jhplot

Class PND

java.lang.Object

jhplot.PND

All Implemented Interfaces:

java.io.Serializable

public class PND
extends java.lang.Object
implements java.io.Serializable

Data holder in 2D for double values. It is similar to a matrix in 2D. It has columns and rows. The number of columns may not be the same. For example, data can be presented as:

 1 2 3 4 5
 12 3 4
 1 3 4 555 5 66 77
 1 2 2 33 434 4
 

All numbers are expected to be in double precision.

It extends ArrayList and adds many new features for data manipulation. The class does not have graphical option (use H1D to show the data or methods of this class which transform P0D to a H1D histogram).

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PND() Construct an empty container with no title
PND(java.lang.String title) Construct an empty container with a title
PND(java.lang.String title, boolean shallow, PND pnd) Construct a copy from a PND.
PND(java.lang.String title, java.lang.String file) Construct a container with a title from external file (see the method toFile() how to write such ASCII file).

Method Summary

Modifier and Type	Method and Description
void	add(double[] values) Adds (appends) the specified element to the end of this list.
void	add(P0D values) Adds (appends) P0D to the end of this list.
void	clear() Clear the container
PND	copy(java.lang.String newtitle) Create an exact copy of the current P0D.
void	doc() Show online documentation.
double[]	get(int row) Return a specific row as array
double	get(int row, int column) Return a specific value.
double[][]	getArray() Get a double array with values.
java.util.ArrayList<double[]>	getArrayList() Get data in form of ArrayList
double[]	getColumn(int column) Return a specific column as an array
P0D	getColumnP0D(int column) Return a specific column as P0D object
int	getDimension() Get last dimension of the data (or number of columns).
int[]	getDimensions() Get the numbers of columns.
H1D	getH1D(int bins) Create histogram.
H1D	getH1D(int bins, double min, double max) Return H1D histogram with PND content.
H1D	getH1D(int bins, double min, double max, int column) Make a histogram from a column of PND.
IDataPointSet	getIDataPointSet() Get the data point set for JAIDA
double	getMax() Get min value
double	getMin() Get max value
java.lang.String	getName() Get a new title
P0D	getP0D(int column) Return a specific column as an array
P1D	getP1D(int c1, int c2) Return 2 columns as P1D to show as a X-Y plot
P2D	getP2D(int c1, int c2, int c3) Return 3 columns as P2D to show as a X-Y-Z plot
P0D	getRow(int row) Return a specific row as array
P0D	getRowP0D(int row) Return a specific row as P0D
PND	getRows(java.lang.String newtitle, int indexMin, int indexMax) Get rows : min is inxluded, max is not;
java.lang.String	getTitle() Get a new title.
static void	main(java.lang.String[] args) Test
PND	oper(PND pnd, java.lang.String what) Operations on PND containers: add, subtract, multiply, divide.
PND	oper(PND pnd, java.lang.String title, java.lang.String what) Operations on PND containers: add, subtract, multiply, divide.
void	operScale(double scale) Scale each element of data
void	print() Print PND to System.out.
int	read(java.io.BufferedReader br) Read the data from an external source.
int	read(java.io.File sfile) Read PND from a file.
int	read(java.lang.String sfile) Read PND from a file.
int	read(java.net.URL url) Read data from URL.
int	readGZip(java.io.File sfile) Read PND from a GZiped file.
int	readGZip(java.lang.String sfile) Read PND from a GZiped file.
PND	readSerialized(java.lang.String name) Read a PND object from a serialized file
int	readZip(java.lang.String sfile) Read the data from ZIPed external file.
PND	remove(int index) Remove a row
PND	rescale(double[][] v) This is an inverse operation to rescale(type) function.
double[][]	rescale(int type) Rescale the column vectors.
void	set(int index, double[] values) Sets (replace) the specified row.
void	set(int index, P0D values) Sets (replace) the specified element with P0D.
PND	setArray(double[][] values) Set values from double array Old content will be lost.
void	setArrayList(java.util.ArrayList<double[]> array) Set the data in form of ArrayList
void	setName(java.lang.String title) Set a new title
void	setTitle(java.lang.String title) Set a new title
int	size() Data size (number of rows)
PND	standardize() Standardize each column.
void	toFile(java.lang.String name) Write a PND to an external file.
java.lang.String	toString() Get a string representing PND
void	toTable() Show container to a Table in a separate Frame.
void	write(java.lang.String name) Write a PND to an external file.
int	writeSerialized(java.lang.String name) Write a P0D object to a serialized file

Methods inherited from class java.lang.Object

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

Constructor Detail

PND

public PND(java.lang.String title)

Construct an empty container with a title

Parameters:

title - A title

PND

public PND(java.lang.String title,
           boolean shallow,
           PND pnd)

Construct a copy from a PND. If the last argument is true, a shallow copy of a collection. In this case a new collection contains references to same objects as the source collection. Data are not cloned

Parameters:

title - new title

shallow - if true, a shallow copy of a collection.

pnd - inpit data

PND

public PND(java.lang.String title,
           java.lang.String file)

Construct a container with a title from external file (see the method toFile() how to write such ASCII file).

Parameters:

title - A title

file - input file name. It can be either a file on a file system or URL location (must start from http or ftp)

PND

public PND()

Construct an empty container with no title

Method Detail

setTitle

public void setTitle(java.lang.String title)

Set a new title

Parameters:

title - New Title

setName

public void setName(java.lang.String title)

Set a new title

Parameters:

title - New Title

getTitle

public java.lang.String getTitle()

Get a new title.

Returns:

Title

getName

public java.lang.String getName()

Get a new title

Returns:

Title

clear

public void clear()

Clear the container

get

public double[] get(int row)

Return a specific row as array

Parameters:

row - index of the row

Returns:

array of values

getRowP0D

public P0D getRowP0D(int row)

Return a specific row as P0D

Parameters:

row - index of the row

Returns:

array of values

get

public double get(int row,
                  int column)

Return a specific value.

Parameters:

row - row index

column - column index

Returns:

value

toString

public java.lang.String toString()

Get a string representing PND

Overrides:

toString in class java.lang.Object

Returns:

String with all values

print

public void print()

Print PND to System.out.

getP0D

public P0D getP0D(int column)

Return a specific column as an array

Parameters:

column - index of the column

Returns:

P0D array with values.

getColumn

public double[] getColumn(int column)

Return a specific column as an array

Parameters:

column - index of the column

Returns:

array with values.

getColumnP0D

public P0D getColumnP0D(int column)

Return a specific column as P0D object

Parameters:

column - index of the column

Returns:

array with values.

getP1D

public P1D getP1D(int c1,
                  int c2)

Return 2 columns as P1D to show as a X-Y plot

Parameters:

c1 - index of the first column

c2 - index of the second column

Returns:

P1D array with X-Y values.

getP2D

public P2D getP2D(int c1,
                  int c2,
                  int c3)

Return 3 columns as P2D to show as a X-Y-Z plot

Parameters:

c1 - index of the first column

c2 - index of the second column

c3 - index of the third column

Returns:

P3D array with X-Y-Z values.

getDimension

public int getDimension()

Get last dimension of the data (or number of columns). The stored dimention is the one set after the last call "add", or if it set manually.

Returns:

dimension (number of elements in a row)

getDimensions

public int[] getDimensions()

Get the numbers of columns. The stored dimention is the one set after the last call "add", or if it set manually.

Returns:

dimension (number of elements in a row)

getRow

public P0D getRow(int row)

Return a specific row as array

Parameters:

row - index of the row

Returns:

array of values

getArrayList

public java.util.ArrayList<double[]> getArrayList()

Get data in form of ArrayList

Returns:

data in form of ArrayList

getIDataPointSet

public IDataPointSet getIDataPointSet()

Get the data point set for JAIDA

Returns:

add

public void add(double[] values)

Adds (appends) the specified element to the end of this list.

Parameters:

values - array of values to be added.

add

public void add(P0D values)

Adds (appends) P0D to the end of this list.

Parameters:

values - array of values to be added.

set

public void set(int index,
                double[] values)

Sets (replace) the specified row.

Parameters:

index - position index

values - array of values to be added.

set

public void set(int index,
                P0D values)

Sets (replace) the specified element with P0D.

Parameters:

index - position index

values - array of values to be added.

read

public int read(java.io.BufferedReader br)

Read the data from an external source. Old data will be lost. Use "#" or "*" for comments. Use a space to separate values in columns and new line to put new row.

Parameters:

br - BufferedReader

Returns:

zero if success.

read

public int read(java.io.File sfile)

Read PND from a file. The old content will be lost. Use a space to separate values in columns and new line to put new row. Comment lines starting with "#" and "*" are ignored.

Parameters:

sfile - input file

Returns:

zero if success

read

public int read(java.net.URL url)

Read data from URL. Use a space to separate values in columns and new line to put new row.

Parameters:

url - URL location of input file

readGZip

public int readGZip(java.lang.String sfile)

Read PND from a GZiped file. It can read URL if the string starts from http or ftp, otherwise a file on the file system is assumed.

Use a space to separate values in columns and new line to put new row.

Parameters:

sfile - File name with input (extension .gz)

Returns:

zero if success

read

public int read(java.lang.String sfile)

Read PND from a file. It can read URL if the string starts from http or ftp, otherwise a file on the file system is assumed.

The old content will be lost. Use a space to separate values in columns and new line to put new row. Comment lines starting with "#" and "*" are ignored.

Parameters:

sfile - File name with input

Returns:

zero if success

readGZip

public int readGZip(java.io.File sfile)

Read PND from a GZiped file. The old content will be lost. Use a space to separate values in columns and ne line to put new row. Comment lines start from "#" and "*" are ignored.

Parameters:

sfile - File name with input (extension .gz)

Returns:

zero if success

readZip

public int readZip(java.lang.String sfile)

Read the data from ZIPed external file. Old data will be lost. Use "#" or "*" for comments.

Parameters:

sfile - File name with the input (extension .zip)

Returns:

zero if success.

write

public void write(java.lang.String name)

Write a PND to an external file. Same method as toFile()

Parameters:

name - File name with output

writeSerialized

public int writeSerialized(java.lang.String name)

Write a P0D object to a serialized file

Parameters:

name - serialized file name for output.

Returns:

zero if no errors

readSerialized

public PND readSerialized(java.lang.String name)

Read a PND object from a serialized file

Parameters:

name - serialized file name for input.

Returns:

new PND object

toFile

public void toFile(java.lang.String name)

Write a PND to an external file.

Parameters:

name - File name with output

remove

public PND remove(int index)

Remove a row

Parameters:

index - row index to be removed

oper

public PND oper(PND pnd,
                java.lang.String what)

Operations on PND containers: add, subtract, multiply, divide. Keep the same graphical attributes and title.

Parameters:

pnd - Input PND container for operation

what - String representing the operation: "+" add a P0D container to the original; "-" subtract a P0D from the original; "*" multiply; "/" divide by P0D

Returns:

original PND after the operation.

oper

public PND oper(PND pnd,
                java.lang.String title,
                java.lang.String what)

Operations on PND containers: add, subtract, multiply, divide. Keep the same graphical attributes

Parameters:

pnd - Input PND container for operation

title - New title

what - String representing the operation: "+" add a P0D container to the original; "-" subtract a P0D from the original; "*" multiply; "/" divide by P0D

Returns:

original PND after the operation.

operScale

public void operScale(double scale)

Scale each element of data

Parameters:

scale - Scale factor

size

public int size()

Data size (number of rows)

Returns:

number of rows

copy

public PND copy(java.lang.String newtitle)

Create an exact copy of the current P0D. New object is created.

Parameters:

newtitle - new title

getRows

public PND getRows(java.lang.String newtitle,
                   int indexMin,
                   int indexMax)

Get rows : min is inxluded, max is not;

Parameters:

title - New title

indexMin - min index of row

indexMax - max index of row

Returns:

new PND with rows indexMin-indexMax

setArrayList

public void setArrayList(java.util.ArrayList<double[]> array)

Set the data in form of ArrayList

Parameters:

array - ArrayList to be set.

getArray

public double[][] getArray()

Get a double array with values.

Returns:

double array with values

setArray

public PND setArray(double[][] values)

Set values from double array Old content will be lost.

Parameters:

values - array to be set: [ROWS][dimension];

Returns:

PND with new values

standardize

public PND standardize()

Standardize each column. Useful for Neural Network studies. This means S(i)= (X(i) - mean) / std; i goes from 0 to size(); for each column in PND. mean - mean value for data in a certain column; std is the standard deviation. Usually used for neural net to standardize the input variables (column vectors). Operates on the original data.

Returns:

PND after standardize

rescale

public double[][] rescale(int type)

Rescale the column vectors. S(i)= (X(i) - v[0]) / v[1], where v[dimension] [2] is the 2D array returned by this function to be able calculate X(i) back. Usually used for a neural net (rescaling of the output).

Parameters:

type - 0: is ths standard rescaling, i.e. all columns are rescaled to the range [0,1] This is done as: v[0] is the min value of X(i), v[1] is the range (max-min).

type 1: midrange rescaling, i.e. all values are in the range [-1,1]. v[0] is 0.5*(min+max), while [1] is (max-min) /2

Returns:

v[][] used to rescale the data: v[column][0] gives v[0], v[column][1] given by v[1]. Use this array to convert the data back.

getH1D

public H1D getH1D(int bins,
                  double min,
                  double max)

Return H1D histogram with PND content. All values are added. Histogram range is defined by Min and Max values.

Parameters:

bins - Number of bins for the histogram.

min - Min value of histogram

max - Max value of histogram

Returns:

H2D histogram filled with P0D.

getH1D

public H1D getH1D(int bins,
                  double min,
                  double max,
                  int column)

Make a histogram from a column of PND.

Parameters:

bins - Number of bins

min - Min value

max - Max value

column - column of PND (

Returns:

histogram

getH1D

public H1D getH1D(int bins)

Create histogram. Min and Max are determined authomatically.

Parameters:

bins - Number of bins

Returns:

getMax

public double getMax()

Get min value

Returns:

minimum value

getMin

public double getMin()

Get max value

Returns:

rescale

public PND rescale(double[][] v)

This is an inverse operation to rescale(type) function. You should give array v[2], from which the original data can be calculated. Each column after the rescaling will be transformed to X(i)=S(i)*v[1]+v[0] (we drop here index for rows).

Parameters:

v - array used to rescale the data. applied as X(i)=S(i)*v[1]+v[0]

Returns:

PND after rescaling

main

public static void main(java.lang.String[] args)

Test

Parameters:

args -

toTable

public void toTable()

Show container to a Table in a separate Frame. The numbers are formatted to scientific format. One can sort and search the data in this table (but not modify)

doc

public void doc()

Show online documentation.