A lot of minor fixes. Moving some code to kotlin

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

@@ -10,7 +10,6 @@ import hep.dataforge.storage.commons.StorageManager;
 import hep.dataforge.storage.filestorage.FileStorage;
 import org.jetbrains.annotations.NotNull;
 
-import java.io.File;
 import java.net.URI;
 import java.nio.file.FileSystem;
 import java.nio.file.FileSystems;
@@ -29,9 +28,15 @@ public class NumassStorageFactory implements StorageType {
      * @return
      */
     @NotNull
-    public static FileStorage buildLocal(Context context, File file, boolean readOnly, boolean monitor) {
+    public static FileStorage buildLocal(Context context, Path file, boolean readOnly, boolean monitor) {
         StorageManager manager = context.loadFeature("hep.dataforge:storage", StorageManager.class);
-        return (FileStorage) manager.buildStorage(buildStorageMeta(file.toURI(),readOnly,monitor));
+        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);
+        return buildLocal(context, file, readOnly, monitor);
     }
 
     @Override

numass-core/src/main/kotlin/inr/numass/data/analyzers/NumassAnalyzer.kt

@@ -116,7 +116,7 @@ interface NumassAnalyzer {
 
         val DEFAULT_ANALYZER: NumassAnalyzer = SmartAnalyzer()
 
-        val ADAPTER: ValuesAdapter = Adapters.buildXYAdapter(CHANNEL_KEY, COUNT_RATE_KEY)
+        val AMPLITUDE_ADAPTER: ValuesAdapter = Adapters.buildXYAdapter(CHANNEL_KEY, COUNT_RATE_KEY)
 
 //        val MAX_CHANNEL = 10000
 
@@ -131,7 +131,7 @@ interface NumassAnalyzer {
          * @param sp2
          * @return
          */
-        fun subtractSpectrum(sp1: Table, sp2: Table): Table {
+        fun subtractAmplitudeSpectrum(sp1: Table, sp2: Table): Table {
             val format = TableFormatBuilder()
                     .addNumber(CHANNEL_KEY, X_VALUE_KEY)
                     .addNumber(COUNT_RATE_KEY, Y_VALUE_KEY)
@@ -144,7 +144,8 @@ interface NumassAnalyzer {
                 val channel = row1.getDouble(CHANNEL_KEY)
                 val row2 = sp2.rows.asSequence().find { it.getDouble(CHANNEL_KEY) == channel }   //t2[channel]
                 if (row2 == null) {
-                    builder.row(row1)
+                    throw RuntimeException("Reference for channel $channel not found");
+
                 } else {
                     val value = Math.max(row1.getDouble(COUNT_RATE_KEY) - row2.getDouble(COUNT_RATE_KEY), 0.0)
                     val error1 = row1.getDouble(COUNT_RATE_ERROR_KEY)

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

@@ -40,6 +40,7 @@ import inr.numass.utils.ExpressionUtils
 import org.apache.commons.math3.analysis.UnivariateFunction
 import org.jfree.chart.plot.IntervalMarker
 import org.jfree.chart.ui.RectangleInsets
+import org.slf4j.Logger
 import tornadofx.*
 import java.awt.Color
 import java.awt.Font
@@ -220,24 +221,24 @@ fun addSetMarkers(frame: JFreeChartFrame, sets: Collection<NumassSet>) {
 }
 
 /**
- * Subtract one energy spectrum from the other one
+ * Subtract one U spectrum from the other one
  */
-fun subtractAmplitudeSpectrum(context: Context, merge: Table, empty: Table): Table {
+fun subtractSpectrum(merge: Table, empty: Table, logger: Logger? = null): Table {
     val builder = ListTable.Builder(merge.format)
     merge.rows.forEach { point ->
         val pointBuilder = ValueMap.Builder(point)
         val referencePoint = empty.rows
-                .filter { p -> Math.abs(p.getDouble(NumassPoint.HV_KEY)!! - point.getDouble(NumassPoint.HV_KEY)!!) < 0.1 }.findFirst()
+                .filter { p -> Math.abs(p.getDouble(NumassPoint.HV_KEY) - point.getDouble(NumassPoint.HV_KEY)) < 0.1 }.findFirst()
         if (referencePoint.isPresent) {
             pointBuilder.putValue(
                     NumassAnalyzer.COUNT_RATE_KEY,
-                    Math.max(0.0, point.getDouble(NumassAnalyzer.COUNT_RATE_KEY)!! - referencePoint.get().getDouble(NumassAnalyzer.COUNT_RATE_KEY)!!)
+                    Math.max(0.0, point.getDouble(NumassAnalyzer.COUNT_RATE_KEY) - referencePoint.get().getDouble(NumassAnalyzer.COUNT_RATE_KEY))
             )
             pointBuilder.putValue(
                     NumassAnalyzer.COUNT_RATE_ERROR_KEY,
-                    Math.sqrt(Math.pow(point.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY)!!, 2.0) + Math.pow(referencePoint.get().getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY)!!, 2.0)))
+                    Math.sqrt(Math.pow(point.getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY), 2.0) + Math.pow(referencePoint.get().getDouble(NumassAnalyzer.COUNT_RATE_ERROR_KEY), 2.0)))
         } else {
-            context.logger.warn("No reference point found for voltage = {}", point.getDouble(NumassPoint.HV_KEY))
+            logger?.warn("No reference point found for voltage = {}", point.getDouble(NumassPoint.HV_KEY))
         }
         builder.row(pointBuilder.build())
     }

numass-main/src/main/kotlin/inr/numass/scripts/DifferentialSpectrum.kt

@@ -0,0 +1,83 @@
+/*
+ * Copyright  2017 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.scripts
+
+import hep.dataforge.fx.plots.PlotManager
+import hep.dataforge.kodex.buildContext
+import hep.dataforge.kodex.buildMeta
+import hep.dataforge.kodex.replaceColumn
+import hep.dataforge.plots.data.DataPlot
+import inr.numass.NumassPlugin
+import inr.numass.data.NumassDataUtils
+import inr.numass.data.analyzers.NumassAnalyzer
+import inr.numass.data.analyzers.SmartAnalyzer
+import inr.numass.data.api.NumassSet
+import inr.numass.data.storage.NumassStorageFactory
+
+fun main(args: Array<String>) {
+
+    val context = buildContext("NUMASS", NumassPlugin::class.java, PlotManager::class.java) {
+        rootDir = "D:\\Work\\Numass\\sterile2017_05"
+        dataDir = "D:\\Work\\Numass\\data\\2017_05"
+    }
+    //val rootDir = File("D:\\Work\\Numass\\data\\2017_05\\Fill_2")
+
+    val storage = NumassStorageFactory.buildLocal(context, "Fill_2", true, false);
+
+    val sets = (2..14).map { "set_$it" }
+
+    val loaders = sets.mapNotNull { set ->
+        storage.provide("loader::$set", NumassSet::class.java).orElse(null)
+    }
+
+    val analyzer = SmartAnalyzer()
+
+    val all = NumassDataUtils.join("sum", loaders)
+
+
+    val meta = buildMeta {
+        "window.lo" to 400
+        "window.up" to 1800
+    }
+
+    val plots = context.getFeature(PlotManager::class.java)
+
+    val frame = plots.getPlotFrame("differential")
+
+    val integralFrame = plots.getPlotFrame("integral")
+
+    for (hv in arrayOf(14000.0, 14200.0, 14400.0, 14600.0, 14800.0, 15000.0)) {
+        val point1 = all.optPoint(hv).get()
+
+        val point0 = all.optPoint(hv + 200.0).get()
+
+        with(NumassAnalyzer) {
+
+            val spectrum1 = analyzer.getSpectrum(point1, meta).withBinning(20)
+
+            val spectrum0 = analyzer.getSpectrum(point0, meta).withBinning(20)
+
+            val res = subtractAmplitudeSpectrum(spectrum1, spectrum0)
+
+            val norm = res.getColumn(COUNT_RATE_KEY).stream().mapToDouble { it.doubleValue() }.sum()
+
+            integralFrame.add(DataPlot.plot("point_$hv", AMPLITUDE_ADAPTER, spectrum0))
+
+            frame.add(DataPlot.plot("point_$hv", AMPLITUDE_ADAPTER, res.replaceColumn(COUNT_RATE_KEY) { getDouble(COUNT_RATE_KEY) / norm }))
+        }
+    }
+}

numass-main/src/main/kotlin/inr/numass/scripts/InversedChain.kt

@@ -30,16 +30,17 @@ import inr.numass.data.analyzers.TimeAnalyzer
 import inr.numass.data.analyzers.getSpectrum
 import inr.numass.data.api.NumassSet
 import inr.numass.data.storage.NumassStorageFactory
-import java.io.File
 import kotlin.streams.asSequence
 
 
 fun main(args: Array<String>) {
 
-    val context = buildContext("NUMASS", NumassPlugin::class.java, PlotManager::class.java)
+    val context = buildContext("NUMASS", NumassPlugin::class.java, PlotManager::class.java){
-    val rootDir = File("D:\\Work\\Numass\\data\\2017_05\\Fill_2")
+        rootDir = "D:\\Work\\Numass\\sterile2017_05"
+    }
+    //val rootDir = File("D:\\Work\\Numass\\data\\2017_05\\Fill_2")
 
-    val storage = NumassStorageFactory.buildLocal(context, rootDir, true, false);
+    val storage = NumassStorageFactory.buildLocal(context, "D:\\Work\\Numass\\data\\2017_05\\Fill_2", true, false);
 
     val sets = (2..14).map { "set_$it" }
 
@@ -99,9 +100,9 @@ fun main(args: Array<String>) {
 
 
         plots.getPlotFrame("amps").apply {
-            add(DataPlot.plot("events", ADAPTER, events.replaceColumn(COUNT_RATE_KEY){getDouble(COUNT_RATE_KEY)/eventsNorming}))
+            add(DataPlot.plot("events", AMPLITUDE_ADAPTER, events.replaceColumn(COUNT_RATE_KEY){getDouble(COUNT_RATE_KEY)/eventsNorming}))
-            add(DataPlot.plot("filtered", ADAPTER, filtered.replaceColumn(COUNT_RATE_KEY){getDouble(COUNT_RATE_KEY)/filteredNorming}))
+            add(DataPlot.plot("filtered", AMPLITUDE_ADAPTER, filtered.replaceColumn(COUNT_RATE_KEY){getDouble(COUNT_RATE_KEY)/filteredNorming}))
-            add(DataPlot.plot("defaultFiltered", ADAPTER, defaultFiltered.replaceColumn(COUNT_RATE_KEY){getDouble(COUNT_RATE_KEY)/defaultFilteredNorming}))
+            add(DataPlot.plot("defaultFiltered", AMPLITUDE_ADAPTER, defaultFiltered.replaceColumn(COUNT_RATE_KEY){getDouble(COUNT_RATE_KEY)/defaultFilteredNorming}))
         }
 
 //        plots.getPlotFrame("ratio").apply {

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

@@ -31,7 +31,7 @@ import inr.numass.addSetMarkers
 import inr.numass.data.analyzers.SmartAnalyzer
 import inr.numass.data.api.NumassPoint
 import inr.numass.data.api.NumassSet
-import inr.numass.subtractAmplitudeSpectrum
+import inr.numass.subtractSpectrum
 import inr.numass.unbox
 import inr.numass.utils.ExpressionUtils
 import java.io.PrintWriter
@@ -170,7 +170,7 @@ val subtractEmptyTask = task("dif") {
                 node("empty", empty.meta)
             }
             val res = DataUtils.combine(input, empty, Table::class.java, resMeta) { mergeData, emptyData ->
-                subtractAmplitudeSpectrum(context, mergeData, emptyData)
+                subtractSpectrum(mergeData, emptyData, context.logger)
             }
 
             res.goal.onComplete { r, _ ->