Provider revising

numass-main/build.gradle

@@ -36,6 +36,15 @@ task repl(dependsOn: classes, type: JavaExec) {
     }
 }
 
+task grindTask(dependsOn: classes, type: JavaExec){
+    group "numass"
+    main 'inr.numass.RunTask'
+    classpath = sourceSets.main.runtimeClasspath
+    description "Run a task in a numass workspace"
+    standardInput = System.in
+    standardOutput = System.out
+}
+
 task simulate(dependsOn: classes, type: JavaExec) {
     group "numass"
     main 'inr.numass.scripts.Simulate'

numass-main/src/main/groovy/inr/numass/LaunchGrindShell.groovy

@@ -22,7 +22,7 @@ println "Starting Grind shell"
 
 if (cfgPath) {
     try {
-        GrindTerminal.dumb().launch {
+        GrindTerminal.system().launch {
             GrindWorkspaceBuilder numass = new GrindWorkspaceBuilder(it.shell.context).read(new File(cfgPath)).startup {
                 it.loadTask(NumassPrepareTask)
                 it.loadTask(NumassTableFilterTask)

numass-main/src/main/groovy/inr/numass/RunTask.groovy

@@ -0,0 +1,23 @@
+package inr.numass
+
+import hep.dataforge.grind.GrindWorkspaceBuilder
+import inr.numass.tasks.*
+
+/**
+ * Created by darksnake on 18-Apr-17.
+ */
+
+
+cfgPath = "D:\\Work\\Numass\\sterile2016_10\\workspace.groovy"
+
+GrindWorkspaceBuilder numass = new GrindWorkspaceBuilder().read(new File(cfgPath)).startup {
+    it.loadTask(NumassPrepareTask)
+    it.loadTask(NumassTableFilterTask)
+    it.loadTask(NumassFitScanTask)
+    it.loadTask(NumassSubstractEmptySourceTask)
+    it.loadTask(NumassFitScanSummaryTask)
+    it.loadTask(NumassFitTask)
+    it.loadTask(NumassFitSummaryTask)
+}
+
+numass.scansum "fill_1"

numass-main/src/main/java/hep/dataforge/plotfit/PlotFitResultAction.java

@@ -27,6 +27,7 @@ import hep.dataforge.plots.PlotFrame;
 import hep.dataforge.plots.PlotUtils;
 import hep.dataforge.plots.data.PlottableData;
 import hep.dataforge.plots.data.PlottableXYFunction;
+import hep.dataforge.stat.fit.FitResult;
 import hep.dataforge.stat.fit.FitState;
 import hep.dataforge.stat.models.XYModel;
 import hep.dataforge.tables.NavigablePointSource;
@@ -41,10 +42,10 @@ import java.util.stream.StreamSupport;
 @TypedActionDef(name = "plotFit", info = "Plot fit result", inputType = FitState.class, outputType = FitState.class)
 @NodeDef(name = "adapter", info = "adapter for DataSet being fitted. By default is taken from model.")
 @ValueDef(name = "plotTitle", def = "", info = "The title of the plot.")
-public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
+public class PlotFitResultAction extends OneToOneAction<FitResult, FitResult> {
 
     @Override
-    protected FitState execute(Context context, String name, FitState input, Laminate metaData) {
+    protected FitResult execute(Context context, String name, FitResult input, Laminate metaData) {
 
         NavigablePointSource data = input.getDataSet();
         if (!(input.getModel() instanceof XYModel)) {

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

@@ -31,9 +31,11 @@ import hep.dataforge.meta.Meta;
 public class Numass {
 
     public static Context buildContext(Context parent, Meta meta) {
-        Context numassContext = Global.getContext("numass").withParent(parent).withProperties(meta);
+        return Context.builder("NUMASS")
-        numassContext.pluginManager().load("inr.numass:numass");
+                .parent(parent)
-        return numassContext;
+                .properties(meta)
+                .plugin(NumassPlugin.class)
+                .build();
     }
 
     public static Context buildContext() {

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

@@ -72,7 +72,7 @@ public class NumassPlugin extends BasicPlugin {
     public void attach(Context context) {
 //        StorageManager.buildFrom(context);
         super.attach(context);
-        context.setIO(new NumassIO());
+        context.pluginManager().load(new NumassIO());
         FitManager fm = context.getFeature(FitManager.class);
         loadModels(fm.getModelManager());
         loadMath(MathPlugin.buildFrom(context));

numass-main/src/main/java/inr/numass/actions/MonitorCorrectAction.java

@@ -58,7 +58,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
 
         TreeMap<Instant, DataPoint> index = getMonitorIndex(monitor, sourceData);
         if (index.isEmpty()) {
-            getReport(context, name).reportError("No monitor points found");
+            context.getLog(name).reportError("No monitor points found");
             return sourceData;
         }
         double norm = 0;

numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java

@@ -80,7 +80,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
             corrections.add(new DeadTimeCorrection(meta.getString("deadTime")));
         }
 
-        if (meta.hasNode("correction")) {
+        if (meta.optMeta("correction").isPresent()) {
             corrections.addAll(meta.getMetaList("correction").stream()
                     .map((Function<Meta, Correction>) this::makeCorrection)
                     .collect(Collectors.toList()));

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

@@ -11,6 +11,7 @@ import hep.dataforge.data.DataTree;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
 import hep.dataforge.stat.fit.FitAction;
+import hep.dataforge.stat.fit.FitResult;
 import hep.dataforge.stat.fit.FitState;
 import hep.dataforge.tables.Table;
 import hep.dataforge.values.Value;
@@ -40,7 +41,7 @@ public class NumassFitScanTask extends AbstractTask<FitState> {
         } else {
             scanValues = config.getValue("scan.values", Value.of("[2.5e5, 1e6, 2.25e6, 4e6, 6.25e6, 9e6]"));
         }
-        Action<Table, FitState> action = new FitAction();
+        Action<Table, FitResult> action = new FitAction();
         DataTree.Builder<FitState> resultBuilder = DataTree.builder(FitState.class);
         DataNode<Table> sourceNode = data.getCheckedNode("prepare", Table.class);
 
@@ -65,7 +66,7 @@ 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<FitState> node = action.run(model.getContext(), DataNode.of("fit_" + i, table, Meta.empty()), overrideMeta);
+                DataNode<FitResult> node = action.run(model.getContext(), DataNode.of("fit_" + i, table, Meta.empty()), overrideMeta);
                 resultBuilder.putData(table.getName() + ".fit_" + i, node.getData());
             }
         });

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

@@ -23,7 +23,7 @@ import hep.dataforge.meta.Meta;
 import hep.dataforge.meta.MetaBuilder;
 import hep.dataforge.plotfit.PlotFitResultAction;
 import hep.dataforge.stat.fit.FitAction;
-import hep.dataforge.stat.fit.FitState;
+import hep.dataforge.stat.fit.FitResult;
 import hep.dataforge.tables.Table;
 import hep.dataforge.workspace.SingleActionTask;
 import hep.dataforge.workspace.TaskModel;
@@ -31,7 +31,7 @@ import hep.dataforge.workspace.TaskModel;
 /**
  * Created by darksnake on 16-Sep-16.
  */
-public class NumassFitTask extends SingleActionTask<Table, FitState> {
+public class NumassFitTask extends SingleActionTask<Table, FitResult> {
 
     @Override
     public String getName() {
@@ -51,8 +51,8 @@ public class NumassFitTask extends SingleActionTask<Table, FitState> {
     }
 
     @Override
-    protected Action<Table, FitState> getAction(TaskModel model) {
+    protected Action<Table, FitResult> getAction(TaskModel model) {
-        Action<Table, FitState> action = new FitAction();
+        Action<Table, FitResult> action = new FitAction();
         if (model.meta().getBoolean("fit.plot", false)) {
             return ActionUtils.compose(action, new PlotFitResultAction());
         } else {

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

@@ -29,6 +29,7 @@ import hep.dataforge.tables.MapPoint;
 import hep.dataforge.tables.Table;
 import hep.dataforge.workspace.AbstractTask;
 import hep.dataforge.workspace.TaskModel;
+import org.slf4j.LoggerFactory;
 
 import java.io.OutputStream;
 import java.util.Optional;
@@ -77,7 +78,7 @@ public class NumassSubstractEmptySourceTask extends AbstractTask<Table> {
 
 
     private Data<? extends Table> subtractBackground(Data<? extends Table> mergeData, Data<? extends Table> emptyData) {
-        return DataUtils.combine(Table.class, mergeData, emptyData, mergeData.meta(), (BiFunction<Table, Table, Table>) this::subtractBackground);
+        return DataUtils.combine(mergeData, emptyData, Table.class, mergeData.meta(), (BiFunction<Table, Table, Table>) this::subtractBackground);
     }
 
     private Table subtractBackground(Table merge, Table empty) {
@@ -90,7 +91,7 @@ public class NumassSubstractEmptySourceTask extends AbstractTask<Table> {
                 pointBuilder.putValue("CR", Math.max(0, point.getDouble("CR") - referencePoint.get().getDouble("CR")));
                 pointBuilder.putValue("CRerr", Math.sqrt(Math.pow(point.getDouble("CRerr"), 2d) + Math.pow(referencePoint.get().getDouble("CRerr"), 2d)));
             } else {
-                getLogger().warn("No reference point found for Uset = {}", point.getDouble("Uset"));
+                LoggerFactory.getLogger(getClass()).warn("No reference point found for Uset = {}", point.getDouble("Uset"));
             }
             builder.row(pointBuilder.build());
         });

numass-viewer/src/main/kotlin/inr/numass/viewer/NumassLoaderView.kt

@@ -50,6 +50,7 @@ class NumassLoaderView : View() {
     lateinit var main: MainView
 
     var data: NumassData? = null
+    val spectrumData = PlottableData("spectrum")
 
     private val detectorPlotPane: AnchorPane by fxid();
     private val tabPane: TabPane by fxid();
@@ -175,13 +176,11 @@ class NumassLoaderView : View() {
         getWorkManager().startWork("viewer.numass.hv") { callback: Work ->
             val t = hvData.get()
             Platform.runLater {
-//                hvPlot.plot.clear()
                 val set = PlottableGroup<TimePlottable>()
                 for (dp in t) {
                     val block = dp.getString("block", "default")
                     if (!set.has(block)) {
-
+                        set.add(TimePlottable(block))
-                        set.add(hvPlot.plot.opt(block).orElseGet{TimePlottable(block)} as TimePlottable)
                     }
                     set.get(block).put(dp.getValue("timestamp").timeValue(), dp.getValue("value"))
                 }
@@ -217,8 +216,7 @@ class NumassLoaderView : View() {
     }
 
     private fun setupSpectrumPane(points: List<NumassPoint>) {
-        val spectrumData = spectrumPlot.plot.opt("spectrum").orElseGet{PlottableData("spectrum")} as PlottableData
+        spectrumPlot.plot.add(spectrumData)
-        spectrumPlot.plot.add(spectrumData) //does nothing if it is the same plottable
 
         val lowChannel = channelSlider.lowValue.toInt()
         val highChannel = channelSlider.highValue.toInt()