Fix orders in DerivativeStructures

kmath-commons/src/main/kotlin/kscience/kmath/commons/expressions/DerivativeStructureExpression.kt

@@ -38,13 +38,13 @@ public class DerivativeStructureField(
         key.identity to DerivativeStructureSymbol(key, value)
     }
 
-    override fun const(value: Double): DerivativeStructure = DerivativeStructure(order, bindings.size, value)
+    override fun const(value: Double): DerivativeStructure = DerivativeStructure(bindings.size, order,  value)
 
     public override fun bindOrNull(symbol: Symbol): DerivativeStructureSymbol? = variables[symbol.identity]
 
     public fun bind(symbol: Symbol): DerivativeStructureSymbol = variables.getValue(symbol.identity)
 
-    public fun Number.const(): DerivativeStructure = const(toDouble())
+    //public fun Number.const(): DerivativeStructure = const(toDouble())
 
     public fun DerivativeStructure.derivative(parameter: Symbol, order: Int = 1): Double {
         return derivative(mapOf(parameter to order))

kmath-commons/src/main/kotlin/kscience/kmath/commons/optimization/CMFit.kt

@@ -17,9 +17,9 @@ public object CMFit {
 
     /**
      * Generate a chi squared expression from given x-y-sigma model represented by an expression. Does not provide derivatives
-     * TODO move to core/separate module
+     * TODO move to prob/stat
      */
-    public fun chiSquaredExpression(
+    public fun chiSquared(
         x: Buffer<Double>,
         y: Buffer<Double>,
         yErr: Buffer<Double>,
@@ -35,7 +35,7 @@ public object CMFit {
                 val yErrValue = yErr[it]
                 val modifiedArgs = arguments + (xSymbol to xValue)
                 val modelValue = model(modifiedArgs)
-                ((yValue - modelValue) / yErrValue).pow(2) / 2
+                ((yValue - modelValue) / yErrValue).pow(2)
             }
         }
     }
@@ -43,7 +43,7 @@ public object CMFit {
     /**
      * Generate a chi squared expression from given x-y-sigma data and inline model. Provides automatic differentiation
      */
-    public fun chiSquaredExpression(
+    public fun chiSquared(
         x: Buffer<Double>,
         y: Buffer<Double>,
         yErr: Buffer<Double>,
@@ -58,7 +58,7 @@ public object CMFit {
                 val yValue = y[it]
                 val yErrValue = yErr[it]
                 val modelValue = model(const(xValue))
-                sum += ((yValue - modelValue) / yErrValue).pow(2) / 2
+                sum += ((yValue - modelValue) / yErrValue).pow(2)
             }
             sum
         }
@@ -92,12 +92,13 @@ public fun DifferentiableExpression<Double>.optimize(
 }
 
 public fun DifferentiableExpression<Double>.minimize(
-    vararg symbols: Symbol,
+    vararg startPoint: Pair<Symbol, Double>,
-    configuration: CMOptimizationProblem.() -> Unit,
+    configuration: CMOptimizationProblem.() -> Unit = {},
 ): OptimizationResult<Double> {
-    require(symbols.isNotEmpty()) { "Must provide a list of symbols for optimization" }
+    require(startPoint.isNotEmpty()) { "Must provide a list of symbols for optimization" }
-    val problem = CMOptimizationProblem(symbols.toList()).apply(configuration)
+    val problem = CMOptimizationProblem(startPoint.map { it.first }).apply(configuration)
     problem.diffExpression(this)
+    problem.initialGuess(startPoint.toMap())
     problem.goal(GoalType.MINIMIZE)
     return problem.optimize()
 }

kmath-commons/src/main/kotlin/kscience/kmath/commons/optimization/CMOptimizationProblem.kt

@@ -17,14 +17,13 @@ public operator fun PointValuePair.component2(): Double = value
 
 public class CMOptimizationProblem(
     override val symbols: List<Symbol>,
-) : OptimizationProblem<Double>, SymbolIndexer {
+) : OptimizationProblem<Double>, SymbolIndexer, OptimizationFeature {
-    protected val optimizationData: HashMap<KClass<out OptimizationData>, OptimizationData> = HashMap()
+    private val optimizationData: HashMap<KClass<out OptimizationData>, OptimizationData> = HashMap()
     private var optimizatorBuilder: (() -> MultivariateOptimizer)? = null
-
     public var convergenceChecker: ConvergenceChecker<PointValuePair> = SimpleValueChecker(DEFAULT_RELATIVE_TOLERANCE,
         DEFAULT_ABSOLUTE_TOLERANCE, DEFAULT_MAX_ITER)
 
-    private fun addOptimizationData(data: OptimizationData) {
+    public fun addOptimizationData(data: OptimizationData) {
         optimizationData[data::class] = data
     }
 
@@ -32,6 +31,8 @@ public class CMOptimizationProblem(
         addOptimizationData(MaxEval.unlimited())
     }
 
+    public fun exportOptimizationData(): List<OptimizationData> = optimizationData.values.toList()
+
     public fun initialGuess(map: Map<Symbol, Double>): Unit {
         addOptimizationData(InitialGuess(map.toDoubleArray()))
     }
@@ -90,7 +91,7 @@ public class CMOptimizationProblem(
     override fun optimize(): OptimizationResult<Double> {
         val optimizer = optimizatorBuilder?.invoke() ?: error("Optimizer not defined")
         val (point, value) = optimizer.optimize(*optimizationData.values.toTypedArray())
-        return OptimizationResult(point.toMap(), value)
+        return OptimizationResult(point.toMap(), value, setOf(this))
     }
 
     public companion object {

kmath-commons/src/main/kotlin/kscience/kmath/commons/optimization/OptimizationProblem.kt

@@ -4,14 +4,19 @@ import kscience.kmath.expressions.DifferentiableExpression
 import kscience.kmath.expressions.Expression
 import kscience.kmath.expressions.Symbol
 
-public interface OptimizationResultFeature
+public interface OptimizationFeature
 
+//TODO move to prob/stat
 
 public class OptimizationResult<T>(
     public val point: Map<Symbol, T>,
     public val value: T,
-    public val features: Set<OptimizationResultFeature> = emptySet(),
+    public val features: Set<OptimizationFeature> = emptySet(),
-)
+){
+    override fun toString(): String {
+        return "OptimizationResult(point=$point, value=$value)"
+    }
+}
 
 /**
  * A configuration builder for optimization problem

kmath-commons/src/main/kotlin/kscience/kmath/commons/random/CMRandomGeneratorWrapper.kt

@@ -2,8 +2,9 @@ package kscience.kmath.commons.random
 
 import kscience.kmath.prob.RandomGenerator
 
-public class CMRandomGeneratorWrapper(public val factory: (IntArray) -> RandomGenerator) :
+public class CMRandomGeneratorWrapper(
-    org.apache.commons.math3.random.RandomGenerator {
+    public val factory: (IntArray) -> RandomGenerator,
+) : org.apache.commons.math3.random.RandomGenerator {
     private var generator: RandomGenerator = factory(intArrayOf())
 
     public override fun nextBoolean(): Boolean = generator.nextBoolean()

kmath-commons/src/test/kotlin/kscience/kmath/commons/optimization/OptimizeTest.kt

@@ -2,14 +2,19 @@ package kscience.kmath.commons.optimization
 
 import kscience.kmath.commons.expressions.DerivativeStructureExpression
 import kscience.kmath.expressions.symbol
+import kscience.kmath.prob.Distribution
+import kscience.kmath.prob.RandomGenerator
+import kscience.kmath.prob.normal
+import kscience.kmath.structures.asBuffer
 import org.junit.jupiter.api.Test
+import kotlin.math.pow
 
 internal class OptimizeTest {
     val x by symbol
     val y by symbol
 
     val normal = DerivativeStructureExpression {
-        exp(-bind(x).pow(2) / 2) + exp(- bind(y).pow(2) / 2)
+        exp(-bind(x).pow(2) / 2) + exp(-bind(y).pow(2) / 2)
     }
 
     @Test
@@ -32,4 +37,29 @@ internal class OptimizeTest {
         println(result.point)
         println(result.value)
     }
+
+    @Test
+    fun testFit() {
+        val a by symbol
+        val b by symbol
+        val c by symbol
+
+        val sigma = 1.0
+        val generator = Distribution.normal(0.0, sigma)
+        val chain = generator.sample(RandomGenerator.default(1126))
+        val x = (1..100).map { it.toDouble() }
+        val y = x.map { it ->
+            it.pow(2) + it + 1 + chain.nextDouble()
+        }
+        val yErr = x.map { sigma }
+        with(CMFit) {
+            val chi2 = chiSquared(x.asBuffer(), y.asBuffer(), yErr.asBuffer()) { x ->
+                bind(a) * x.pow(2) + bind(b) * x + bind(c)
+            }
+
+            val result = chi2.minimize(a to 1.5, b to 0.9, c to 1.0)
+            println(result)
+            println("Chi2/dof = ${result.value / (x.size - 3)}")
+        }
+    }
 }