Made ActionManager optional. ActionUtils searches all plugins for exported actions.

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

@@ -81,9 +81,9 @@ ListTable data = readData("c:\\Users\\Darksnake\\Dropbox\\PlayGround\\RUN23.DAT"
 
 FitState state = new FitState(data, model, allPars);
 
-FitState res = fm.runDefaultTask(state, "E0", "N", "bkg");
+FitState res = fm.runDefaultStage(state, "E0", "N", "bkg");
 
-res = fm.runDefaultTask(res, "E0", "N", "bkg", "mnu2");
+res = fm.runDefaultStage(res, "E0", "N", "bkg", "mnu2");
 
 res.print(out);
 
@@ -91,7 +91,7 @@ res.print(out);
 //
 ////        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 = fm.runStage(res, "MINUIT", "run", "E0", "N", "bkg", "mnu2");
 ////
 //res.print(onComplete);
 

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

@@ -3,7 +3,7 @@ package inr.numass.scripts
 import hep.dataforge.context.Global
 import hep.dataforge.grind.Grind
 import hep.dataforge.meta.Meta
-import hep.dataforge.stat.fit.FitPlugin
+import hep.dataforge.stat.fit.FitManager
 import hep.dataforge.stat.fit.ParamSet
 import hep.dataforge.stat.models.XYModel
 import inr.numass.NumassPlugin
@@ -17,7 +17,7 @@ Locale.setDefault(Locale.US);
 new NumassPlugin().startGlobal();
 
 
-def fm = Global.instance().provide("fitting", FitPlugin.class).getFitManager();
+def fm = Global.instance().provide("fitting", FitManager.class).getFitManager();
 def mm = fm.modelManager
 
 

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

@@ -91,7 +91,7 @@ FitState state = new FitState(data, model, allPars);
 //new PlotFitResultAction().eval(state);
         
         
-FitState res = fm.runTask(state, "QOW", FitStage.TASK_RUN, "N", "bkg", "E0", "U2");
+FitState res = fm.runStage(state, "QOW", FitStage.TASK_RUN, "N", "bkg", "E0", "U2");
 
         
 

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

@@ -61,7 +61,7 @@ FittingIOUtils.printSpectrum(new PrintWriter(System.out), spectrum, allPars, 184
 ////        allPars.setParValue("X", 0.4);
 //        FitState state = FitTaskManager.buildState(data, model, allPars);
 //
-//        FitState res = fm.runTask(state, "QOW", FitTask.TASK_RUN, "N", "bkg", "pos", "sigma");
+//        FitState res = fm.runStage(state, "QOW", FitTask.TASK_RUN, "N", "bkg", "pos", "sigma");
 //
 //        res.print(onComplete());
 

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

@@ -40,7 +40,7 @@ List<NMPoint> pileup = new ArrayList<>();
 lowerChannel = 400;
 upperChannel = 1800;
 
-PileUpSimulator buildSimulator(NMPoint point, double cr, NMPoint reference = null, boolean extrapolate = true, double scale = 1d) {
+PileUpSimulator buildSimulator(NMPoint point, double cr, NMPoint reference = null, boolean extrapolate = false, double scale = 1d) {
     def cfg = Grind.buildMeta(cr: cr) {
         pulser(mean: 3450, sigma: 86.45, freq: 66.43)
     }

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

@@ -73,7 +73,7 @@ FittingIOUtils.printSpectrum(Global.out(), spectrum, allPars, 14000, 18600.0, 40
 ////new PlotFitResultAction().eval(state);
 //        
 //        
-//FitState res = fm.runTask(state, "QOW", FitTask.TASK_RUN, "N", "bkg", "E0", "U2", "trap");
+//FitState res = fm.runStage(state, "QOW", FitTask.TASK_RUN, "N", "bkg", "E0", "U2", "trap");
 //
 //        
 //

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

@@ -95,7 +95,7 @@ FitState state = fm.buildState(data, model, allPars);
 //       fm.checkDerivs();
 //        res.print(Out.onComplete);
 //        fm.checkFitDerivatives();
-FitState res = fm.runDefaultTask(state, "U2", "N", "trap");
+FitState res = fm.runDefaultStage(state, "U2", "N", "trap");
 
 res.print(out);
 

numass-main/src/main/java/inr/numass/Numass.java

@@ -19,16 +19,13 @@ import hep.dataforge.actions.ActionManager;
 import hep.dataforge.context.Context;
 import hep.dataforge.context.Global;
 import hep.dataforge.description.ActionDescriptor;
-import hep.dataforge.description.DescriptorFormatter;
 import hep.dataforge.description.DescriptorUtils;
-import hep.dataforge.description.TextDescriptorFormatter;
 import hep.dataforge.exceptions.DescriptorException;
+import hep.dataforge.io.markup.MarkupBuilder;
+import hep.dataforge.io.markup.MarkupUtils;
 import hep.dataforge.meta.Meta;
 
-import java.io.PrintWriter;
-
 /**
- *
  * @author Darksnake
  */
 public class Numass {
@@ -44,22 +41,30 @@ public class Numass {
     }
 
     public static void printDescription(Context context, boolean allowANSI) throws DescriptorException {
-        PrintWriter writer = new PrintWriter(context.io().out());
 
-        DescriptorFormatter formatter = new TextDescriptorFormatter(writer, allowANSI);
+        MarkupBuilder builder = new MarkupBuilder()
-        writer.println("***Data description***");
+                .addText("***Data description***", "red")
-        writer.print("  ");
+                .ln()
-        formatter.showDescription(
+                .addText("\t")
-                DescriptorUtils.buildDescriptor(
+                .addContent(
-                        DescriptorUtils.findAnnotatedElement("method::hep.dataforge.data.DataManager.read")
+                        MarkupUtils.markupDescriptor(DescriptorUtils.buildDescriptor("method::hep.dataforge.data.DataManager.read"))
-                ));
+                )
-        writer.println("***Allowed actions***");
+                .ln()
+                .addText("***Allowed actions***", "red")
+                .ln();
+
+
+        for (ActionDescriptor descriptor : context.getPlugin(ActionManager.class).list()) {
+            builder
+                    .addText("\t")
+                    .addContent(
+                            MarkupUtils.markupDescriptor(descriptor)
+                    );
 
-        for (ActionDescriptor descriptor : ActionManager.buildFrom(context).list()) {
-            writer.print("  ");
-            formatter.showDescription(descriptor);
         }
-        writer.println("***End of actions list***");
+        builder.addText("***End of actions list***", "red");
-        writer.flush();
+
+
+        context.io().getMarkupRenderer().render(builder.build());
     }
 }

numass-main/src/main/java/inr/numass/NumassPlugin.java

@@ -27,7 +27,6 @@ import hep.dataforge.plots.fx.FXPlotUtils;
 import hep.dataforge.plots.fx.PlotContainer;
 import hep.dataforge.plots.jfreechart.JFreeChartFrame;
 import hep.dataforge.stat.fit.FitManager;
-import hep.dataforge.stat.fit.FitPlugin;
 import hep.dataforge.stat.models.ModelManager;
 import hep.dataforge.stat.models.WeightedXYModel;
 import hep.dataforge.stat.models.XYModel;
@@ -74,11 +73,13 @@ public class NumassPlugin extends BasicPlugin {
 //        StorageManager.buildFrom(context);
         super.attach(context);
         context.setIO(new NumassIO());
-        FitManager fm = context.provide("fitting", FitPlugin.class).getFitManager();
+        FitManager fm = context.provide("fitting", FitManager.class);
         loadModels(fm.getModelManager());
         loadMath(MathPlugin.buildFrom(context));
 
-        ActionManager actions = ActionManager.buildFrom(context);
+        ActionManager actions = new ActionManager();
+        actions.attach(context);
+
         actions.register(SlicingAction.class);
         actions.register(PrepareDataAction.class);
         actions.register(ReadLegacyDataAction.class);
@@ -88,7 +89,6 @@ public class NumassPlugin extends BasicPlugin {
         actions.register(SummaryAction.class);
         actions.register(PlotDataAction.class);
         actions.register(PlotFitResultAction.class);
-        actions.register(ShowLossSpectrumAction.class);
         actions.register(AdjustErrorsAction.class);
         actions.register(ShowEnergySpectrumAction.class);
         actions.register(SubstractSpectrumAction.class);
@@ -124,16 +124,16 @@ public class NumassPlugin extends BasicPlugin {
      */
     private void loadModels(ModelManager manager) {
 
-        manager.addModel("modularbeta", (context, an) -> {
+//        manager.addModel("modularbeta", (context, an) -> {
-            double A = an.getDouble("resolution", 8.3e-5);//8.3e-5
+//            double A = an.getDouble("resolution", 8.3e-5);//8.3e-5
-            double from = an.getDouble("from", 14400d);
+//            double from = an.getDouble("from", 14400d);
-            double to = an.getDouble("to", 19010d);
+//            double to = an.getDouble("to", 19010d);
-            RangedNamedSetSpectrum beta = new BetaSpectrum(getClass().getResourceAsStream("/data/FS.txt"));
+//            RangedNamedSetSpectrum beta = new BetaSpectrum(getClass().getResourceAsStream("/data/FS.txt"));
-            ModularSpectrum sp = new ModularSpectrum(beta, A, from, to);
+//            ModularSpectrum sp = new ModularSpectrum(beta, A, from, to);
-            NBkgSpectrum spectrum = new NBkgSpectrum(sp);
+//            NBkgSpectrum spectrum = new NBkgSpectrum(sp);
-
+//
-            return new XYModel(spectrum, getAdapter(an));
+//            return new XYModel(spectrum, getAdapter(an));
-        });
+//        });
 
         manager.addModel("scatter", (context, an) -> {
             double A = an.getDouble("resolution", 8.3e-5);//8.3e-5

numass-main/src/main/java/inr/numass/models/sterile/TestModels.java

@@ -62,6 +62,7 @@ public class TestModels {
         }
     }
 
+    @SuppressWarnings("deprecation")
     private static ParametricFunction oldModel(Context context, Meta meta) {
         double A = meta.getDouble("resolution", meta.getDouble("resolution.width", 8.3e-5));//8.3e-5
         double from = meta.getDouble("from", 13900d);

numass-main/src/main/java/inr/numass/tasks/NumassFitScanTask.java

@@ -52,11 +52,11 @@ public class NumassFitScanTask extends AbstractTask<FitState> {
         //do fit
 
         Meta fitConfig = config.getMeta("fit");
-        sourceNode.forEachDataWithType(Table.class, d -> {
+        sourceNode.dataStream().forEach(table -> {
             for (int i = 0; i < scanValues.listValue().size(); i++) {
                 Value val = scanValues.listValue().get(i);
                 MetaBuilder overrideMeta = new MetaBuilder(fitConfig);
-                overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", d.getName(), scanParameter, val.stringValue()));
+                overrideMeta.setValue("@resultName", String.format("%s[%s=%s]", table.getName(), scanParameter, val.stringValue()));
 
                 if (overrideMeta.hasMeta("params." + scanParameter)) {
                     overrideMeta.setValue("params." + scanParameter + ".value", val);
@@ -65,8 +65,8 @@ public class NumassFitScanTask extends AbstractTask<FitState> {
                             .filter(par -> par.getString("name") == scanParameter).forEach(par -> par.setValue("value", val));
                 }
 //                Data<Table> newData = new Data<Table>(data.getGoal(),data.type(),overrideMeta);
-                DataNode node = action.run(model.getContext(), DataNode.of("fit_" + i, d, Meta.empty()), overrideMeta);
+                DataNode<FitState> node = action.run(model.getContext(), DataNode.of("fit_" + i, table, Meta.empty()), overrideMeta);
-                resultBuilder.putData(d.getName() + ".fit_" + i, node.getData());
+                resultBuilder.putData(table.getName() + ".fit_" + i, node.getData());
             }
         });
 

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

@@ -100,7 +100,7 @@ public class PileUpSimulator {
      * @return
      */
     private boolean nextEventRegistered(short prevChanel, double delay) {
-        double average = 6.76102 - 4.31897E-4 * prevChanel + 7.88429E-8 * prevChanel * prevChanel;
+        double average = 6.76102 - 4.31897E-4 * prevChanel + 7.88429E-8 * prevChanel * prevChanel + 0.2;
         double prob = 1d - 1d / (1d + Math.pow(delay / average, 75.91));
         return random(prob);
     }