Document ShapeND.asArray()

Co-authored-by: Gleb Minaev <43728100+lounres@users.noreply.github.com>

build.gradle.kts

@@ -6,7 +6,7 @@ plugins {
     id("org.jetbrains.kotlinx.kover") version "0.7.6"
 }
 
-val attributesVersion by extra("0.1.0")
+val attributesVersion by extra("0.2.0")
 
 allprojects {
     repositories {

docs/buffers.md

@@ -17,4 +17,4 @@ own `MemoryBuffer.create()` factory).
 ## Buffer performance
 
 One should avoid using default boxing buffer wherever it is possible. Try to use primitive buffers or memory buffers
-instead .
+instead.

kmath-core/src/commonMain/kotlin/space/kscience/kmath/nd/ShapeND.kt

@@ -68,6 +68,9 @@ public operator fun ShapeND.component3(): Int = get(2)
  */
 public fun ShapeND.toArray(): IntArray = array.copyOf()
 
+/**
+ * Provide internal content of [ShapeND]. Must not be modified.
+ */
 @UnsafeKMathAPI
 public fun ShapeND.asArray(): IntArray = array
 

kmath-optimization/src/commonMain/tmp/minuit/MinuitParameter.kt

@@ -38,9 +38,9 @@ class MinuitParameter {
      * @param name a [String] object.
      * @param val a double.
      */
-    constructor(num: Int, name: String, `val`: Double) {
+    constructor(num: Int, name: String, value: Double) {
         theNum = num
-        theValue = `val`
+        theValue = value
         theConst = true
         theName = name
     }
@@ -53,9 +53,9 @@ class MinuitParameter {
      * @param val a double.
      * @param err a double.
      */
-    constructor(num: Int, name: String, `val`: Double, err: Double) {
+    constructor(num: Int, name: String, value: Double, err: Double) {
         theNum = num
-        theValue = `val`
+        theValue = value
         theError = err
         theName = name
     }
@@ -70,9 +70,9 @@ class MinuitParameter {
      * @param min a double.
      * @param max a double.
      */
-    constructor(num: Int, name: String, `val`: Double, err: Double, min: Double, max: Double) {
+    constructor(num: Int, name: String, value: Double, err: Double, min: Double, max: Double) {
         theNum = num
-        theValue = `val`
+        theValue = value
         theError = err
         theLoLimit = min
         theUpLimit = max
@@ -288,8 +288,8 @@ class MinuitParameter {
      *
      * @param val a double.
      */
-    fun setValue(`val`: Double) {
+    fun setValue(value: Double) {
-        theValue = `val`
+        theValue = value
     }
 
     /**

kmath-optimization/src/commonMain/tmp/minuit/MnApplication.kt

@@ -77,8 +77,8 @@ abstract class MnApplication {
      * @param val a double.
      * @param name a [String] object.
      */
-    fun add(name: String, `val`: Double, err: Double) {
+    fun add(name: String, value: Double, err: Double) {
-        theState.add(name, `val`, err)
+        theState.add(name, value, err)
     }
 
     /**
@@ -90,8 +90,8 @@ abstract class MnApplication {
      * @param val a double.
      * @param err a double.
      */
-    fun add(name: String, `val`: Double, err: Double, low: Double, up: Double) {
+    fun add(name: String, value: Double, err: Double, low: Double, up: Double) {
-        theState.add(name, `val`, err, low, up)
+        theState.add(name, value, err, low, up)
     }
 
     /**
@@ -100,8 +100,8 @@ abstract class MnApplication {
      * @param name a [String] object.
      * @param val a double.
      */
-    fun add(name: String, `val`: Double) {
+    fun add(name: String, value: Double) {
-        theState.add(name, `val`)
+        theState.add(name, value)
     }
 
     /**
@@ -471,8 +471,8 @@ abstract class MnApplication {
      * @param index a int.
      * @param val a double.
      */
-    fun setValue(index: Int, `val`: Double) {
+    fun setValue(index: Int, value: Double) {
-        theState.setValue(index, `val`)
+        theState.setValue(index, value)
     }
 
     /**
@@ -482,8 +482,8 @@ abstract class MnApplication {
      * @param name a [String] object.
      * @param val a double.
      */
-    fun setValue(name: String?, `val`: Double) {
+    fun setValue(name: String?, value: Double) {
-        theState.setValue(name, `val`)
+        theState.setValue(name, value)
     }
 
     /**

kmath-optimization/src/commonMain/tmp/minuit/MnMinos.kt

@@ -106,8 +106,8 @@ class MnMinos(fcn: MultiFunction?, min: FunctionMinimum?, stra: MnStrategy?) {
         val para = intArrayOf(par)
         val upar: MnUserParameterState = theMinimum!!.userState().copy()
         val err: Double = upar.error(par)
-        val `val`: Double = upar.value(par) - err
+        val value: Double = upar.value(par) - err
-        val xmid = doubleArrayOf(`val`)
+        val xmid = doubleArrayOf(value)
         val xdir = doubleArrayOf(-err)
         val ind: Int = upar.intOfExt(par)
         val m: MnAlgebraicSymMatrix = theMinimum!!.error().matrix()
@@ -121,7 +121,7 @@ class MnMinos(fcn: MultiFunction?, min: FunctionMinimum?, stra: MnStrategy?) {
             upar.setValue(ext, upar.value(ext) - xdev)
         }
         upar.fix(par)
-        upar.setValue(par, `val`)
+        upar.setValue(par, value)
         val toler = 0.1
         val cross = MnFunctionCross(theFCN, upar, theMinimum!!.fval(), theStrategy, errDef)
         val aopt: MnCross = cross.cross(para, xmid, xdir, toler, maxcalls)
@@ -330,8 +330,8 @@ class MnMinos(fcn: MultiFunction?, min: FunctionMinimum?, stra: MnStrategy?) {
         val para = intArrayOf(par)
         val upar: MnUserParameterState = theMinimum!!.userState().copy()
         val err: Double = upar.error(par)
-        val `val`: Double = upar.value(par) + err
+        val value: Double = upar.value(par) + err
-        val xmid = doubleArrayOf(`val`)
+        val xmid = doubleArrayOf(value)
         val xdir = doubleArrayOf(err)
         val ind: Int = upar.intOfExt(par)
         val m: MnAlgebraicSymMatrix = theMinimum!!.error().matrix()
@@ -345,7 +345,7 @@ class MnMinos(fcn: MultiFunction?, min: FunctionMinimum?, stra: MnStrategy?) {
             upar.setValue(ext, upar.value(ext) + xdev)
         }
         upar.fix(par)
-        upar.setValue(par, `val`)
+        upar.setValue(par, value)
         val toler = 0.1
         val cross = MnFunctionCross(theFCN, upar, theMinimum!!.fval(), theStrategy, errDef)
         val aopt: MnCross = cross.cross(para, xmid, xdir, toler, maxcalls)

kmath-optimization/src/commonMain/tmp/minuit/MnSeedGenerator.kt

@@ -52,17 +52,9 @@ internal class MnSeedGenerator : MinimumSeedGenerator {
                     val delta: Double = hgrd.getSecond().getEntry(i)
                     if (abs(calculated - provided) > delta) {
                         MINUITPlugin.logStatic(
-                            ""
+                            """gradient discrepancy of external parameter "%d" (internal parameter "%d") too large. Expected: "%f", provided: "%f"""",
-                                    + "gradient discrepancy of external parameter \"%d\" "
-                                    + "(internal parameter \"%d\") too large. Expected: \"%f\", provided: \"%f\"",
                             st.getTransformation().extOfInt(i), i, provided, calculated
                         )
-
-//                        
-//                        MINUITPlugin.logStatic("gradient discrepancy of external parameter "
-//                                + st.getTransformation().extOfInt(i) 
-//                                + " (internal parameter " + i + ") too large.");
-//                        good = false;
                     }
                 }
                 if (!good) {
@@ -84,10 +76,7 @@ internal class MnSeedGenerator : MinimumSeedGenerator {
             dcovar = 0.0
         } else {
             for (i in 0 until n) {
-                mat[i, i] = if (abs(
+                mat[i, i] = if (abs(dgrad.getGradientDerivative().getEntry(i)) > prec.eps2()
-                        dgrad.getGradientDerivative()
-                            .getEntry(i)
-                    ) > prec.eps2()
                 ) 1.0 / dgrad.getGradientDerivative().getEntry(i) else 1.0
             }
         }

kmath-optimization/src/commonMain/tmp/minuit/MnUserParameterState.kt

@@ -235,9 +235,9 @@ class MnUserParameterState {
      * @param val a double.
      * @param name a [String] object.
      */
-    fun add(name: String, `val`: Double, err: Double) {
+    fun add(name: String, value: Double, err: Double) {
-        theParameters.add(name, `val`, err)
+        theParameters.add(name, value, err)
-        theIntParameters.add(`val`)
+        theIntParameters.add(value)
         theCovarianceValid = false
         theGCCValid = false
         theValid = true
@@ -252,10 +252,10 @@ class MnUserParameterState {
      * @param err a double.
      * @param up a double.
      */
-    fun add(name: String, `val`: Double, err: Double, low: Double, up: Double) {
+    fun add(name: String, value: Double, err: Double, low: Double, up: Double) {
-        theParameters.add(name, `val`, err, low, up)
+        theParameters.add(name, value, err, low, up)
         theCovarianceValid = false
-        theIntParameters.add(ext2int(index(name), `val`))
+        theIntParameters.add(ext2int(index(name), value))
         theGCCValid = false
         theValid = true
     }
@@ -266,8 +266,8 @@ class MnUserParameterState {
      * @param name a [String] object.
      * @param val a double.
      */
-    fun add(name: String, `val`: Double) {
+    fun add(name: String, value: Double) {
-        theParameters.add(name, `val`)
+        theParameters.add(name, value)
         theValid = true
     }
 
@@ -331,8 +331,8 @@ class MnUserParameterState {
         return theParameters.errors()
     }
 
-    fun ext2int(i: Int, `val`: Double): Double {
+    fun ext2int(i: Int, value: Double): Double {
-        return theParameters.trafo().ext2int(i, `val`)
+        return theParameters.trafo().ext2int(i, value)
     }
 
     /**
@@ -426,8 +426,8 @@ class MnUserParameterState {
     }
 
     // transformation internal <-> external
-    fun int2ext(i: Int, `val`: Double): Double {
+    fun int2ext(i: Int, value: Double): Double {
-        return theParameters.trafo().int2ext(i, `val`)
+        return theParameters.trafo().int2ext(i, value)
     }
 
     fun intCovariance(): MnUserCovariance {
@@ -700,14 +700,14 @@ class MnUserParameterState {
      * @param e a int.
      * @param val a double.
      */
-    fun setValue(e: Int, `val`: Double) {
+    fun setValue(e: Int, value: Double) {
-        theParameters.setValue(e, `val`)
+        theParameters.setValue(e, value)
         if (!parameter(e).isFixed() && !parameter(e).isConst()) {
             val i = intOfExt(e)
             if (parameter(e).hasLimits()) {
-                theIntParameters[i] = ext2int(e, `val`)
+                theIntParameters[i] = ext2int(e, value)
             } else {
-                theIntParameters[i] = `val`
+                theIntParameters[i] = value
             }
         }
     }
@@ -719,8 +719,8 @@ class MnUserParameterState {
      * @param name a [String] object.
      * @param val a double.
      */
-    fun setValue(name: String?, `val`: Double) {
+    fun setValue(name: String?, value: Double) {
-        setValue(index(name), `val`)
+        setValue(index(name), value)
     }
 
     /** {@inheritDoc}  */

kmath-optimization/src/commonMain/tmp/minuit/MnUserParameters.kt

@@ -65,8 +65,8 @@ class MnUserParameters {
      * @param val a double.
      * @param name a [String] object.
      */
-    fun add(name: String, `val`: Double, err: Double) {
+    fun add(name: String, value: Double, err: Double) {
-        theTransformation.add(name, `val`, err)
+        theTransformation.add(name, value, err)
     }
 
     /**
@@ -78,8 +78,8 @@ class MnUserParameters {
      * @param val a double.
      * @param err a double.
      */
-    fun add(name: String, `val`: Double, err: Double, low: Double, up: Double) {
+    fun add(name: String, value: Double, err: Double, low: Double, up: Double) {
-        theTransformation.add(name, `val`, err, low, up)
+        theTransformation.add(name, value, err, low, up)
     }
 
     /**
@@ -88,8 +88,8 @@ class MnUserParameters {
      * @param name a [String] object.
      * @param val a double.
      */
-    fun add(name: String, `val`: Double) {
+    fun add(name: String, value: Double) {
-        theTransformation.add(name, `val`)
+        theTransformation.add(name, value)
     }
 
     /**
@@ -344,8 +344,8 @@ class MnUserParameters {
      * @param index a int.
      * @param val a double.
      */
-    fun setValue(index: Int, `val`: Double) {
+    fun setValue(index: Int, value: Double) {
-        theTransformation.setValue(index, `val`)
+        theTransformation.setValue(index, value)
     }
 
     /**
@@ -355,8 +355,8 @@ class MnUserParameters {
      * @param name a [String] object.
      * @param val a double.
      */
-    fun setValue(name: String?, `val`: Double) {
+    fun setValue(name: String?, value: Double) {
-        theTransformation.setValue(name, `val`)
+        theTransformation.setValue(name, value)
     }
 
     /** {@inheritDoc}  */

kmath-optimization/src/commonMain/tmp/minuit/MnUserTransformation.kt

@@ -64,12 +64,12 @@ class MnUserTransformation {
      * @param err
      * @param val
      */
-    fun add(name: String, `val`: Double, err: Double) {
+    fun add(name: String, value: Double, err: Double) {
         require(!nameMap.containsKey(name)) { "duplicate name: $name" }
         nameMap[name] = theParameters.size
         theExtOfInt.add(theParameters.size)
-        theCache.add(`val`)
+        theCache.add(value)
-        theParameters.add(MinuitParameter(theParameters.size, name, `val`, err))
+        theParameters.add(MinuitParameter(theParameters.size, name, value, err))
     }
 
     /**
@@ -77,12 +77,12 @@ class MnUserTransformation {
      * @param up
      * @param low
      */
-    fun add(name: String, `val`: Double, err: Double, low: Double, up: Double) {
+    fun add(name: String, value: Double, err: Double, low: Double, up: Double) {
         require(!nameMap.containsKey(name)) { "duplicate name: $name" }
         nameMap[name] = theParameters.size
         theExtOfInt.add(theParameters.size)
-        theCache.add(`val`)
+        theCache.add(value)
-        theParameters.add(MinuitParameter(theParameters.size, name, `val`, err, low, up))
+        theParameters.add(MinuitParameter(theParameters.size, name, value, err, low, up))
     }
 
     /**
@@ -90,11 +90,11 @@ class MnUserTransformation {
      * @param name
      * @param val
      */
-    fun add(name: String, `val`: Double) {
+    fun add(name: String, value: Double) {
         require(!nameMap.containsKey(name)) { "duplicate name: $name" }
         nameMap[name] = theParameters.size
-        theCache.add(`val`)
+        theCache.add(value)
-        theParameters.add(MinuitParameter(theParameters.size, name, `val`))
+        theParameters.add(MinuitParameter(theParameters.size, name, value))
     }
 
     /**
@@ -107,20 +107,20 @@ class MnUserTransformation {
         return MnUserTransformation(this)
     }
 
-    fun dInt2Ext(i: Int, `val`: Double): Double {
+    fun dInt2Ext(i: Int, value: Double): Double {
         var dd = 1.0
         val parm: MinuitParameter = theParameters[theExtOfInt[i]]
         if (parm.hasLimits()) {
             dd = if (parm.hasUpperLimit() && parm.hasLowerLimit()) {
                 theDoubleLimTrafo.dInt2Ext(
-                    `val`,
+                    value,
                     parm.upperLimit(),
                     parm.lowerLimit()
                 )
             } else if (parm.hasUpperLimit() && !parm.hasLowerLimit()) {
-                theUpperLimTrafo.dInt2Ext(`val`, parm.upperLimit())
+                theUpperLimTrafo.dInt2Ext(value, parm.upperLimit())
             } else {
-                theLowerLimTrafo.dInt2Ext(`val`, parm.lowerLimit())
+                theLowerLimTrafo.dInt2Ext(value, parm.lowerLimit())
             }
         }
         return dd
@@ -143,30 +143,30 @@ class MnUserTransformation {
         return result
     }
 
-    fun ext2int(i: Int, `val`: Double): Double {
+    fun ext2int(i: Int, value: Double): Double {
         val parm: MinuitParameter = theParameters[i]
         return if (parm.hasLimits()) {
             if (parm.hasUpperLimit() && parm.hasLowerLimit()) {
                 theDoubleLimTrafo.ext2int(
-                    `val`,
+                    value,
                     parm.upperLimit(),
                     parm.lowerLimit(),
                     precision()
                 )
             } else if (parm.hasUpperLimit() && !parm.hasLowerLimit()) {
                 theUpperLimTrafo.ext2int(
-                    `val`,
+                    value,
                     parm.upperLimit(),
                     precision()
                 )
             } else {
                 theLowerLimTrafo.ext2int(
-                    `val`,
+                    value,
                     parm.lowerLimit(),
                     precision()
                 )
             }
-        } else `val`
+        } else value
     }
 
     fun extOfInt(internal: Int): Int {
@@ -200,21 +200,21 @@ class MnUserTransformation {
         return nameMap[name]!!
     }
 
-    fun int2ext(i: Int, `val`: Double): Double {
+    fun int2ext(i: Int, value: Double): Double {
         val parm: MinuitParameter = theParameters[theExtOfInt[i]]
         return if (parm.hasLimits()) {
             if (parm.hasUpperLimit() && parm.hasLowerLimit()) {
                 theDoubleLimTrafo.int2ext(
-                    `val`,
+                    value,
                     parm.upperLimit(),
                     parm.lowerLimit()
                 )
             } else if (parm.hasUpperLimit() && !parm.hasLowerLimit()) {
-                theUpperLimTrafo.int2ext(`val`, parm.upperLimit())
+                theUpperLimTrafo.int2ext(value, parm.upperLimit())
             } else {
-                theLowerLimTrafo.int2ext(`val`, parm.lowerLimit())
+                theLowerLimTrafo.int2ext(value, parm.lowerLimit())
             }
-        } else `val`
+        } else value
     }
 
     fun int2extCovariance(vec: RealVector, cov: MnAlgebraicSymMatrix): MnUserCovariance {
@@ -235,13 +235,13 @@ class MnUserTransformation {
         return result
     }
 
-    fun int2extError(i: Int, `val`: Double, err: Double): Double {
+    fun int2extError(i: Int, value: Double, err: Double): Double {
         var dx = err
         val parm: MinuitParameter = theParameters[theExtOfInt[i]]
         if (parm.hasLimits()) {
-            val ui = int2ext(i, `val`)
+            val ui = int2ext(i, value)
-            var du1 = int2ext(i, `val` + dx) - ui
+            var du1 = int2ext(i, value + dx) - ui
-            val du2 = int2ext(i, `val` - dx) - ui
+            val du2 = int2ext(i, value - dx) - ui
             if (parm.hasUpperLimit() && parm.hasLowerLimit()) {
                 if (dx > 1.0) {
                     du1 = parm.upperLimit() - parm.lowerLimit()
@@ -354,13 +354,13 @@ class MnUserTransformation {
         setUpperLimit(index(name), up)
     }
 
-    fun setValue(index: Int, `val`: Double) {
+    fun setValue(index: Int, value: Double) {
-        theParameters[index].setValue(`val`)
+        theParameters[index].setValue(value)
-        theCache[index] = `val`
+        theCache[index] = value
     }
 
-    fun setValue(name: String?, `val`: Double) {
+    fun setValue(name: String?, value: Double) {
-        setValue(index(name), `val`)
+        setValue(index(name), value)
     }
 
     fun transform(pstates: RealVector): ArrayRealVector {

kmath-optimization/src/commonMain/tmp/minuit/NegativeG2LineSearch.kt

@@ -71,10 +71,7 @@ internal object NegativeG2LineSearch {
         } while (iter++ < 2 * n && iterate)
         val mat = MnAlgebraicSymMatrix(n)
         for (i in 0 until n) {
-            mat[i, i] = if (abs(
+            mat[i, i] = if (abs(dgrad.getGradientDerivative().getEntry(i)) > prec.eps2()
-                    dgrad.getGradientDerivative()
-                        .getEntry(i)
-                ) > prec.eps2()
             ) 1.0 / dgrad.getGradientDerivative().getEntry(i) else 1.0
         }
         val err = MinimumError(mat, 1.0)

kmath-optimization/src/commonMain/tmp/minuit/SimplexSeedGenerator.kt

@@ -41,10 +41,7 @@ internal class SimplexSeedGenerator : MinimumSeedGenerator {
         val mat = MnAlgebraicSymMatrix(n)
         val dcovar = 1.0
         for (i in 0 until n) {
-            mat[i, i] = if (abs(
+            mat[i, i] = if (abs(dgrad.getGradientDerivative().getEntry(i)) > prec.eps2()
-                    dgrad.getGradientDerivative()
-                        .getEntry(i)
-                ) > prec.eps2()
             ) 1.0 / dgrad.getGradientDerivative().getEntry(i) else 1.0
         }
         val err = MinimumError(mat, dcovar)