maltcms.tools

Class ArrayTools

java.lang.Object

maltcms.tools.ArrayTools

public class ArrayTools
extends Object

Utility class providing methods for Sparse and Dense Arrays.

Author:

Nils.Hoffmann@cebitec.uni-bielefeld.de

Constructor Summary

Constructors

Constructor and Description
ArrayTools()

Method Summary

Methods

Modifier and Type	Method and Description
static double	calcPercentDone(long elements, long elemCnt)
static ArrayDouble.D2	combine(ArrayDouble.D1 a1, ArrayDouble.D1 a2, boolean asColumns)
static ArrayDouble.D1	compress(List<Array> sourceA, int source, int length)
static List<ArrayDouble.D1>	convertArrays(List<Array> al)
static List<ArrayInt.D1>	convertArraysIntD1(List<Array> al)
static TreeMap<Double,Integer>	convertScan(Array masses, Array intensities)
static Tuple2D<Array,Tuple2D<Array,Array>>	createCombinedArray(List<Sparse> al) Returns a Tuple2D holding an ArrayInt.D1 as scan indices to the arrays held in the Tuple2D, mass values and intensity values.
static void	createDenseArray(Array source_ind, Array source_val, Tuple2D<Array,Array> tiv, double min, double max, int nbins, double resolution, double fillvalue) Create binned arrays from source mass_values and intensity_values arrays.
static Sparse	createSparseIndexArray(ArrayDouble.D1 index, ArrayDouble.D1 values, int minindex, int maxindex, int nbins, double massBinResolution)
static Array	diff(Array a, Array b) Calculates A-B elementwise.
static Array	div(Array a, Array b) Calculates A/B elementwise.
static Array	divBy60(Array a) Divides values in array by 60, convenience method for second to minute conversion.
static List<ArrayDouble.D1>	expand(Array source, int length) Expansion, as used in Dynamic Time Warping, defined as copying the expanded element length times.
static ArrayDouble.D1	factory(double... d)
static ArrayFloat.D1	factory(float... d)
static ArrayInt.D1	factory(int... d)
static Array	factoryScalar(Object o) This factory is usable for scalar values and primitive array instances.
static void	fill(Array a, double d) Fill array a with double value d.
static void	fillArray(Array a, Double d) Fill array a with Double value d.
static void	fillArray(Array a, int i) Fill array a with int value i.
static void	fillArray(Array a, Integer i) Fill array a with Integer value i.
static Array	filterIndices(Array a, List<Integer> removeIndices, boolean invert, double defaultValue) Given an array and a list of indices within that array, removes all values at those indices and returns a new array where the respective values have been set to a definable minimum value.
static Array	filterIndices(Array a, List<Integer> removeIndices, double defaultValue)
static List<Array>	fromCRS(ArrayInt.D1 indices, Array values) Restore List of Array objects from contiguous representation, using an index array containing the offsets for each individual array.
static List<Array>	generalizeList(List<ArrayDouble.D1> al) Return a list, which is more generally typed than the input list.
static int	getNewIndexOnLHS(int oldIndex, List<Tuple2DI> al)
static int	getNewIndexOnRHS(int oldIndex, List<Tuple2DI> al)
static int	getRequiredSize(List<Sparse> al) Compute total number of elements for all Sparse arrays in list.
static int	getSizeForFlattenedArray(Array a) Returns the number of elements required for a one-dimensional representation of multidimensional array.
static ArrayInt.D1	indexArray(int size, int begin_index) Create an index array with given size, whose integer indexing begins at begin_index.
static void	initRandom()
static void	initRandom(long seed)
static List<Array>	insertRandomGauss(List<Array> intensity_values, int at_position, int number_of_scans, int dim1)
static double	integrate(Array a)
static ArrayDouble.D1	integrate(List<Array> values) Sum over all values of all arrays within a list.
static ArrayDouble.D2	matrix(int rows, int columns)
static TreeMap<Double,Integer>	merge(List<TreeMap<Double,Integer>> rhs, boolean average)
static Tuple2D<List<Array>,List<Array>>	merge2(List<Array> lhsMasses, List<Array> lhsIntensities, List<Array> rhsMasses, List<Array> rhsIntensities, List<Tuple2DI> al, boolean average)
static Array	mult(Array a, Array b) Calculates A*B elementwise.
static Array	mult(Array a, double d)
static double	nextGaussian()
static double	nextUniform()
static Array	pow(Array a, double exp)
static long	printPercentDone(double percentDone, long parts, long partCnt1, org.slf4j.Logger log)
static long	printPercentDone(double percentDone, long parts, long partCnt1, OutputStream os)
static Tuple2D<List<Array>,List<Array>>	project2(boolean toLHS, List<Array> massesRef, List<Array> intenRef, List<Tuple2DI> al, List<Array> massesToBeWarped, List<Array> intenToBeWarped, boolean average)
static Array	projectToLHS(Array lhs, List<Tuple2DI> al, Array rhs, boolean average)
static Array	projectToRHS(Array rhs, List<Tuple2DI> al, Array lhs, boolean average)
static ArrayDouble.D1	randomGaussian(int size, double mean, double stddev)
static ArrayDouble.D1	randomUniform(int size, double mean, double scale)
static double	rootMeanSquareError(List<Tuple2DI> map, List<Array> refInt, List<Array> queryInt)
static ArrayDouble.D0	scalar(double d)
static Array	sq(Array a)
static Array	sum(Array a, Array b) Calculates A + B elementwise.
static List<Array>	tilt(List<Array> al) Creates a new Array containing all values of elements in al along every dimension.
static List<ArrayDouble.D1>	tiltD1(List<ArrayDouble.D1> al) Creates a new Array containing all values of elements in al along every dimension.
static Tuple2D<Array,Array>	toArrays(TreeMap<Double,Integer> s)
static Tuple2D<ArrayDouble.D1,ArrayDouble.D1>	toCRS(List<Array> values)
static ArrayDouble.D1	vector(int elems)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ArrayTools

public ArrayTools()

Method Detail

calcPercentDone

public static double calcPercentDone(long elements,
                     long elemCnt)

combine

public static ArrayDouble.D2 combine(ArrayDouble.D1 a1,
                     ArrayDouble.D1 a2,
                     boolean asColumns)

factory

public static ArrayDouble.D1 factory(double... d)

factory

public static ArrayInt.D1 factory(int... d)

factory

public static ArrayFloat.D1 factory(float... d)

factoryScalar

public static Array factoryScalar(Object o)
                           throws IllegalArgumentException

This factory is usable for scalar values and primitive array instances.

Parameters:

o -

Returns:

Throws:

IllegalArgumentException

compress

public static ArrayDouble.D1 compress(List<Array> sourceA,
                      int source,
                      int length)

convertArrays

public static List<ArrayDouble.D1> convertArrays(List<Array> al)

convertArraysIntD1

public static List<ArrayInt.D1> convertArraysIntD1(List<Array> al)

convertScan

public static TreeMap<Double,Integer> convertScan(Array masses,
                                  Array intensities)

createCombinedArray

public static Tuple2D<Array,Tuple2D<Array,Array>> createCombinedArray(List<Sparse> al)

Returns a Tuple2D holding an ArrayInt.D1 as scan indices to the arrays held in the Tuple2D, mass values and intensity values.

Parameters:

al -

Returns:

createDenseArray

public static void createDenseArray(Array source_ind,
                    Array source_val,
                    Tuple2D<Array,Array> tiv,
                    double min,
                    double max,
                    int nbins,
                    double resolution,
                    double fillvalue)

Create binned arrays from source mass_values and intensity_values arrays. Takes a Tuple of two initially null or intialized arrays which are the binned representations. Requires minimum and maximum mass values, number of bins, resolution and the fillvalue for empty bins.

Parameters:

source_ind -

source_val -

tiv -

min -

max -

nbins -

resolution -

fillvalue -

createSparseIndexArray

public static Sparse createSparseIndexArray(ArrayDouble.D1 index,
                            ArrayDouble.D1 values,
                            int minindex,
                            int maxindex,
                            int nbins,
                            double massBinResolution)

diff

public static Array diff(Array a,
         Array b)

Calculates A-B elementwise.

Parameters:

a -

b -

Returns:

div

public static Array div(Array a,
        Array b)

Calculates A/B elementwise.

Parameters:

a -

b -

Returns:

mult

public static Array mult(Array a,
         Array b)

Calculates A*B elementwise.

Parameters:

a -

b -

Returns:

divBy60

public static Array divBy60(Array a)

Divides values in array by 60, convenience method for second to minute conversion.

Parameters:

a -

Returns:

expand

public static List<ArrayDouble.D1> expand(Array source,
                          int length)

Expansion, as used in Dynamic Time Warping, defined as copying the expanded element length times.

Parameters:

source -

length -

Returns:

fill

public static void fill(Array a,
        double d)

Fill array a with double value d.

Parameters:

a -

d -

fillArray

public static void fillArray(Array a,
             Double d)

Fill array a with Double value d.

Parameters:

a -

d -

fillArray

public static void fillArray(Array a,
             int i)

Fill array a with int value i.

Parameters:

a -

i -

fillArray

public static void fillArray(Array a,
             Integer i)

Fill array a with Integer value i.

Parameters:

a -

i -

fromCRS

public static List<Array> fromCRS(ArrayInt.D1 indices,
                  Array values)

Restore List of Array objects from contiguous representation, using an index array containing the offsets for each individual array.

Parameters:

indices -

values -

Returns:

generalizeList

public static List<Array> generalizeList(List<ArrayDouble.D1> al)

Return a list, which is more generally typed than the input list.

Parameters:

al -

Returns:

getNewIndexOnLHS

public static int getNewIndexOnLHS(int oldIndex,
                   List<Tuple2DI> al)

getNewIndexOnRHS

public static int getNewIndexOnRHS(int oldIndex,
                   List<Tuple2DI> al)

getRequiredSize

public static int getRequiredSize(List<Sparse> al)

Compute total number of elements for all Sparse arrays in list.

Parameters:

al -

Returns:

getSizeForFlattenedArray

public static int getSizeForFlattenedArray(Array a)

Returns the number of elements required for a one-dimensional representation of multidimensional array.

Parameters:

a -

Returns:

indexArray

public static ArrayInt.D1 indexArray(int size,
                     int begin_index)

Create an index array with given size, whose integer indexing begins at begin_index.

Parameters:

size -

begin_index -

Returns:

initRandom

public static void initRandom()

initRandom

public static void initRandom(long seed)

insertRandomGauss

public static List<Array> insertRandomGauss(List<Array> intensity_values,
                            int at_position,
                            int number_of_scans,
                            int dim1)

integrate

public static double integrate(Array a)

integrate

public static ArrayDouble.D1 integrate(List<Array> values)

Sum over all values of all arrays within a list.

Parameters:

valuesvalues -

Returns:

matrix

public static ArrayDouble.D2 matrix(int rows,
                    int columns)

merge

public static TreeMap<Double,Integer> merge(List<TreeMap<Double,Integer>> rhs,
                            boolean average)

merge2

public static Tuple2D<List<Array>,List<Array>> merge2(List<Array> lhsMasses,
                                      List<Array> lhsIntensities,
                                      List<Array> rhsMasses,
                                      List<Array> rhsIntensities,
                                      List<Tuple2DI> al,
                                      boolean average)

mult

public static Array mult(Array a,
         double d)

nextGaussian

public static double nextGaussian()

nextUniform

public static double nextUniform()

pow

public static Array pow(Array a,
        double exp)

printPercentDone

public static long printPercentDone(double percentDone,
                    long parts,
                    long partCnt1,
                    org.slf4j.Logger log)

printPercentDone

public static long printPercentDone(double percentDone,
                    long parts,
                    long partCnt1,
                    OutputStream os)

project2

public static Tuple2D<List<Array>,List<Array>> project2(boolean toLHS,
                                        List<Array> massesRef,
                                        List<Array> intenRef,
                                        List<Tuple2DI> al,
                                        List<Array> massesToBeWarped,
                                        List<Array> intenToBeWarped,
                                        boolean average)

projectToLHS

public static Array projectToLHS(Array lhs,
                 List<Tuple2DI> al,
                 Array rhs,
                 boolean average)

projectToRHS

public static Array projectToRHS(Array rhs,
                 List<Tuple2DI> al,
                 Array lhs,
                 boolean average)

randomGaussian

public static ArrayDouble.D1 randomGaussian(int size,
                            double mean,
                            double stddev)

randomUniform

public static ArrayDouble.D1 randomUniform(int size,
                           double mean,
                           double scale)

rootMeanSquareError

public static double rootMeanSquareError(List<Tuple2DI> map,
                         List<Array> refInt,
                         List<Array> queryInt)

scalar

public static ArrayDouble.D0 scalar(double d)

sq

public static Array sq(Array a)

sum

public static Array sum(Array a,
        Array b)

Calculates A + B elementwise.

Parameters:

a -

b -

Returns:

tilt

public static List<Array> tilt(List<Array> al)

Creates a new Array containing all values of elements in al along every dimension. The list returned is a CachedList implementation. It creates the tilted arrays lazily from the original supplied list.

Parameters:

al -

Returns:

tiltD1

public static List<ArrayDouble.D1> tiltD1(List<ArrayDouble.D1> al)

Creates a new Array containing all values of elements in al along every dimension.

Parameters:

al -

Returns:

toArrays

public static Tuple2D<Array,Array> toArrays(TreeMap<Double,Integer> s)

toCRS

public static Tuple2D<ArrayDouble.D1,ArrayDouble.D1> toCRS(List<Array> values)

vector

public static ArrayDouble.D1 vector(int elems)

filterIndices

public static Array filterIndices(Array a,
                  List<Integer> removeIndices,
                  double defaultValue)

filterIndices

public static Array filterIndices(Array a,
                  List<Integer> removeIndices,
                  boolean invert,
                  double defaultValue)

Given an array and a list of indices within that array, removes all values at those indices and returns a new array where the respective values have been set to a definable minimum value.

Parameters:

a -

removeIndices -

Returns: