org.micromanager.data

Interface Coords

public interface Coords

The multi-dimensional coordinate of a 2D image within a dataset.

This is typically used to represent the time point, stage position, z slice, and channel indices of images.

The Coords object is a mapping from axes (represented by strings) to positive integer indices. Because an arbitrary number of axes may be included in the Coords, the index zero is meaningless and will be omitted. Therefore, the axis index for any index not included in the Coords will be zero. The Coords of an image that is zero for all axes is an empty Coords.

The equals operator can be relied upon to establish whether two different Coords contain the same axes and the same indices to those axes.

Although methods are included to support any arbitrary axes, such usage is not yet fully supported. If you do use custom axes, give them names that include upper case letters so that they do not clash with standard axes added in the future.

Coords objects are immutable.

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static interface	Coords.Builder The real Builder for Coords.
static interface	Coords.CoordsBuilder Not sure why there is a Builder and CoordsBuilder.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	C Axis label for the channel axis (short form).
static java.lang.String	CHANNEL Axis label for the channel axis.
static java.lang.String	P Axis label for the stage position axis (short form).
static java.lang.String	STAGE_POSITION Axis label for the stage position axis.
static java.lang.String	T Axis label for the time point (frame) axis (short form).
static java.lang.String	TIME Deprecated. Use discouraged because it reads like a physical time rather than the time point index that it is.
static java.lang.String	TIME_POINT Axis label for the time point (frame) axis.
static java.lang.String	Z Axis label for the Z slice axis (short form).
static java.lang.String	Z_SLICE Axis label for the Z slice axis.

Method Summary

Modifier and Type	Method and Description
Coords.CoordsBuilder	copy() Deprecated. Use copyBuilder instead
Coords.Builder	copyBuilder() Provides a Builder pre-loaded with a copy of this Coords.
Coords	copyRemovingAxes(java.lang.String... axes) Removes the axes provided as varargs from this Coord.
Coords	copyRetainingAxes(java.lang.String... axes) Name of this function is very unclear.
java.util.List<java.lang.String>	getAxes() Return all axes that this Coords has an index for.
int	getC() Shorthand for getChannel.
int	getChannel() Get the channel index.
int	getIndex(java.lang.String axis) Get the index for the given axis.
int	getP() Shorthand for getStagePosition.
int	getStagePosition() Get the stage position index.
int	getT() Shorthand for getTimePoint.
int	getTime() Deprecated. Due to looking like the physical time rather than an index. Use getTmePoint
int	getTimePoint() Get the time point (frame) index.
int	getZ() Shorthand for getZSlice.
int	getZSlice() Get the Z slice index.
boolean	hasAxis(java.lang.String axis) Returns whether this coords has the given axis.
boolean	hasC()
boolean	hasChannelAxis()
boolean	hasP()
boolean	hasStagePositionAxis()
boolean	hasT()
boolean	hasTimePointAxis()
boolean	hasZ()
boolean	hasZSliceAxis()
boolean	matches(Coords alt) Deprecated. Use equality (after removing specific axes) instead

Field Detail

TIME_POINT

static final java.lang.String TIME_POINT

Axis label for the time point (frame) axis.

See Also:

Constant Field Values

TIME

@Deprecated
static final java.lang.String TIME

Deprecated. Use discouraged because it reads like a physical time rather than the time point index that it is.

Same as TIME_POINT or T.

See Also:

Constant Field Values

T

static final java.lang.String T

Axis label for the time point (frame) axis (short form). Same as TIME_POINT.

See Also:

Constant Field Values

STAGE_POSITION

static final java.lang.String STAGE_POSITION

Axis label for the stage position axis.

See Also:

Constant Field Values

P

static final java.lang.String P

Axis label for the stage position axis (short form). Same as STAGE_POSTITION.

See Also:

Constant Field Values

Z_SLICE

static final java.lang.String Z_SLICE

Axis label for the Z slice axis.

See Also:

Constant Field Values

Z

static final java.lang.String Z

Axis label for the Z slice axis (short form). Same as Z_SLICE.

See Also:

Constant Field Values

CHANNEL

static final java.lang.String CHANNEL

Axis label for the channel axis.

See Also:

Constant Field Values

C

static final java.lang.String C

Axis label for the channel axis (short form). Same as CHANNEL.

See Also:

Constant Field Values

Method Detail

getIndex

int getIndex(java.lang.String axis)

Get the index for the given axis.

Parameters:

axis - coordinate axis such as Coords.CHANNEL

Returns:

index along axis, or 0 if axis does not exist

getChannel

int getChannel()

Get the channel index.

Equivalent to getIndex(Coords.CHANNEL).

Returns:

channel index, or 0 if this Coords doesn't contain a channel index.

getC

int getC()

Shorthand for getChannel.

Returns:

channel index, or 0 if this Coords doesn't contain a channel index.

getTimePoint

int getTimePoint()

Get the time point (frame) index.

Equivalent to getIndex(Coords.TIME_POINT).

Returns:

time point index, or 0 if this Coords doesn't contain a time point index.

getTime

@Deprecated
int getTime()

Deprecated. Due to looking like the physical time rather than an index. Use getTmePoint

Same as getTimePoint.

Returns:

time index (0-based)

getT

int getT()

Shorthand for getTimePoint.

Returns:

time point index, or 0 if this Coords doesn't contain a time point index.

getZSlice

int getZSlice()

Get the Z slice index.

Equivalent to getIndex(Coords.Z_SLICE).

Returns:

Z slice index, or 0 if this Coords doesn't contain a Z slice index.

getZ

int getZ()

Shorthand for getZSlice.

Returns:

Z slice index, or 0 if this Coords doesn't contain a Z slice index.

getStagePosition

int getStagePosition()

Get the stage position index.

Equivalent to getIndex(Coords.STAGE_POSITION).

Returns:

stage position index, or 0 if this Coords doesn't contain a stage position index.

getP

int getP()

Shorthand for getStagePosition.

Returns:

stage position index, or 0 if this Coords doesn't contain a stage position index.

getAxes

java.util.List<java.lang.String> getAxes()

Return all axes that this Coords has an index for.

Returns:

List of all axis

hasAxis

boolean hasAxis(java.lang.String axis)

Returns whether this coords has the given axis.

Parameters:

axis - the axis to test for presence

Returns:

true if this coords includes axis

hasTimePointAxis

boolean hasTimePointAxis()

hasT

boolean hasT()

hasStagePositionAxis

boolean hasStagePositionAxis()

hasP

boolean hasP()

hasZSliceAxis

boolean hasZSliceAxis()

hasZ

boolean hasZ()

hasChannelAxis

boolean hasChannelAxis()

hasC

boolean hasC()

matches

@Deprecated
boolean matches(Coords alt)

Deprecated. Use equality (after removing specific axes) instead

Deprecated.

Parameters:

alt - the instance to compare with

Returns:

whether this instance is a superspace coords of other

copyBuilder

Coords.Builder copyBuilder()

Provides a Builder pre-loaded with a copy of this Coords.

Returns:

copyBuilder

copy

@Deprecated
Coords.CoordsBuilder copy()

Deprecated. Use copyBuilder instead

Deprecated.

Returns:

Builder

copyRemovingAxes

Coords copyRemovingAxes(java.lang.String... axes)

Removes the axes provided as varargs from this Coord.

Parameters:

axes - One or more Strings naming the axes to be removed

Returns:

Copy of this Coords without the listed axes

copyRetainingAxes

Coords copyRetainingAxes(java.lang.String... axes)

Name of this function is very unclear. It seems that its functionality is to provide a copy of the given Coords, but only for the axes provided in the input strings. A more useful name may be: copyProvidedAxes, or copyAxes

Parameters:

axes - Names of axes to be represented in the output

Returns:

Copy of this Coords, but only with the subset of axes provided in the axes param