WIP histograms refactor

kmath-histograms/build.gradle.kts

@@ -1,4 +1,10 @@
-plugins { id("ru.mipt.npm.mpp") }
+plugins {
+    id("ru.mipt.npm.mpp")
+}
+
+kscience {
+    useAtomic()
+}
 
 kotlin.sourceSets {
     commonMain {
@@ -6,8 +12,8 @@ kotlin.sourceSets {
             api(project(":kmath-core"))
         }
     }
-    commonTest{
+    commonTest {
-        dependencies{
+        dependencies {
             implementation(project(":kmath-for-real"))
         }
     }

kmath-histograms/src/commonMain/kotlin/kscience/kmath/histogram/Counters.kt

@@ -1,20 +1,47 @@
 package kscience.kmath.histogram
 
+import kotlinx.atomicfu.atomic
+import kotlinx.atomicfu.getAndUpdate
+import kscience.kmath.operations.Space
+
 /*
  * Common representation for atomic counters
  * TODO replace with atomics
  */
 
-public expect class LongCounter() {
+public interface Counter<T : Any> {
-    public fun decrement()
+    public fun add(delta: T)
-    public fun increment()
+    public val value: T
-    public fun reset()
-    public fun sum(): Long
-    public fun add(l: Long)
 }
 
-public expect class DoubleCounter() {
+public class IntCounter : Counter<Int> {
-    public fun reset()
+    private val innerValue = atomic(0)
-    public fun sum(): Double
+
-    public fun add(d: Double)
+    override fun add(delta: Int) {
+        innerValue += delta
+    }
+
+    override val value: Int get() = innerValue.value
 }
+
+public class LongCounter : Counter<Long> {
+    private val innerValue = atomic(0L)
+
+    override fun add(delta: Long) {
+        innerValue += delta
+    }
+
+    override val value: Long get() = innerValue.value
+}
+
+public class ObjectCounter<T : Any>(public val space: Space<T>) : Counter<T> {
+    private val innerValue = atomic(space.zero)
+
+    override fun add(delta: T) {
+        innerValue.getAndUpdate { space.run { it + delta } }
+    }
+
+    override val value: T get() = innerValue.value
+}
+
+

kmath-histograms/src/commonMain/kotlin/kscience/kmath/histogram/Histogram.kt

@@ -6,7 +6,7 @@ import kscience.kmath.structures.ArrayBuffer
 import kscience.kmath.structures.RealBuffer
 
 /**
- * The bin in the histogram. The histogram is by definition always done in the real space
+ * The binned data element. Could be a histogram bin with a number of counts or an artificial construct
  */
 public interface Bin<T : Any> : Domain<T> {
     /**
@@ -17,7 +17,7 @@ public interface Bin<T : Any> : Domain<T> {
     public val center: Point<T>
 }
 
-public interface Histogram<T : Any, out B : Bin<T>> : Iterable<B> {
+public interface Histogram<T : Any, out B : Bin<T>> {
     /**
      * Find existing bin, corresponding to given coordinates
      */
@@ -27,9 +27,11 @@ public interface Histogram<T : Any, out B : Bin<T>> : Iterable<B> {
      * Dimension of the histogram
      */
     public val dimension: Int
+
+    public val bins: Collection<B>
 }
 
-public interface MutableHistogram<T : Any, out B : Bin<T>> : Histogram<T, B> {
+public interface HistogramBuilder<T : Any, out B : Bin<T>> : Histogram<T, B> {
 
     /**
      * Increment appropriate bin
@@ -39,16 +41,16 @@ public interface MutableHistogram<T : Any, out B : Bin<T>> : Histogram<T, B> {
     public fun put(point: Point<out T>): Unit = putWithWeight(point, 1.0)
 }
 
-public fun <T : Any> MutableHistogram<T, *>.put(vararg point: T): Unit = put(ArrayBuffer(point))
+public fun <T : Any> HistogramBuilder<T, *>.put(vararg point: T): Unit = put(ArrayBuffer(point))
 
-public fun MutableHistogram<Double, *>.put(vararg point: Number): Unit =
+public fun HistogramBuilder<Double, *>.put(vararg point: Number): Unit =
     put(RealBuffer(point.map { it.toDouble() }.toDoubleArray()))
 
-public fun MutableHistogram<Double, *>.put(vararg point: Double): Unit = put(RealBuffer(point))
+public fun HistogramBuilder<Double, *>.put(vararg point: Double): Unit = put(RealBuffer(point))
-public fun <T : Any> MutableHistogram<T, *>.fill(sequence: Iterable<Point<T>>): Unit = sequence.forEach { put(it) }
+public fun <T : Any> HistogramBuilder<T, *>.fill(sequence: Iterable<Point<T>>): Unit = sequence.forEach { put(it) }
 
 /**
  * Pass a sequence builder into histogram
  */
-public fun <T : Any> MutableHistogram<T, *>.fill(block: suspend SequenceScope<Point<T>>.() -> Unit): Unit =
+public fun <T : Any> HistogramBuilder<T, *>.fill(block: suspend SequenceScope<Point<T>>.() -> Unit): Unit =
     fill(sequence(block).asIterable())

kmath-histograms/src/commonMain/kotlin/kscience/kmath/histogram/RealHistogram.kt

@@ -43,7 +43,7 @@ public class RealHistogram(
     private val lower: Buffer<Double>,
     private val upper: Buffer<Double>,
     private val binNums: IntArray = IntArray(lower.size) { 20 },
-) : MutableHistogram<Double, MultivariateBin<Double>> {
+) : HistogramBuilder<Double, MultivariateBin<Double>> {
     private val strides = DefaultStrides(IntArray(binNums.size) { binNums[it] + 2 })
     private val counts: NDStructure<LongCounter> = NDStructure.auto(strides) { LongCounter() }
     private val values: NDStructure<DoubleCounter> = NDStructure.auto(strides) { DoubleCounter() }
@@ -88,11 +88,12 @@ public class RealHistogram(
         return MultivariateBinDefinition(RealBufferFieldOperations, center, binSize)
     }
 
-    public fun getBinDefinition(point: Buffer<out Double>): MultivariateBinDefinition<Double> = getBinDefinition(getIndex(point))
+    public fun getBinDefinition(point: Buffer<out Double>): MultivariateBinDefinition<Double> =
+        getBinDefinition(getIndex(point))
 
     public override operator fun get(point: Buffer<out Double>): MultivariateBin<Double>? {
         val index = getIndex(point)
-        return MultivariateBin(getBinDefinition(index), getCount(index),getValue(index))
+        return MultivariateBin(getBinDefinition(index), getCount(index), getValue(index))
     }
 
 //    fun put(point: Point<out Double>){
@@ -106,10 +107,10 @@ public class RealHistogram(
         values[index].add(weight)
     }
 
-    public override operator fun iterator(): Iterator<MultivariateBin<Double>> =
+    override val bins: Collection<MultivariateBin<Double>>
-        strides.indices().map { index->
+        get() = strides.indices().map { index ->
             MultivariateBin(getBinDefinition(index), counts[index].sum(), values[index].sum())
-        }.iterator()
+        }.toList()
 
     /**
      * NDStructure containing number of events in bins without weights

kmath-histograms/src/commonTest/kotlin/scietifik/kmath/histogram/MultivariateHistogramTest.kt

@@ -16,7 +16,7 @@ internal class MultivariateHistogramTest {
             (-1.0..1.0)
         )
         histogram.put(0.55, 0.55)
-        val bin = histogram.find { it.value.toInt() > 0 } ?: fail()
+        val bin = histogram.bins.find { it.value.toInt() > 0 } ?: fail()
         assertTrue { bin.contains(RealVector(0.55, 0.55)) }
         assertTrue { bin.contains(RealVector(0.6, 0.5)) }
         assertFalse { bin.contains(RealVector(-0.55, 0.55)) }
@@ -40,6 +40,6 @@ internal class MultivariateHistogramTest {
                 yield(RealVector(nextDouble(), nextDouble(), nextDouble()))
             }
         }
-        assertEquals(n, histogram.sumBy { it.value.toInt() })
+        assertEquals(n, histogram.bins.sumBy { it.value.toInt() })
     }
 }

kmath-histograms/src/jsMain/kotlin/kscience/kmath/histogram/Counters.kt

@@ -1,37 +0,0 @@
-package kscience.kmath.histogram
-
-public actual class LongCounter {
-    private var sum: Long = 0L
-
-    public actual fun decrement() {
-        sum--
-    }
-
-    public actual fun increment() {
-        sum++
-    }
-
-    public actual fun reset() {
-        sum = 0
-    }
-
-    public actual fun sum(): Long = sum
-
-    public actual fun add(l: Long) {
-        sum += l
-    }
-}
-
-public actual class DoubleCounter {
-    private var sum: Double = 0.0
-
-    public actual fun reset() {
-        sum = 0.0
-    }
-
-    public actual fun sum(): Double = sum
-
-    public actual fun add(d: Double) {
-        sum += d
-    }
-}

kmath-histograms/src/jvmMain/kotlin/kscience/kmath/histogram/AbstractUnivariateHistogram.kt

@@ -0,0 +1,33 @@
+package kscience.kmath.histogram
+
+
+/**
+ * Univariate histogram with log(n) bin search speed
+ */
+//private abstract class AbstractUnivariateHistogram<B: UnivariateBin>{
+//
+//    public abstract val bins: TreeMap<Double, B>
+//
+//    public open operator fun get(value: Double): B? {
+//        // check ceiling entry and return it if it is what needed
+//        val ceil = bins.ceilingEntry(value)?.value
+//        if (ceil != null && value in ceil) return ceil
+//        //check floor entry
+//        val floor = bins.floorEntry(value)?.value
+//        if (floor != null && value in floor) return floor
+//        //neither is valid, not found
+//        return null
+//    }
+
+//    public override operator fun get(point: Buffer<out Double>): B? = get(point[0])
+//
+//    public override val dimension: Int get() = 1
+//
+//    public override operator fun iterator(): Iterator<B> = bins.values.iterator()
+//
+//    public companion object {
+
+//    }
+//}
+
+

kmath-histograms/src/jvmMain/kotlin/kscience/kmath/histogram/Counters.kt

@@ -1,7 +0,0 @@
-package kscience.kmath.histogram
-
-import java.util.concurrent.atomic.DoubleAdder
-import java.util.concurrent.atomic.LongAdder
-
-public actual typealias LongCounter = LongAdder
-public actual typealias DoubleCounter = DoubleAdder

kmath-histograms/src/jvmMain/kotlin/kscience/kmath/histogram/UnivariateHistogram.kt

@@ -6,71 +6,47 @@ import kscience.kmath.operations.SpaceElement
 import kscience.kmath.structures.Buffer
 import kscience.kmath.structures.asBuffer
 import kscience.kmath.structures.asSequence
-import java.util.*
-import kotlin.math.floor
 
-//TODO move to common
+public data class UnivariateHistogramBinDefinition(
+    val position: Double,
+    val size: Double,
+) : Comparable<UnivariateHistogramBinDefinition> {
+    override fun compareTo(other: UnivariateHistogramBinDefinition): Int = this.position.compareTo(other.position)
+}
 
-public class UnivariateBin(
+public interface UnivariateBin : Bin<Double> {
-    public val position: Double,
+    public val def: UnivariateHistogramBinDefinition
-    public val size: Double,
-) : Bin<Double> {
-    //internal mutation operations
-    internal val counter: LongCounter = LongCounter()
-    internal val weightCounter: DoubleCounter = DoubleCounter()
 
-    /**
+    public val position: Double get() = def.position
-     * The precise number of events ignoring weighting
+    public val size: Double get() = def.size
-     */
-    public val count: Long get() = counter.sum()
 
     /**
      * The value of histogram including weighting
      */
-    public override val value: Double get() = weightCounter.sum()
+    public override val value: Double
+
+    /**
+     * Standard deviation of the bin value. Zero if not applicable
+     */
+    public val standardDeviation: Double
 
     public override val center: Point<Double> get() = doubleArrayOf(position).asBuffer()
+
     public override val dimension: Int get() = 1
 
-    public operator fun contains(value: Double): Boolean = value in (position - size / 2)..(position + size / 2)
     public override fun contains(point: Buffer<Double>): Boolean = contains(point[0])
 }
 
-/**
+public operator fun UnivariateBin.contains(value: Double): Boolean =
- * Univariate histogram with log(n) bin search speed
+    value in (position - size / 2)..(position + size / 2)
- */
+
 @OptIn(UnstableKMathAPI::class)
-public abstract class UnivariateHistogram protected constructor(
+public interface UnivariateHistogram : Histogram<Double, UnivariateBin>,
-    protected val bins: TreeMap<Double, UnivariateBin> = TreeMap(),
+    SpaceElement<UnivariateHistogram, UnivariateHistogramSpace> {
-) : Histogram<Double, UnivariateBin>, SpaceElement<UnivariateHistogram, UnivariateHistogramSpace> {
+    public operator fun get(value: Double): UnivariateBin?
-
-    public operator fun get(value: Double): UnivariateBin? {
-        // check ceiling entry and return it if it is what needed
-        val ceil = bins.ceilingEntry(value)?.value
-        if (ceil != null && value in ceil) return ceil
-        //check floor entry
-        val floor = bins.floorEntry(value)?.value
-        if (floor != null && value in floor) return floor
-        //neither is valid, not found
-        return null
-    }
-
     public override operator fun get(point: Buffer<out Double>): UnivariateBin? = get(point[0])
 
-    public override val dimension: Int get() = 1
-
-    public override operator fun iterator(): Iterator<UnivariateBin> = bins.values.iterator()
-
     public companion object {
-        /**
-         * Build a histogram with a uniform binning with a start at [start] and a bin size of [binSize]
-         */
-        public fun uniformBuilder(binSize: Double, start: Double = 0.0): UnivariateHistogramBuilder =
-            UnivariateHistogramSpace { value ->
-                val center = start + binSize * floor((value - start) / binSize + 0.5)
-                UnivariateBin(center, binSize)
-            }.builder()
-
         /**
          * Build and fill a [UnivariateHistogram]. Returns a read-only histogram.
          */
@@ -78,35 +54,7 @@ public abstract class UnivariateHistogram protected constructor(
             binSize: Double,
             start: Double = 0.0,
             builder: UnivariateHistogramBuilder.() -> Unit,
-        ): UnivariateHistogram = uniformBuilder(binSize, start).apply(builder)
+        ): UnivariateHistogram = UnivariateHistogramSpace.uniform(binSize, start).produce(builder)
-
-        /**
-         * Create a histogram with custom cell borders
-         */
-        public fun customBuilder(borders: DoubleArray): UnivariateHistogramBuilder {
-            val sorted = borders.sortedArray()
-
-            return UnivariateHistogramSpace { value ->
-                when {
-                    value < sorted.first() -> UnivariateBin(
-                        Double.NEGATIVE_INFINITY,
-                        Double.MAX_VALUE
-                    )
-
-                    value > sorted.last() -> UnivariateBin(
-                        Double.POSITIVE_INFINITY,
-                        Double.MAX_VALUE
-                    )
-
-                    else -> {
-                        val index = sorted.indices.first { value > sorted[it] }
-                        val left = sorted[index]
-                        val right = sorted[index + 1]
-                        UnivariateBin((left + right) / 2, (right - left))
-                    }
-                }
-            }.builder()
-        }
 
         /**
          * Build and fill a histogram with custom borders. Returns a read-only histogram.
@@ -114,41 +62,24 @@ public abstract class UnivariateHistogram protected constructor(
         public fun custom(
             borders: DoubleArray,
             builder: UnivariateHistogramBuilder.() -> Unit,
-        ): UnivariateHistogram = customBuilder(borders).apply(builder)
+        ): UnivariateHistogram = UnivariateHistogramSpace.custom(borders).produce(builder)
+
     }
 }
 
-public class UnivariateHistogramBuilder internal constructor(
+public interface UnivariateHistogramBuilder {
-    override val context: UnivariateHistogramSpace,
-) : UnivariateHistogram(), MutableHistogram<Double, UnivariateBin> {
-
-    private fun createBin(value: Double): UnivariateBin = context.binFactory(value).also {
-        synchronized(this) { bins[it.position] = it }
-    }
-
     /**
      * Thread safe put operation
      */
-    public fun put(value: Double, weight: Double = 1.0) {
+    public fun put(value: Double, weight: Double = 1.0)
-        (get(value) ?: createBin(value)).apply {
+    public fun putWithWeight(point: Buffer<out Double>, weight: Double)
-            counter.increment()
-            weightCounter.add(weight)
-        }
-    }
-
-    override fun putWithWeight(point: Buffer<out Double>, weight: Double) {
-        put(point[0], weight)
-    }
 
     /**
      * Put several items into a single bin
      */
-    public fun putMany(value: Double, count: Int, weight: Double = count.toDouble()) {
+    public fun putMany(value: Double, count: Int, weight: Double = count.toDouble())
-        (get(value) ?: createBin(value)).apply {
+
-            counter.add(count.toLong())
+    public fun build(): UnivariateHistogram
-            weightCounter.add(weight)
-        }
-    }
 }
 
 @UnstableKMathAPI

kmath-histograms/src/jvmMain/kotlin/kscience/kmath/histogram/UnivariateHistogramSpace.kt

@@ -1,25 +1,185 @@
 package kscience.kmath.histogram
 
 import kscience.kmath.operations.Space
+import kscience.kmath.structures.Buffer
+import java.util.*
+import kotlin.math.abs
+import kotlin.math.sqrt
 
-public class UnivariateHistogramSpace(public val binFactory: (Double) -> UnivariateBin) : Space<UnivariateHistogram> {
+private fun <B : UnivariateBin> TreeMap<Double, B>.getBin(value: Double): B? {
+    // check ceiling entry and return it if it is what needed
+    val ceil = ceilingEntry(value)?.value
+    if (ceil != null && value in ceil) return ceil
+    //check floor entry
+    val floor = floorEntry(value)?.value
+    if (floor != null && value in floor) return floor
+    //neither is valid, not found
+    return null
+}
 
-    public fun builder(): UnivariateHistogramBuilder = UnivariateHistogramBuilder(this)
 
-    public fun produce(builder: UnivariateHistogramBuilder.() -> Unit): UnivariateHistogram = builder().apply(builder)
+private class UnivariateHistogramImpl(
+    override val context: UnivariateHistogramSpace,
+    val binMap: TreeMap<Double, out UnivariateBin>,
+) : UnivariateHistogram {
+    override fun get(value: Double): UnivariateBin? = binMap.getBin(value)
+    override val dimension: Int get() = 1
+    override val bins: Collection<UnivariateBin> get() = binMap.values
+}
+
+private class UnivariateBinCounter(
+    override val def: UnivariateHistogramBinDefinition,
+) : UnivariateBin {
+    val counter: LongCounter = LongCounter()
+    val valueCounter: DoubleCounter = DoubleCounter()
+
+    /**
+     * The precise number of events ignoring weighting
+     */
+    val count: Long get() = counter.sum()
+
+    override val standardDeviation: Double get() = sqrt(count.toDouble()) / count * value
+
+    /**
+     * The value of histogram including weighting
+     */
+    override val value: Double get() = valueCounter.sum()
+
+    public fun increment(count: Long, value: Double) {
+        counter.add(count)
+        valueCounter.add(value)
+    }
+}
+
+private class UnivariateBinValue(
+    override val def: UnivariateHistogramBinDefinition,
+    override val value: Double,
+    override val standardDeviation: Double,
+) : UnivariateBin
+
+
+public class UnivariateHistogramSpace(
+    public val binFactory: (Double) -> UnivariateHistogramBinDefinition,
+) : Space<UnivariateHistogram> {
+
+    private inner class UnivariateHistogramBuilderImpl : UnivariateHistogramBuilder {
+
+        val bins: TreeMap<Double, UnivariateBinCounter> = TreeMap()
+        fun get(value: Double): UnivariateBinCounter? = bins.getBin(value)
+
+        private fun createBin(value: Double): UnivariateBinCounter {
+            val binDefinition = binFactory(value)
+            val newBin = UnivariateBinCounter(binDefinition)
+            synchronized(this) { bins[binDefinition.position] = newBin }
+            return newBin
+        }
+
+        /**
+         * Thread safe put operation
+         */
+        override fun put(value: Double, weight: Double) {
+            (get(value) ?: createBin(value)).apply {
+                increment(1, weight)
+            }
+        }
+
+        override fun putWithWeight(point: Buffer<out Double>, weight: Double) {
+            put(point[0], weight)
+        }
+
+        /**
+         * Put several items into a single bin
+         */
+        override fun putMany(value: Double, count: Int, weight: Double) {
+            (get(value) ?: createBin(value)).apply {
+                increment(count.toLong(), weight)
+            }
+        }
+
+        override fun build(): UnivariateHistogram = UnivariateHistogramImpl(this@UnivariateHistogramSpace, bins)
+    }
+
+
+    public fun builder(): UnivariateHistogramBuilder = UnivariateHistogramBuilderImpl()
+
+    public fun produce(builder: UnivariateHistogramBuilder.() -> Unit): UnivariateHistogram =
+        UnivariateHistogramBuilderImpl().apply(builder).build()
 
     override fun add(
         a: UnivariateHistogram,
         b: UnivariateHistogram,
     ): UnivariateHistogram {
-        require(a.context == this){"Histogram $a does not belong to this context"}
+        require(a.context == this) { "Histogram $a does not belong to this context" }
-        require(b.context == this){"Histogram $b does not belong to this context"}
+        require(b.context == this) { "Histogram $b does not belong to this context" }
-        TODO()
+        val bins = TreeMap<Double, UnivariateBin>().apply {
+            (a.bins.map { it.def } union b.bins.map { it.def }).forEach { def ->
+                val newBin = UnivariateBinValue(
+                    def,
+                    value = (a[def.position]?.value ?: 0.0) + (b[def.position]?.value ?: 0.0),
+                    standardDeviation = (a[def.position]?.standardDeviation
+                        ?: 0.0) + (b[def.position]?.standardDeviation ?: 0.0)
+                )
+            }
+        }
+        return UnivariateHistogramImpl(this, bins)
     }
 
     override fun multiply(a: UnivariateHistogram, k: Number): UnivariateHistogram {
-        TODO("Not yet implemented")
+        val bins = TreeMap<Double, UnivariateBin>().apply {
+            a.bins.forEach { bin ->
+                put(bin.position,
+                    UnivariateBinValue(
+                        bin.def,
+                        value = bin.value * k.toDouble(),
+                        standardDeviation = abs(bin.standardDeviation * k.toDouble())
+                    )
+                )
+            }
+        }
+
+        return UnivariateHistogramImpl(this, bins)
     }
 
-    override val zero: UnivariateHistogram = produce {  }
+    override val zero: UnivariateHistogram = produce { }
+
+    public companion object {
+        /**
+         * Build and fill a [UnivariateHistogram]. Returns a read-only histogram.
+         */
+        public fun uniform(
+            binSize: Double,
+            start: Double = 0.0
+        ): UnivariateHistogramSpace = UnivariateHistogramSpace { value ->
+            val center = start + binSize * Math.floor((value - start) / binSize + 0.5)
+            UnivariateHistogramBinDefinition(center, binSize)
+        }
+
+        /**
+         * Create a histogram with custom cell borders
+         */
+        public fun custom(borders: DoubleArray): UnivariateHistogramSpace {
+            val sorted = borders.sortedArray()
+
+            return UnivariateHistogramSpace { value ->
+                when {
+                    value < sorted.first() -> UnivariateHistogramBinDefinition(
+                        Double.NEGATIVE_INFINITY,
+                        Double.MAX_VALUE
+                    )
+
+                    value > sorted.last() -> UnivariateHistogramBinDefinition(
+                        Double.POSITIVE_INFINITY,
+                        Double.MAX_VALUE
+                    )
+
+                    else -> {
+                        val index = sorted.indices.first { value > sorted[it] }
+                        val left = sorted[index]
+                        val right = sorted[index + 1]
+                        UnivariateHistogramBinDefinition((left + right) / 2, (right - left))
+                    }
+                }
+            }
+        }
+    }
 }