io.scif

Class AxisGuesser

java.lang.Object

io.scif.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

Field Summary

Fields

Modifier and Type	Field and Description
static int	C_AXIS Axis type for channels.
static int	S_AXIS Axis type for series.
static int	T_AXIS Axis type for time points.
static int	UNKNOWN_AXIS Axis type for unclassified axes.
static int	Z_AXIS Axis type for focal planes.

Constructor Summary

Constructors

Constructor and Description
AxisGuesser(FilePattern fp, net.imagej.axis.AxisType[] dimOrder, long sizeZ, long sizeT, long 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

Modifier and Type	Method and Description
net.imagej.axis.AxisType[]	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 length of the Z axes in the pattern.
static int	getAxisType(String label) Returns a best guess of the given label's axis type.
net.imagej.axis.AxisType[]	getAxisTypes() Gets the guessed axis type for each dimensional block.
FilePattern	getFilePattern() Gets the file pattern.
net.imagej.axis.AxisType[]	getOriginalOrder() Gets the original dimension order.
boolean	isCertain() Gets whether the guesser is confident that all axes are correct.
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

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

Constructor Detail

AxisGuesser

public AxisGuesser(FilePattern fp,
                   net.imagej.axis.AxisType[] dimOrder,
                   long sizeZ,
                   long sizeT,
                   long 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 net.imagej.axis.AxisType[] getOriginalOrder()

Gets the original dimension order.

getAdjustedOrder

public net.imagej.axis.AxisType[] getAdjustedOrder()

Gets the adjusted dimension order.

isCertain

public boolean isCertain()

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

getAxisTypes

public net.imagej.axis.AxisType[] 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 length of the 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.