org.micromanager

Class MultiStagePosition

java.lang.Object

org.micromanager.MultiStagePosition

public final class MultiStagePosition
extends java.lang.Object

Definition of a position in space in terms of available stages/drives.

The current implementation uses the concept of "DefaultXYStage", and "DefaultZStage". This is problematic. The concept of "default" stages originates in the Micro-Manager core, that always has only 1 stage that is the "active" one. However, MultiStagePosition devices can record the position of multiple stages, sometimes even lacking those of the "default" stages, so it can not rely on the Micro-manager "Default" stages being in the list.

It would be nice to be able to rely on the getX, getY, and getZ functions, but these will return bogus values if the system's default stages are not included. To avoid surprises, you may need to parse the MultiStagePosition yourself.

Constructor Summary

Constructors

Constructor and Description
MultiStagePosition() Default constructor.
MultiStagePosition(java.lang.String xyStage, double x, double y, java.lang.String zStage, double z) Convenient constructor where the motion system consists of one XY stage and one focus stage.

Method Summary

Modifier and Type	Method and Description
void	add(StagePosition sp) Add one stage position point.
boolean	equals(java.lang.Object alt) Compares this MultiStagePosition to another, and returns true if they are equal in all aspects.
static MultiStagePosition	fromPropertyMap(PropertyMap pmap) Generates a multistagePosition from the given PropertyMap.
StagePosition	get(int idx) Return stage position based on index.
StagePosition	get(java.lang.String stageName) Returns position for a specific stage.
java.lang.String	getDefaultXYStage() Return the default XY stage, i,e, the one used if no stage is named explicitly.
java.lang.String	getDefaultZStage() Returns the Default Z stage, i.e.
int	getGridColumn() Returns rectangular grid column.
int	getGridRow() Returns rectangular grid row.
java.lang.String	getLabel() Returns position label.
java.lang.String	getProperty(java.lang.String key) Returns property value for a given key (name).
java.lang.String[]	getPropertyNames() Return the array of property keys (names) associated with this position.
double	getX() Returns "X" coordinate of the position.
double	getY() Returns "Y" coordinate of the position.
double	getZ() Returns "Z" - focus coordinate of the position.
static void	goToPosition(MultiStagePosition msp, mmcorej.CMMCore core) Moves all stages to the specified positions.
int	hashCode()
boolean	hasProperty(java.lang.String key) Checks if the position has a particular property.
static MultiStagePosition	newInstance(MultiStagePosition aMps) Copy constructor.
void	remove(StagePosition sp) Removed one stage position point.
void	setDefaultXYStage(java.lang.String stage) Defines which stage serves as the default XY motion control device.
void	setDefaultZStage(java.lang.String stage) Defines which stage serves as focus control.
void	setGridCoordinates(int row, int col) Sets grid parameters for the rectangular grid.
void	setLabel(java.lang.String lab) Sets position label (such as well name, etc.).
void	setProperty(java.lang.String key, java.lang.String value) Add a generalized property-value par to the position.
int	size() Number of stages.
PropertyMap	toPropertyMap() Returns a propertymap describing this MultiStagePosition.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MultiStagePosition

public MultiStagePosition()

Default constructor.

MultiStagePosition

public MultiStagePosition(java.lang.String xyStage,
                          double x,
                          double y,
                          java.lang.String zStage,
                          double z)

Convenient constructor where the motion system consists of one XY stage and one focus stage.

Parameters:

xyStage - name

x - - coordinate in microns

y - - coordinate in microns

zStage - name

z - - focus position in microns

Method Detail

newInstance

public static MultiStagePosition newInstance(MultiStagePosition aMps)

Copy constructor.

Parameters:

aMps - - another instance of the MultiStagePoswition class

Returns:

multistageposition

add

public void add(StagePosition sp)

Add one stage position point.

Parameters:

sp - Stageposition to be added

remove

public void remove(StagePosition sp)

Removed one stage position point.

Parameters:

sp - stage position point to be removed

size

public int size()

Number of stages.

Returns:

number of stages in this MultiStagePosition object

get

public StagePosition get(int idx)

Return stage position based on index.

Parameters:

idx - - position index

Returns:

stageposition

get

public StagePosition get(java.lang.String stageName)

Returns position for a specific stage.

Parameters:

stageName - Name of the stage

Returns:

position of the specified stage

setProperty

public void setProperty(java.lang.String key,
                        java.lang.String value)

Add a generalized property-value par to the position.

Parameters:

key - Key of the property

value - Value of the property

getPropertyNames

public java.lang.String[] getPropertyNames()

Return the array of property keys (names) associated with this position.

Returns:

array with property names

hasProperty

public boolean hasProperty(java.lang.String key)

Checks if the position has a particular property.

Parameters:

key - Key or property

Returns:

true if the position has this key

getProperty

public java.lang.String getProperty(java.lang.String key)

Returns property value for a given key (name).

Parameters:

key - Key of the property

Returns:

value associated with the key

getLabel

public java.lang.String getLabel()

Returns position label.

Returns:

label associated with this MultiStagePosition

setLabel

public void setLabel(java.lang.String lab)

Sets position label (such as well name, etc.).

Parameters:

lab - new MultiStagePosition Label

setDefaultZStage

public void setDefaultZStage(java.lang.String stage)

Defines which stage serves as focus control.

Parameters:

stage - new focus stage

getDefaultZStage

public java.lang.String getDefaultZStage()

Returns the Default Z stage, i.e. the one that will be used if not named explicitly.

Returns:

Default Z stage (defined by the user in MMCore)

getDefaultXYStage

public java.lang.String getDefaultXYStage()

Return the default XY stage, i,e, the one used if no stage is named explicitly.

Returns:

Default XY stage (defined by the user in MMCore)

setDefaultXYStage

public void setDefaultXYStage(java.lang.String stage)

Defines which stage serves as the default XY motion control device.

Parameters:

stage - new default XY stage

goToPosition

public static void goToPosition(MultiStagePosition msp,
                                mmcorej.CMMCore core)
                         throws java.lang.Exception

Moves all stages to the specified positions.

Parameters:

msp - position to move to

core - - microscope API

Throws:

java.lang.Exception - If there is an error moving the stage.

getX

public double getX()

Returns "X" coordinate of the position.

Returns:

X position of the default XY stage

getY

public double getY()

Returns "Y" coordinate of the position.

Returns:

Y position of the default XY stage

getZ

public double getZ()

Returns "Z" - focus coordinate of the position.

Returns:

Position of the default Focus stage

setGridCoordinates

public void setGridCoordinates(int row,
                               int col)

Sets grid parameters for the rectangular grid.

Parameters:

row - Row number of the grid coordinate

col - Column number of the grid coordinate

getGridRow

public int getGridRow()

Returns rectangular grid row.

Returns:

row

getGridColumn

public int getGridColumn()

Returns rectangular grid column.

Returns:

column

equals

public boolean equals(java.lang.Object alt)

Compares this MultiStagePosition to another, and returns true if they are equal in all aspects.

Overrides:

equals in class java.lang.Object

Parameters:

alt - The MultiStagePosition to compare against.

Returns:

true if every field of this MultiStagePosition matches every field of the provided MultiStagePosition, false otherwise.

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toPropertyMap

public PropertyMap toPropertyMap()

Returns a propertymap describing this MultiStagePosition.

Returns:

PropertyMap describing this MultiStagePosition

fromPropertyMap

public static MultiStagePosition fromPropertyMap(PropertyMap pmap)

Generates a multistagePosition from the given PropertyMap.

Parameters:

pmap - PropertyMap

Returns:

MultiStagePosition