A lot of fixes. IO needs work

numass-core/src/main/java/inr/numass/NumassProperties.java

@@ -21,7 +21,7 @@ import java.util.Properties;
 public class NumassProperties {
 
     private static File getNumassPropertiesFile() throws IOException {
-        File file = new File(Global.Companion.instance().getUserDirectory(), "numass");
+        File file = new File(Global.INSTANCE.getUserDirectory(), "numass");
         if (!file.exists()) {
             file.mkdirs();
         }
@@ -54,7 +54,7 @@ public class NumassProperties {
             }
             props.store(new FileOutputStream(store), "");
         } catch (IOException ex) {
-            Global.Companion.instance().getLogger().error("Failed to save numass properties", ex);
+            Global.INSTANCE.getLogger().error("Failed to save numass properties", ex);
         }
     }
 }

numass-core/src/main/java/inr/numass/data/api/SimpleNumassPoint.java

@@ -23,9 +23,9 @@ public class SimpleNumassPoint extends MetaHolder implements NumassPoint {
      * @param blocks
      */
     public SimpleNumassPoint(double voltage, Collection<? extends NumassBlock> blocks) {
+        super(new MetaBuilder("point").setValue(HV_KEY, voltage));
         this.blocks = new ArrayList<>(blocks);
         this.blocks.sort(Comparator.comparing(NumassBlock::getStartTime));
-        super.setMeta(new MetaBuilder("point").setValue(HV_KEY, voltage));
     }
 
     public SimpleNumassPoint(Meta meta, Collection<? extends NumassBlock> blocks) {

numass-core/src/main/java/inr/numass/data/storage/NumassDataFactory.java

@@ -27,7 +27,7 @@ public class NumassDataFactory extends DataFactory<NumassSet> {
     @Override
     protected void fill(DataTree.Builder<NumassSet> builder, Context context, Meta meta) {
         Meta newMeta = meta.getBuilder().setValue("type", "numass");
-        Storage storage = context.loadFeature("hep.dataforge:storage", StorageManager.class).buildStorage(newMeta);
+        Storage storage = context.load(StorageManager.class, Meta.empty()).buildStorage(newMeta);
         StorageUtils.loaderStream(storage).forEach(loader -> {
             if (loader instanceof NumassSet) {
                 builder.putStatic(loader.getFullName().toUnescaped(), (NumassSet) loader);

numass-core/src/main/java/inr/numass/data/storage/NumassStorageFactory.java

@@ -29,13 +29,13 @@ public class NumassStorageFactory implements StorageType {
      */
     @NotNull
     public static FileStorage buildLocal(Context context, Path file, boolean readOnly, boolean monitor) {
-        StorageManager manager = context.loadFeature("hep.dataforge:storage", StorageManager.class);
+        StorageManager manager = context.load(StorageManager.class, Meta.empty());
         return (FileStorage) manager.buildStorage(buildStorageMeta(file.toUri(), readOnly, monitor));
     }
 
     @NotNull
     public static FileStorage buildLocal(Context context, String path, boolean readOnly, boolean monitor) {
-        Path file = context.getIo().getDataFile(path);
+        Path file = context.getIo().getDataDir().resolve(path);
         return buildLocal(context, file, readOnly, monitor);
     }
 

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

@@ -31,5 +31,5 @@ try {
 } catch (Exception ex) {
     ex.printStackTrace();
 } finally {
-    Global.terminate();
+    Global.INSTANCE.terminate();
 }

numass-main/src/main/groovy/inr/numass/scripts/models/TristanModel.groovy

@@ -13,7 +13,6 @@ import hep.dataforge.stat.fit.ParamSet
 import hep.dataforge.stat.models.XYModel
 import hep.dataforge.stat.parametric.ParametricFunction
 import hep.dataforge.tables.Table
-import inr.numass.NumassIOKt
 import inr.numass.NumassPlugin
 import inr.numass.data.SpectrumAdapter
 import inr.numass.data.SpectrumGenerator
@@ -23,7 +22,6 @@ import inr.numass.models.misc.ModGauss
 import inr.numass.models.sterile.NumassBeta
 import inr.numass.utils.DataModelUtils
 
-import static hep.dataforge.grind.Grind.morph
 
 Context ctx = Global.instance()
 ctx.getPluginManager().load(FXPlotManager)

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

@@ -48,7 +48,7 @@ public class PlotFitResultAction extends OneToOneAction<FitResult, FitResult> {
 
         NavigableValuesSource data = input.getData();
         if (!(state.getModel() instanceof XYModel)) {
-            context.getChronicle(name).reportError("The fit model should be instance of XYModel for this action. Action failed!");
+            context.getHistory().getChronicle(name).reportError("The fit model should be instance of XYModel for this action. Action failed!");
             return input;
         }
         XYModel model = (XYModel) state.getModel();

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

@@ -19,7 +19,6 @@ import hep.dataforge.actions.ActionUtils;
 import hep.dataforge.context.Context;
 import hep.dataforge.context.Global;
 import hep.dataforge.context.IOManager;
-import hep.dataforge.data.FileDataFactory;
 import hep.dataforge.io.MetaFileReader;
 import hep.dataforge.meta.Meta;
 import org.apache.commons.cli.*;
@@ -34,7 +33,6 @@ import java.io.FileNotFoundException;
 import java.nio.file.Files;
 import java.util.Locale;
 
-import static hep.dataforge.context.Global.out;
 import static inr.numass.Numass.printDescription;
 import static java.util.Locale.setDefault;
 
@@ -52,7 +50,7 @@ public class Main {
 
     public static void run(Context context, String[] args) throws Exception {
         if(context == null){
-            context = Global.Companion.instance();
+            context = Global.INSTANCE;
         }
         Logger logger = LoggerFactory.getLogger("numass-main");
 
@@ -78,7 +76,7 @@ public class Main {
         if (args.length == 0) {
             HelpFormatter formatter = new HelpFormatter();
             formatter.printHelp("java -jar DataReader.jar [OPTIONS]", options);
-            Companion.out().println("Trying to use default config location...");
+            System.out.println("Trying to use default config location...");
         }
 
         if (line.hasOption("c")) {
@@ -88,7 +86,7 @@ public class Main {
                 return;
             }
 
-            java.nio.file.Path configFile = context.getIo().getFile(cfgPath);
+            java.nio.file.Path configFile = context.getIo().getRootDir().resolve(cfgPath);
 
             if (!Files.exists(configFile)) {
                 throw new FileNotFoundException("Configuration file not found");
@@ -119,7 +117,7 @@ public class Main {
                 dataDir = new File(workDir, dataPath);
             }
             if (dataDir.exists() && dataDir.isDirectory()) {
-                context.setValue(FileDataFactory.Companion.getDATA_DIR_KEY(), dataDir.getAbsolutePath());
+                context.setValue(IOManager.DATA_DIRECTORY_CONTEXT_KEY, dataDir.getAbsolutePath());
             } else {
                 throw new FileNotFoundException("Data directory not found");
             }
@@ -134,7 +132,7 @@ public class Main {
             if (!outDir.exists()) {
                 outDir.mkdirs();
             }
-            context.setValue(NumassIO.Companion.getNUMASS_OUTPUT_CONTEXT_KEY(), outDir.toString());
+            context.setValue(IOManager.WORK_DIRECTORY_CONTEXT_KEY, outDir.toString());
         }
     }
 

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

@@ -17,6 +17,7 @@ package inr.numass;
 
 import hep.dataforge.actions.ActionManager;
 import hep.dataforge.context.Context;
+import hep.dataforge.context.ContextBuilder;
 import hep.dataforge.context.Global;
 import hep.dataforge.description.ActionDescriptor;
 import hep.dataforge.description.Descriptors;
@@ -31,14 +32,14 @@ import hep.dataforge.meta.Meta;
 public class Numass {
 
     public static Context buildContext(Context parent, Meta meta) {
-        return Context.Companion.builder("NUMASS", parent)
+        return new ContextBuilder("NUMASS", parent)
                 .properties(meta)
                 .plugin(NumassPlugin.class)
                 .build();
     }
 
     public static Context buildContext() {
-        return buildContext(Global.Companion.instance(), Meta.empty());
+        return buildContext(Global.INSTANCE, Meta.empty());
     }
 
     public static void printDescription(Context context) throws DescriptorException {
@@ -66,6 +67,6 @@ public class Numass {
         builder.text("***End of actions list***", "red");
 
 
-        context.getIo().getMarkupRenderer().render(builder.build());
+        context.getIo().getOutput().push(builder.build(), Meta.empty());
     }
 }

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

@@ -58,7 +58,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
 
         TreeMap<Instant, Values> index = getMonitorIndex(monitor, sourceData);
         if (index.isEmpty()) {
-            context.getChronicle(name).reportError("No monitor points found");
+            context.getHistory().getChronicle(name).reportError("No monitor points found");
             return sourceData;
         }
         double norm = 0;
@@ -129,7 +129,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
 //        }
         Table res = new ListTable(dataList);
 
-        output(context, name, stream -> NumassUtils.INSTANCE.write(stream, meta, res));
+        context.getIo().output(name, getName()).push(NumassUtils.INSTANCE.wrap(res, meta), Meta.empty());
 
         return res;
     }
@@ -194,7 +194,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
             String monitorFileName = meta.getString("monitorFile", "monitor");
             ListTable data = new ListTable(monitorPoints);
 
-            output(context, monitorFileName, stream -> NumassUtils.INSTANCE.write(stream, meta, data));
+            context.getIo().output(monitorFileName, getName()).push(NumassUtils.INSTANCE.wrap(data, meta), Meta.empty());
 //            ColumnedDataWriter.writeTable(stream, TableTransform.sort(data, "Timestamp", true), "Monitor points", monitorNames);
         }
     }

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

@@ -10,6 +10,7 @@ import hep.dataforge.context.Context;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.io.ColumnedDataReader;
 import hep.dataforge.meta.Laminate;
+import hep.dataforge.meta.Meta;
 import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.Table;
 import hep.dataforge.tables.ValueMap;
@@ -30,7 +31,7 @@ public class SubstractSpectrumAction extends OneToOneAction<Table, Table> {
     protected Table execute(Context context, String name, Table input, Laminate inputMeta) {
         try {
             String referencePath = inputMeta. getString("file", "empty.dat");
-            Path referenceFile = context.getIo().getFile(referencePath);
+            Path referenceFile = context.getIo().getRootDir().resolve(referencePath);
             Table referenceTable = new ColumnedDataReader(referenceFile).toTable();
             ListTable.Builder builder = new ListTable.Builder(input.getFormat());
             input.getRows().forEach(point -> {
@@ -47,7 +48,8 @@ public class SubstractSpectrumAction extends OneToOneAction<Table, Table> {
             });
 
             Table res = builder.build();
-            output(context,name, stream -> NumassUtils.INSTANCE.write(stream,inputMeta,res));
+
+            context.getIo().output(name, getName()).push(NumassUtils.INSTANCE.wrap(res, inputMeta), Meta.empty());
             return res;
         } catch (IOException ex) {
             throw new RuntimeException("Could not read reference file", ex);

numass-main/src/main/java/inr/numass/data/MonitorCorrector.java

@@ -1,92 +0,0 @@
-/* 
- * Copyright 2015 Alexander Nozik.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package inr.numass.data;
-
-import hep.dataforge.context.Global;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.text.ParseException;
-import java.time.LocalDateTime;
-import java.util.ArrayList;
-import java.util.List;
-
-import static java.time.temporal.ChronoUnit.SECONDS;
-
-/**
- * Заплатка для задания поправки на масс-спектрометр
- *
- * @author Darksnake
- */
-public class MonitorCorrector {
-
-    private final double average;
-    private final List<MonitorPoint> list;
-
-    public MonitorCorrector(String path) throws ParseException, IOException {
-        this(Global.Companion.instance().getIo().getFile(path));
-    }
-
-    public MonitorCorrector(Path monitorFile) throws ParseException, IOException {
-        list = new ArrayList<>();
-        
-        BufferedReader reader = new BufferedReader(Files.newBufferedReader(monitorFile));
-//        Scanner sc = new Scanner(monitorFile);
-
-        double sum = 0;
-        String str = reader.readLine();
-        while ((str!=null)&&(!str.isEmpty())) {
-            MonitorPoint point = new MonitorPoint(str);
-            str = reader.readLine();
-            list.add(point);
-            sum += point.getMonitorValue();
-        }
-        average = sum / list.size();
-    }
-
-    /**
-     * возвращает ближайшую по времени точку
-     *
-     * @param time
-     * @return
-     */
-    public MonitorPoint findNearestMonitorPoint(LocalDateTime time) {
-        MonitorPoint nearest = this.list.get(0);
-        for (MonitorPoint point : this.list) {
-            if (Math.abs(point.getTime().until(time, SECONDS)) 
-                    < Math.abs(nearest.getTime().until(time, SECONDS))) {
-                nearest = point;
-            }
-        }
-        return nearest;
-
-    }
-
-    public double getCorrection(LocalDateTime start, double length) {
-        LocalDateTime finish = start.plusSeconds((long) length);
-
-        return (findNearestMonitorPoint(start).getMonitorValue() + findNearestMonitorPoint(finish).getMonitorValue()) / 2 / average;
-    }
-
-    public double getCorrectionError(LocalDateTime start, double length) {
-        LocalDateTime finish = start.plusSeconds((long) length);
-
-        return (findNearestMonitorPoint(start).getMonitorError() + findNearestMonitorPoint(finish).getMonitorError()) / 2 / average;
-    }
-
-}

numass-main/src/main/java/inr/numass/models/TransmissionInterpolator.java

@@ -40,7 +40,7 @@ public class TransmissionInterpolator implements UnivariateFunction {
 
     public static TransmissionInterpolator fromFile(Context context, String path, String xName, String yName, int nSmooth, double w, double border) {
         try {
-            Path dataFile = context.getIo().getFile(path);
+            Path dataFile = context.getIo().getRootDir().resolve(path);
             ColumnedDataReader reader = new ColumnedDataReader(Files.newInputStream(dataFile));
             return new TransmissionInterpolator(reader, xName, yName, nSmooth, w, border);
         } catch (IOException ex) {

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

@@ -40,7 +40,7 @@ public class OldDataReader {
     public static Table readConfig(String path) throws IOException {
         String[] list = {"X", "time", "ushift"};
         ListTable.Builder res = new ListTable.Builder(list);
-        Path file = Global.Companion.instance().getIo().getFile(path);
+        Path file = Global.INSTANCE.getIo().getRootDir().resolve(path);
         Scanner sc = new Scanner(file);
         sc.nextLine();
 
@@ -62,7 +62,7 @@ public class OldDataReader {
     public static Table readData(String path, double Elow) {
         SpectrumAdapter factory = new SpectrumAdapter(Meta.empty());
         ListTable.Builder res = new ListTable.Builder(Adapters.getFormat(factory));
-        Path file = Global.Companion.instance().getIo().getFile(path);
+        Path file = Global.INSTANCE.getIo().getRootDir().resolve(path);
         double x;
         int count;
         int time;
@@ -114,7 +114,7 @@ public class OldDataReader {
     public static Table readDataAsGun(String path, double Elow) {
         SpectrumAdapter factory = new SpectrumAdapter(Meta.empty());
         ListTable.Builder res = new ListTable.Builder(Adapters.getFormat(factory));
-        Path file = Global.Companion.instance().getIo().getFile(path);
+        Path file = Global.INSTANCE.getIo().getRootDir().resolve(path);
         double x;
         long count;
         int time;
@@ -147,7 +147,7 @@ public class OldDataReader {
     public static Table readSpectrumData(String path) {
         SpectrumAdapter factory = new SpectrumAdapter(Meta.empty());
         ListTable.Builder res = new ListTable.Builder(Adapters.getFormat(factory));
-        Path file = Global.Companion.instance().getIo().getFile(path);
+        Path file = Global.INSTANCE.getIo().getRootDir().resolve(path);
         double x;
         double count;
         double time;

numass-main/src/main/kotlin/inr/numass/NumassIO.kt

@@ -1,179 +0,0 @@
-/* 
- * Copyright 2015 Alexander Nozik.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package inr.numass
-
-import ch.qos.logback.classic.LoggerContext
-import ch.qos.logback.classic.encoder.PatternLayoutEncoder
-import ch.qos.logback.classic.spi.ILoggingEvent
-import ch.qos.logback.core.Appender
-import ch.qos.logback.core.FileAppender
-import hep.dataforge.context.Context
-import hep.dataforge.context.DefaultIOManager
-import hep.dataforge.context.IOManager
-import hep.dataforge.fx.plots.plusAssign
-import hep.dataforge.meta.Meta
-import hep.dataforge.names.Name
-import hep.dataforge.plots.PlotUtils
-import hep.dataforge.plots.XYFunctionPlot
-import hep.dataforge.plots.data.DataPlot
-import hep.dataforge.stat.fit.FitResult
-import hep.dataforge.stat.models.XYModel
-import hep.dataforge.tables.Adapters
-import hep.dataforge.utils.ReferenceRegistry
-import org.apache.commons.io.output.TeeOutputStream
-import org.slf4j.LoggerFactory
-import java.io.File
-import java.io.IOException
-import java.io.OutputStream
-import java.nio.file.Files
-import java.nio.file.Path
-import java.util.*
-
-/**
- * @author Darksnake
- */
-class NumassIO : DefaultIOManager() {
-
-    internal var registry = ReferenceRegistry<OutputStream>()
-    //    FileAppender<ILoggingEvent> appender;
-
-
-    override fun attach(context: Context) {
-        super.attach(context)
-    }
-
-    override fun createLoggerAppender(): Appender<ILoggingEvent> {
-        val lc = LoggerFactory.getILoggerFactory() as LoggerContext
-        val ple = PatternLayoutEncoder()
-
-        ple.pattern = "%date %level [%thread] %logger{10} [%file:%line] %msg%n"
-        ple.context = lc
-        ple.start()
-        val appender = FileAppender<ILoggingEvent>()
-        appender.file = File(workDir.toFile(), meta.getString("logFileName", "numass.log")).toString()
-        appender.encoder = ple
-        return appender
-    }
-
-    override fun detach() {
-        super.detach()
-        registry.forEach { it ->
-            try {
-                it.close()
-            } catch (e: IOException) {
-                LoggerFactory.getLogger(javaClass).error("Failed to close output", e)
-            }
-        }
-    }
-
-    private fun getExtension(type: String): String {
-        return when (type) {
-            IOManager.DEFAULT_OUTPUT_TYPE -> ".out"
-            else -> "." + type
-        }
-    }
-
-    override fun out(stage: Name?, name: Name, type: String): OutputStream {
-        val tokens = ArrayList<String>()
-        if (context.hasValue("numass.path")) {
-            val path = context.getString("numass.path")
-            if (path.contains(".")) {
-                tokens.addAll(Arrays.asList(*path.split(".".toRegex()).dropLastWhile { it.isEmpty() }.toTypedArray()))
-            } else {
-                tokens.add(path)
-            }
-        }
-
-        if (stage != null && stage.length != 0) {
-            tokens.addAll(Arrays.asList(*stage.asArray()))
-        }
-
-        val dirName = tokens.joinToString(File.separator)
-        val fileName = name.toString() + getExtension(type)
-        val out = buildOut(workDir, dirName, fileName)
-        registry.add(out)
-        return out
-    }
-
-    private fun buildOut(parentDir: Path, dirName: String?, fileName: String): OutputStream {
-        val outputFile: Path
-
-        if (!Files.exists(parentDir)) {
-            throw RuntimeException("Working directory does not exist")
-        }
-        try {
-            val dir = if (dirName.isNullOrEmpty()) {
-                parentDir
-            } else {
-                parentDir.resolve(dirName).also {
-                    Files.createDirectories(it)
-                }
-            }
-
-            //        String output = source.meta().getString("output", this.meta().getString("output", fileName + ".onComplete"));
-            outputFile = dir.resolve(fileName)
-
-            return if (context.getBoolean("numass.consoleOutput", false)) {
-                TeeOutputStream(Files.newOutputStream(outputFile), System.out)
-            } else {
-                Files.newOutputStream(outputFile)
-            }
-        } catch (ex: IOException) {
-            throw RuntimeException(ex)
-        }
-
-    }
-
-    companion object {
-
-        val NUMASS_OUTPUT_CONTEXT_KEY = "numass.outputDir"
-    }
-}
-
-fun FitResult.display(context: Context, stage: String = "fit") {
-    val model = optModel(context).get() as XYModel
-
-    val adapter = model.adapter
-
-    val frame = PlotUtils.getPlotManager(context)
-            .getPlotFrame(stage, "plot", Meta.empty())
-
-    val func = { x: Double -> model.spectrum.value(x, parameters) }
-
-    val fit = XYFunctionPlot("fit",func)
-    fit.density = 100
-    // ensuring all data points are calculated explicitly
-    data.rows.map { dp -> Adapters.getXValue(adapter, dp).doubleValue() }.sorted().forEach { fit.calculateIn(it) }
-
-    frame.add(fit)
-
-    frame.add(DataPlot.plot("data", adapter, data))
-
-    val residualsFrame = PlotUtils.getPlotManager(context)
-            .getPlotFrame(stage, "residuals", Meta.empty())
-
-    val residual = DataPlot("residuals");
-
-    data.rows.forEach {
-        val x = Adapters.getXValue(adapter, it).doubleValue()
-        val y = Adapters.getYValue(adapter, it).doubleValue()
-        val err = Adapters.optYError(adapter,it).orElse(1.0)
-        residual += Adapters.buildXYDataPoint(x, (y - func(x)) / err, 1.0)
-    }
-
-    residualsFrame.add(residual)
-
-}

numass-main/src/main/kotlin/inr/numass/NumassPlugin.kt

@@ -41,7 +41,7 @@ import org.apache.commons.math3.util.FastMath
 @PluginDef(
         group = "inr.numass",
         name = "numass",
-        dependsOn = arrayOf("hep.dataforge:math", "hep.dataforge:MINUIT", "hep.dataforge:actions"),
+        dependsOn = arrayOf("hep.dataforge:math", "hep.dataforge:MINUIT", "hep.dataforge:actions", "hep.dataforge:io.dir"),
         support = false,
         info = "Numass data analysis tools"
 )
@@ -50,8 +50,7 @@ class NumassPlugin : BasicPlugin() {
     override fun attach(context: Context) {
         //        StorageManager.buildFrom(context);
         super.attach(context)
-        context.pluginManager.load(NumassIO())
+        loadModels(context[ModelManager::class.java])
-        loadModels(context.get(ModelManager::class.java))
         loadMath(MathPlugin.buildFrom(context))
 
         context.get(ActionManager::class.java).apply {
@@ -266,10 +265,8 @@ class NumassPlugin : BasicPlugin() {
         }
     }
 
-    class Factory : PluginFactory {
+    class Factory : PluginFactory() {
-        override fun type(): Class<out Plugin> {
+        override val type: Class<out Plugin> = NumassPlugin::class.java
-            return NumassPlugin::class.java
-        }
 
         override fun build(meta: Meta): Plugin {
             return NumassPlugin()

numass-main/src/main/kotlin/inr/numass/NumassUtils.kt

@@ -19,6 +19,7 @@ import hep.dataforge.context.Context
 import hep.dataforge.data.DataNode
 import hep.dataforge.data.DataSet
 import hep.dataforge.data.binary.Binary
+import hep.dataforge.fx.plots.plusAssign
 import hep.dataforge.io.envelopes.DefaultEnvelopeType
 import hep.dataforge.io.envelopes.Envelope
 import hep.dataforge.io.envelopes.EnvelopeBuilder
@@ -28,7 +29,13 @@ import hep.dataforge.io.markup.SimpleMarkupRenderer
 import hep.dataforge.kodex.nullable
 import hep.dataforge.meta.Meta
 import hep.dataforge.meta.MetaBuilder
+import hep.dataforge.plots.PlotUtils
+import hep.dataforge.plots.XYFunctionPlot
+import hep.dataforge.plots.data.DataPlot
 import hep.dataforge.plots.jfreechart.JFreeChartFrame
+import hep.dataforge.stat.fit.FitResult
+import hep.dataforge.stat.models.XYModel
+import hep.dataforge.tables.Adapters
 import hep.dataforge.tables.ListTable
 import hep.dataforge.tables.Table
 import hep.dataforge.tables.ValueMap
@@ -132,11 +139,11 @@ object NumassUtils {
 
     }
 
-    fun write(stream: OutputStream, meta: Meta, something: Markedup) {
+//    fun write(stream: OutputStream, meta: Meta, something: Markedup) {
-        writeEnvelope(stream, meta) { out ->
+//        writeEnvelope(stream, meta) { out ->
-            SimpleMarkupRenderer(out).render(something.markup(meta))
+//            SimpleMarkupRenderer(out).render(something.markup(meta))
-        }
+//        }
-    }
+//    }
 
     /**
      * Convert numass set to DataNode
@@ -261,4 +268,39 @@ fun Values.unbox(): Map<String, Any?> {
         res.put(field, obj)
     }
     return res
-}
+}
+
+fun FitResult.display(context: Context, stage: String = "fit") {
+    val model = optModel(context).get() as XYModel
+
+    val adapter = model.adapter
+
+    val frame = PlotUtils.getPlotManager(context)
+            .getPlotFrame(stage, "plot", Meta.empty())
+
+    val func = { x: Double -> model.spectrum.value(x, parameters) }
+
+    val fit = XYFunctionPlot("fit",func)
+    fit.density = 100
+    // ensuring all data points are calculated explicitly
+    data.rows.map { dp -> Adapters.getXValue(adapter, dp).doubleValue() }.sorted().forEach { fit.calculateIn(it) }
+
+    frame.add(fit)
+
+    frame.add(DataPlot.plot("data", adapter, data))
+
+    val residualsFrame = PlotUtils.getPlotManager(context)
+            .getPlotFrame(stage, "residuals", Meta.empty())
+
+    val residual = DataPlot("residuals");
+
+    data.rows.forEach {
+        val x = Adapters.getXValue(adapter, it).doubleValue()
+        val y = Adapters.getYValue(adapter, it).doubleValue()
+        val err = Adapters.optYError(adapter,it).orElse(1.0)
+        residual += Adapters.buildXYDataPoint(x, (y - func(x)) / err, 1.0)
+    }
+
+    residualsFrame.add(residual)
+
+}

numass-main/src/main/kotlin/inr/numass/actions/MergeDataAction.kt

@@ -28,7 +28,6 @@ import hep.dataforge.values.Values
 import inr.numass.NumassUtils
 import inr.numass.data.analyzers.NumassAnalyzer
 import inr.numass.data.api.NumassPoint
-
 import java.util.*
 
 /**
@@ -57,7 +56,8 @@ class MergeDataAction : ManyToOneAction<Table, Table>() {
     }
 
     override fun afterGroup(context: Context, groupName: String, outputMeta: Meta, output: Table) {
-        output(context, groupName) { stream -> NumassUtils.write(stream, outputMeta, output) }
+        context.io.output(groupName, name).push(NumassUtils.wrap(output, outputMeta))
+        super.afterGroup(context, groupName, outputMeta, output)
     }
 
     private fun mergeDataPoints(dp1: Values?, dp2: Values?): Values? {

numass-main/src/main/kotlin/inr/numass/actions/SummaryAction.kt

@@ -85,7 +85,7 @@ class SummaryAction : ManyToOneAction<FitState, Table>() {
                 weights[i] += weight
             }
             values[values.size - 1] = Value.of(value.chi2)
-            val point = ValueMap.of(names, *values as Array<Any>)
+            val point = ValueMap.of(names, *values)
             res.row(point)
         }
 
@@ -98,13 +98,13 @@ class SummaryAction : ManyToOneAction<FitState, Table>() {
             averageValues[2 * i + 2] = Value.of(1 / Math.sqrt(weights[i]))
         }
 
-        res.row(ValueMap.of(names, *averageValues as Array<Any>))
+        res.row(ValueMap.of(names, *averageValues))
 
         return res.build()
     }
 
     override fun afterGroup(context: Context, groupName: String, outputMeta: Meta, output: Table) {
-        output(context, groupName) { stream -> NumassUtils.write(stream, outputMeta, output) }
+        context.io.output(groupName, name).push(NumassUtils.wrap(output, outputMeta))
         super.afterGroup(context, groupName, outputMeta, output)
     }
 

numass-main/src/main/kotlin/inr/numass/actions/TransformDataAction.kt

@@ -99,7 +99,7 @@ class TransformDataAction : OneToOneAction<Table, Table>() {
         val res = table.addColumn(ListColumn.build(table.getColumn(COUNT_RATE_KEY).format, cr.stream()))
                 .addColumn(ListColumn.build(table.getColumn(COUNT_RATE_ERROR_KEY).format, crErr.stream()))
 
-        output(context, name) { stream -> NumassUtils.write(stream, meta, res) }
+        context.io.output(name, name).push(NumassUtils.wrap(res, meta))
         return res
     }
 

numass-main/src/main/kotlin/inr/numass/models/mc/BetaSampler.kt

@@ -1,5 +1,6 @@
 package inr.numass.models.mc
 
+import hep.dataforge.context.Global
 import hep.dataforge.fx.plots.FXPlotManager
 import hep.dataforge.kodex.buildMeta
 import hep.dataforge.maths.chain.Chain
@@ -34,7 +35,7 @@ fun main(args: Array<String>) {
             .setPar("X", 0.0, 0.01, 0.0, java.lang.Double.POSITIVE_INFINITY)
             .setPar("trap", 1.0, 0.01, 0.0, java.lang.Double.POSITIVE_INFINITY)
 
-    val sp = SterileNeutrinoSpectrum(global, meta)
+    val sp = SterileNeutrinoSpectrum(Global, meta)
 
     val spectrumPlot = XYFunctionPlot.plot("spectrum", 14000.0, 18600.0, 500) {
         sp.value(it, allPars)

numass-main/src/main/kotlin/inr/numass/scripts/utils/ScanTree.kt

@@ -1,8 +1,8 @@
 package inr.numass.scripts.utils
 
+import hep.dataforge.context.Global
 import hep.dataforge.io.XMLMetaWriter
 import hep.dataforge.kodex.buildMeta
-import hep.dataforge.kodex.global
 import hep.dataforge.kodex.useValue
 import hep.dataforge.meta.Meta
 import hep.dataforge.meta.MetaBuilder
@@ -14,7 +14,7 @@ import java.io.File
 import java.nio.file.Paths
 
 private fun createSummaryNode(storage: Storage): MetaBuilder {
-    global.logger.info("Reading content of shelf {}", storage.fullName)
+    Global.logger.info("Reading content of shelf {}", storage.fullName)
 
     val builder = MetaBuilder("shelf")
             .setValue("name", storage.name)
@@ -24,7 +24,7 @@ private fun createSummaryNode(storage: Storage): MetaBuilder {
     }
     storage.loaders().filterIsInstance(NumassDataLoader::class.java).forEach { set ->
 
-        global.logger.info("Reading content of set {}", set.fullName)
+        Global.logger.info("Reading content of set {}", set.fullName)
 
         val setBuilder = MetaBuilder("set")
                 .setValue("name", set.name)
@@ -83,14 +83,14 @@ fun main(args: Array<String>) {
     output.createNewFile()
 
 
-    val storage = NumassStorageFactory.buildLocal(global, path, true, false)
+    val storage = NumassStorageFactory.buildLocal(Global, path, true, false)
     val summary = createSummaryNode(storage)
 
-    global.logger.info("Writing output meta")
+    Global.logger.info("Writing output meta")
     output.outputStream().use {
         XMLMetaWriter().write(it, summary)
     }
-    global.logger.info("Calculating statistics")
+    Global.logger.info("Calculating statistics")
     val statistics = MetaBuilder("statistics")
     (14000..18600).step(100).map { it.toDouble() }.forEach {
         statistics.putNode(calculateStatistics(summary, it))

numass-main/src/main/kotlin/inr/numass/tasks/NumassFitScanSummaryTask.kt

@@ -69,7 +69,7 @@ class NumassFitScanSummaryTask : AbstractTask<Table>() {
                         pars.getValue("trap"))
             }
             val res = TableTransform.sort(builder.build(), "m", true)
-            output(context, nodeName) { stream -> NumassUtils.write(stream, meta, res) }
+            context.io.output(nodeName, stage = name).push(NumassUtils.wrap(res, meta))
             return res
         }
 

numass-main/src/main/kotlin/inr/numass/tasks/NumassTasks.kt

@@ -80,20 +80,17 @@ val monitorTableTask = task("monitor") {
                     }
                     plots + DataPlot.plot(name, Adapters.buildXYAdapter("timestamp", "cr", "crErr"), res)
                 }.also { frame ->
-                    if (frame is JFreeChartFrame) {
+                            if (frame is JFreeChartFrame) {
-                        //add set markers
+                                //add set markers
-                        addSetMarkers(frame, data.values)
+                                addSetMarkers(frame, data.values)
-                    }
+                            }
-                    context.io.out("numass.monitor", name, "dfp").use {
+                            context.io.output(name, stage = "numass.monitor", type = "dfp").push(PlotFrame.Wrapper().wrap(frame))
-                        NumassUtils.writeEnvelope(it, PlotFrame.Wrapper().wrap(frame))
+
-                    }
+                        }
-                }
             }
         }
 
-        context.io.out("numass.monitor", name).use {
+        context.io.output(name, stage = "numass.monitor").push(NumassUtils.wrap(res, meta))
-            NumassUtils.write(it, meta, res)
-        }
 
         return@join res;
     }
@@ -107,9 +104,7 @@ val analyzeTask = task("analyze") {
     pipe<NumassSet, Table> { set ->
         SmartAnalyzer().analyzeSet(set, meta).also { res ->
             val outputMeta = meta.builder.putNode("data", set.meta)
-            context.io.out("numass.analyze", name).use {
+            context.io.output(name, stage = "numass.analyze").push(NumassUtils.wrap(res, outputMeta))
-                NumassUtils.write(it, outputMeta, res)
-            }
         }
     }
 }
@@ -175,9 +170,7 @@ val subtractEmptyTask = task("dif") {
 
             res.goal.onComplete { r, _ ->
                 if (r != null) {
-                    context.io.out("numass.merge", input.name + "_subtract").use {
+                    context.io.output(input.name + "_subtract", stage = "numass.merge").push(NumassUtils.wrap(r,resMeta))
-                        NumassUtils.write(it, resMeta, r)
-                    }
                 }
             }
 
@@ -228,7 +221,7 @@ val fitTask = task("fit") {
         configure(meta.getMeta("fit"))
     }
     pipe<Table, FitResult> { data ->
-        context.io.out("numass.fit", name).use { out ->
+        context.io.stream(name, "numass.fit").use { out ->
             val writer = PrintWriter(out)
             writer.printf("%n*** META ***%n")
             writer.println(meta.toString())

numass-main/src/test/java/inr/numass/models/TransmissionInterpolatorTest.java

@@ -30,7 +30,7 @@ public class TransmissionInterpolatorTest {
     public static void main(String[] args) {
         JFreeChartFrame frame = NumassPluginKt.displayJFreeChart("TransmissionInterpolatorTest");
 //JFreeChartFrame.drawFrame("TransmissionInterpolatorTest", null);
-        TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(Global.Companion.instance(),
+        TransmissionInterpolator interpolator = TransmissionInterpolator.fromFile(Global.INSTANCE,
                 "d:\\sterile-new\\loss2014-11\\.dataforge\\merge\\empty_sum.onComplete", "Uset", "CR", 15, 0.8, 19002d);
         frame.add(DataPlot.plot("data", interpolator.getX(), interpolator.getY()));
         frame.add(XYFunctionPlot.Companion.plot("interpolated", interpolator.getXmin(), interpolator.getXmax(), 2000, interpolator::value));