public class InferFromMatrix extends Object
| Modifier and Type | Class and Description |
|---|---|
static class |
InferFromMatrix.BorderRegularization |
static class |
InferFromMatrix.IdentityRegularization |
static class |
InferFromMatrix.ModelRegularization |
static class |
InferFromMatrix.NoRegularization |
static class |
InferFromMatrix.RegularizationType |
static interface |
InferFromMatrix.Regularizer |
| Constructor and Description |
|---|
InferFromMatrix(AbstractCorrelationFit correlationFit) |
| Modifier and Type | Method and Description |
|---|---|
void |
applyShifts(double[] coordinates,
double[] shifts,
double[] regularizerCoordinates,
PermutationTransform permutation,
Options options) |
<T extends RealType<T> & NativeType<T>,W extends RealType<W>> |
estimateZCoordinates(RandomAccessibleInterval<T> inputMatrix,
double[] startingCoordinates,
double[] functionEstimate,
double[] scalingFactors,
RandomAccessibleInterval<W> estimateWeights,
double[] shiftWeights,
Visitor visitor,
Options options) |
<T extends RealType<T> & NativeType<T>> |
estimateZCoordinates(RandomAccessibleInterval<T> matrix,
double[] startingCoordinates,
Options options) |
<T extends RealType<T> & NativeType<T>> |
estimateZCoordinates(RandomAccessibleInterval<T> inputMatrix,
double[] startingCoordinates,
Visitor visitor,
Options options) |
static <T extends RealType<T>> |
fillWeightStrip(RandomAccessibleInterval<T> strip,
double[] weights,
T t) |
<T extends RealType<T>,W extends RealType<W>> |
getMediatedShifts(RandomAccessibleInterval<T> matrix,
RandomAccessibleInterval<T> scaledMatrix,
double[] lut,
double[] scalingFactors,
int iteration,
RandomAccessibleInterval<double[]>[] correlationFitsStore,
double[] shiftsArray,
double[] weightSums,
RandomAccessibleInterval<W> estimateWeightMatrix,
double[] shiftWeights,
Options options) |
static boolean |
isIdentity(double[] mapping) |
static void |
mediateShifts(double[] shifts,
double[] weightSums,
double[] mediatedShifts) |
void |
preventReorder(double[] coordinates,
Options options) |
void |
updateArray(double[] source,
double[] target,
int[] permutation) |
public InferFromMatrix(AbstractCorrelationFit correlationFit)
public <T extends RealType<T> & NativeType<T>> double[] estimateZCoordinates(RandomAccessibleInterval<T> matrix, double[] startingCoordinates, Options options) throws Exception
Exceptionpublic <T extends RealType<T> & NativeType<T>> double[] estimateZCoordinates(RandomAccessibleInterval<T> inputMatrix, double[] startingCoordinates, Visitor visitor, Options options) throws Exception
Exceptionpublic <T extends RealType<T> & NativeType<T>,W extends RealType<W>> double[] estimateZCoordinates(RandomAccessibleInterval<T> inputMatrix, double[] startingCoordinates, double[] functionEstimate, double[] scalingFactors, RandomAccessibleInterval<W> estimateWeights, double[] shiftWeights, Visitor visitor, Options options) throws Exception
Exceptionpublic <T extends RealType<T>,W extends RealType<W>> double[] getMediatedShifts(RandomAccessibleInterval<T> matrix, RandomAccessibleInterval<T> scaledMatrix, double[] lut, double[] scalingFactors, int iteration, RandomAccessibleInterval<double[]>[] correlationFitsStore, double[] shiftsArray, double[] weightSums, RandomAccessibleInterval<W> estimateWeightMatrix, double[] shiftWeights, Options options) throws NotEnoughDataPointsException, IllDefinedDataPointsException
public void applyShifts(double[] coordinates,
double[] shifts,
double[] regularizerCoordinates,
PermutationTransform permutation,
Options options)
public void preventReorder(double[] coordinates,
Options options)
public void updateArray(double[] source,
double[] target,
int[] permutation)
public static void mediateShifts(double[] shifts,
double[] weightSums,
double[] mediatedShifts)
public static <T extends RealType<T>> void fillWeightStrip(RandomAccessibleInterval<T> strip, double[] weights, T t)
public static boolean isIdentity(double[] mapping)
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