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A

add(double[], double[]) - Method in class wsh.opt.CoordinateTransform

Add an observation of a set of input and output coordinates You should add enough of these to determine (or overdetermine) a unique linear mapping.

add(double, double, VectConst) - Method in class wsh.opt.ArrayVect1

add(double, double, VectConst) - Method in interface wsh.opt.Vect

Add a scaled version of another vector to a scaled version of this vector.

addGlobalLogFile(String) - Static method in class wsh.util.CleanHandler

All CleanHandlers will also log to this file.

addTranspose(VectConst, Vect) - Method in interface wsh.opt.LinearTransform

Apply the transpose of a linear transform model = F' data Add to existing data.

addTranspose(VectConst, Vect, VectConst) - Method in class wsh.opt.LinearTransformWrapper

addTranspose(VectConst, Vect, VectConst) - Method in interface wsh.opt.Transform

The transpose of the linearized approximation of the forward transform for a small perturbation (model) to a reference model (modelReference): model = F' data.

adjustRobustErrors(Vect) - Method in interface wsh.opt.LinearTransform

Apply any robust trimming of outliers, or scale all errors for an approximate L1 norm when squared.

adjustRobustErrors(Vect) - Method in class wsh.opt.LinearTransformWrapper

adjustRobustErrors(Vect) - Method in interface wsh.opt.Transform

Apply any robust trimming of outliers, or scale all errors for an approximate L1 norm when squared.

Almost - Class in wsh.util

This class allows safe comparisons of floating point numbers with limited precision.

Almost() - Constructor for class wsh.util.Almost

Accept default precision, appropriate for arithmetic on floats.

Almost(boolean) - Constructor for class wsh.util.Almost

Constructor that allows either double or float precision.

Almost(double) - Constructor for class wsh.util.Almost

Specify precision to be used for operations.

Almost(double, double) - Constructor for class wsh.util.Almost

Specify precision to be used for operations.

Almost(int) - Constructor for class wsh.util.Almost

Specify precision to be used for operations.

ALMOST_DOT - Static variable in class wsh.opt.VectUtil

AlmostTest - Class in wsh.util.test

Wrap another class Almost for junit testing.

AlmostTest(String) - Constructor for class wsh.util.test.AlmostTest

Standard constructor calls TestCase(name) constructor

areSame(VectConst, VectConst) - Static method in class wsh.opt.VectUtil

See if two vectors are the same.

ArrayMath - Class in wsh.util

Utility method required by a test.

ArrayMath() - Constructor for class wsh.util.ArrayMath

ArrayVect1 - Class in wsh.opt

Implements a Vect by wrapping an array of doubles.

ArrayVect1() - Constructor for class wsh.opt.ArrayVect1

To be used with init()

ArrayVect1(double[], double) - Constructor for class wsh.opt.ArrayVect1

Construct from an array of data.

ArrayVect1Test - Class in wsh.opt.test

Wrap wsh.opt.ArrayVect1 for junit testing.

ArrayVect1Test(String) - Constructor for class wsh.opt.test.ArrayVect1Test

Standard constructor calls TestCase(name) constructor

B

between(double, double, double) - Method in class wsh.util.Almost

See if value is between two other values, including almost equality

C

cancel() - Method in class wsh.util.LogMonitor

Interrupt any further work.

checkError() - Method in class wsh.util.LoggerStream

CleanFormatter - Class in wsh.util

Format log messages without any extras.

CleanFormatter() - Constructor for class wsh.util.CleanFormatter

CleanFormatterTest - Class in wsh.util.test

Wrap wsh.util.CleanFormatter for junit testing.

CleanFormatterTest(String) - Constructor for class wsh.util.test.CleanFormatterTest

Standard constructor calls TestCase(name) constructor

CleanHandler - Class in wsh.util

An alternative to ConsoleHandler.

CleanHandler() - Constructor for class wsh.util.CleanHandler

Construct a new CleanHandler.

clone() - Method in class wsh.opt.ArrayVect1

clone() - Method in interface wsh.opt.Vect

clone() - Method in interface wsh.opt.VectConst

cloneZero(VectConst) - Static method in class wsh.opt.VectUtil

Clone a vector and initialized to zero, so that out.dot(out) == 0.

close() - Method in class wsh.util.CleanHandler

close() - Method in class wsh.util.LoggerStream

cmp(double, double) - Method in class wsh.util.Almost

Check order of two numbers, within precision.

compare(Number, Number) - Method in class wsh.util.Almost

constrain() - Method in class wsh.opt.ArrayVect1

constrain() - Method in interface wsh.opt.Vect

Optionally apply a hard constraint (such as an inequality) to the current vector.

CoordinateTransform - Class in wsh.opt

Find a best linear combination of input coordinates to fit output coordinates.

CoordinateTransform(int, int) - Constructor for class wsh.opt.CoordinateTransform

Constructor sets number of input and output coordinates.

CoordinateTransformTest - Class in wsh.opt.test

Wrap wsh.opt.CoordinateTransform for junit testing.

CoordinateTransformTest(String) - Constructor for class wsh.opt.test.CoordinateTransformTest

Standard constructor calls TestCase(name) constructor

copy(double[][]) - Static method in class wsh.util.ArrayMath

Deep copy of a double array

copy(Vect, VectConst) - Static method in class wsh.opt.VectUtil

Copy the state of one vector onto another.

D

DBL_EPSILON - Static variable in class wsh.util.MathPlus

The smallest double value e such that (1+e) does not equal 1.

dispose() - Method in class wsh.opt.ArrayVect1

dispose() - Method in class wsh.opt.TransformQuadratic

Free up internal cached vectors

dispose() - Method in interface wsh.opt.Vect

Optionally free any resources held by this object.

divide(double, double, boolean) - Method in class wsh.util.Almost

Safely divide one number by another.

divide(double, double, double) - Method in class wsh.util.Almost

Safely divide one number by another.

dot(VectConst) - Method in class wsh.opt.ArrayVect1

dot(VectConst) - Method in interface wsh.opt.VectConst

Return the Cartesian dot product of this vector with another vector (not including any inverse covariance).

DOUBLE - Static variable in class wsh.util.Almost

This instance uses default double precision

E

equal(double, double) - Method in class wsh.util.Almost

See if two numbers are almost equal.

equals(Object) - Method in class wsh.util.Almost

evalFullObjectiveFunction(VectConst) - Method in class wsh.opt.TransformQuadratic

Evaluate the full objective function without approximation.

F

filter(String, Class<?>) - Static method in class wsh.util.Localize

Deprecated.

Prefer other methods for standard localization.

filter(String, ResourceBundle) - Static method in class wsh.util.Localize

Filter the specified string with the specified resource bundle.

FLOAT - Static variable in class wsh.util.Almost

This instance uses default float precision

FLT_EPSILON - Static variable in class wsh.util.MathPlus

The smallest float value e such that (1+e) does not equal 1.

flush() - Method in class wsh.util.CleanHandler

flush() - Method in class wsh.util.LoggerStream

format(String, Object...) - Method in class wsh.util.Localize

Format a localized message, with java.util.Formatter and the appropriate resource.

format(LogRecord) - Method in class wsh.util.CleanFormatter

forward(Vect, VectConst) - Method in interface wsh.opt.LinearTransform

Apply the linear transform data = F model Zero the current data, and do not add.

forwardLinearized(Vect, VectConst, VectConst) - Method in class wsh.opt.LinearTransformWrapper

forwardLinearized(Vect, VectConst, VectConst) - Method in interface wsh.opt.Transform

A linearized approximation of the forward transform for a small perturbation (model) to a reference model (modelReference).

forwardNonlinear(Vect, VectConst) - Method in class wsh.opt.LinearTransformWrapper

forwardNonlinear(Vect, VectConst) - Method in interface wsh.opt.Transform

Non-linear transform: data = f(model).

function(double) - Method in interface wsh.opt.ScalarSolver.Function

Return a single value as a function of the argument

G

GaussNewtonSolver - Class in wsh.opt

Solve least-squares inverse of a non-linear Transform.

GaussNewtonSolverTest - Class in wsh.opt.test

Solve least-squares inverse of a Transform.

GaussNewtonSolverTest(String) - Constructor for class wsh.opt.test.GaussNewtonSolverTest

Standard constructor calls TestCase(name) constructor

ge(double, double) - Method in class wsh.util.Almost

Check whether first number is greater than or equal to second.

get(double[]) - Method in class wsh.opt.CoordinateTransform

For a given set of input coordinates, return the linearly predicted output coordinates.

getB() - Method in interface wsh.opt.Quadratic

Get the linear gradient term b of the quadratic expression.

getB() - Method in class wsh.opt.TransformQuadratic

Return gradient term of quadratic.

getData() - Method in class wsh.opt.ArrayVect1

Get the embedded data

getEpsilon() - Method in class wsh.util.Almost

Get the smallest positive number that can be added to 1 before the number is considered different from 1.

getMessage(Throwable) - Static method in class wsh.util.Localize

Get the best localized message from a Throwable that may contain other Throwables as a cause.

getMinValue() - Method in class wsh.util.Almost

Get the smallest positive value that should be distinguished from zero.

getProgressReport(long, long, double, double) - Static method in class wsh.util.LogMonitor

Get a user-viewable String describing the progress and completion time.

getResourceBundle(Class<?>, String, Locale) - Static method in class wsh.util.Localize

Get a resource bundle associated with a class.

getSize() - Method in class wsh.opt.ArrayVect1

Return the size of the embedded array

getTransposePrecision() - Method in class wsh.opt.TransformQuadratic

Run a few tests to ensure that transpose satisfies definition.

getTransposePrecision(VectConst, VectConst, LinearTransform) - Static method in class wsh.opt.VectUtil

Return the number of significant digits in the dot product when calculated with and without the transpose.

getTransposePrecision(VectConst, VectConst, Transform) - Static method in class wsh.opt.VectUtil

Return the number of significant digits in the dot product when calculated with and without the transpose.

gt(double, double) - Method in class wsh.util.Almost

Check whether first number is strictly greater than second.

H

hashCode() - Method in class wsh.util.Almost

hashCodeOf(Number) - Method in class wsh.util.Almost

Return a hashcode consistent with imprecise floating-point equality.

hashCodeOf(Number, int) - Method in class wsh.util.Almost

Return a hashcode consistent with imprecise floating-point equality.

I

init(double[], double) - Method in class wsh.opt.ArrayVect1

Construct from an array of data.

initReport(double) - Method in class wsh.util.LogMonitor

initReport(double) - Method in interface wsh.util.Monitor

Initialize the fraction of the work that was completed when the process started.

initReport(double) - Method in class wsh.util.PartialMonitor

inverseHessian(Vect) - Method in interface wsh.opt.LinearTransform

To speed convergence multiple a model by an approximate inverse Hessian.

inverseHessian(Vect) - Method in interface wsh.opt.Quadratic

Multiply vector by an approximate inverse of the Hessian.

inverseHessian(Vect) - Method in class wsh.opt.TransformQuadratic

inverseHessian(Vect, VectConst) - Method in class wsh.opt.LinearTransformWrapper

inverseHessian(Vect, VectConst) - Method in interface wsh.opt.Transform

To speed convergence multiple a model by an approximate inverse Hessian.

isCanceled() - Method in class wsh.util.LogMonitor

isCanceled() - Method in interface wsh.util.Monitor

If true, then any further progress should be cancelled.

isCanceled() - Method in class wsh.util.PartialMonitor

L

le(double, double) - Method in class wsh.util.Almost

Check whether first number is less than or equal to second.

LinearTransform - Interface in wsh.opt

Define methods applying a linear transform and its transpose

LinearTransformWrapper - Class in wsh.opt

Wrap a LinearTransform as a non-linear Transform, by ignoring reference model.

LinearTransformWrapper(LinearTransform) - Constructor for class wsh.opt.LinearTransformWrapper

Constructor.

Localize - Class in wsh.util

Localize messages for end users, using a Formatter pattern and a localized resource bundle.

Localize(Class<?>) - Constructor for class wsh.util.Localize

Construct for localized messages.

Localize(Class<?>, String) - Constructor for class wsh.util.Localize

Construct for localized messages.

Localize(Class<?>, String, Locale) - Constructor for class wsh.util.Localize

Construct for localized messages.

LocalizeTest - Class in wsh.util.test

Wrap wsh.util.Localize for junit testing.

LocalizeTest(String) - Constructor for class wsh.util.test.LocalizeTest

Standard constructor calls TestCase(name) constructor

LoggerStream - Class in wsh.util

Wrap a Logger as a PrintStream.

LoggerStream(Logger, Level) - Constructor for class wsh.util.LoggerStream

Wrap a Logger as a PrintStream .

LogMonitor - Class in wsh.util

Report progress to default Logger

LogMonitor(String, Logger) - Constructor for class wsh.util.LogMonitor

Progress will be reported to this Logger.

lt(double, double) - Method in class wsh.util.Almost

Check whether first number is strictly less than second.

M

magnitude() - Method in class wsh.opt.ArrayVect1

magnitude() - Method in interface wsh.opt.VectConst

This is the dot product of the vector with itself premultiplied by the inverse covariance.

main(String[]) - Static method in class wsh.opt.test.ArrayVect1Test

Run all tests with text gui if this class main is invoked

main(String[]) - Static method in class wsh.opt.test.CoordinateTransformTest

Run all tests with text gui if this class main is invoked

main(String[]) - Static method in class wsh.opt.test.GaussNewtonSolverTest

Run all tests with text gui if this class main is invoked

main(String[]) - Static method in class wsh.opt.test.QuadraticSolverTest

Run all tests with text gui if this class main is invoked

main(String[]) - Static method in class wsh.opt.test.ScalarSolverTest

Run all tests with text gui if this class main is invoked

main(String[]) - Static method in class wsh.util.CleanHandler

Test code

main(String[]) - Static method in class wsh.util.LoggerStream

test code

main(String[]) - Static method in class wsh.util.LogMonitor

run tests

main(String[]) - Static method in class wsh.util.test.AlmostTest

Run all tests with text gui if this class main is invoked

main(String[]) - Static method in class wsh.util.test.CleanFormatterTest

Run all tests with text gui if this class main is invoked

main(String[]) - Static method in class wsh.util.test.LocalizeTest

Run all tests with text gui if this class main is invoked

MathPlus - Class in wsh.util

Constants required by a test.

MathPlus() - Constructor for class wsh.util.MathPlus

Monitor - Interface in wsh.util

Implement this interface to receive notifications of progress

multiplyHessian(Vect) - Method in interface wsh.opt.Quadratic

Multiply vector by the quadratic Hessian H.

multiplyHessian(Vect) - Method in class wsh.opt.TransformQuadratic

Multiply by Hessian H = F'NF + M

multiplyInverseCovariance() - Method in class wsh.opt.ArrayVect1

multiplyInverseCovariance() - Method in interface wsh.opt.Vect

Optionally multiply a vector by the inverse covariance matrix.

N

NULL_MONITOR - Static variable in interface wsh.util.Monitor

Empty implementation that does nothing.

O

outside(double, double, double) - Method in class wsh.util.Almost

See if value is outside two other values.

overrideExistingHandlers(Level) - Static method in class wsh.util.CleanHandler

Override any previously specified Handlers with the CleanHandler, and set Level.

P

PartialMonitor - Class in wsh.util

Wrap an existing Monitor with a partial range.

PartialMonitor(Monitor, double, double) - Constructor for class wsh.util.PartialMonitor

An existing Monitor will be wrapped for progress in a limited range.

postCondition() - Method in class wsh.opt.ArrayVect1

postCondition() - Method in interface wsh.opt.Vect

Apply a linear filter that enhances components that should be optimized first, and suppresses components of lesser importance.

prependToLines(String, String) - Static method in class wsh.util.CleanFormatter

Prepend a string to every line of text in a String

println() - Method in class wsh.util.LoggerStream

println(Object) - Method in class wsh.util.LoggerStream

println(String) - Method in class wsh.util.LoggerStream

project(double, double, VectConst) - Method in class wsh.opt.ArrayVect1

project(double, double, VectConst) - Method in interface wsh.opt.Vect

Project another vector onto the space of this vector, then scale, and add to a scaled version of this vector.

publish(LogRecord) - Method in class wsh.util.CleanHandler

Q

Quadratic - Interface in wsh.opt

Define a second-order quadratic operation on a Vector 0.5 x'Hx + b'x where H is a positive semidefinite quadratic and b is a linear gradient.

QuadraticSolver - Class in wsh.opt

Minimize a simple quadratic objective function.

QuadraticSolver(Quadratic) - Constructor for class wsh.opt.QuadraticSolver

Implement the Quadratic interface and pass to this constructor.

QuadraticSolverTest - Class in wsh.opt.test

Wrap wsh.opt.QuadraticSolver for junit testing.

QuadraticSolverTest(String) - Constructor for class wsh.opt.test.QuadraticSolverTest

Standard constructor calls TestCase(name) constructor

R

reciprocal(double) - Method in class wsh.util.Almost

Safely take the reciprocal of a number.

report(double) - Method in class wsh.util.LogMonitor

report(double) - Method in interface wsh.util.Monitor

This method will be called with the current fraction of work done.

report(double) - Method in class wsh.util.PartialMonitor

S

ScalarSolver - Class in wsh.opt

Search a single variable for a value that minimizes a function

ScalarSolver(ScalarSolver.Function) - Constructor for class wsh.opt.ScalarSolver

Constructor

ScalarSolver.Function - Interface in wsh.opt

Implement a function of one variable to be minimized

ScalarSolverTest - Class in wsh.opt.test

Wrap wsh.opt.ScalarSolver for junit testing.

ScalarSolverTest(String) - Constructor for class wsh.opt.test.ScalarSolverTest

Standard constructor calls TestCase(name) constructor

scale(Vect, double) - Static method in class wsh.opt.VectUtil

Scale a vector by a scalar constant.

serialVersionUID - Static variable in class wsh.util.Almost

setDefaultHandler() - Static method in class wsh.util.CleanHandler

If the user has not specified a java property for the global Handler, then set the default global handler to this CleanHandler at an INFO level.

setExpensiveDebug(boolean) - Static method in class wsh.opt.GaussNewtonSolver

Turn on expensive checking of transform and vector properties during solving of equations.

setUp() - Method in class wsh.opt.test.ArrayVect1Test

setUp() - Method in class wsh.opt.test.CoordinateTransformTest

setUp() - Method in class wsh.opt.test.GaussNewtonSolverTest

setUp() - Method in class wsh.opt.test.QuadraticSolverTest

setUp() - Method in class wsh.opt.test.ScalarSolverTest

setUp() - Method in class wsh.util.test.AlmostTest

setUp() - Method in class wsh.util.test.CleanFormatterTest

setUp() - Method in class wsh.util.test.LocalizeTest

setWarningPrefix(String) - Static method in class wsh.util.CleanFormatter

Prefix a string to all warnings or severe errors We use this method only for unit tests, to distinguish the source of warnings.

solve(double, double, double, double, int, Monitor) - Method in class wsh.opt.ScalarSolver

Minimize a function of scalar and return the optimum value.

solve(int, Monitor) - Method in class wsh.opt.QuadraticSolver

Return a new solution after the number of conjugate gradient iterations.

solve(VectConst, VectConst, LinearTransform, boolean, int, Monitor) - Static method in class wsh.opt.QuadraticSolver

Solve quadratic objective function for linear transform.

solve(VectConst, VectConst, VectConst, Transform, boolean, int, int, int, double, Monitor) - Static method in class wsh.opt.GaussNewtonSolver

Solve nonquadratic objective function with Gauss Newton iterations.

suite() - Static method in class wsh.opt.test.ArrayVect1Test

This automatically generates a suite of all "test" methods

suite() - Static method in class wsh.opt.test.CoordinateTransformTest

This automatically generates a suite of all "test" methods

suite() - Static method in class wsh.opt.test.GaussNewtonSolverTest

This automatically generates a suite of all "test" methods

suite() - Static method in class wsh.opt.test.QuadraticSolverTest

This automatically generates a suite of all "test" methods.

suite() - Static method in class wsh.opt.test.ScalarSolverTest

This automatically generates a suite of all "test" methods.

suite() - Static method in class wsh.util.test.AlmostTest

This automatically generates a suite of all "test" methods

suite() - Static method in class wsh.util.test.CleanFormatterTest

This automatically generates a suite of all "test" methods.

suite() - Static method in class wsh.util.test.LocalizeTest

This automatically generates a suite of all "test" methods.

T

tearDown() - Method in class wsh.opt.test.ArrayVect1Test

tearDown() - Method in class wsh.opt.test.CoordinateTransformTest

tearDown() - Method in class wsh.opt.test.GaussNewtonSolverTest

tearDown() - Method in class wsh.opt.test.QuadraticSolverTest

tearDown() - Method in class wsh.opt.test.ScalarSolverTest

tearDown() - Method in class wsh.util.test.AlmostTest

tearDown() - Method in class wsh.util.test.CleanFormatterTest

tearDown() - Method in class wsh.util.test.LocalizeTest

test(VectConst) - Static method in class wsh.opt.VectUtil

Exercise all methods of Vect.

testAll() - Method in class wsh.opt.test.ArrayVect1Test

Run unit tests.

testAll() - Method in class wsh.opt.test.CoordinateTransformTest

Test CoordinateTransform class

testAll() - Method in class wsh.util.test.LocalizeTest

Junit test code

testAlmostObjectMethod() - Method in class wsh.util.test.AlmostTest

test Object methods

testEverything() - Method in class wsh.util.test.AlmostTest

Run some test code.

testFormatter() - Method in class wsh.util.test.CleanFormatterTest

Unit tests

testHashCode() - Method in class wsh.util.test.AlmostTest

test the hash code algorithm

testLeftHandSide2() - Method in class wsh.opt.test.ScalarSolverTest

Unit test

testLinearObjFunc() - Method in class wsh.opt.test.ScalarSolverTest

Unit test

testLogger() - Static method in class wsh.util.CleanHandler

Call this from your code to test each type of log message

testMain() - Method in class wsh.opt.test.GaussNewtonSolverTest

Unit test code.

testNaNs() - Method in class wsh.util.test.AlmostTest

test handling of nans

testNonUnitScalarRange() - Method in class wsh.opt.test.ScalarSolverTest

Unit test

testParabola() - Method in class wsh.opt.test.ScalarSolverTest

Unit test

testPositiveCurvature() - Method in class wsh.opt.test.ScalarSolverTest

Unit test

testPrepend() - Method in class wsh.util.test.CleanFormatterTest

Test prependToLines method

testQS() - Method in class wsh.opt.test.QuadraticSolverTest

Junit test of QuadraticSolver

testRightHandSide() - Method in class wsh.opt.test.ScalarSolverTest

Unit test

testStepFunction() - Method in class wsh.opt.test.ScalarSolverTest

Unit test

timeWords(long) - Static method in class wsh.util.Localize

Convert a number of seconds into words

toString() - Method in class wsh.opt.ArrayVect1

toString() - Method in class wsh.util.Almost

toString() - Method in class wsh.util.Localize

Transform - Interface in wsh.opt

Implement a non-linear transform and its linearizations for a non-linear optimization.

TransformQuadratic - Class in wsh.opt

For a linearized transform, implement the Gauss-Newton quadratic approximation of a damped least-squares objective function.

TransformQuadratic(VectConst, VectConst, VectConst, Transform, boolean) - Constructor for class wsh.opt.TransformQuadratic

Wrap known data, reference mode, and transform as a Gauss-Newton objectiveFunction.

V

Vect - Interface in wsh.opt

Implement a vector supporting linear vector-space methods Test your implementation with VectUtil.test().

VectConst - Interface in wsh.opt

Vector operations that do not change the state of the vector

VectUtil - Class in wsh.opt

Implements convenience methods for Vect.

W

wsh.opt - package wsh.opt

wsh.opt.test - package wsh.opt.test

wsh.util - package wsh.util

wsh.util.test - package wsh.util.test

Z

zero(double) - Method in class wsh.util.Almost

See if the number is almost zero

zero(Vect) - Static method in class wsh.opt.VectUtil

Set the magnitude of this vector to zero, so that this.dot(this) == 0.

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