org.youscope.plugin.microplatemeasurement

Class MicroplatePositionConfiguration

java.lang.Object

org.youscope.common.measurement.microplate.MicroplateConfiguration

org.youscope.plugin.microplatemeasurement.MicroplatePositionConfiguration

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Configuration

public class MicroplatePositionConfiguration
extends MicroplateConfiguration

Configuration of the positions to measure in a microplate measurement.

Author:

langmo

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
MicroplatePositionConfiguration() Default constructor.
MicroplatePositionConfiguration(int numPositions) Constructor for a microplate type, when no microplate is used, but the functionality of the microplate measurement methods should be used for custom positions.
MicroplatePositionConfiguration(int numWellsX, int numWellsY, double wellWidth, double wellHeight) Constructor for a custom defined microplate.
MicroplatePositionConfiguration(Microplate microplateType) Constructor for a predefined microplate type.

Method Summary

Modifier and Type	Method and Description
java.lang.Object	clone()
void	createDefaultPath(double zeroPositionX, double zeroPositionY) Creates a default path given this configuration.
void	createDefaultPath(double zeroPositionX, double zeroPositionY, double zeroPositionFocus) Creates a default path given this configuration.
boolean[][]	getMeasuredPositionsInWell() Returns a matrix of the size of the positions in a well, where each element is indicating if the respective position should be measured or not.
boolean[][]	getMeasuredWells() Returns a matrix of the size of the microplate, where each element is indicating if the respective well should be measured or not.
int	getNumMeasuredPos() Returns the number of positions in a well which are measured.
int	getNumMeasuredWells() Returns the number of wells which are measured in the microplate.
XYAndFocusPosition	getPosition(Well well, int posY, int posX) Returns the previously initialized x, y, and focus value for the given position in the given well, or NULL if the data was yet not initialized or the given position or the given well should not be measured.
int	getTotalMeasuredPositions() Returns the total number of measured positions in a well times the number of measured wells.
boolean	isAllPositionsSelected() Returns true if all positions in each well of the microplate are selected to be measured.
boolean	isAllWellsSelected() Returns true if all wells of the microplate are selected to be measured.
boolean	isInitialized() Returns true if the exact x/y position for every well is initialized.
boolean	isMeasurePosition(int posY, int posX) Returns if a given position in a well should be measured.
boolean	isMeasureWell(Well well) Returns true if the given well should be measured.
boolean	isNoneSelected() Returns if either no well or no position inside a well is selected/should be measured.
boolean	isSinglePosition() Returns true if this configuration is configured such that only one position per well is defined (and not necessarily if only one position is activated).
void	setMeasurePosition(boolean measure, int posY, int posX) Sets if a given position in a well should be measured.
void	setMeasureWell(boolean measure, Well well) Sets if the given well should be measured or not.
boolean	setMicroplateDimensions(int numWellsX, int numWellsY, double wellWidth, double wellHeight, int wellPositionsX, int wellPositionsY, double wellMarginX, double wellMarginY) Sets the dimensions of the microplate and the measured positions.
boolean	setNumPositions(int numPositions) Microplate measurements can be "misused" to measure just some arbitrary positions.
void	setPosition(XYAndFocusPosition position, Well well, int posY, int posX) Sets the x, y, and focus value for the given position in the given well.
void	setSelectAllWellPositions(boolean select) Select or unselects all positions in a well.
void	setSelectAllWells(boolean select) Select or unselects all wells in a microplate.

Methods inherited from class org.youscope.common.measurement.microplate.MicroplateConfiguration

checkConfiguration, getMicroplateTypeID, getNumPositions, getNumWellsX, getNumWellsY, getTypeIdentifier, getWellHeight, getWellMarginX, getWellMarginY, getWellNumPositionsX, getWellNumPositionsY, getWellPositionDistanceX, getWellPositionDistanceY, getWellWidth, isAliasMicroplate, setMicroplateType, setNumWellsX, setNumWellsY, setWellHeight, setWellMarginX, setWellMarginY, setWellNumPositionsX, setWellNumPositionsY, setWellWidth

Methods inherited from class java.lang.Object

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

Constructor Detail

MicroplatePositionConfiguration

public MicroplatePositionConfiguration()

Default constructor. Initializes a 96 well plate.

MicroplatePositionConfiguration

public MicroplatePositionConfiguration(Microplate microplateType)

Constructor for a predefined microplate type.

Parameters:

microplateType - The predefined microplate type.

MicroplatePositionConfiguration

public MicroplatePositionConfiguration(int numWellsX,
                                       int numWellsY,
                                       double wellWidth,
                                       double wellHeight)

Constructor for a custom defined microplate.

Parameters:

numWellsX - number of wells in the horizontal direction.

numWellsY - number of wells in the vertical direction.

wellWidth - width of a well (well-well distance).

wellHeight - height of a well (well-well distance).

MicroplatePositionConfiguration

public MicroplatePositionConfiguration(int numPositions)

Constructor for a microplate type, when no microplate is used, but the functionality of the microplate measurement methods should be used for custom positions.

Parameters:

numPositions - Number of positions.

Method Detail

setMeasureWell

public void setMeasureWell(boolean measure,
                           Well well)

Sets if the given well should be measured or not.

Parameters:

measure - True if the given well should be measured during the microplate measurement.

well - The well.

isSinglePosition

public boolean isSinglePosition()

Returns true if this configuration is configured such that only one position per well is defined (and not necessarily if only one position is activated).

Returns:

True if only one position per well is defined.

isMeasureWell

public boolean isMeasureWell(Well well)

Returns true if the given well should be measured.

Parameters:

well - The well.

Returns:

True if the given well should be measured, false otherwise.

setMeasurePosition

public void setMeasurePosition(boolean measure,
                               int posY,
                               int posX)

Sets if a given position in a well should be measured.

Parameters:

measure - True if the position should be measured.

posY - The y-index of the position in a well, starting with 0.

posX - The x-index of the position in a well, starting with 0.

isMeasurePosition

public boolean isMeasurePosition(int posY,
                                 int posX)

Returns if a given position in a well should be measured.

Parameters:

posY - The y-index of the position in a well, starting with 0.

posX - The x-index of the position in a well, starting with 0.

Returns:

True if the position should be measured.

setNumPositions

public boolean setNumPositions(int numPositions)

Description copied from class: MicroplateConfiguration

Microplate measurements can be "misused" to measure just some arbitrary positions. Call this function to define the number of positions. Automatically sets isAliasMicroplate() to true.

Overrides:

setNumPositions in class MicroplateConfiguration

Parameters:

numPositions - The number of abitrary positions to measure.

Returns:

Returns TRUE if microplate dimensions changed.

setMicroplateDimensions

public boolean setMicroplateDimensions(int numWellsX,
                                       int numWellsY,
                                       double wellWidth,
                                       double wellHeight,
                                       int wellPositionsX,
                                       int wellPositionsY,
                                       double wellMarginX,
                                       double wellMarginY)

Description copied from class: MicroplateConfiguration

Sets the dimensions of the microplate and the measured positions.

Overrides:

setMicroplateDimensions in class MicroplateConfiguration

Parameters:

numWellsX - Number of wells in the x-direction.

numWellsY - Number of wells in the y-direction.

wellWidth - Width of a well.

wellHeight - Height of a well.

wellPositionsX - Number of measured positions in one well in the x-direction.

wellPositionsY - Number of measured positions in one well in the y-direction.

wellMarginX - Relative margin between the well border and the first measured position in the x-direction.

wellMarginY - Relative margin between the well border and the first measured position in the y-direction.

Returns:

Returns TRUE if microplate dimensions changed.

getMeasuredWells

public boolean[][] getMeasuredWells()

Returns a matrix of the size of the microplate, where each element is indicating if the respective well should be measured or not.

Returns:

Matrix of measured wells.

getMeasuredPositionsInWell

public boolean[][] getMeasuredPositionsInWell()

Returns a matrix of the size of the positions in a well, where each element is indicating if the respective position should be measured or not.

Returns:

Matrix of measured positions.

createDefaultPath

public void createDefaultPath(double zeroPositionX,
                              double zeroPositionY)

Creates a default path given this configuration. Same as createDefaultPath(zeroPositionX, zeroPositionY, 0).

Parameters:

zeroPositionX - The x-position of the center of the well A1;

zeroPositionY - The y-position of the center of the well A1;

createDefaultPath

public void createDefaultPath(double zeroPositionX,
                              double zeroPositionY,
                              double zeroPositionFocus)

Creates a default path given this configuration.

Parameters:

zeroPositionX - The x-position of the center of the well A1;

zeroPositionY - The y-position of the center of the well A1;

zeroPositionFocus - The focus with which the positions should be initialized.

isInitialized

public boolean isInitialized()

Returns true if the exact x/y position for every well is initialized.

Returns:

True if each position in each well has an associated x/y/focus value

getNumMeasuredWells

public int getNumMeasuredWells()

Returns the number of wells which are measured in the microplate.

Returns:

Number of wells which should be measured.

getNumMeasuredPos

public int getNumMeasuredPos()

Returns the number of positions in a well which are measured.

Returns:

Number of positions which should be measured.

getTotalMeasuredPositions

public int getTotalMeasuredPositions()

Returns the total number of measured positions in a well times the number of measured wells.

Returns:

Overall number of measured positions.

setSelectAllWells

public void setSelectAllWells(boolean select)

Select or unselects all wells in a microplate.

Parameters:

select - True if all wells should be selected/measured, false if all wells should be unselected.

setSelectAllWellPositions

public void setSelectAllWellPositions(boolean select)

Select or unselects all positions in a well.

Parameters:

select - True if all positions should be selected/measured, false if all positions should be unselected.

isNoneSelected

public boolean isNoneSelected()

Returns if either no well or no position inside a well is selected/should be measured.

Returns:

True if no position in no well should be measured, false if at least one position in one well should be measured.

isAllWellsSelected

public boolean isAllWellsSelected()

Returns true if all wells of the microplate are selected to be measured.

Returns:

True if all wells should be measured.

isAllPositionsSelected

public boolean isAllPositionsSelected()

Returns true if all positions in each well of the microplate are selected to be measured.

Returns:

True if all positions should be measured.

setPosition

public void setPosition(XYAndFocusPosition position,
                        Well well,
                        int posY,
                        int posX)

Sets the x, y, and focus value for the given position in the given well.

Parameters:

position - The x, y, and focus value.

well - The well.

posY - The y-index of the position in the well, starting with 0.

posX - The x-index of the position in the well, starting with 0.

getPosition

public XYAndFocusPosition getPosition(Well well,
                                      int posY,
                                      int posX)

Returns the previously initialized x, y, and focus value for the given position in the given well, or NULL if the data was yet not initialized or the given position or the given well should not be measured.

Parameters:

well - The well.

posY - The y-index of the position in the well, starting with 0.

posX - The x-index of the position in the well, starting with 0.

Returns:

The previously initialized x, y, and focus value for the given position in the given well.

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class MicroplateConfiguration

Throws:

java.lang.CloneNotSupportedException