technetwork/java/javase/overview/index.html delete mode 100644 numass-main/src/main/groovy/inr/numass/scripts/TestWorkspace.groovy create mode 100644 numass-main/src/main/groovy/inr/numass/scripts/workspace/TestActions.groovy create mode 100644 numass-main/src/main/groovy/inr/numass/scripts/workspace/TestWorkspace.groovy create mode 100644 numass-main/src/main/java/inr/numass/tasks/GrindCaller.java diff --git a/numass-main/private/cache/retriever/catalog.xml b/numass-main/private/cache/retriever/catalog.xml deleted file mode 100644 index a63b4498..00000000 --- a/numass-main/private/cache/retriever/catalog.xml +++ /dev/null @@ -1,4 +0,0 @@ - - - - \ No newline at end of file diff --git a/numass-main/private/cache/retriever/www.oracle.com/technetwork/java/javase/overview/index.html b/numass-main/private/cache/retriever/www.oracle.com/technetwork/java/javase/overview/index.html deleted file mode 100644 index 39ff197c..00000000 --- a/numass-main/private/cache/retriever/www.oracle.com/technetwork/java/javase/overview/index.html +++ /dev/null @@ -1,1087 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Java SE | Oracle Technology Network | Oracle - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Java SE at a Glance

  
 

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers, as well as in today's demanding embedded environments. Java offers the rich user interface, performance, versatility, portability, and security that today's applicationsrequire.


Auto-update Notice & End of Public Updates for Oracle JDK 7

Coincident with the January 2015 CPU release users with the auto-update feature enabled were migrated from Oracle JRE 7 to Oracle JRE 8. Also, please note the April 2015 CPU release was the last Oracle JDK 7 publicly available update. For more information, and details on how to receive longer term support for Oracle JDK 7, please see the Oracle Java SE Support Roadmap.
 
 

What's New

Java Platform, Standard Edition 8 Update 91 (Java SE 8u91) and 8 Update 92 (Java SE 8u92) are Now Available
This latest release of the Java Platform includes important security fixes. Oracle strongly recommends that all Java SE 8 users upgrade to this release.
JDK for ARM releases are available on the same page as the downloads for other platforms
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Advanced Management Console 2.3
Provides system administrators an effective control over diverse Java versions running on desktops in the enterprise enabling a more secure environment and enhanced application experience and availability. Documentation

Java SE 8 is Now Available
The Java Platform, Standard Edition 8 (Java SE 8) is a major feature release. It contains new features and enhancements in many functional areas. Java SE 8 delivers enhanced developer productivity and significant application performance increases through reduced boilerplate code, improved collections and annotations, simpler parallel programming models and more efficient use of modern, multi-core processors. See what's new in JDK 8 for more details.
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Security of the Java Platform
A description of security information provided by role. For developers, system administrators, home users, and security professionals.

Java RIA Security Checklist
Recently announced changes scheduled for Java 7 update 51 (January 2014) have established that the default security slider will require code signatures and the Permissions Manifest attribute. This checklist is intended to provide best practices to help development teams track work necessary to accommodate user prompts.

LiveConnect changes in 7u45 
Java 7 update 45 (October 2013) introduces a new warning to users of LiveConnect applications. LiveConnect is a technology for Rich Internet Applications that allows JavaScript on a web page to make calls into an RIA, allowing the two to work together and load content. RIAs that do not use LiveConnect are unaffected by this change. Read More

Oracle Releases New Diagnostic, Monitoring, Security and Deployment Capabilities for Java SE 7 (Press Release)  Video

Java Mission Control 
Java Flight Recorder and Java Mission Control together create a complete tool chain to continuously collect low level and detailed runtime information enabling after-the-fact incident analysis.
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Deployment Rule Set 
Deployment rule set allows a desktop administrator to control the level of Java client compatibility and default prompts across an organization. Documentation 

Java API Documentation Updater Tool 

Java Usage Tracking and Visualization with Oracle Fusion Middleware 

Server JRE 
Starting with Java SE 7u21, a Server Java Runtime Environment (Server JRE) package is available for deploying Java applications on servers. Learn More

Java Applet & Web Start - Code Signing 
Starting with Java SE 7u21 all Java Applets and Web Start Applications are encouraged to be signed with a trusted certificate. Learn More

Archive of Technical Articles

 

Updates

Java SE 8u91 and 8u92 Released
Java SE 8u91 is the latest Security Alert releases for JDK 8. Java SE 8u92 is the latest patch-set update with additional features.

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Expert monitoring, diagnostics, and centralized management for enterprise and ISV Java-based applications.
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Access Oracle Premier Support for the components and features included with Java SE.

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JavaOne
JavaOne 2015 has concluded, but the Learning Lives On
Did you miss a JavaOne keynote or session? You can find those here. And 'Save the Date' for Oracle OpenWorld 2016 September 18-22, 2016!

Java 8 Event Kit
Access the "Create the Future with Java 8 Event Kit" - run your own Java 8 event using the resources designed for Java User Groups (JUGs). The kit includes a fully scripted technical presentation, intro video, promotional tools and more. Learn More

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Read about and share ideas and suggestions about Java technology on the discussion forums. Start with the New to Java or the more advanced Java Programming category.

Gimme Java - Show your true colors!
These Java designs are yours to take and use. Post on your Website, put them on t-shirts or coffee mugs—use them just about anywhere except on a Java product—and let the world know about your passion for Java.

 
 

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- - - - - - - - - - - - - diff --git a/numass-main/src/main/groovy/inr/numass/scripts/OldTest.groovy b/numass-main/src/main/groovy/inr/numass/scripts/OldTest.groovy index 1538503d..4080598a 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/OldTest.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/OldTest.groovy @@ -87,18 +87,18 @@ res = fm.runDefaultTask(res, "E0", "N", "bkg", "mnu2"); res.print(out); -//spectrum.counter.print(out); +//spectrum.counter.print(onComplete); // //// fm.setPriorProb(new GaussianPrior("X", 0.47, 0.47*0.03)); //// fm.setPriorProb(new MultivariateGaussianPrior(allPars.getSubSet("X","trap"))); //res = fm.runTask(res, "MINUIT", "run", "E0", "N", "bkg", "mnu2"); //// -//res.print(out); +//res.print(onComplete); //sp.setCaching(true); //sp.setSuppressWarnings(true); // //BayesianManager bm = new BayesianManager(); -//bm.printMarginalLikelihood(out, "U2", res, ["E0", "N", "bkg", "U2", "X"], 10000); +//bm.printMarginalLikelihood(onComplete, "U2", res, ["E0", "N", "bkg", "U2", "X"], 10000); -// PrintNamed.printLike2D(Out.out, "like", res, "N", "E0", 30, 60, 2); +// PrintNamed.printLike2D(Out.onComplete, "like", res, "N", "E0", 30, 60, 2); diff --git a/numass-main/src/main/groovy/inr/numass/scripts/ResolutionTest.groovy b/numass-main/src/main/groovy/inr/numass/scripts/ResolutionTest.groovy index 505f0d4b..e0df5b46 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/ResolutionTest.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/ResolutionTest.groovy @@ -72,8 +72,8 @@ allPars.setParValue("trap", 0); allPars.setParError("trap", 0.01d); allPars.setParDomain("trap", 0d, Double.POSITIVE_INFINITY); -// PrintNamed.printSpectrum(GlobalContext.out(), spectrum, allPars, 0.0, 18700.0, 600); -//String fileName = "d:\\PlayGround\\merge\\scans.out"; +// PrintNamed.printSpectrum(GlobalContext.onComplete(), spectrum, allPars, 0.0, 18700.0, 600); +//String fileName = "d:\\PlayGround\\merge\\scans.onComplete"; // String configName = "d:\\PlayGround\\SCAN.CFG"; // ListTable config = OldDataReader.readConfig(configName); SpectrumGenerator generator = new SpectrumGenerator(model, allPars, 12316); diff --git a/numass-main/src/main/groovy/inr/numass/scripts/RunScriptsFromDirectory.groovy b/numass-main/src/main/groovy/inr/numass/scripts/RunScriptsFromDirectory.groovy index 39777ceb..d7748876 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/RunScriptsFromDirectory.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/RunScriptsFromDirectory.groovy @@ -15,9 +15,10 @@ */ package inr.numass.scripts -import static groovy.io.FileType.* import org.apache.commons.io.FilenameUtils +import static groovy.io.FileType.FILES + File dir = new File("D:\\loss-2014\\"); File resultDir = new File(dir, ".dataforge\\showLoss\\"); @@ -33,7 +34,7 @@ resultFile.setText("name\tX\tX_err\texPos\texPos_err\tionPos\tionPos_err\texW\te dir.eachFileMatch FILES, {it ==~ /[dh]2_\d\d_\d(?:_bkg)?\.xml/}, { try{ inr.numass.Main.main("-c", it.getAbsolutePath()) - File outFile = new File(resultDir, FilenameUtils.getBaseName(it.getName())+"_loss.out") + File outFile = new File(resultDir, FilenameUtils.getBaseName(it.getName()) + "_loss.onComplete") resultFile.append(outFile.readLines().get(50)); resultFile.append("\r\n"); } catch(Exception ex){ diff --git a/numass-main/src/main/groovy/inr/numass/scripts/SignificanceTest.groovy b/numass-main/src/main/groovy/inr/numass/scripts/SignificanceTest.groovy index da96f73c..1ce04d8d 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/SignificanceTest.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/SignificanceTest.groovy @@ -13,22 +13,19 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package inr.numass.scripts; +package inr.numass.scripts -import hep.dataforge.meta.MetaBuilder; -import hep.dataforge.context.GlobalContext; -import hep.dataforge.stat.fit.ParamSet; -import inr.numass.data.SpectrumInformation; -import inr.numass.models.ModularSpectrum; -import inr.numass.models.BetaSpectrum; -import inr.numass.models.NBkgSpectrum; -import inr.numass.models.ResolutionFunction; -import java.util.HashMap; -import java.util.Locale; -import static java.util.Locale.setDefault; -import java.util.Map; -import org.apache.commons.math3.analysis.UnivariateFunction; +import hep.dataforge.context.GlobalContext +import hep.dataforge.meta.MetaBuilder +import hep.dataforge.stat.fit.ParamSet +import inr.numass.data.SpectrumInformation +import inr.numass.models.BetaSpectrum +import inr.numass.models.ModularSpectrum +import inr.numass.models.NBkgSpectrum +import inr.numass.models.ResolutionFunction +import org.apache.commons.math3.analysis.UnivariateFunction +import static java.util.Locale.setDefault setDefault(Locale.US); GlobalContext global = GlobalContext.instance(); @@ -86,7 +83,7 @@ SpectrumInformation sign = new SpectrumInformation(spectrum); // PrintNamed.printNamedMatrix(Out.out, infoMatrix); // NamedMatrix cov = sign.getExpetedCovariance(allPars, config,"U2","E0","N"); // -// PrintWriter out = GlobalContext.out(); +// PrintWriter onComplete = GlobalContext.onComplete(); // // printNamedMatrix(out, cov); // diff --git a/numass-main/src/main/groovy/inr/numass/scripts/Simulate.groovy b/numass-main/src/main/groovy/inr/numass/scripts/Simulate.groovy index cd2f379c..b82d8e0c 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/Simulate.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/Simulate.groovy @@ -15,7 +15,10 @@ */ package inr.numass.scripts -import hep.dataforge.stat.fit.* +import hep.dataforge.stat.fit.FitManager +import hep.dataforge.stat.fit.FitState +import hep.dataforge.stat.fit.MINUITPlugin +import hep.dataforge.stat.fit.ParamSet import hep.dataforge.stat.models.XYModel import hep.dataforge.tables.ListTable import inr.numass.data.SpectrumDataAdapter @@ -70,8 +73,8 @@ allPars.setParValue("trap", 1d); allPars.setParError("trap", 0.01d); allPars.setParDomain("trap", 0d, Double.POSITIVE_INFINITY); -// PrintNamed.printSpectrum(GlobalContext.out(), spectrum, allPars, 0.0, 18700.0, 600); -//String fileName = "d:\\PlayGround\\merge\\scans.out"; +// PrintNamed.printSpectrum(GlobalContext.onComplete(), spectrum, allPars, 0.0, 18700.0, 600); +//String fileName = "d:\\PlayGround\\merge\\scans.onComplete"; // String configName = "d:\\PlayGround\\SCAN.CFG"; // ListTable config = OldDataReader.readConfig(configName); SpectrumGenerator generator = new SpectrumGenerator(model, allPars, 12316); diff --git a/numass-main/src/main/groovy/inr/numass/scripts/SimulateGun.groovy b/numass-main/src/main/groovy/inr/numass/scripts/SimulateGun.groovy index f4005fa0..e08acf60 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/SimulateGun.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/SimulateGun.groovy @@ -16,10 +16,10 @@ package inr.numass.scripts import hep.dataforge.context.GlobalContext +import hep.dataforge.io.FittingIOUtils import hep.dataforge.stat.fit.FitManager import hep.dataforge.stat.fit.ParamSet import hep.dataforge.stat.models.XYModel -import hep.dataforge.io.FittingIOUtils import inr.numass.data.SpectrumDataAdapter import inr.numass.models.GunSpectrum import inr.numass.models.NBkgSpectrum @@ -50,7 +50,7 @@ allPars.setParValue("sigma", 0.6); FittingIOUtils.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 18495, 18505, 100); -// //String fileName = "d:\\PlayGround\\merge\\scans.out"; +// //String fileName = "d:\\PlayGround\\merge\\scans.onComplete"; //// String configName = "d:\\PlayGround\\SCAN.CFG"; //// ListTable config = OldDataReader.readConfig(configName); // SpectrumGenerator generator = new SpectrumGenerator(model, allPars, 12316); @@ -63,5 +63,5 @@ FittingIOUtils.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 184 // // FitState res = fm.runTask(state, "QOW", FitTask.TASK_RUN, "N", "bkg", "pos", "sigma"); // -// res.print(out()); +// res.print(onComplete()); diff --git a/numass-main/src/main/groovy/inr/numass/scripts/SterileDemo.groovy b/numass-main/src/main/groovy/inr/numass/scripts/SterileDemo.groovy index 882c72e3..065db734 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/SterileDemo.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/SterileDemo.groovy @@ -77,5 +77,5 @@ FittingIOUtils.printSpectrum(GlobalContext.out(), spectrum, allPars, 14000, 1860 // // // -//res.print(out()); +//res.print(onComplete()); // diff --git a/numass-main/src/main/groovy/inr/numass/scripts/TestWorkspace.groovy b/numass-main/src/main/groovy/inr/numass/scripts/TestWorkspace.groovy deleted file mode 100644 index cdc51658..00000000 --- a/numass-main/src/main/groovy/inr/numass/scripts/TestWorkspace.groovy +++ /dev/null @@ -1,10 +0,0 @@ -package inr.numass.scripts - -import hep.dataforge.grind.GrindLauncher - -/** - * Created by darksnake on 11-Aug-16. - */ - - -new GrindLauncher().from { new File("D:\\Work\\Numass\\sterile2016\\workspace.groovy") }.runTask("numass.prepare", "fill_2") diff --git a/numass-main/src/main/groovy/inr/numass/scripts/TritiumTest.groovy b/numass-main/src/main/groovy/inr/numass/scripts/TritiumTest.groovy index ce930380..f6424718 100644 --- a/numass-main/src/main/groovy/inr/numass/scripts/TritiumTest.groovy +++ b/numass-main/src/main/groovy/inr/numass/scripts/TritiumTest.groovy @@ -69,10 +69,10 @@ allPars.setParDomain("trap", 0d, Double.POSITIVE_INFINITY); // PlotManager pm = new PlotManager(); // String plotTitle = "Tritium spectrum"; // pm.plotFunction(FunctionUtils.getSpectrumFunction(spectrum, allPars), 14000, 18600, 500,plotTitle, null); -// PrintNamed.printSpectrum(Out.out, beta.trapping, allPars, 14000d, 18600d, 500); +// PrintNamed.printSpectrum(Out.onComplete, beta.trapping, allPars, 14000d, 18600d, 500); // double e = 18570d; // trans.alpha = 1e-4; -// trans.plotTransmission(System.out, allPars, e, e-1000d, e+100d, 200); +// trans.plotTransmission(System.onComplete, allPars, e, e-1000d, e+100d, 200); SpectrumGenerator generator = new SpectrumGenerator(model, allPars); // ColumnedDataFile file = new ColumnedDataFile("d:\\PlayGround\\RUN36.cfg"); @@ -93,7 +93,7 @@ ListTable data = generator.generateData(config); FitState state = fm.buildState(data, model, allPars); // fm.checkDerivs(); -// res.print(Out.out); +// res.print(Out.onComplete); // fm.checkFitDerivatives(); FitState res = fm.runDefaultTask(state, "U2", "N", "trap"); @@ -107,14 +107,14 @@ beta.setSuppressWarnings(true); BayesianManager bm = new BayesianManager(); // bm.setPriorProb(new OneSidedUniformPrior("trap", 0, true)); // bm.setPriorProb(new GaussianPrior("trap", 1d, 0.002)); -// bm.printMarginalLikelihood(Out.out,"U2", res); +// bm.printMarginalLikelihood(Out.onComplete,"U2", res); FitState conf = bm.getConfidenceInterval("U2", res, ["U2", "N", "trap"]); // plotTitle = String.format("Marginal likelihood for parameter \'%s\'", "U2"); // pm.plotFunction(bm.getMarginalLikelihood("U2", res), 0, 2e-3, 40,plotTitle, null); conf.print(out); -// PrintNamed.printLogProbRandom(Out.out, res, 5000,0.5d, "E0","N"); +// PrintNamed.printLogProbRandom(Out.onComplete, res, 5000,0.5d, "E0","N"); spectrum.counter.print(out); diff --git a/numass-main/src/main/groovy/inr/numass/scripts/workspace/TestActions.groovy b/numass-main/src/main/groovy/inr/numass/scripts/workspace/TestActions.groovy new file mode 100644 index 00000000..1e4284ff --- /dev/null +++ b/numass-main/src/main/groovy/inr/numass/scripts/workspace/TestActions.groovy @@ -0,0 +1,16 @@ +package inr.numass.scripts.workspace + +import hep.dataforge.actions.ActionUtils +import hep.dataforge.context.Context +import hep.dataforge.io.IOManager +import inr.numass.NumassPlugin + +/** + * Created by darksnake on 12-Aug-16. + */ + + +Context context = new Context("numass"); +context.loadPlugin(new NumassPlugin()); +context.putValue(IOManager.ROOT_DIRECTORY_CONTEXT_KEY, "D:\\Work\\Numass\\sterile2016"); +ActionUtils.runConfig(context, "test.xml").computeAll() \ No newline at end of file diff --git a/numass-main/src/main/groovy/inr/numass/scripts/workspace/TestWorkspace.groovy b/numass-main/src/main/groovy/inr/numass/scripts/workspace/TestWorkspace.groovy new file mode 100644 index 00000000..930aeb74 --- /dev/null +++ b/numass-main/src/main/groovy/inr/numass/scripts/workspace/TestWorkspace.groovy @@ -0,0 +1,13 @@ +package inr.numass.scripts.workspace + +import hep.dataforge.grind.GrindLauncher + +/** + * Created by darksnake on 11-Aug-16. + */ + + +new GrindLauncher().from { + new File("D:\\Work\\Numass\\sterile2016\\workspace.groovy") +}.runTask("numass.prepare", "fill_2").computeAll() + diff --git a/numass-main/src/main/java/inr/numass/Main.java b/numass-main/src/main/java/inr/numass/Main.java index f5de0b93..4d6f0738 100644 --- a/numass-main/src/main/java/inr/numass/Main.java +++ b/numass-main/src/main/java/inr/numass/Main.java @@ -17,29 +17,24 @@ package inr.numass; import hep.dataforge.actions.ActionUtils; import hep.dataforge.context.Context; -import hep.dataforge.context.GlobalContext; -import static hep.dataforge.context.GlobalContext.out; import hep.dataforge.data.FileDataFactory; -import hep.dataforge.stat.fit.MINUITPlugin; import hep.dataforge.io.IOManager; import hep.dataforge.io.MetaFileReader; import hep.dataforge.meta.Meta; -import static inr.numass.Numass.printDescription; +import hep.dataforge.stat.fit.MINUITPlugin; +import org.apache.commons.cli.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import javax.swing.*; +import javax.swing.filechooser.FileFilter; +import javax.swing.filechooser.FileNameExtensionFilter; import java.io.File; import java.io.FileNotFoundException; import java.util.Locale; -import javax.swing.JFileChooser; -import javax.swing.JFrame; -import javax.swing.filechooser.FileFilter; -import javax.swing.filechooser.FileNameExtensionFilter; -import org.apache.commons.cli.CommandLine; -import org.apache.commons.cli.CommandLineParser; -import org.apache.commons.cli.DefaultParser; -import org.apache.commons.cli.HelpFormatter; -import org.apache.commons.cli.Options; -import org.apache.commons.cli.ParseException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; + +import static hep.dataforge.context.GlobalContext.out; +import static inr.numass.Numass.printDescription; import static java.util.Locale.setDefault; /** @@ -152,7 +147,7 @@ public class Main { options.addOption("h", "home", true, "Working directory (by default the working directory is the directory where config file is placed)"); options.addOption("d", "data", true, "Data directory (absolute or relative to working directory)"); - options.addOption("o", "out", true, "Output directory (absolute or relative to working directory)"); + options.addOption("o", "onComplete", true, "Output directory (absolute or relative to working directory)"); options.addOption("l", "list", false, "List of available actions"); options.addOption("lc", "list-color", false, "List of available actions with ANSI coloring"); diff --git a/numass-main/src/main/java/inr/numass/NumassIO.java b/numass-main/src/main/java/inr/numass/NumassIO.java index 9768b8aa..1a3e8190 100644 --- a/numass-main/src/main/java/inr/numass/NumassIO.java +++ b/numass-main/src/main/java/inr/numass/NumassIO.java @@ -20,19 +20,16 @@ import hep.dataforge.data.binary.Binary; import hep.dataforge.io.BasicIOManager; import hep.dataforge.meta.Meta; import hep.dataforge.names.Name; -import inr.numass.storage.NumassDataReader; import inr.numass.data.NumassPawReader; +import inr.numass.storage.NumassDataReader; import inr.numass.storage.RawNMFile; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.OutputStream; +import org.apache.commons.io.FilenameUtils; +import org.apache.commons.io.output.TeeOutputStream; + +import java.io.*; 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; /** * @@ -42,25 +39,8 @@ public class NumassIO extends BasicIOManager { public static final String NUMASS_OUTPUT_CONTEXT_KEY = "numass.outputDir"; - @Override - public OutputStream out(Name stage, Name name) { - List tokens = new ArrayList<>(); - if (getContext().hasValue("numass.path")) { - String path = getContext().getString("numass.path"); - if (path.contains(".")) { - tokens.addAll(Arrays.asList(path.split("."))); - } else { - tokens.add(path); - } - } - - if (stage != null) { - tokens.addAll(Arrays.asList(stage.asArray())); - } - - String dirName = String.join(File.separator, tokens); - String fileName = name.removeNameSpace().toString() + ".out"; - return buildOut(getWorkDirectory(), dirName, fileName); + public static RawNMFile readAsDat(Binary source, Meta config) throws IOException { + return new NumassDataReader(source, config).read(); } // private File getOutputDir() { @@ -73,36 +53,6 @@ public class NumassIO extends BasicIOManager { // // } - protected OutputStream buildOut(File parentDir, String dirName, String fileName) { - File outputFile; - - if (!parentDir.exists()) { - throw new RuntimeException("Working directory does not exist"); - } - if (dirName != null && !dirName.isEmpty()) { - parentDir = new File(parentDir, dirName); - if (!parentDir.exists()) { - parentDir.mkdirs(); - } - } - -// String output = source.meta().getString("output", this.meta().getString("output", fileName + ".out")); - outputFile = new File(parentDir, fileName); - try { - if (getContext().getBoolean("numass.consoleOutput", false)) { - return new TeeOutputStream(new FileOutputStream(outputFile), System.out); - } else { - return new FileOutputStream(outputFile); - } - } catch (FileNotFoundException ex) { - throw new RuntimeException(ex); - } - } - - public static RawNMFile readAsDat(Binary source, Meta config) throws IOException { - return new NumassDataReader(source, config).read(); - } - public static RawNMFile readAsPaw(Binary source, Meta config) throws IOException { return new NumassPawReader().readPaw(source, config.getString(FileDataFactory.FILE_NAME_KEY)); } @@ -126,4 +76,51 @@ public class NumassIO extends BasicIOManager { throw new RuntimeException(ex); } } + + @Override + public OutputStream out(Name stage, Name name) { + List tokens = new ArrayList<>(); + if (getContext().hasValue("numass.path")) { + String path = getContext().getString("numass.path"); + if (path.contains(".")) { + tokens.addAll(Arrays.asList(path.split("."))); + } else { + tokens.add(path); + } + } + + if (stage != null) { + tokens.addAll(Arrays.asList(stage.asArray())); + } + + String dirName = String.join(File.separator, tokens); + String fileName = name.removeNameSpace().toString() + ".out"; + return buildOut(getWorkDirectory(), dirName, fileName); + } + + protected OutputStream buildOut(File parentDir, String dirName, String fileName) { + File outputFile; + + if (!parentDir.exists()) { + throw new RuntimeException("Working directory does not exist"); + } + if (dirName != null && !dirName.isEmpty()) { + parentDir = new File(parentDir, dirName); + if (!parentDir.exists()) { + parentDir.mkdirs(); + } + } + +// String output = source.meta().getString("output", this.meta().getString("output", fileName + ".onComplete")); + outputFile = new File(parentDir, fileName); + try { + if (getContext().getBoolean("numass.consoleOutput", false)) { + return new TeeOutputStream(new FileOutputStream(outputFile), System.out); + } else { + return new FileOutputStream(outputFile); + } + } catch (FileNotFoundException ex) { + throw new RuntimeException(ex); + } + } } diff --git a/numass-main/src/main/java/inr/numass/actions/MergeDataAction.java b/numass-main/src/main/java/inr/numass/actions/MergeDataAction.java index cd32c49b..18ca4e2e 100644 --- a/numass-main/src/main/java/inr/numass/actions/MergeDataAction.java +++ b/numass-main/src/main/java/inr/numass/actions/MergeDataAction.java @@ -24,21 +24,12 @@ import hep.dataforge.io.ColumnedDataWriter; import hep.dataforge.io.reports.Reportable; import hep.dataforge.meta.Meta; import hep.dataforge.meta.MetaBuilder; -import hep.dataforge.tables.DataPoint; -import hep.dataforge.tables.ListTable; -import hep.dataforge.tables.MapPoint; -import hep.dataforge.tables.PointSource; -import hep.dataforge.tables.Table; -import hep.dataforge.tables.TableFormat; +import hep.dataforge.tables.*; + import java.io.OutputStream; -import java.util.ArrayList; -import java.util.Collection; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; +import java.util.*; /** - * * @author Darksnake */ @TypedActionDef(name = "merge", inputType = Table.class, outputType = Table.class, info = "Merge different numass data files into one.") @@ -64,7 +55,7 @@ public class MergeDataAction extends ManyToOneAction { @Override protected Table execute(Reportable log, String nodeName, Map data, Meta meta) { Table res = mergeDataSets(nodeName, data.values()); - return new ListTable(res.getFormat(),res.sort("Uset", true)); + return new ListTable(res.getFormat(), res.sort("Uset", true)); } @Override @@ -76,7 +67,7 @@ public class MergeDataAction extends ManyToOneAction { @Override protected MetaBuilder outputMeta(DataNode input) { - String numassPath = input.dataStream().map(item -> item.getValue().meta().getString("numass.path", null)) + String numassPath = input.dataStream().map(data -> data.meta().getString("numass.path", null)) .reduce("", (String path, String newPath) -> { if (path == null) { return null; @@ -168,8 +159,8 @@ public class MergeDataAction extends ManyToOneAction { }).forEach((curPoint) -> { res.add(curPoint); }); - - return new ListTable(TableFormat.forNames(parnames),res); + + return new ListTable(TableFormat.forNames(parnames), res); } diff --git a/numass-main/src/main/java/inr/numass/actions/MonitorCorrectAction.java b/numass-main/src/main/java/inr/numass/actions/MonitorCorrectAction.java index 6054d5b5..bbd00118 100644 --- a/numass-main/src/main/java/inr/numass/actions/MonitorCorrectAction.java +++ b/numass-main/src/main/java/inr/numass/actions/MonitorCorrectAction.java @@ -28,6 +28,10 @@ import hep.dataforge.tables.ListTable; import hep.dataforge.tables.MapPoint; import hep.dataforge.tables.Table; import hep.dataforge.values.Value; +import javafx.util.Pair; +import org.apache.commons.math3.analysis.interpolation.SplineInterpolator; +import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction; + import java.io.OutputStream; import java.time.Instant; import java.util.ArrayList; @@ -35,9 +39,6 @@ import java.util.List; import java.util.Map.Entry; import java.util.TreeMap; import java.util.concurrent.CopyOnWriteArrayList; -import javafx.util.Pair; -import org.apache.commons.math3.analysis.interpolation.SplineInterpolator; -import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction; /** * @@ -45,7 +46,7 @@ import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction; */ @TypedActionDef(name = "monitor", inputType = Table.class, outputType = Table.class) @ValueDef(name = "monitorPoint", type = "NUMBER", required = true, info = "The Uset for monitor point") -@ValueDef(name = "monitorFile", info = "The outputfile for monitor points", def = "monitor.out") +@ValueDef(name = "monitorFile", info = "The outputfile for monitor points", def = "monitor.onComplete") @ValueDef(name = "calculateRelative", info = "Calculate count rate relative to average monitor point", def = "false") public class MonitorCorrectAction extends OneToOneAction { diff --git a/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java b/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java index 3fb63bef..d7907d8c 100644 --- a/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java +++ b/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java @@ -24,23 +24,21 @@ import hep.dataforge.io.XMLMetaWriter; import hep.dataforge.io.reports.Reportable; import hep.dataforge.meta.Laminate; import hep.dataforge.meta.Meta; -import hep.dataforge.tables.DataPoint; -import hep.dataforge.tables.ListTable; -import hep.dataforge.tables.MapPoint; -import hep.dataforge.tables.Table; -import hep.dataforge.tables.TableFormat; +import hep.dataforge.tables.*; import inr.numass.storage.NMPoint; import inr.numass.storage.NumassData; import inr.numass.storage.RawNMPoint; import inr.numass.utils.TritiumUtils; -import static inr.numass.utils.TritiumUtils.evaluateExpression; import inr.numass.utils.UnderflowCorrection; + import java.io.OutputStream; import java.time.Instant; import java.util.ArrayList; import java.util.List; import java.util.function.Function; +import static inr.numass.utils.TritiumUtils.evaluateExpression; + /** * * @author Darksnake @@ -143,7 +141,6 @@ public class PrepareDataAction extends OneToOneAction { * @param log * @param point * @param meta - * @param countRate precalculated count rate in main window * @return */ private double correction(Reportable log, NMPoint point, Laminate meta) { diff --git a/numass-main/src/main/java/inr/numass/actions/ShowLossSpectrumAction.java b/numass-main/src/main/java/inr/numass/actions/ShowLossSpectrumAction.java index 21dd6564..cf35326d 100644 --- a/numass-main/src/main/java/inr/numass/actions/ShowLossSpectrumAction.java +++ b/numass-main/src/main/java/inr/numass/actions/ShowLossSpectrumAction.java @@ -16,11 +16,6 @@ package inr.numass.actions; import hep.dataforge.actions.OneToOneAction; -import hep.dataforge.stat.fit.FitState; -import hep.dataforge.stat.fit.FitTaskResult; -import hep.dataforge.stat.fit.Param; -import hep.dataforge.stat.fit.ParamSet; -import hep.dataforge.stat.models.Histogram; import hep.dataforge.description.TypedActionDef; import hep.dataforge.io.ColumnedDataWriter; import hep.dataforge.io.PrintFunction; @@ -34,6 +29,11 @@ import hep.dataforge.plots.PlotsPlugin; import hep.dataforge.plots.XYPlotFrame; import hep.dataforge.plots.data.PlottableData; import hep.dataforge.plots.data.PlottableXYFunction; +import hep.dataforge.stat.fit.FitState; +import hep.dataforge.stat.fit.FitTaskResult; +import hep.dataforge.stat.fit.Param; +import hep.dataforge.stat.fit.ParamSet; +import hep.dataforge.stat.models.Histogram; import hep.dataforge.stat.simulation.GaussianParameterGenerator; import hep.dataforge.tables.ListTable; import hep.dataforge.tables.MapPoint; @@ -41,13 +41,8 @@ import hep.dataforge.tables.Table; import hep.dataforge.tables.XYAdapter; import hep.dataforge.values.NamedValueSet; import inr.numass.NumassIntegrator; -import inr.numass.Numass; import inr.numass.models.ExperimentalVariableLossSpectrum; import inr.numass.models.LossCalculator; -import java.io.OutputStreamWriter; -import java.io.PrintWriter; -import java.nio.charset.Charset; -import java.util.Arrays; import org.apache.commons.math3.analysis.UnivariateFunction; import org.apache.commons.math3.analysis.interpolation.LinearInterpolator; import org.apache.commons.math3.analysis.interpolation.UnivariateInterpolator; @@ -55,6 +50,11 @@ import org.apache.commons.math3.stat.StatUtils; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.slf4j.LoggerFactory; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.nio.charset.Charset; +import java.util.Arrays; + /** * * @author darksnake @@ -65,6 +65,55 @@ public class ShowLossSpectrumAction extends OneToOneAction { private static final String[] names = {"X", "exPos", "ionPos", "exW", "ionW", "exIonRatio"}; + public static double calcultateIonRatio(NamedValueSet set, double threshold) { + UnivariateIntegrator integrator = NumassIntegrator.getHighDensityIntegrator(); + UnivariateFunction integrand = LossCalculator.getSingleScatterFunction(set); + return 1d - integrator.integrate(integrand, 5d, threshold); + } + + public static Table generateSpread(PrintWriter writer, String name, NamedValueSet parameters, NamedMatrix covariance) { + int numCalls = 1000; + int gridPoints = 200; + double a = 8; + double b = 32; + + double[] grid = GridCalculator.getUniformUnivariateGrid(a, b, gridPoints); + + double[] upper = new double[gridPoints]; + double[] lower = new double[gridPoints]; + double[] dispersion = new double[gridPoints]; + + double[] central = new double[gridPoints]; + + UnivariateFunction func = LossCalculator.getSingleScatterFunction(parameters); + for (int j = 0; j < gridPoints; j++) { + central[j] = func.value(grid[j]); + } + + Arrays.fill(upper, Double.NEGATIVE_INFINITY); + Arrays.fill(lower, Double.POSITIVE_INFINITY); + Arrays.fill(dispersion, 0); + + GaussianParameterGenerator generator = new GaussianParameterGenerator(parameters, covariance); + + for (int i = 0; i < numCalls; i++) { + func = LossCalculator.getSingleScatterFunction(generator.generate()); + for (int j = 0; j < gridPoints; j++) { + double val = func.value(grid[j]); + upper[j] = Math.max(upper[j], val); + lower[j] = Math.min(lower[j], val); + dispersion[j] += (val - central[j]) * (val - central[j]) / numCalls; + } + } + String[] pointNames = {"e", "central", "lower", "upper", "dispersion"}; + ListTable.Builder res = new ListTable.Builder(pointNames); + for (int i = 0; i < gridPoints; i++) { + res.row(new MapPoint(pointNames, grid[i], central[i], lower[i], upper[i], dispersion[i])); + + } + return res.build(); + } + @Override protected FitState execute(Reportable log, String name, Laminate meta, FitState input) { ParamSet pars = input.getParameters(); @@ -115,7 +164,7 @@ public class ShowLossSpectrumAction extends OneToOneAction { // writer.println(param.toString()); // } // writer.println(); -// out.printf("Chi squared over degrees of freedom: %g/%d = %g", input.getChi2(), input.ndf(), chi2 / this.ndf()); +// onComplete.printf("Chi squared over degrees of freedom: %g/%d = %g", input.getChi2(), input.ndf(), chi2 / this.ndf()); writer.println(); @@ -178,12 +227,6 @@ public class ShowLossSpectrumAction extends OneToOneAction { return input; } - public static double calcultateIonRatio(NamedValueSet set, double threshold) { - UnivariateIntegrator integrator = NumassIntegrator.getHighDensityIntegrator(); - UnivariateFunction integrand = LossCalculator.getSingleScatterFunction(set); - return 1d - integrator.integrate(integrand, 5d, threshold); - } - private double calculateIntegralExIonRatio(Table data, double X, double integralThreshold) { double scatterProb = 1 - Math.exp(-X); @@ -233,47 +276,4 @@ public class ShowLossSpectrumAction extends OneToOneAction { return new DescriptiveStatistics(res).getStandardDeviation(); } - public static Table generateSpread(PrintWriter writer, String name, NamedValueSet parameters, NamedMatrix covariance) { - int numCalls = 1000; - int gridPoints = 200; - double a = 8; - double b = 32; - - double[] grid = GridCalculator.getUniformUnivariateGrid(a, b, gridPoints); - - double[] upper = new double[gridPoints]; - double[] lower = new double[gridPoints]; - double[] dispersion = new double[gridPoints]; - - double[] central = new double[gridPoints]; - - UnivariateFunction func = LossCalculator.getSingleScatterFunction(parameters); - for (int j = 0; j < gridPoints; j++) { - central[j] = func.value(grid[j]); - } - - Arrays.fill(upper, Double.NEGATIVE_INFINITY); - Arrays.fill(lower, Double.POSITIVE_INFINITY); - Arrays.fill(dispersion, 0); - - GaussianParameterGenerator generator = new GaussianParameterGenerator(parameters, covariance); - - for (int i = 0; i < numCalls; i++) { - func = LossCalculator.getSingleScatterFunction(generator.generate()); - for (int j = 0; j < gridPoints; j++) { - double val = func.value(grid[j]); - upper[j] = Math.max(upper[j], val); - lower[j] = Math.min(lower[j], val); - dispersion[j] += (val - central[j]) * (val - central[j]) / numCalls; - } - } - String[] pointNames = {"e", "central", "lower", "upper", "dispersion"}; - ListTable.Builder res = new ListTable.Builder(pointNames); - for (int i = 0; i < gridPoints; i++) { - res.row(new MapPoint(pointNames, grid[i], central[i], lower[i], upper[i], dispersion[i])); - - } - return res.build(); - } - } diff --git a/numass-main/src/main/java/inr/numass/tasks/GrindCaller.java b/numass-main/src/main/java/inr/numass/tasks/GrindCaller.java new file mode 100644 index 00000000..d0a29ffc --- /dev/null +++ b/numass-main/src/main/java/inr/numass/tasks/GrindCaller.java @@ -0,0 +1,16 @@ +package inr.numass.tasks; + +import hep.dataforge.grind.JavaGrindLauncher; + +import java.io.File; + +/** + * Created by darksnake on 12-Aug-16. + */ +public class GrindCaller { + + public static void main(String[] args) throws Exception { + JavaGrindLauncher.buildWorkspace(new File("D:\\Work\\Numass\\sterile2016\\workspace.groovy")).runTask("numass.prepare", "fill_2").computeAll(); + } + +} diff --git a/numass-main/src/main/java/inr/numass/tasks/NumassFitScanSummaryTask.java b/numass-main/src/main/java/inr/numass/tasks/NumassFitScanSummaryTask.java index 308ec4f6..898486fb 100644 --- a/numass-main/src/main/java/inr/numass/tasks/NumassFitScanSummaryTask.java +++ b/numass-main/src/main/java/inr/numass/tasks/NumassFitScanSummaryTask.java @@ -8,7 +8,6 @@ package inr.numass.tasks; import hep.dataforge.actions.ManyToOneAction; import hep.dataforge.computation.WorkManager; import hep.dataforge.context.Context; -import hep.dataforge.data.Data; import hep.dataforge.data.DataNode; import hep.dataforge.description.TypedActionDef; import hep.dataforge.io.reports.Reportable; @@ -20,6 +19,7 @@ import hep.dataforge.tables.Table; import hep.dataforge.workspace.GenericTask; import hep.dataforge.workspace.TaskModel; import hep.dataforge.workspace.TaskState; + import java.util.Map; /** @@ -29,8 +29,8 @@ import java.util.Map; public class NumassFitScanSummaryTask extends GenericTask { @Override - protected TaskState transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { - return state.finish(new FitSummaryAction().withContext(context).run((DataNode) state.getData(), config)); + protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { + state.finish(new FitSummaryAction().withContext(context).run((DataNode) state.getData(), config)); } @Override diff --git a/numass-main/src/main/java/inr/numass/tasks/NumassFitScanTask.java b/numass-main/src/main/java/inr/numass/tasks/NumassFitScanTask.java index ea613a42..1f1cc79d 100644 --- a/numass-main/src/main/java/inr/numass/tasks/NumassFitScanTask.java +++ b/numass-main/src/main/java/inr/numass/tasks/NumassFitScanTask.java @@ -23,13 +23,12 @@ import hep.dataforge.workspace.TaskModel; import hep.dataforge.workspace.TaskState; /** - * * @author Alexander Nozik */ public class NumassFitScanTask extends GenericTask { @Override - protected TaskState transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { + protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { String scanParameter = config.getString("scanPar", "msterile2"); Value scanValues = config.getValue("scanValues", Value.of(new String[]{"0.5, 1, 1.5, 2, 2.5, 3"})); Action action = new FitAction().withContext(context).withParentProcess(callback.workName()); @@ -42,25 +41,24 @@ public class NumassFitScanTask extends GenericTask { } //do fit - sourceNode.forEachDataWithType(Table.class, (name, data) -> { + sourceNode.forEachDataWithType(Table.class, data -> { DataNode res = scanValues.listValue().stream().parallel().map(val -> { MetaBuilder overrideMeta = new MetaBuilder("override"); - overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", name, scanParameter, val.stringValue())); - MetaBuilder paramMeta = MetaUtils.findNodeByValue(config, "params.param", name, scanParameter).getBuilder() + overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", data.getName(), scanParameter, val.stringValue())); + MetaBuilder paramMeta = MetaUtils.findNodeByValue(config, "params.param", data.getName(), scanParameter).getBuilder() .setValue("value", val); overrideMeta.setNode("params.param", paramMeta); - return action.run(DataNode.of(name, data, overrideMeta), config); + return action.run(DataNode.of(data.getName(), data, overrideMeta), config); }).collect( () -> DataSet.builder(FitState.class), (DataSet.Builder builder, DataNode node) -> builder.putData(node.getName(), node.getData()), (DataSet.Builder builder1, DataSet.Builder builder2) -> builder1.putAll(builder2.getDataMap()) ).build(); - resultBuilder.putData(name, res.getData()); + resultBuilder.putData(data.getName(), res.getData()); }); state.finish(resultBuilder.build()); - return state; } @Override diff --git a/numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java b/numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java index 44728bab..fb287370 100644 --- a/numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java +++ b/numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java @@ -6,8 +6,8 @@ package inr.numass.tasks; import hep.dataforge.actions.Action; -import hep.dataforge.context.Context; import hep.dataforge.computation.WorkManager; +import hep.dataforge.context.Context; import hep.dataforge.data.DataNode; import hep.dataforge.data.DataTree; import hep.dataforge.meta.Meta; @@ -47,7 +47,7 @@ public class NumassPrepareTask extends GenericTask { */ @Override @SuppressWarnings("unchecked") - protected TaskState transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { + protected void transform(WorkManager.Callback callback, Context context, TaskState state, Meta config) { //acquiring initial data. Data node could not be empty Meta dataMeta = Template.compileTemplate(config.getNode("data"), config); DataNode data = runAction(new ReadNumassStorageAction(), callback, context, DataNode.empty(), dataMeta); @@ -66,13 +66,13 @@ public class NumassPrepareTask extends GenericTask { //merging if needed if (config.hasNode("merge")) { DataTree.Builder resultBuilder = DataTree.builder(Table.class); - tables.dataStream().forEach(pair -> resultBuilder.putData(pair.getKey(), pair.getValue())); +// tables.dataStream().forEach(d -> resultBuilder.putData(d)); DataNode
finalTables = tables; config.getNodes("merge").forEach(mergeNode -> { Meta mergeMeta = Template.compileTemplate(mergeNode, config); DataNode
mergeData = runAction(new MergeDataAction(), callback, context, finalTables, mergeMeta); - mergeData.dataStream().forEach(pair -> { - resultBuilder.putData("merge." + pair.getKey(), pair.getValue()); + mergeData.dataStream().forEach(d -> { + resultBuilder.putData("merge." + d.getName(), d.anonymize()); }); }); tables = resultBuilder.build(); @@ -84,7 +84,6 @@ public class NumassPrepareTask extends GenericTask { } state.finish(tables); - return state; } private DataNode runAction(Action action, WorkManager.Callback callback, Context context, DataNode data, Meta meta) { diff --git a/numass-main/src/main/java/inr/numass/workbench/TextOutputTab.java b/numass-main/src/main/java/inr/numass/workbench/TextOutputTab.java index f5f26c3a..122b930e 100644 --- a/numass-main/src/main/java/inr/numass/workbench/TextOutputTab.java +++ b/numass-main/src/main/java/inr/numass/workbench/TextOutputTab.java @@ -6,11 +6,12 @@ package inr.numass.workbench; import hep.dataforge.fx.FXDataOutputPane; -import java.io.OutputStream; import javafx.event.Event; +import java.io.OutputStream; + /** - * A text output tab. Basically it is attached to IOManager::out + * A text output tab. Basically it is attached to IOManager::onComplete * * @author Alexander Nozik */ @@ -27,7 +28,7 @@ public class TextOutputTab extends OutputTab { */ public TextOutputTab(String name) { super(name); -// out = new DataOutputPane(); +// onComplete = new DataOutputPane(); out = new FXDataOutputPane(); setContent(out.getRoot()); setOnClosed((Event event) -> close()); diff --git a/numass-main/src/main/java/inr/numass/workbench/WorkbenchIOManager.java b/numass-main/src/main/java/inr/numass/workbench/WorkbenchIOManager.java index 14e6a10d..5cf265a3 100644 --- a/numass-main/src/main/java/inr/numass/workbench/WorkbenchIOManager.java +++ b/numass-main/src/main/java/inr/numass/workbench/WorkbenchIOManager.java @@ -8,10 +8,11 @@ package inr.numass.workbench; import hep.dataforge.context.Context; import hep.dataforge.io.IOManager; import hep.dataforge.names.Name; +import org.apache.commons.io.output.TeeOutputStream; + import java.io.File; import java.io.InputStream; import java.io.OutputStream; -import org.apache.commons.io.output.TeeOutputStream; /** * An IOManager wrapper that redirects output to appropriate FX components @@ -32,6 +33,11 @@ public class WorkbenchIOManager implements IOManager { return manager.getContext(); } + @Override + public void setContext(Context context) { + manager.setContext(context); + } + @Override public File getFile(String path) { return manager.getFile(path); @@ -63,12 +69,7 @@ public class WorkbenchIOManager implements IOManager { @Override public OutputStream out() { return manager.out(); -// return new ConsoleStream(holder.getLogArea(), new PrintStream(manager.out())); - } - - @Override - public void setContext(Context context) { - manager.setContext(context); +// return new ConsoleStream(holder.getLogArea(), new PrintStream(manager.onComplete())); } } diff --git a/numass-main/src/test/java/inr/numass/models/TransmissionInterpolatorTest.java b/numass-main/src/test/java/inr/numass/models/TransmissionInterpolatorTest.java index 7885caa3..57335066 100644 --- a/numass-main/src/test/java/inr/numass/models/TransmissionInterpolatorTest.java +++ b/numass-main/src/test/java/inr/numass/models/TransmissionInterpolatorTest.java @@ -31,11 +31,11 @@ public class TransmissionInterpolatorTest { JFreeChartFrame frame = FXPlotUtils.displayJFreeChart("TransmissionInterpolatorTest", null); //JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null); TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(GlobalContext.instance(), - "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.out", "Uset", "CR", 15, 0.8, 19002d); + "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.onComplete", "Uset", "CR", 15, 0.8, 19002d); frame.add(PlottableData.plot("data", interpolator.getX(), interpolator.getY())); frame.add(PlottableXYFunction.plotFunction("interpolated", x->interpolator.value(x), interpolator.getXmin(), interpolator.getXmax(), 2000)); -// PrintFunction.printFuntionSimple(new PrintWriter(System.out), interpolator, interpolator.getXmin(), interpolator.getXmax(), 500); +// PrintFunction.printFuntionSimple(new PrintWriter(System.onComplete), interpolator, interpolator.getXmin(), interpolator.getXmax(), 500); } } diff --git a/numass-viewer/src/main/java/inr/numass/viewer/NumassLoaderViewComponent.java b/numass-viewer/src/main/java/inr/numass/viewer/NumassLoaderViewComponent.java index f7051d2e..39629828 100644 --- a/numass-viewer/src/main/java/inr/numass/viewer/NumassLoaderViewComponent.java +++ b/numass-viewer/src/main/java/inr/numass/viewer/NumassLoaderViewComponent.java @@ -20,37 +20,22 @@ package inr.numass.viewer; * To change this template file, choose Tools | Templates * and open the template in the editor. */ -import hep.dataforge.context.Context; + import hep.dataforge.computation.WorkManager; +import hep.dataforge.context.Context; import hep.dataforge.io.ColumnedDataWriter; import hep.dataforge.meta.Meta; import hep.dataforge.meta.MetaBuilder; import hep.dataforge.plots.PlotFrame; import hep.dataforge.plots.XYPlotFrame; -import hep.dataforge.plots.data.ChangeablePlottableData; -import hep.dataforge.plots.data.DynamicPlottable; -import hep.dataforge.plots.data.DynamicPlottableSet; -import hep.dataforge.plots.data.PlotDataUtils; -import hep.dataforge.plots.data.PlottableData; +import hep.dataforge.plots.data.*; import hep.dataforge.plots.fx.PlotContainer; import hep.dataforge.plots.jfreechart.JFreeChartFrame; import hep.dataforge.storage.commons.JSONMetaWriter; -import hep.dataforge.tables.DataPoint; -import hep.dataforge.tables.ListTable; -import hep.dataforge.tables.MapPoint; -import hep.dataforge.tables.Table; -import hep.dataforge.tables.XYAdapter; +import hep.dataforge.tables.*; import inr.numass.storage.NMPoint; import inr.numass.storage.NumassData; import inr.numass.utils.TritiumUtils; -import java.io.File; -import java.io.IOException; -import java.net.URL; -import java.util.List; -import java.util.ResourceBundle; -import java.util.function.Predicate; -import java.util.function.Supplier; -import java.util.stream.Collectors; import javafx.application.Platform; import javafx.beans.value.ChangeListener; import javafx.beans.value.ObservableValue; @@ -61,14 +46,7 @@ import javafx.fxml.FXMLLoader; import javafx.fxml.Initializable; import javafx.geometry.Insets; import javafx.geometry.Orientation; -import javafx.scene.control.Button; -import javafx.scene.control.CheckBox; -import javafx.scene.control.ChoiceBox; -import javafx.scene.control.Label; -import javafx.scene.control.Separator; -import javafx.scene.control.Tab; -import javafx.scene.control.TextArea; -import javafx.scene.control.TextField; +import javafx.scene.control.*; import javafx.scene.layout.AnchorPane; import javafx.scene.layout.VBox; import javafx.stage.FileChooser; @@ -80,6 +58,15 @@ import org.controlsfx.validation.Validator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.io.File; +import java.io.IOException; +import java.net.URL; +import java.util.List; +import java.util.ResourceBundle; +import java.util.function.Predicate; +import java.util.function.Supplier; +import java.util.stream.Collectors; + /** * FXML Controller class * @@ -387,7 +374,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab if (points != null && !points.isEmpty()) { FileChooser fileChooser = new FileChooser(); fileChooser.setTitle("Choose text export destination"); - fileChooser.setInitialFileName(data.getName() + "_spectrum.out"); + fileChooser.setInitialFileName(data.getName() + "_spectrum.onComplete"); File destination = fileChooser.showSaveDialog(spectrumPlotPane.getScene().getWindow()); if (destination != null) { String[] names = new String[]{"Uset", "Uread", "Length", "Total", "Window", "CR", "CRerr", "Timestamp"}; @@ -428,7 +415,7 @@ public class NumassLoaderViewComponent extends AnchorPane implements Initializab private void onExportButtonClick(ActionEvent event) { FileChooser fileChooser = new FileChooser(); fileChooser.setTitle("Choose text export destination"); - fileChooser.setInitialFileName(data.getName() + "_detector.out"); + fileChooser.setInitialFileName(data.getName() + "_detector.onComplete"); File destination = fileChooser.showSaveDialog(detectorPlotPane.getScene().getWindow()); if (destination != null) { Table detectorData = PlotDataUtils.collectXYDataFromPlot((XYPlotFrame) detectorPlot.getPlot(), true);