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, C or S), 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.
static int	C_AXIS Axis type for channels.
static Set<String>	C_PREFIXES Prefixes indicating channel dimension.
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 Logger for this class.
protected String	newOrder Adjusted ordering of internal dimensional axes.
protected static String	ONE
static int	S_AXIS Axis type for series.
static Set<String>	S_PREFIXES Prefixes indicating series dimension.
static int	T_AXIS Axis type for time points.
static Set<String>	T_PREFIXES Prefixes indicating time dimension.
protected static String	THREE
protected static String	TWO
static int	UNKNOWN_AXIS Axis type for unclassified axes.
static int	Z_AXIS Axis type for focal planes.
static Set<String>	Z_PREFIXES Prefixes indicating space dimension.

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

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) Convert the given label to an 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.
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

Logger for this class.

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_PREFIXES

public static final Set<String> Z_PREFIXES

Prefixes indicating space dimension.

T_PREFIXES

public static final Set<String> T_PREFIXES

Prefixes indicating time dimension.

C_PREFIXES

public static final Set<String> C_PREFIXES

Prefixes indicating channel dimension.

S_PREFIXES

public static final Set<String> S_PREFIXES

Prefixes 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.

The algorithm first assigns pattern blocks based on known prefixes. For instance, a block preceded by "time" is assigned to the time points (T) axis. Blocks that don't have a known prefix are checked for special cases (Bio-Rad .pic, RGB). Remaining blocks are assigned according to the given dimensional sizes: dimensions with size greater than 1 are assumed to be already contained within each file, while those with size equal to 1 can be scattered across multiple files and thus are assigned to pattern blocks.

If isCertain is false, the algorithm checks for cases where the reader might have mixed up the Z and T dimensions. For instance, if the pattern string is z<*>_<*> and size{Z,T,C} = 2,1,1, then the reader is assumed to be wrong about the relative positions of Z and T in the given dimOrder. The new suggested order (see getAdjustedOrder()) will have Z and T swapped and the second block will be assigned to C (the actual dimensional sizes are assumed to be 1,2,1).

If after trying all of the above there are still unassigned blocks, they will be assigned to the last dimension in the (possibly adjusted) order.

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)

Convert the given label to an axis type. If the label ends with one of the known prefixes for the Z, C, T or S axis (as defined in Z_PREFIXES, C_PREFIXES, T_PREFIXES, S_PREFIXES), return the corresponding axis type; otherwise, return UNKNOWN_AXIS. Note that the match is case-insensitive.