Minor fixes

numass-core/build.gradle

@@ -14,10 +14,11 @@ description = "A bse package with minimal dependencies for numass"
 
 dependencies {
     compile "hep.dataforge:dataforge-storage" //project(':dataforge-storage')
+    compile "hep.dataforge:kodex"
     compile 'com.google.protobuf:protobuf-java:3.5.0'
 
     // https://mvnrepository.com/artifact/com.github.robtimus/sftp-fs
-    compile group: 'com.github.robtimus', name: 'sftp-fs', version: '1.1.1'
+    compile group: 'com.github.robtimus', name: 'sftp-fs', version: '1.1.3'
 }
 
 protobuf {

numass-main/build.gradle

@@ -74,3 +74,9 @@ task underflow(dependsOn: classes, type: JavaExec) {
     classpath = sourceSets.main.runtimeClasspath
 }
 
+task scanTreeStartScript(type: CreateStartScripts, dependsOn: installDist) {
+    applicationName = 'scanTree'
+    classpath = fileTree('build/install/numass-main/lib')
+    mainClassName = 'inr.numass.scripts.ScanTreeKt'
+    outputDir = file('build/install/numass-main/bin')
+}

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

@@ -21,7 +21,7 @@ import inr.numass.data.api.NumassPoint
 @ValueDefs(
         ValueDef(name = "normalize", type = arrayOf(ValueType.BOOLEAN), def = "true", info = "Normalize t0 dependencies"),
         ValueDef(name = "t0", type = arrayOf(ValueType.NUMBER), def = "30e3", info = "The default t0 in nanoseconds"),
-        ValueDef(name = "window.lo", type = arrayOf(ValueType.NUMBER), def = "500", info = "Lower boundary for amplitude window"),
+        ValueDef(name = "window.lo", type = arrayOf(ValueType.NUMBER), def = "0", info = "Lower boundary for amplitude window"),
         ValueDef(name = "window.up", type = arrayOf(ValueType.NUMBER), def = "10000", info = "Upper boundary for amplitude window"),
         ValueDef(name = "binNum", type = arrayOf(ValueType.NUMBER), def = "1000", info = "Number of bins for time histogram"),
         ValueDef(name = "binSize", type = arrayOf(ValueType.NUMBER), info = "Size of bin for time histogram. By default is defined automatically")
@@ -39,8 +39,8 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
 
 
         //val t0 = inputMeta.getDouble("t0", 30e3);
-        val loChannel = inputMeta.getInt("window.lo", 500);
+//        val loChannel = inputMeta.getInt("window.lo", 500);
-        val upChannel = inputMeta.getInt("window.up", 10000);
+//        val upChannel = inputMeta.getInt("window.up", 10000);
         val pm = context.getFeature(PlotPlugin::class.java);
 
 
@@ -101,7 +101,7 @@ class TimeAnalyzerAction : OneToOneAction<NumassPoint, Table>() {
 
             pm.getPlotFrame(getName(), "stat-method").add(statPlot)
 
-            (1..100).map { 1000 * it }.map { t ->
+            (1..100).map { inputMeta.getDouble("t0Step", 1000.0) * it }.map { t ->
                 val result = analyzer.analyze(input, inputMeta.builder.setValue("t0", t))
 
 

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

@@ -1,8 +1,8 @@
 package inr.numass.scripts
 
+import hep.dataforge.fx.plots.PlotManager
 import hep.dataforge.kodex.buildMeta
-import inr.numass.data.analyzers.NumassAnalyzer
+import inr.numass.actions.TimeAnalyzerAction
-import inr.numass.data.analyzers.SmartAnalyzer
 import inr.numass.data.api.SimpleNumassPoint
 import inr.numass.data.buildBunchChain
 import inr.numass.data.buildSimpleEventChain
@@ -12,13 +12,15 @@ import java.time.Instant
 
 fun main(args: Array<String>) {
 
+    PlotManager().startGlobal()
+
     val cr = 10.0
     val length = 1e12.toLong()
-    val num = 20;
+    val num = 60;
 
     val blocks = (1..num).map {
         val regularChain = buildSimpleEventChain(cr)
-        val bunchChain = buildBunchChain(20.0, 0.01, 5.0)
+        val bunchChain = buildBunchChain(40.0, 0.01, 5.0)
 
         val generator = mergeEventChains(regularChain, bunchChain)
         generateBlock(Instant.now().plusNanos(it * length), length, generator)
@@ -27,14 +29,19 @@ fun main(args: Array<String>) {
     val point = SimpleNumassPoint(10000.0, blocks)
 
     val meta = buildMeta {
-        "t0.crFraction" to 0.1
+        "t0" to 1e7
+        "t0Step" to 4e6
+        "normalize" to false
+        "t0.crFraction" to 0.5
     }
 
     println("actual count rate: ${point.events.count().toDouble() / point.length.seconds}")
 
-    val res = SmartAnalyzer().analyze(point, meta)
+    TimeAnalyzerAction().simpleRun(point,meta)
-            .getDouble(NumassAnalyzer.COUNT_RATE_KEY)
 
-    println("estimated count rate: $res")
+//    val res = SmartAnalyzer().analyze(point, meta)
+//            .getDouble(NumassAnalyzer.COUNT_RATE_KEY)
+//
+//    println("estimated count rate: $res")
 
 }

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

@@ -0,0 +1,103 @@
+package inr.numass.scripts
+
+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
+import hep.dataforge.meta.MetaUtils
+import hep.dataforge.storage.api.Storage
+import inr.numass.data.storage.NumassDataLoader
+import inr.numass.data.storage.NumassStorageFactory
+import java.io.File
+import java.nio.file.Paths
+
+private fun createSummaryNode(storage: Storage): MetaBuilder {
+    global.logger.info("Reading content of shelf {}", storage.fullName)
+
+    val builder = MetaBuilder("shelf")
+            .setValue("name", storage.name)
+            .setValue("path", storage.fullName)
+    storage.shelves().filter { it.name.startsWith("Fill") }.forEach {
+        builder.putNode(createSummaryNode(it))
+    }
+    storage.loaders().filterIsInstance(NumassDataLoader::class.java).forEach { set ->
+
+        global.logger.info("Reading content of set {}", set.fullName)
+
+        val setBuilder = MetaBuilder("set")
+                .setValue("name", set.name)
+                .setValue("path", set.fullName)
+
+        if (set.name.endsWith("bad")) {
+            setBuilder.setValue("bad", true)
+        }
+
+        set.points.forEach { point ->
+            val pointBuilder = MetaBuilder("point")
+                    .setValue("index", point.index)
+                    .setValue("hv", point.voltage)
+                    .setValue("startTime", point.startTime)
+//                    .setNode("meta", point.meta)
+
+            point.meta.useValue("acquisition_time") {
+                pointBuilder.setValue("length", it.doubleValue())
+            }
+
+            point.meta.useValue("events") {
+                pointBuilder.setValue("count", it.listValue().stream().mapToInt { it.intValue() }.sum())
+            }
+
+            setBuilder.putNode(pointBuilder)
+        }
+        builder.putNode(setBuilder)
+    }
+    return builder
+}
+
+fun calculateStatistics(summary: Meta, hv: Double): Meta {
+    var totalLength = 0.0
+    var totalCount = 0L
+    MetaUtils.nodeStream(summary).map { it.value }.filter { it.name == "point" && it.getDouble("hv") == hv }.forEach {
+        totalCount += it.getInt("count")
+        totalLength += it.getDouble("length")
+    }
+    return buildMeta("point") {
+        "hv" to hv
+        "time" to totalLength
+        "count" to totalCount
+    }
+}
+
+fun main(args: Array<String>) {
+    val directory = if (args.isNotEmpty()) {
+        args.first()
+    } else {
+        "."
+    }
+
+    val path = Paths.get(directory)
+
+    val output = File(directory, "summary.xml")
+    output.createNewFile()
+
+
+    val storage = NumassStorageFactory.buildLocal(global, path, true, false)
+    val summary = createSummaryNode(storage)
+
+    global.logger.info("Writing output meta")
+    output.outputStream().use {
+        XMLMetaWriter().write(it, summary)
+    }
+    global.logger.info("Calculating statistics")
+    val statistics = MetaBuilder("statistics")
+    (14000..18600).step(100).map { it.toDouble() }.forEach {
+        statistics.putNode(calculateStatistics(summary, it))
+    }
+
+    File(directory, "statistics.xml").outputStream().use {
+        XMLMetaWriter().write(it, statistics)
+    }
+
+}

numass-server/build.gradle

@@ -6,7 +6,7 @@ buildscript {
     }
     dependencies {
         classpath 'io.ratpack:ratpack-gradle:1.4.6'
-        classpath 'com.github.jengelman.gradle.plugins:shadow:1.2.3'
+        classpath 'com.github.jengelman.gradle.plugins:shadow:2.+'
     }
 }