add cli parser to fit.kt

# Conflicts:
#	numass-data-proto/src/gen/kotlin/ru/inr/mass/data/proto/Point.kt
#	numass-workspace/src/main/kotlin/ru/inr/mass/scripts/fit.kt

build.gradle.kts

@@ -1,3 +1,6 @@
+import space.kscience.gradle.useApache2Licence
+import space.kscience.gradle.useSPCTeam
+
 plugins {
     id("space.kscience.gradle.project")
 }
@@ -10,17 +13,21 @@ allprojects {
     }
 
     group = "ru.inr.mass"
-    version = "0.1.3"
+    version = "0.1.4-dev-2"
 }
 
-val dataforgeVersion by extra("0.6.0-dev-15")
+val dataforgeVersion by extra("0.6.2")
 val tablesVersion: String by extra("0.2.0-dev-3")
-val kmathVersion by extra("0.3.1-dev-6")
+val kmathVersion by extra("0.3.1")
-val visionForgeVersion: String by rootProject.extra("0.3.0-dev-4")
+val visionForgeVersion: String by rootProject.extra("0.3.0-dev-6")
 
 
 ksciencePublish {
-    space("https://maven.pkg.jetbrains.space/mipt-npm/p/numass/maven")
+    pom("https://spc.jetbrains.space/p/numass/repositories/numass/") {
+        useApache2Licence()
+        useSPCTeam()
+    }
+    space("https://maven.pkg.jetbrains.space/spc/p/numass/maven")
 }
 
 apiValidation {

gradle.properties

@@ -5,11 +5,11 @@
 
 kotlin.code.style=official
 kotlin.mpp.stability.nowarn=true
-
+kotlin.js.compiler=ir
-kotlin.jupyter.add.scanner=false
 
 org.gradle.configureondemand=true
 org.gradle.parallel=true
 org.gradle.jvmargs=-XX:MaxMetaspaceSize=1G
 
-toolsVersion=0.13.3-kotlin-1.7.20
+toolsVersion=0.14.10-kotlin-1.9.0
+compose.version=1.5.1

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

numass-analysis/build.gradle.kts

@@ -8,7 +8,9 @@ val dataforgeVersion: String by rootProject.extra
 val kmathVersion: String by rootProject.extra
 val tablesVersion: String by rootProject.extra
 
-kotlin.sourceSets {
+kscience {
+    jvm()
+    js()
     commonMain {
         dependencies {
             api(projects.numass.numassDataModel)
@@ -20,7 +22,7 @@ kotlin.sourceSets {
         }
     }
 }
-
+//
 //kscience{
 //    useAtomic()
 //}

numass-data-model/build.gradle.kts

@@ -6,7 +6,11 @@ plugins {
 
 val dataforgeVersion: String by rootProject.extra
 
-kotlin.sourceSets {
+kscience{
+    jvm()
+    js()
+    useSerialization()
+
     commonMain {
         dependencies {
             api("space.kscience:dataforge-context:$dataforgeVersion")
@@ -14,15 +18,14 @@ kotlin.sourceSets {
             api("org.jetbrains.kotlinx:kotlinx-datetime:${space.kscience.gradle.KScienceVersions.dateTimeVersion}")
         }
     }
-    jvmMain{
+}
+
+kotlin.sourceSets{
+    getByName("jvmMain"){
         dependencies{
             api("ch.qos.logback:logback-classic:1.2.3")
         }
     }
 }
 
-kscience{
-    useSerialization()
-}
-
 

numass-data-proto/build.gradle.kts

@@ -1,6 +1,6 @@
 plugins {
     id("space.kscience.gradle.jvm")
-    id("com.squareup.wire") version "4.4.1"
+    id("com.squareup.wire") version "4.9.1"
     `maven-publish`
 }
 

numass-data-proto/src/gen/kotlin/ru/inr/mass/data/proto/Point.kt

@@ -2,10 +2,27 @@
 // Source: ru.inr.mass.data.proto.Point in numass-proto.proto
 package ru.inr.mass.`data`.proto
 
-import com.squareup.wire.*
+import com.squareup.wire.FieldEncoding
+import com.squareup.wire.Message
+import com.squareup.wire.ProtoAdapter
+import com.squareup.wire.ProtoReader
+import com.squareup.wire.ProtoWriter
+import com.squareup.wire.ReverseProtoWriter
 import com.squareup.wire.Syntax.PROTO_3
-import com.squareup.wire.internal.immutableCopyOf
+import com.squareup.wire.WireField
-import com.squareup.wire.internal.redactElements
+import com.squareup.wire.`internal`.JvmField
+import com.squareup.wire.`internal`.immutableCopyOf
+import com.squareup.wire.`internal`.redactElements
+import kotlin.Any
+import kotlin.AssertionError
+import kotlin.Boolean
+import kotlin.Deprecated
+import kotlin.DeprecationLevel
+import kotlin.Int
+import kotlin.Long
+import kotlin.Nothing
+import kotlin.String
+import kotlin.collections.List
 import okio.ByteString
 
 public class Point(
@@ -19,6 +36,7 @@ public class Point(
     tag = 1,
     adapter = "ru.inr.mass.data.proto.Point${'$'}Channel#ADAPTER",
     label = WireField.Label.REPEATED,
+    schemaIndex = 0,
   )
   public val channels: List<Channel> = immutableCopyOf("channels", channels)
 
@@ -26,10 +44,10 @@ public class Point(
     message = "Shouldn't be used in Kotlin",
     level = DeprecationLevel.HIDDEN,
   )
-  public override fun newBuilder(): Nothing = throw
+  override fun newBuilder(): Nothing = throw
       AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-  public override fun equals(other: Any?): Boolean {
+  override fun equals(other: Any?): Boolean {
     if (other === this) return true
     if (other !is Point) return false
     if (unknownFields != other.unknownFields) return false
@@ -37,7 +55,7 @@ public class Point(
     return true
   }
 
-  public override fun hashCode(): Int {
+  override fun hashCode(): Int {
     var result = super.hashCode
     if (result == 0) {
       result = unknownFields.hashCode()
@@ -47,7 +65,7 @@ public class Point(
     return result
   }
 
-  public override fun toString(): String {
+  override fun toString(): String {
     val result = mutableListOf<String>()
     if (channels.isNotEmpty()) result += """channels=$channels"""
     return result.joinToString(prefix = "Point{", separator = ", ", postfix = "}")
@@ -66,23 +84,23 @@ public class Point(
       null, 
       "numass-proto.proto"
     ) {
-      public override fun encodedSize(`value`: Point): Int {
+      override fun encodedSize(`value`: Point): Int {
         var size = value.unknownFields.size
         size += Channel.ADAPTER.asRepeated().encodedSizeWithTag(1, value.channels)
         return size
       }
 
-      public override fun encode(writer: ProtoWriter, `value`: Point): Unit {
+      override fun encode(writer: ProtoWriter, `value`: Point) {
         Channel.ADAPTER.asRepeated().encodeWithTag(writer, 1, value.channels)
         writer.writeBytes(value.unknownFields)
       }
 
-      public override fun encode(writer: ReverseProtoWriter, `value`: Point): Unit {
+      override fun encode(writer: ReverseProtoWriter, `value`: Point) {
         writer.writeBytes(value.unknownFields)
         Channel.ADAPTER.asRepeated().encodeWithTag(writer, 1, value.channels)
       }
 
-      public override fun decode(reader: ProtoReader): Point {
+      override fun decode(reader: ProtoReader): Point {
         val channels = mutableListOf<Channel>()
         val unknownFields = reader.forEachTag { tag ->
           when (tag) {
@@ -96,7 +114,7 @@ public class Point(
         )
       }
 
-      public override fun redact(`value`: Point): Point = value.copy(
+      override fun redact(`value`: Point): Point = value.copy(
         channels = value.channels.redactElements(Channel.ADAPTER),
         unknownFields = ByteString.EMPTY
       )
@@ -116,6 +134,7 @@ public class Point(
       tag = 1,
       adapter = "com.squareup.wire.ProtoAdapter#UINT64",
       label = WireField.Label.OMIT_IDENTITY,
+      schemaIndex = 0,
     )
     public val id: Long = 0L,
     blocks: List<Block> = emptyList(),
@@ -128,6 +147,7 @@ public class Point(
       tag = 2,
       adapter = "ru.inr.mass.data.proto.Point${'$'}Channel${'$'}Block#ADAPTER",
       label = WireField.Label.REPEATED,
+      schemaIndex = 1,
     )
     public val blocks: List<Block> = immutableCopyOf("blocks", blocks)
 
@@ -135,10 +155,10 @@ public class Point(
       message = "Shouldn't be used in Kotlin",
       level = DeprecationLevel.HIDDEN,
     )
-    public override fun newBuilder(): Nothing = throw
+    override fun newBuilder(): Nothing = throw
         AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-    public override fun equals(other: Any?): Boolean {
+    override fun equals(other: Any?): Boolean {
       if (other === this) return true
       if (other !is Channel) return false
       if (unknownFields != other.unknownFields) return false
@@ -147,7 +167,7 @@ public class Point(
       return true
     }
 
-    public override fun hashCode(): Int {
+    override fun hashCode(): Int {
       var result = super.hashCode
       if (result == 0) {
         result = unknownFields.hashCode()
@@ -158,7 +178,7 @@ public class Point(
       return result
     }
 
-    public override fun toString(): String {
+    override fun toString(): String {
       val result = mutableListOf<String>()
       result += """id=$id"""
       if (blocks.isNotEmpty()) result += """blocks=$blocks"""
@@ -181,26 +201,26 @@ public class Point(
         null, 
         "numass-proto.proto"
       ) {
-        public override fun encodedSize(`value`: Channel): Int {
+        override fun encodedSize(`value`: Channel): Int {
           var size = value.unknownFields.size
           if (value.id != 0L) size += ProtoAdapter.UINT64.encodedSizeWithTag(1, value.id)
           size += Block.ADAPTER.asRepeated().encodedSizeWithTag(2, value.blocks)
           return size
         }
 
-        public override fun encode(writer: ProtoWriter, `value`: Channel): Unit {
+        override fun encode(writer: ProtoWriter, `value`: Channel) {
           if (value.id != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.id)
           Block.ADAPTER.asRepeated().encodeWithTag(writer, 2, value.blocks)
           writer.writeBytes(value.unknownFields)
         }
 
-        public override fun encode(writer: ReverseProtoWriter, `value`: Channel): Unit {
+        override fun encode(writer: ReverseProtoWriter, `value`: Channel) {
           writer.writeBytes(value.unknownFields)
           Block.ADAPTER.asRepeated().encodeWithTag(writer, 2, value.blocks)
           if (value.id != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.id)
         }
 
-        public override fun decode(reader: ProtoReader): Channel {
+        override fun decode(reader: ProtoReader): Channel {
           var id: Long = 0L
           val blocks = mutableListOf<Block>()
           val unknownFields = reader.forEachTag { tag ->
@@ -217,7 +237,7 @@ public class Point(
           )
         }
 
-        public override fun redact(`value`: Channel): Channel = value.copy(
+        override fun redact(`value`: Channel): Channel = value.copy(
           blocks = value.blocks.redactElements(Block.ADAPTER),
           unknownFields = ByteString.EMPTY
         )
@@ -237,6 +257,7 @@ public class Point(
         tag = 1,
         adapter = "com.squareup.wire.ProtoAdapter#UINT64",
         label = WireField.Label.OMIT_IDENTITY,
+        schemaIndex = 0,
       )
       public val time: Long = 0L,
       frames: List<Frame> = emptyList(),
@@ -247,6 +268,7 @@ public class Point(
         tag = 3,
         adapter = "ru.inr.mass.data.proto.Point${'$'}Channel${'$'}Block${'$'}Events#ADAPTER",
         label = WireField.Label.OMIT_IDENTITY,
+        schemaIndex = 2,
       )
       public val events: Events? = null,
       /**
@@ -256,6 +278,7 @@ public class Point(
         tag = 4,
         adapter = "com.squareup.wire.ProtoAdapter#UINT64",
         label = WireField.Label.OMIT_IDENTITY,
+        schemaIndex = 3,
       )
       public val length: Long = 0L,
       /**
@@ -266,6 +289,7 @@ public class Point(
         adapter = "com.squareup.wire.ProtoAdapter#UINT64",
         label = WireField.Label.OMIT_IDENTITY,
         jsonName = "binSize",
+        schemaIndex = 4,
       )
       public val bin_size: Long = 0L,
       unknownFields: ByteString = ByteString.EMPTY,
@@ -277,6 +301,7 @@ public class Point(
         tag = 2,
         adapter = "ru.inr.mass.data.proto.Point${'$'}Channel${'$'}Block${'$'}Frame#ADAPTER",
         label = WireField.Label.REPEATED,
+        schemaIndex = 1,
       )
       public val frames: List<Frame> = immutableCopyOf("frames", frames)
 
@@ -284,10 +309,10 @@ public class Point(
         message = "Shouldn't be used in Kotlin",
         level = DeprecationLevel.HIDDEN,
       )
-      public override fun newBuilder(): Nothing = throw
+      override fun newBuilder(): Nothing = throw
           AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-      public override fun equals(other: Any?): Boolean {
+      override fun equals(other: Any?): Boolean {
         if (other === this) return true
         if (other !is Block) return false
         if (unknownFields != other.unknownFields) return false
@@ -299,7 +324,7 @@ public class Point(
         return true
       }
 
-      public override fun hashCode(): Int {
+      override fun hashCode(): Int {
         var result = super.hashCode
         if (result == 0) {
           result = unknownFields.hashCode()
@@ -313,7 +338,7 @@ public class Point(
         return result
       }
 
-      public override fun toString(): String {
+      override fun toString(): String {
         val result = mutableListOf<String>()
         result += """time=$time"""
         if (frames.isNotEmpty()) result += """frames=$frames"""
@@ -342,7 +367,7 @@ public class Point(
           null, 
           "numass-proto.proto"
         ) {
-          public override fun encodedSize(`value`: Block): Int {
+          override fun encodedSize(`value`: Block): Int {
             var size = value.unknownFields.size
             if (value.time != 0L) size += ProtoAdapter.UINT64.encodedSizeWithTag(1, value.time)
             size += Frame.ADAPTER.asRepeated().encodedSizeWithTag(2, value.frames)
@@ -353,7 +378,7 @@ public class Point(
             return size
           }
 
-          public override fun encode(writer: ProtoWriter, `value`: Block): Unit {
+          override fun encode(writer: ProtoWriter, `value`: Block) {
             if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
             Frame.ADAPTER.asRepeated().encodeWithTag(writer, 2, value.frames)
             if (value.events != null) Events.ADAPTER.encodeWithTag(writer, 3, value.events)
@@ -362,7 +387,7 @@ public class Point(
             writer.writeBytes(value.unknownFields)
           }
 
-          public override fun encode(writer: ReverseProtoWriter, `value`: Block): Unit {
+          override fun encode(writer: ReverseProtoWriter, `value`: Block) {
             writer.writeBytes(value.unknownFields)
             if (value.bin_size != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 5, value.bin_size)
             if (value.length != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 4, value.length)
@@ -371,7 +396,7 @@ public class Point(
             if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
           }
 
-          public override fun decode(reader: ProtoReader): Block {
+          override fun decode(reader: ProtoReader): Block {
             var time: Long = 0L
             val frames = mutableListOf<Frame>()
             var events: Events? = null
@@ -397,7 +422,7 @@ public class Point(
             )
           }
 
-          public override fun redact(`value`: Block): Block = value.copy(
+          override fun redact(`value`: Block): Block = value.copy(
             frames = value.frames.redactElements(Frame.ADAPTER),
             events = value.events?.let(Events.ADAPTER::redact),
             unknownFields = ByteString.EMPTY
@@ -418,6 +443,7 @@ public class Point(
           tag = 1,
           adapter = "com.squareup.wire.ProtoAdapter#UINT64",
           label = WireField.Label.OMIT_IDENTITY,
+          schemaIndex = 0,
         )
         public val time: Long = 0L,
         /**
@@ -428,6 +454,7 @@ public class Point(
           adapter = "com.squareup.wire.ProtoAdapter#BYTES",
           label = WireField.Label.OMIT_IDENTITY,
           declaredName = "data",
+          schemaIndex = 1,
         )
         public val data_: ByteString = ByteString.EMPTY,
         unknownFields: ByteString = ByteString.EMPTY,
@@ -436,10 +463,10 @@ public class Point(
           message = "Shouldn't be used in Kotlin",
           level = DeprecationLevel.HIDDEN,
         )
-        public override fun newBuilder(): Nothing = throw
+        override fun newBuilder(): Nothing = throw
             AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-        public override fun equals(other: Any?): Boolean {
+        override fun equals(other: Any?): Boolean {
           if (other === this) return true
           if (other !is Frame) return false
           if (unknownFields != other.unknownFields) return false
@@ -448,7 +475,7 @@ public class Point(
           return true
         }
 
-        public override fun hashCode(): Int {
+        override fun hashCode(): Int {
           var result = super.hashCode
           if (result == 0) {
             result = unknownFields.hashCode()
@@ -459,7 +486,7 @@ public class Point(
           return result
         }
 
-        public override fun toString(): String {
+        override fun toString(): String {
           val result = mutableListOf<String>()
           result += """time=$time"""
           result += """data_=$data_"""
@@ -482,7 +509,7 @@ public class Point(
             null, 
             "numass-proto.proto"
           ) {
-            public override fun encodedSize(`value`: Frame): Int {
+            override fun encodedSize(`value`: Frame): Int {
               var size = value.unknownFields.size
               if (value.time != 0L) size += ProtoAdapter.UINT64.encodedSizeWithTag(1, value.time)
               if (value.data_ != ByteString.EMPTY) size += ProtoAdapter.BYTES.encodedSizeWithTag(2,
@@ -490,21 +517,21 @@ public class Point(
               return size
             }
 
-            public override fun encode(writer: ProtoWriter, `value`: Frame): Unit {
+            override fun encode(writer: ProtoWriter, `value`: Frame) {
               if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
               if (value.data_ != ByteString.EMPTY) ProtoAdapter.BYTES.encodeWithTag(writer, 2,
                   value.data_)
               writer.writeBytes(value.unknownFields)
             }
 
-            public override fun encode(writer: ReverseProtoWriter, `value`: Frame): Unit {
+            override fun encode(writer: ReverseProtoWriter, `value`: Frame) {
               writer.writeBytes(value.unknownFields)
               if (value.data_ != ByteString.EMPTY) ProtoAdapter.BYTES.encodeWithTag(writer, 2,
                   value.data_)
               if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
             }
 
-            public override fun decode(reader: ProtoReader): Frame {
+            override fun decode(reader: ProtoReader): Frame {
               var time: Long = 0L
               var data_: ByteString = ByteString.EMPTY
               val unknownFields = reader.forEachTag { tag ->
@@ -521,7 +548,7 @@ public class Point(
               )
             }
 
-            public override fun redact(`value`: Frame): Frame = value.copy(
+            override fun redact(`value`: Frame): Frame = value.copy(
               unknownFields = ByteString.EMPTY
             )
           }
@@ -547,6 +574,7 @@ public class Point(
           tag = 1,
           adapter = "com.squareup.wire.ProtoAdapter#UINT64",
           label = WireField.Label.PACKED,
+          schemaIndex = 0,
         )
         public val times: List<Long> = immutableCopyOf("times", times)
 
@@ -557,6 +585,7 @@ public class Point(
           tag = 2,
           adapter = "com.squareup.wire.ProtoAdapter#UINT64",
           label = WireField.Label.PACKED,
+          schemaIndex = 1,
         )
         public val amplitudes: List<Long> = immutableCopyOf("amplitudes", amplitudes)
 
@@ -564,10 +593,10 @@ public class Point(
           message = "Shouldn't be used in Kotlin",
           level = DeprecationLevel.HIDDEN,
         )
-        public override fun newBuilder(): Nothing = throw
+        override fun newBuilder(): Nothing = throw
             AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-        public override fun equals(other: Any?): Boolean {
+        override fun equals(other: Any?): Boolean {
           if (other === this) return true
           if (other !is Events) return false
           if (unknownFields != other.unknownFields) return false
@@ -576,7 +605,7 @@ public class Point(
           return true
         }
 
-        public override fun hashCode(): Int {
+        override fun hashCode(): Int {
           var result = super.hashCode
           if (result == 0) {
             result = unknownFields.hashCode()
@@ -587,7 +616,7 @@ public class Point(
           return result
         }
 
-        public override fun toString(): String {
+        override fun toString(): String {
           val result = mutableListOf<String>()
           if (times.isNotEmpty()) result += """times=$times"""
           if (amplitudes.isNotEmpty()) result += """amplitudes=$amplitudes"""
@@ -610,43 +639,61 @@ public class Point(
             null, 
             "numass-proto.proto"
           ) {
-            public override fun encodedSize(`value`: Events): Int {
+            override fun encodedSize(`value`: Events): Int {
               var size = value.unknownFields.size
               size += ProtoAdapter.UINT64.asPacked().encodedSizeWithTag(1, value.times)
               size += ProtoAdapter.UINT64.asPacked().encodedSizeWithTag(2, value.amplitudes)
               return size
             }
 
-            public override fun encode(writer: ProtoWriter, `value`: Events): Unit {
+            override fun encode(writer: ProtoWriter, `value`: Events) {
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 1, value.times)
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 2, value.amplitudes)
               writer.writeBytes(value.unknownFields)
             }
 
-            public override fun encode(writer: ReverseProtoWriter, `value`: Events): Unit {
+            override fun encode(writer: ReverseProtoWriter, `value`: Events) {
               writer.writeBytes(value.unknownFields)
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 2, value.amplitudes)
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 1, value.times)
             }
 
-            public override fun decode(reader: ProtoReader): Events {
+            override fun decode(reader: ProtoReader): Events {
-              val times = mutableListOf<Long>()
+              var times: MutableList<Long>? = null
-              val amplitudes = mutableListOf<Long>()
+              var amplitudes: MutableList<Long>? = null
               val unknownFields = reader.forEachTag { tag ->
                 when (tag) {
-                  1 -> times.add(ProtoAdapter.UINT64.decode(reader))
+                  1 -> {
-                  2 -> amplitudes.add(ProtoAdapter.UINT64.decode(reader))
+                    if (times == null) {
+                      val minimumByteSize = 1
+                      val initialCapacity = (reader.nextFieldMinLengthInBytes() / minimumByteSize)
+                        .coerceAtMost(Int.MAX_VALUE.toLong())
+                        .toInt()
+                      times = ArrayList(initialCapacity)
+                    }
+                    times!!.add(ProtoAdapter.UINT64.decode(reader))
+                  }
+                  2 -> {
+                    if (amplitudes == null) {
+                      val minimumByteSize = 1
+                      val initialCapacity = (reader.nextFieldMinLengthInBytes() / minimumByteSize)
+                        .coerceAtMost(Int.MAX_VALUE.toLong())
+                        .toInt()
+                      amplitudes = ArrayList(initialCapacity)
+                    }
+                    amplitudes!!.add(ProtoAdapter.UINT64.decode(reader))
+                  }
                   else -> reader.readUnknownField(tag)
                 }
               }
               return Events(
-                times = times,
+                times = times ?: listOf(),
-                amplitudes = amplitudes,
+                amplitudes = amplitudes ?: listOf(),
                 unknownFields = unknownFields
               )
             }
 
-            public override fun redact(`value`: Events): Events = value.copy(
+            override fun redact(`value`: Events): Events = value.copy(
               unknownFields = ByteString.EMPTY
             )
           }

numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/NumassProtoPlugin.kt

@@ -20,7 +20,6 @@ import java.nio.file.Path
 import kotlin.io.path.exists
 import kotlin.io.path.isDirectory
 import kotlin.io.path.relativeTo
-import kotlin.reflect.KClass
 
 public class NumassProtoPlugin : AbstractPlugin() {
     public val io: IOPlugin by require(IOPlugin)
@@ -35,7 +34,6 @@ public class NumassProtoPlugin : AbstractPlugin() {
     public companion object : PluginFactory<NumassProtoPlugin> {
         override fun build(context: Context, meta: Meta): NumassProtoPlugin = NumassProtoPlugin()
         override val tag: PluginTag = PluginTag("numass-proto", group = "ru.inr.mass")
-        override val type: KClass<out NumassProtoPlugin> = NumassProtoPlugin::class
     }
 }
 

numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/TaggedNumassEnvelopeFormat.kt

@@ -39,24 +39,8 @@ public class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeForm
         writeRawString(END_SEQUENCE)
     }
 
-    override fun writeEnvelope(
+    override fun writeObject(output: Output, obj: Envelope) {
-        output: Output,
-        envelope: Envelope,
-        metaFormatFactory: MetaFormatFactory,
-        formatMeta: Meta,
-    ) {
         error("Don't write legacy formats")
-//        val metaFormat = metaFormatFactory.invoke(formatMeta, io.context)
-//        val metaBytes = metaFormat.toBinary(envelope.meta)
-//        val actualSize: ULong = (envelope.data?.size ?: 0).toULong()
-//        val tag = Tag(metaFormatFactory.key, metaBytes.size.toUInt() + 2u, actualSize)
-//        output.writeBinary(tag.toBinary())
-//        output.writeBinary(metaBytes)
-//        output.writeRawString("\r\n")
-//        envelope.data?.let {
-//            output.writeBinary(it)
-//        }
-//        output.flush()
     }
 
     /**
@@ -68,31 +52,30 @@ public class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeForm
     override fun readObject(input: Input): Envelope {
         val tag = input.readTag()
 
-        val metaFormat = io.resolveMetaFormat(tag.metaFormatKey)
+        val metaFormat = io.resolveMetaFormat(tag.metaFormatKey) ?: JsonMetaFormat
-            ?: error("Meta format with key ${tag.metaFormatKey} not found")
 
         val meta: Meta = metaFormat.readObjectFrom(input.readBinary(tag.metaSize.toInt()))
 
         val data = input.readBinary(tag.dataSize.toInt())
 
-        return SimpleEnvelope(meta, data)
+        return Envelope(meta, data)
-    }
-
-    override fun readPartial(input: Input): PartialEnvelope {
-        val tag = input.readTag()
-
-        val metaFormat = if (tag.metaFormatKey == 1.toShort()) {
-            JsonMetaFormat
-        } else {
-            io.resolveMetaFormat(tag.metaFormatKey)
-                ?: error("Meta format with key ${tag.metaFormatKey} not found")
-        }
-
-        val meta: Meta = metaFormat.readObjectFrom(input.readBinary(tag.metaSize.toInt()))
-
-
-        return PartialEnvelope(meta, 30 + tag.metaSize.toInt(), tag.dataSize)
     }
+//
+//    override fun readPartial(input: Input): PartialEnvelope {
+//        val tag = input.readTag()
+//
+//        val metaFormat = if (tag.metaFormatKey == 1.toShort()) {
+//            JsonMetaFormat
+//        } else {
+//            io.resolveMetaFormat(tag.metaFormatKey)
+//                ?: error("Meta format with key ${tag.metaFormatKey} not found")
+//        }
+//
+//        val meta: Meta = metaFormat.readObjectFrom(input.readBinary(tag.metaSize.toInt()))
+//
+//
+//        return PartialEnvelope(meta, 30 + tag.metaSize.toInt(), tag.dataSize)
+//    }
 
     private data class Tag(
         val metaFormatKey: Short,
@@ -149,23 +132,11 @@ public class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeForm
 
         private val default by lazy { invoke() }
 
-        override fun readPartial(input: Input): PartialEnvelope =
+        override fun writeObject(output: Output, obj: Envelope) {
-            default.run { readPartial(input) }
+            error("Don't write legacy formats")
-
-        override fun writeEnvelope(
-            output: Output,
-            envelope: Envelope,
-            metaFormatFactory: MetaFormatFactory,
-            formatMeta: Meta,
-        ): Unit = default.run {
-            writeEnvelope(
-                output,
-                envelope,
-                metaFormatFactory,
-                formatMeta
-            )
         }
 
+
         override fun readObject(input: Input): Envelope = default.readObject(input)
     }
 }

numass-data-server/build.gradle.kts

@@ -1,5 +1,6 @@
 plugins {
     id("space.kscience.gradle.mpp")
+    id("org.jetbrains.compose")
     `maven-publish`
 }
 
@@ -7,17 +8,17 @@ val visionForgeVersion: String by rootProject.extra
 
 val production: Boolean by rootProject.extra(true)
 
-kotlin {
+
-    js(IR) {
+kscience {
-        browser {
+    fullStack("js/numass-web.js")
-            webpackTask {
+
-                this.outputFileName = "js/numass-web.js"
+    useSerialization {
-            }
+        json()
-        }
-        binaries.executable()
     }
 
-    sourceSets {
+    useContextReceivers()
+    useKtor()
+
     commonMain {
         dependencies {
             implementation(project(":numass-data-model"))
@@ -25,36 +26,23 @@ kotlin {
             implementation("space.kscience:visionforge-plotly:$visionForgeVersion")
         }
     }
-        jvmMain {
+}
+
+kotlin{
+    sourceSets{
+        getByName("jvmMain"){
             dependencies{
+                implementation(compose.runtime)
                 implementation(project(":numass-data-proto"))
-                implementation("space.kscience:visionforge-server:$visionForgeVersion")
+                implementation("io.ktor:ktor-server-cio")
+                implementation("io.ktor:ktor-server-html-builder")
+                implementation("space.kscience:visionforge-plotly:$visionForgeVersion")
             }
         }
-
+        getByName("jsMain"){
-    }
+            dependencies{
-}
+                implementation(compose.html.core)
-
-afterEvaluate {
-    val distributionTask = if (production) {
-        tasks.getByName("jsBrowserDistribution")
-    } else {
-        tasks.getByName("jsBrowserDevelopmentExecutableDistribution")
-    }
-
-    tasks.getByName<ProcessResources>("jvmProcessResources") {
-        dependsOn(distributionTask)
-        from(distributionTask)
-        include("**/*.js")
-        if (production) {
-            include("**/*.map")
             }
         }
     }
-
-kscience {
-    useSerialization {
-        json()
-    }
-    withContextReceivers()
 }

numass-data-server/src/commonMain/kotlin/ru/inr/mass/data/server/NumassCommonPlugin.kt

@@ -9,7 +9,6 @@ import space.kscience.dataforge.context.PluginTag
 import space.kscience.dataforge.meta.Meta
 import space.kscience.visionforge.Vision
 import space.kscience.visionforge.VisionPlugin
-import kotlin.reflect.KClass
 
 public class NumassCommonPlugin(meta: Meta = Meta.EMPTY) : VisionPlugin(meta) {
     override val tag: PluginTag get() = Companion.tag
@@ -18,7 +17,6 @@ public class NumassCommonPlugin(meta: Meta = Meta.EMPTY) : VisionPlugin(meta) {
 
     public companion object : PluginFactory<NumassCommonPlugin> {
         override val tag: PluginTag = PluginTag("numass.common", "ru.inr.mass")
-        override val type: KClass<NumassCommonPlugin> = NumassCommonPlugin::class
 
         override fun build(context: Context, meta: Meta): NumassCommonPlugin = NumassCommonPlugin()
 

numass-data-server/src/jsMain/kotlin/ru/inr/mass/data/server/NumassJsPlugin.kt

@@ -18,7 +18,6 @@ import space.kscience.visionforge.ElementVisionRenderer
 import space.kscience.visionforge.Vision
 import space.kscience.visionforge.VisionClient
 import space.kscience.visionforge.plotly.PlotlyPlugin
-import kotlin.reflect.KClass
 
 public class NumassJsPlugin : AbstractPlugin(), ElementVisionRenderer {
     public val client: VisionClient by require(VisionClient)
@@ -37,7 +36,7 @@ public class NumassJsPlugin : AbstractPlugin(), ElementVisionRenderer {
         else -> super.content(target)
     }
 
-    override fun render(element: Element, vision: Vision, meta: Meta) {
+    override fun render(element: Element, name: Name, vision: Vision, meta: Meta) {
         when (vision) {
             is VisionOfNumassHv -> element.append {
                 h1 { +"HV" }
@@ -64,7 +63,7 @@ public class NumassJsPlugin : AbstractPlugin(), ElementVisionRenderer {
                     vision.spectra.forEach { (channel, spectrum) ->
                         val pairs = spectrum.entries.sortedBy { it.key }
                         scatter {
-                            name = channel
+                            this.name = channel
                             mode = ScatterMode.lines
                             line {
                                 shape = LineShape.hv
@@ -83,8 +82,6 @@ public class NumassJsPlugin : AbstractPlugin(), ElementVisionRenderer {
 
     public companion object : PluginFactory<NumassJsPlugin> {
         override val tag: PluginTag = PluginTag("numass.js", "ru.inr.mass")
-        override val type: KClass<NumassJsPlugin> = NumassJsPlugin::class
-
         override fun build(context: Context, meta: Meta): NumassJsPlugin = NumassJsPlugin()
 
     }

numass-data-server/src/jsMain/kotlin/ru/inr/mass/data/server/NumassViewerApplication.kt

@@ -0,0 +1,27 @@
+package ru.inr.mass.data.server
+
+import org.jetbrains.compose.web.dom.Div
+import org.jetbrains.compose.web.renderComposable
+import org.w3c.dom.Document
+import space.kscience.dataforge.context.Context
+import space.kscience.visionforge.Application
+
+public class NumassViewerApplication : Application {
+    private val context = Context("NumassViewer") {
+        plugin(NumassJsPlugin)
+    }
+
+    override fun start(document: Document, state: Map<String, Any>) {
+        renderComposable(rootElementId = "application") {
+            Div({ classes("container") }) {
+                Div({ classes("row") })
+                Div({ classes("col-md-3") }) {
+
+                }
+                Div({ classes("col-md-9") }) {
+
+                }
+            }
+        }
+    }
+}

numass-data-server/src/jvmMain/kotlin/ru/inr/mass/data/server/server.kt

@@ -1,15 +1,20 @@
 package ru.inr.mass.data.server
 
+import io.ktor.http.ContentType
 import io.ktor.http.HttpStatusCode
-import io.ktor.http.URLBuilder
+import io.ktor.server.application.Application
 import io.ktor.server.application.call
 import io.ktor.server.cio.CIO
 import io.ktor.server.engine.embeddedServer
+import io.ktor.server.html.respondHtml
+import io.ktor.server.http.content.resources
 import io.ktor.server.response.respondText
 import io.ktor.server.routing.get
 import io.ktor.server.routing.routing
 import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.runBlocking
 import kotlinx.coroutines.withContext
+import kotlinx.html.*
 import ru.inr.mass.data.api.NumassPoint
 import ru.inr.mass.data.proto.NumassDirectorySet
 import ru.inr.mass.data.proto.NumassProtoPlugin
@@ -22,12 +27,15 @@ import space.kscience.dataforge.names.Name
 import space.kscience.dataforge.names.NameToken
 import space.kscience.dataforge.names.cutLast
 import space.kscience.dataforge.names.lastOrNull
-import space.kscience.visionforge.server.close
-import space.kscience.visionforge.server.openInBrowser
-import space.kscience.visionforge.server.visionServer
 
 
-public suspend fun main() {
+public fun main() {
+    val port = 7777
+    val host = "localhost"
+    embeddedServer(CIO, port, host, module = Application::numassModule).start()
+}
+
+public fun Application.numassModule(repositoryName: String = "D:\\Work\\Numass\\data\\test") {
     val context = Context("Numass") {
         plugin(NumassProtoPlugin)
         plugin(NumassCommonPlugin)
@@ -37,23 +45,47 @@ public suspend fun main() {
     val numassCommon = context.fetch(NumassCommonPlugin)
 
     val visionManager = numassCommon.visionManager
+    val repository: DataTree<NumassDirectorySet> = runBlocking { numassProto.readRepository(repositoryName) }
 
-    val repositroyName = "D:\\Work\\Numass\\data\\test"
-
-    val port = 7777
-    val host = "localhost"
-
-    val url = URLBuilder(host = host, port = port).build()
-
-    val repository: DataTree<NumassDirectorySet> = numassProto.readRepository(repositroyName)
-
-    val visionOfNumassRepository = VisionOfNumassRepository(Name.EMPTY, repository)
-
-    val server = context.embeddedServer(CIO, port, host) {
     routing {
+        resources()
+
+        get("/") {
+            call.respondHtml {
+                head {
+                    meta { charset = "utf-8" }
+                    meta {
+                        name = "viewport"
+                        content = "width=device-width, initial-scale=1"
+                    }
+                    title("Numass Data Viewer")
+                    link {
+                        href = "https://cdn.jsdelivr.net/npm/bootstrap@5.2.3/dist/css/bootstrap.min.css"
+                        rel = "stylesheet"
+                        attributes["integrity"] =
+                            "sha384-rbsA2VBKQhggwzxH7pPCaAqO46MgnOM80zW1RWuH61DGLwZJEdK2Kadq2F9CUG65"
+                        attributes["crossorigin"] = "anonymous"
+                    }
+                }
+                body {
+                    div {
+                        id = "application"
+                    }
+                    script {
+                        src = "js/numass-web.js"
+                    }
+                    script {
+                        src = "https://cdn.jsdelivr.net/npm/bootstrap@5.2.3/dist/js/bootstrap.bundle.min.js"
+                        integrity = "sha384-kenU1KFdBIe4zVF0s0G1M5b4hcpxyD9F7jL+jjXkk+Q2h455rYXK/7HAuoJl+0I4"
+                        attributes["crossorigin"] = "anonymous"
+                    }
+                }
+            }
+        }
+
         get("/repository") {
-                call.respondText {
+            call.respondText(ContentType.Application.Json) {
-                    visionManager.encodeToString(visionOfNumassRepository)
+                visionManager.encodeToString(VisionOfNumassRepository(Name.EMPTY, repository))
             }
         }
 
@@ -72,7 +104,7 @@ public suspend fun main() {
                 return@get
             }
 
-                call.respondText {
+            call.respondText(ContentType.Application.Json) {
                 visionManager.encodeToString(VisionOfNumassSet(setName, set))
             }
         }
@@ -101,32 +133,10 @@ public suspend fun main() {
                 call.respondText(status = HttpStatusCode.NotFound) { "A point with name $setName/$pointIndex not found in the repository" }
                 return@get
             }
-                call.respondText {
+            call.respondText(ContentType.Application.Json) {
                 visionManager.encodeToString(point.toVision())
             }
         }
     }
-        visionServer(numassCommon.visionManager, url)
+    //serveVisionData(VisionRoute("/visions", visionManager))
-    }.start()
-
-//    val server = context.visionManager.serve {
-//        header("numass", VisionPage.scriptHeader("js/numass-web.js"))
-//        page {
-//            div("flex-column") {
-//                h1 { +"Visionforge file demo" }
-//                vision { visionOfNumass }
-//            }
-//        }
-//    }
-
-    server.openInBrowser()
-
-
-    println("Enter 'exit' to close server")
-    while (readLine() != "exit") {
-        //
-    }
-
-    server.close()
-
 }

numass-data-server/src/jvmMain/kotlin/ru/inr/mass/data/server/serverExtensions.kt

@@ -2,11 +2,8 @@ package ru.inr.mass.data.server
 
 import space.kscience.dataforge.context.Context
 import space.kscience.dataforge.misc.DFExperimental
-import space.kscience.visionforge.html.HtmlVisionFragment
+import space.kscience.visionforge.html.*
-import space.kscience.visionforge.html.ResourceLocation
+import space.kscience.visionforge.visionManager
-import space.kscience.visionforge.html.VisionPage
-import space.kscience.visionforge.html.importScriptHeader
-import space.kscience.visionforge.makeFile
 import java.awt.Desktop
 import java.nio.file.Path
 
@@ -19,7 +16,7 @@ public fun Context.makeNumassWebFile(
     show: Boolean = true,
     content: HtmlVisionFragment,
 ): Unit {
-    val actualPath = VisionPage(this, content = content).makeFile(path) { actualPath: Path ->
+    val actualPath = VisionPage(visionManager, content = content).makeFile(path) { actualPath: Path ->
         mapOf(
             "title" to VisionPage.title(title),
             "numassWeb" to VisionPage.importScriptHeader("js/numass-web.js", resourceLocation, actualPath)

numass-model/build.gradle.kts

@@ -7,7 +7,9 @@ plugins {
 val dataforgeVersion: String by rootProject.extra
 val kmathVersion: String by rootProject.extra
 
-kotlin.sourceSets {
+kscience{
+    jvm()
+    js()
     commonMain {
         dependencies {
             api("space.kscience:dataforge-context:$dataforgeVersion")
@@ -15,7 +17,10 @@ kotlin.sourceSets {
             api("space.kscience:kmath-functions:$kmathVersion")
         }
     }
-    jvmMain {
+}
+
+kotlin.sourceSets{
+    getByName("jvmMain"){
         dependencies {
             api("space.kscience:kmath-commons:$kmathVersion")
             api("ch.qos.logback:logback-classic:1.2.3")

numass-model/src/commonMain/kotlin/ru/inr/mass/models/FSS.kt

@@ -15,10 +15,10 @@
  */
 package ru.inr.mass.models
 
+import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.data.ColumnarData
 import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.expressions.symbol
-import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.structures.Buffer
 
 

numass-model/src/commonMain/kotlin/ru/inr/mass/models/NBkgSpectrum.kt

@@ -32,8 +32,8 @@ public class NBkgSpectrum(public val source: Spectrum) : DifferentiableSpectrum
     override fun derivativeOrNull(symbols: List<Symbol>): Spectrum? = when {
         symbols.isEmpty() -> this
         symbols.size == 1 -> when (symbols.first()) {
-            norm -> Spectrum { x, arguments -> source(x, arguments) + (arguments[bkg] ?: 0.0) }
+            norm -> Spectrum { x, arguments -> source(x, arguments) }
-            bkg -> Spectrum { x, arguments -> (arguments[norm] ?: 1.0) * source(x, arguments) }
+            bkg -> Spectrum { _, _ -> 1.0 }
             else -> (source as? DifferentiableSpectrum)?.derivativeOrNull(symbols)?.let { NBkgSpectrum(it) }
         }
         else -> null

numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassBeta.kt

@@ -3,6 +3,8 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
+@file:Suppress("PARAMETER_NAME_CHANGED_ON_OVERRIDE")
+
 package ru.inr.mass.models
 
 import space.kscience.kmath.expressions.Symbol

numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassResolution.kt

@@ -12,10 +12,13 @@ import kotlin.math.sqrt
 /**
  * @author [Alexander Nozik](mailto:altavir@gmail.com)
  */
+
+@Suppress("PARAMETER_NAME_CHANGED_ON_OVERRIDE")
 public class NumassResolution(
-    public val resA: Double = 8.3e-5,
+    public val resA: Double = 1.7e-4,
     public val resB: Double = 0.0,
-    public val tailFunction: (Double, Double) -> Double = { _, _ -> 1.0 },
+    // Recent formula for adiabacity
+    public val tailFunction: (Double, Double) -> Double = { e, u -> -1.75559e-13 * (e - u) * (e - u) * (e - u) - 5.97479e-11 * (e - u) * (e - u) + 3.26473e-7 * (e - u) + 1.0 },
 ) : DifferentiableKernel {
 
 //    private val tailFunction: Kernel = when {
@@ -43,12 +46,12 @@ public class NumassResolution(
 //        else -> ResolutionFunction.getConstantTail()
 //    }
 
-    private fun getValueFast(E: Double, U: Double): Double {
+    private fun getValueFast(e: Double, u: Double): Double {
-        val delta = resA * E
+        val delta = resA * e
         return when {
-            E - U < 0 -> 0.0
+            e - u < 0 -> 0.0
-            E - U > delta -> tailFunction(E, U)
+            e - u > delta -> tailFunction(e, u)
-            else -> (E - U) / delta
+            else -> (e - u) / delta
         }
     }
 
@@ -57,15 +60,15 @@ public class NumassResolution(
     override val x: Symbol get() = e
     override val y: Symbol get() = u
 
-    override fun invoke(E: Double, U: Double, arguments: Map<Symbol, Double>): Double {
+    override fun invoke(e: Double, u: Double, arguments: Map<Symbol, Double>): Double {
         if (resB <= 0) {
-            return this.getValueFast(E, U)
+            return this.getValueFast(e, u)
         }
-        val delta = resA * E
+        val delta = resA * e
         return when {
-            E - U < 0 -> 0.0
+            e - u < 0 -> 0.0
-            E - U > delta -> tailFunction(E, U)
+            e - u > delta -> tailFunction(e, u)
-            else -> (1 - sqrt(1 - (E - U) / E * resB)) / (1 - sqrt(1 - resA * resB))
+            else -> (1 - sqrt(1 - (e - u) / e * resB)) / (1 - sqrt(1 - resA * resB))
         }
     }
 

numass-model/src/commonMain/kotlin/ru/inr/mass/models/NumassTransmission.kt

@@ -20,7 +20,7 @@ import kotlin.math.*
  * @author [Alexander Nozik](mailto:altavir@gmail.com)
  */
 public class NumassTransmission(
-    public val trapFunc: Kernel = defaultTrapping,
+    public val trapFunc: Kernel = trapFunction,
 //    private val adjustX: Boolean = false,
 ) : DifferentiableKernel {
     //    private val trapFunc: Kernel =         if (meta.hasValue("trapping")) {
@@ -54,8 +54,10 @@ public class NumassTransmission(
                 }
                 sum
             }
+
             else -> null
         }
+
         else -> null
     }
 
@@ -63,6 +65,7 @@ public class NumassTransmission(
         // loss part
         val thickness = arguments[thickness] ?: 0.0
         val loss = getTotalLossValue(thickness, ei, ef)
+        //val loss = 0.0
         //        double loss;
         //
         //        if(eIn-eOut >= 300){
@@ -76,7 +79,9 @@ public class NumassTransmission(
         //        }
 
         //trapping part
+        //
         val trap = (arguments[trap] ?: 1.0) * trapFunc(ei, ef, arguments)
+        //val trap = 0.0
         return loss + trap
     }
 
@@ -86,7 +91,7 @@ public class NumassTransmission(
 
         private val cache = HashMap<Int, Function1D<Double>>()
 
-        private const val ION_POTENTIAL = 15.4//eV
+        private const val ION_POTENTIAL = 13.6//eV
 
 
         private fun getX(arguments: Map<Symbol, Double>, eIn: Double, adjustX: Boolean = false): Double {
@@ -131,6 +136,7 @@ public class NumassTransmission(
         }
 
         private fun getCachedSpectrum(order: Int): Function1D<Double> {
+            //println("-------------------ORDER $order ------------------------")
             return when {
                 order <= 0 -> error("Non-positive loss cache order")
                 order == 1 -> singleScatterFunction
@@ -274,13 +280,13 @@ public class NumassTransmission(
          * Значение полной производной функции потерь с учетом всех неисчезающих
          * порядков
          *
-         * @param X
+         * @param thickness
          * @param eIn
          * @param eOut
          * @return
          */
-        private fun getTotalLossDeriv(X: Double, eIn: Double, eOut: Double): Double {
+        private fun getTotalLossDeriv(thickness: Double, eIn: Double, eOut: Double): Double {
-            val probs = getLossProbDerivs(X)
+            val probs = getLossProbDerivs(thickness)
 
             var sum = 0.0
             for (i in 1 until probs.size) {
@@ -331,6 +337,7 @@ public class NumassTransmission(
                     val z = eps - pos1
                     A1 * exp(-2.0 * z * z / w1 / w1)
                 }
+
                 else -> {
                     val z = 4.0 * (eps - pos2) * (eps - pos2)
                     A2 / (1 + z / w2 / w2)
@@ -399,8 +406,8 @@ public class NumassTransmission(
 //            return getSingleScatterFunction(exPos, ionPos, exW, ionW, exIonRatio)
 //        }
 
-        public val trapFunction: (Double, Double) -> Double = { Ei: Double, Ef: Double ->
+        public val trapFunction: Kernel = Kernel { ei: Double, ef: Double, _ ->
-            val eps = Ei - Ef
+            val eps = ei - ef
             if (eps > 10) {
                 1.86e-04 * exp(-eps / 25.0) + 5.5e-05
             } else {

numass-workspace/build.gradle.kts

@@ -2,6 +2,7 @@ plugins {
     id("space.kscience.gradle.jvm")
     id("com.github.johnrengelman.shadow") version "7.1.2"
     `maven-publish`
+    application
 }
 
 kotlin {
@@ -9,7 +10,7 @@ kotlin {
 }
 
 val dataforgeVersion: String by rootProject.extra
-val visionForgeVersion: String by rootProject.extra
+val plotlyKtVersion = "0.6.0"
 val kmathVersion: String by rootProject.extra
 val tablesVersion: String by rootProject.extra
 
@@ -21,9 +22,15 @@ dependencies {
 
     implementation("space.kscience:kmath-jupyter:$kmathVersion")
     implementation("space.kscience:tables-kt:$tablesVersion")
-    implementation("space.kscience:visionforge-plotly:$visionForgeVersion")
+    implementation("space.kscience:plotlykt-core:$plotlyKtVersion")
+
+    implementation("com.github.ajalt.clikt:clikt:4.2.1")
 }
 
 kscience{
     jupyterLibrary("ru.inr.mass.notebook.NumassJupyter")
 }
+
+//application {
+//    mainClass.set("ru.inr.mass.scripts.Get_spectrumKt")
+//}

numass-workspace/src/main/kotlin/ru/inr/mass/scripts/fit.kt

@@ -0,0 +1,196 @@
+package ru.inr.mass.scripts
+
+import com.github.ajalt.clikt.core.CliktCommand
+import com.github.ajalt.clikt.core.context
+import com.github.ajalt.clikt.output.MordantHelpFormatter
+import com.github.ajalt.clikt.parameters.arguments.argument
+import com.github.ajalt.clikt.parameters.arguments.help
+import com.github.ajalt.clikt.parameters.options.default
+import com.github.ajalt.clikt.parameters.options.help
+import com.github.ajalt.clikt.parameters.options.option
+import com.github.ajalt.clikt.parameters.options.prompt
+import com.github.ajalt.clikt.parameters.types.double
+import com.github.ajalt.clikt.parameters.types.int
+import kotlinx.coroutines.runBlocking
+import ru.inr.mass.models.*
+import ru.inr.mass.workspace.buffer
+import ru.inr.mass.workspace.fitWith
+import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.data.XYColumnarData
+import space.kscience.kmath.data.XYErrorColumnarData
+import space.kscience.kmath.data.indices
+import space.kscience.kmath.expressions.Symbol
+import space.kscience.kmath.expressions.derivative
+import space.kscience.kmath.operations.asSequence
+import space.kscience.kmath.optimization.*
+import space.kscience.kmath.real.step
+import space.kscience.kmath.structures.asBuffer
+import space.kscience.plotly.*
+import space.kscience.plotly.models.ScatterMode
+import java.io.File
+import kotlin.math.pow
+
+@OptIn(UnstableKMathAPI::class)
+fun parse(filename: String): XYErrorColumnarData<Double, Double, Double> {
+    val x: MutableList<Double> = mutableListOf()
+    val y: MutableList<Double> = mutableListOf()
+    val errors: MutableList<Double> = mutableListOf()
+
+    File(filename).forEachLine {
+        val array = it.split("\t").map { it.toDouble() }
+        x.add(array[0])
+        y.add(array[1])
+        errors.add(array[2])
+        //errors.add(array[1] / 100)
+    }
+    return XYErrorColumnarData.of(
+        x.asBuffer(),
+        y.asBuffer(),
+        errors.map { it }.asBuffer()
+    )
+}
+class Args : CliktCommand() {
+
+    init {
+        context {
+            helpFormatter = { MordantHelpFormatter(it, showDefaultValues = true) }
+        }
+    }
+
+    val spectrum: String by argument().help("path to spectrum TSV file")
+
+    val norm: Double by option().double().default(8.311751921319484E8).help("NBkgSpectrum.norm")
+    val bkg: Double by option().double().default(1612.626961212948).help("NBkgSpectrum.bkg")
+
+    val mnu2: Double by option().double().default(0.0).help("NumassBeta.mnu2")
+    val e0: Double by option().double().default(18572.0).help("NumassBeta.e0")
+    val msterile2: Double by option().double().default(0.0.pow(2)).help("NumassBeta.msterile2")
+    val u2: Double by option().double().default(1e-2).help("NumassBeta.u2")
+
+    val thickness: Double by option().double().default(0.3).help("NumassTransmission.thickness")
+    val trap: Double by option().double().default(1.0).help("NumassTransmission.trap")
+
+    @UnstableKMathAPI
+    override fun run() {
+        val fitParams: Map<Symbol, Double> = mapOf(
+            NBkgSpectrum.norm to norm,
+            NBkgSpectrum.bkg to bkg,
+            NumassBeta.mnu2 to mnu2,
+            NumassBeta.e0 to e0,
+            NumassBeta.msterile2 to msterile2,
+            NumassBeta.u2 to u2,
+            NumassTransmission.thickness to thickness,
+            NumassTransmission.trap to trap
+        )
+
+        runBlocking {
+            process(spectrum, fitParams)
+        }
+    }
+}
+
+fun main(args: Array<String>) = Args().main(args)
+
+suspend fun fitNumassSpectrum(data: XYErrorColumnarData<Double, Double, Double>, initial: Map<Symbol, Double>): XYFit {
+    val spectrum: NBkgSpectrum = SterileNeutrinoSpectrum(
+//        fss = FSS.default,
+        transmission = NumassTransmission(NumassTransmission.trapFunction),
+//        resolution = NumassResolution(1.7e-4)
+    ).withNBkg()
+
+    return data.fitWith(
+        optimizer = QowOptimizer,
+        modelExpression = spectrum,
+        startingPoint = initial,
+        OptimizationParameters(NumassBeta.e0, NBkgSpectrum.norm, NBkgSpectrum.bkg,
+//            NumassTransmission.trap
+        ),
+        OptimizationIterations(20)
+    )
+}
+
+
+@UnstableKMathAPI
+suspend fun process(spectrumFile: String, fitParams: Map<Symbol, Double>) {
+
+    val data = parse(spectrumFile)
+
+    val spectrum: NBkgSpectrum = SterileNeutrinoSpectrum(
+//        fss = FSS.default,
+        transmission = NumassTransmission(NumassTransmission.trapFunction),
+//        resolution = NumassResolution(1.7e-4)
+    ).withNBkg()
+
+    val fit = fitNumassSpectrum(data, fitParams)
+
+    println(fit.resultPoint)
+
+    Plotly.page {
+        plot {
+
+            scatter {
+                name = "Data"
+                mode = ScatterMode.markers
+                x.buffer = data.x
+                y.buffer = data.y
+            }
+
+
+            scatter {
+                name = "Initial"
+                mode = ScatterMode.lines
+                x.buffer = data.x
+                y.numbers = x.doubles.map { spectrum(it, fitParams + fit.resultPoint) }
+                File(spectrumFile + "-fit").printWriter().use { out ->
+                    out.println("U_sp\tcounts\tresidials")
+
+                    data.indices.map{
+                        val value = spectrum(data.x[it], fitParams + fit.resultPoint)
+                        val dif = data.y[it] - value
+                        out.println("${data.x[it]}\t${data.y[it]}\t${dif/data.yErr[it]}")
+                    }
+                }
+            }
+            scatter {
+                name = "Fit"
+                mode = ScatterMode.lines
+                x.buffer = 12000.0..18600.0 step 10.0
+                y.numbers = x.doubles.map { spectrum(it, fitParams + fit.resultPoint) }
+            }
+        }
+        plot{
+            scatter {
+                name = "Residuals"
+                mode = ScatterMode.markers
+                x.buffer = data.x
+                y.numbers = data.indices.map{
+                    val value = spectrum(data.x[it], fitParams + fit.resultPoint)
+                    val dif = data.y[it] - value
+                    dif/data.yErr[it]
+                }
+            }
+        }
+        plot{
+            histogram {
+                    x.numbers = data.indices.map{
+                        val value = spectrum(data.x[it], fitParams + fit.resultPoint)
+                        val dif = data.y[it] - value
+                        dif/data.yErr[it]
+                    }
+                    name = "Res histo"
+            }
+        }
+        plot {
+            scatter {
+                name = "Residuals_lines"
+                mode = ScatterMode.lines
+                x.buffer = data.x
+                y.numbers = data.indices.map {
+                    val value = spectrum(data.x[it], fitParams + fit.resultPoint)
+                    val dif = data.y[it] - value
+                    dif / data.yErr[it]
+                }
+            }
+        }
+    }.makeFile()
+}

numass-workspace/src/main/kotlin/ru/inr/mass/scripts/get-spectrum.kt

@@ -0,0 +1,89 @@
+package ru.inr.mass.scripts
+
+import com.github.ajalt.clikt.core.CliktCommand
+import com.github.ajalt.clikt.core.context
+import com.github.ajalt.clikt.output.MordantHelpFormatter
+import com.github.ajalt.clikt.parameters.arguments.argument
+import com.github.ajalt.clikt.parameters.arguments.help
+import com.github.ajalt.clikt.parameters.options.default
+import com.github.ajalt.clikt.parameters.options.help
+import com.github.ajalt.clikt.parameters.options.option
+import com.github.ajalt.clikt.parameters.types.double
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.async
+import kotlinx.coroutines.runBlocking
+import ru.inr.mass.models.*
+import space.kscience.kmath.data.XYErrorColumnarData
+import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.expressions.Symbol
+import space.kscience.kmath.operations.toTypedArray
+import space.kscience.kmath.real.plus
+import space.kscience.kmath.real.step
+import space.kscience.plotly.models.HoverMode
+import kotlin.math.pow
+
+private class CalcSpectrum : CliktCommand() {
+
+    init {
+        context {
+            helpFormatter = { MordantHelpFormatter(it, showDefaultValues = true) }
+        }
+    }
+
+    val spectrum: String by argument().help("path to spectrum TSV file")
+
+    val norm: Double by option().double().default(8.84e8).help("NBkgSpectrum.norm")
+    val bkg: Double by option().double().default(-1.702).help("NBkgSpectrum.bkg")
+
+    val mnu2: Double by option().double().default(0.0).help("NumassBeta.mnu2")
+    val e0: Double by option().double().default(18572.0).help("NumassBeta.e0")
+    val msterile2: Double by option().double().default(0.0.pow(2)).help("NumassBeta.msterile2")
+    val u2: Double by option().double().default(1e-2).help("NumassBeta.u2")
+
+    val thickness: Double by option().double().default(0.3).help("NumassTransmission.thickness")
+    val trap: Double by option().double().default(1.0).help("NumassTransmission.trap")
+
+    @UnstableKMathAPI
+    override fun run() {
+        val fitParams: Map<Symbol, Double> = mapOf(
+            NBkgSpectrum.norm to norm,
+            NBkgSpectrum.bkg to bkg,
+            NumassBeta.mnu2 to mnu2,
+            NumassBeta.e0 to e0,
+            NumassBeta.msterile2 to msterile2,
+            NumassBeta.u2 to u2,
+            NumassTransmission.thickness to thickness,
+            NumassTransmission.trap to trap
+        )
+
+        runBlocking {
+            calcSpectrum(spectrum, fitParams)
+        }
+    }
+}
+
+fun main(args: Array<String>) = CalcSpectrum().main(args)
+
+suspend fun calcSpectrum(spectrumFile: String, fitParams: Map<Symbol, Double>) {
+
+    val data = parse(spectrumFile)
+
+    val range = data.x.toTypedArray();
+
+    runBlocking(Dispatchers.Default) {
+
+        val handles = range.map {
+
+            async(Dispatchers.Default) {
+                val spectrum: NBkgSpectrum = SterileNeutrinoSpectrum(
+                    transmission = NumassTransmission(NumassTransmission.trapFunction),
+                ).withNBkg()
+
+                val res = spectrum.invoke(it, fitParams)
+                return@async res
+            }
+        }
+        val out = handles.map { it.await() }
+        println(out.joinToString("\n"))
+    }
+}

numass-workspace/src/main/kotlin/ru/inr/mass/scripts/readGCPoint.kt

@@ -0,0 +1,17 @@
+package ru.inr.mass.scripts
+
+//import com.google.cloud.storage.contrib.nio.CloudStorageFileSystem
+//import ru.inr.mass.data.proto.NumassDirectorySet
+//import ru.inr.mass.workspace.Numass
+//import space.kscience.dataforge.data.DataTree
+//
+//// https://storage.cloud.google.com/numass-data/2020_12/Adiabaticity/16/set_3/p10(10s)(HV1%3D13750)
+//
+//suspend fun main() {
+//    CloudStorageFileSystem.forBucket("numass-data").use { fs ->
+//        val repo: DataTree<NumassDirectorySet> = Numass.readRepository(fs.getPath("2020_12/Adiabaticity"))
+//        repo.items().forEach{ (key,item)->
+//            println(key)
+//        }
+//    }
+//}

numass-workspace/src/main/kotlin/ru/inr/mass/workspace/NumassWorkspacePlugin.kt

@@ -18,7 +18,6 @@ import space.kscience.dataforge.workspace.WorkspacePlugin
 import space.kscience.dataforge.workspace.pipeFrom
 import space.kscience.dataforge.workspace.task
 import space.kscience.tables.Table
-import kotlin.reflect.KClass
 
 class NumassWorkspacePlugin : WorkspacePlugin() {
     override val tag: PluginTag get() = Companion.tag
@@ -128,7 +127,6 @@ class NumassWorkspacePlugin : WorkspacePlugin() {
 
     companion object : PluginFactory<NumassWorkspacePlugin> {
         override val tag: PluginTag = PluginTag("numass", "ru.mipt.npm")
-        override val type: KClass<out NumassWorkspacePlugin> = NumassWorkspacePlugin::class
         override fun build(context: Context, meta: Meta): NumassWorkspacePlugin = NumassWorkspacePlugin()
     }
 }

numass-workspace/src/main/kotlin/ru/inr/mass/workspace/dataUtils.kt

@@ -0,0 +1,67 @@
+@file:OptIn(UnstableKMathAPI::class)
+
+package ru.inr.mass.workspace
+
+import ru.inr.mass.models.Spectrum
+import space.kscience.kmath.UnstableKMathAPI
+import space.kscience.kmath.data.XYColumnarData
+import space.kscience.kmath.data.XYErrorColumnarData
+import space.kscience.kmath.expressions.DifferentiableExpression
+import space.kscience.kmath.expressions.Symbol
+import space.kscience.kmath.misc.FeatureSet
+import space.kscience.kmath.misc.Loggable
+import space.kscience.kmath.optimization.*
+import space.kscience.kmath.random.RandomGenerator
+import space.kscience.kmath.samplers.PoissonSampler
+import space.kscience.kmath.stat.next
+import space.kscience.kmath.structures.asBuffer
+import kotlin.math.sqrt
+
+public suspend fun XYColumnarData<Double, Double, Double>.fitWith(
+    optimizer: Optimizer<Double, XYFit>,
+    modelExpression: DifferentiableExpression<Double>,
+    startingPoint: Map<Symbol, Double>,
+    vararg features: OptimizationFeature = emptyArray(),
+    xSymbol: Symbol = Symbol.x,
+    pointToCurveDistance: PointToCurveDistance = PointToCurveDistance.byY,
+    pointWeight: PointWeight = PointWeight.byYSigma,
+): XYFit {
+    var actualFeatures = FeatureSet.of(*features, OptimizationStartPoint(startingPoint))
+
+    if (actualFeatures.getFeature<OptimizationLog>() == null) {
+        actualFeatures = actualFeatures.with(OptimizationLog(Loggable.console))
+    }
+    val problem = XYFit(
+        this,
+        modelExpression,
+        actualFeatures,
+        pointToCurveDistance,
+        pointWeight,
+        xSymbol
+    )
+    return optimizer.optimize(problem)
+}
+
+public suspend fun Spectrum.generate(
+    strategy: Map<Double, Double>,
+    arguments: Map<Symbol, Double>,
+    generator: RandomGenerator = RandomGenerator.default,
+): XYErrorColumnarData<Double, Double, Double> {
+    val xs = mutableListOf<Double>()
+    val ys = mutableListOf<Double>()
+    val errors = mutableListOf<Double>()
+
+    strategy.forEach { (x, time) ->
+        xs.add(x)
+        val mu = invoke(x, arguments) * time
+        val y = PoissonSampler(mu).next(generator) / time
+        val error = sqrt(mu) / time
+        ys.add(y)
+        errors.add(error)
+    }
+    return XYErrorColumnarData.of(
+        xs.toTypedArray().asBuffer(),
+        ys.toTypedArray().asBuffer(),
+        errors.toTypedArray().asBuffer()
+    )
+}

numass-workspace/src/main/kotlin/ru/inr/mass/workspace/plots.kt

@@ -12,9 +12,9 @@ import ru.inr.mass.data.proto.HVData
 import ru.inr.mass.data.proto.NumassDirectorySet
 import space.kscience.dataforge.meta.asValue
 import space.kscience.dataforge.meta.double
+import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.domains.center
 import space.kscience.kmath.histogram.Histogram1D
-import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.operations.asIterable
 import space.kscience.kmath.structures.Buffer
 import space.kscience.kmath.structures.DoubleBuffer

settings.gradle.kts

@@ -1,7 +1,6 @@
 rootProject.name = "numass"
 
 enableFeaturePreview("TYPESAFE_PROJECT_ACCESSORS")
-enableFeaturePreview("VERSION_CATALOGS")
 
 pluginManagement {
 
@@ -15,6 +14,7 @@ pluginManagement {
     }
 
     plugins {
+        id("org.jetbrains.compose").version(extra["compose.version"] as String)
         id("space.kscience.gradle.project") version toolsVersion
         id("space.kscience.gradle.mpp") version toolsVersion
         id("space.kscience.gradle.jvm") version toolsVersion