loci.formats

Class AxisGuesser

java.lang.Object

loci.formats.AxisGuesser

public class AxisGuesser
extends Object

AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T or C), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.

Author:

Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	axisTypes Guessed axis types.
protected static String[]	C Prefix endings indicating channel dimension.
static int	C_AXIS Axis type for channels.
protected boolean	certain Whether the guesser is confident that all axis types are correct.
protected String	dimOrder Original ordering of internal dimensional axes.
protected FilePattern	fp File pattern identifying dimensional axis blocks.
private static org.slf4j.Logger	LOGGER
protected String	newOrder Adjusted ordering of internal dimensional axes.
protected static String	ONE
protected static String[]	S Prefix endings indicating series dimension.
static int	S_AXIS Axis type for series.
protected static String[]	T Prefix endings indicating time dimension.
static int	T_AXIS Axis type for time points.
protected static String	THREE
protected static String	TWO
static int	UNKNOWN_AXIS Axis type for unclassified axes.
protected static String[]	Z Prefix endings indicating space dimension.
static int	Z_AXIS Axis type for focal planes.

Constructor Summary

Constructors

Constructor and Description
AxisGuesser(FilePattern fp, String dimOrder, int sizeZ, int sizeT, int sizeC, boolean isCertain) Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.

Method Summary

Methods

Modifier and Type	Method and Description
String	getAdjustedOrder() Gets the adjusted dimension order.
int	getAxisCount(int axisType) Gets the number of axes in the pattern of the given type.
int	getAxisCountC() Gets the number of C axes in the pattern.
int	getAxisCountS() Gets the number of S axes in the pattern.
int	getAxisCountT() Gets the number of T axes in the pattern.
int	getAxisCountZ() Gets the number of Z axes in the pattern.
static int	getAxisType(String label) Returns a best guess of the given label's axis type.
int[]	getAxisTypes() Gets the guessed axis type for each dimensional block.
FilePattern	getFilePattern() Gets the file pattern.
String	getOriginalOrder() Gets the original dimension order.
boolean	isCertain() Gets whether the guesser is confident that all axes are correct.
static void	main(String[] args) Method for testing pattern guessing logic.
void	setAxisTypes(int[] axes) Sets the axis type for each dimensional block.

Methods inherited from class java.lang.Object

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

Field Detail

LOGGER

private static final org.slf4j.Logger LOGGER

UNKNOWN_AXIS

public static final int UNKNOWN_AXIS

Axis type for unclassified axes.

See Also:

Constant Field Values

Z_AXIS

public static final int Z_AXIS

Axis type for focal planes.

See Also:

Constant Field Values

T_AXIS

public static final int T_AXIS

Axis type for time points.

See Also:

Constant Field Values

C_AXIS

public static final int C_AXIS

Axis type for channels.

See Also:

Constant Field Values

S_AXIS

public static final int S_AXIS

Axis type for series.

See Also:

Constant Field Values

Z

protected static final String[] Z

Prefix endings indicating space dimension.

T

protected static final String[] T

Prefix endings indicating time dimension.

C

protected static final String[] C

Prefix endings indicating channel dimension.

S

protected static final String[] S

Prefix endings indicating series dimension.

ONE

protected static final String ONE

See Also:

Constant Field Values

TWO

protected static final String TWO

See Also:

Constant Field Values

THREE

protected static final String THREE

See Also:

Constant Field Values

fp

protected FilePattern fp

File pattern identifying dimensional axis blocks.

dimOrder

protected String dimOrder

Original ordering of internal dimensional axes.

newOrder

protected String newOrder

Adjusted ordering of internal dimensional axes.

axisTypes

protected int[] axisTypes

Guessed axis types.

certain

protected boolean certain

Whether the guesser is confident that all axis types are correct.

Constructor Detail

AxisGuesser

public AxisGuesser(FilePattern fp,
           String dimOrder,
           int sizeZ,
           int sizeT,
           int sizeC,
           boolean isCertain)

Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide.

Parameters:

fp - The file pattern of the files

dimOrder - The dimension order (e.g., XYZTC) within each file

sizeZ - The number of Z positions within each file

sizeT - The number of T positions within each file

sizeC - The number of C positions within each file

isCertain - Whether the dimension order given is known to be good, or merely a guess

See Also:

FilePattern

Method Detail

getFilePattern

public FilePattern getFilePattern()

Gets the file pattern.

getOriginalOrder

public String getOriginalOrder()

Gets the original dimension order.

getAdjustedOrder

public String getAdjustedOrder()

Gets the adjusted dimension order.

isCertain

public boolean isCertain()

Gets whether the guesser is confident that all axes are correct.

getAxisTypes

public int[] getAxisTypes()

Gets the guessed axis type for each dimensional block.

Returns:

An array containing values from the enumeration:

• Z_AXIS: focal planes
• T_AXIS: time points
• C_AXIS: channels
• S_AXIS: series

setAxisTypes

public void setAxisTypes(int[] axes)

Sets the axis type for each dimensional block.

Parameters:

axes - An array containing values from the enumeration:

• Z_AXIS: focal planes
• T_AXIS: time points
• C_AXIS: channels
• S_AXIS: series

getAxisCountZ

public int getAxisCountZ()

Gets the number of Z axes in the pattern.

getAxisCountT

public int getAxisCountT()

Gets the number of T axes in the pattern.

getAxisCountC

public int getAxisCountC()

Gets the number of C axes in the pattern.

getAxisCountS

public int getAxisCountS()

Gets the number of S axes in the pattern.

getAxisCount

public int getAxisCount(int axisType)

Gets the number of axes in the pattern of the given type.

Parameters:

axisType - One of:

• Z_AXIS: focal planes
• T_AXIS: time points
• C_AXIS: channels
• S_AXIS: series

getAxisType

public static int getAxisType(String label)

Returns a best guess of the given label's axis type.

main

public static void main(String[] args)
                 throws FormatException,
                        IOException

Method for testing pattern guessing logic.

Throws:

FormatException

IOException