org.micromanager

Interface AutofocusPlugin

All Superinterfaces:

MMGenericPlugin, MMPlugin, org.scijava.plugin.SciJavaPlugin

public interface AutofocusPlugin
extends MMPlugin

This interface is used for a java-based autofocus plugin. Properly compiled jars can be added to the mmplugins directory of Micro-Manager and they will be loaded into the autofocus menu. It also wraps autofocus devices implemented in C++ and exposed by the core, so both java and C++ based autofocus plugins can be used by this common interface.

Method Summary

Modifier and Type	Method and Description
void	applySettings() Pushes setting to the hardware or software autofocus.
double	computeScore(ij.process.ImageProcessor impro) Computes a focus score for the given image.
void	enableContinuousFocus(boolean enable) Turns on continuous autofocus.
double	fullFocus() Runs a full, one-shot autofocus protocol.
double	getCurrentFocusScore() Returns the current focus "score" (goodness of focus).
int	getNumberOfImages() Returns the number of images acquired.
org.micromanager.internal.utils.PropertyItem[]	getProperties() Returns an array of the properties for this autofocus plugin.
org.micromanager.internal.utils.PropertyItem	getProperty(java.lang.String key) Returns the name and value of properties for the autofocus plugin.
java.lang.String[]	getPropertyNames() Returns an array of the names of properties for this autofocus plugin.
java.lang.String	getPropertyValue(java.lang.String name) Gets the value of a named property.
java.lang.String	getVerboseStatus() Returns a detailed status of the autofocus plugin/device.
double	incrementalFocus() Runs a single, incremental focusing step.
void	initialize() Initializes the plugin.
boolean	isContinuousFocusEnabled() Returns true if continuous autofocus has been enabled.
boolean	isContinuousFocusLocked() Returns true if continuous autofocus is currently locked (successfully following the specimen).
void	saveSettings() Stores settings.
void	setProperty(org.micromanager.internal.utils.PropertyItem p) Sets the value of a particular property.
void	setPropertyValue(java.lang.String name, java.lang.String value) Sets the value of a named property.

Methods inherited from interface org.micromanager.MMPlugin

getCopyright, getHelpText, getName, getVersion, setContext

Method Detail

initialize

void initialize()

Initializes the plugin. Can be called multiple times, for instance after a change in hardware configuration. Conversely, the plugin can trust that the hardware never changes without a call to this function.

applySettings

void applySettings()

Pushes setting to the hardware or software autofocus.

saveSettings

void saveSettings()

Stores settings.

fullFocus

double fullFocus()
          throws java.lang.Exception

Runs a full, one-shot autofocus protocol. Blocks until focusing is finished.

Returns:

focus score

Throws:

java.lang.Exception - Mainly exceptions coming from the hardware.

incrementalFocus

double incrementalFocus()
                 throws java.lang.Exception

Runs a single, incremental focusing step.

Returns:

focus score

Throws:

java.lang.Exception - Mainly exceptions coming from the hardware.

getNumberOfImages

int getNumberOfImages()

Returns the number of images acquired.

Returns:

number of images for autofocussing

getVerboseStatus

java.lang.String getVerboseStatus()

Returns a detailed status of the autofocus plugin/device.

Returns:

description of the autofocus Status

getProperties

org.micromanager.internal.utils.PropertyItem[] getProperties()

Returns an array of the properties for this autofocus plugin.

Returns:

array with Property descriptors, representing MMCore data

getPropertyNames

java.lang.String[] getPropertyNames()

Returns an array of the names of properties for this autofocus plugin.

Returns:

array with the names of properties for this autofocus plugin

getProperty

org.micromanager.internal.utils.PropertyItem getProperty(java.lang.String key)
                                                  throws java.lang.Exception

Returns the name and value of properties for the autofocus plugin.

Parameters:

key - PropertyName for which we want the value

Returns:

value for given property

Throws:

java.lang.Exception - thrown by MMCore when key is not found.

setProperty

void setProperty(org.micromanager.internal.utils.PropertyItem p)
          throws java.lang.Exception

Sets the value of a particular property.

Parameters:

p - Property to be set

Throws:

java.lang.Exception - Not sure what this may be

getPropertyValue

java.lang.String getPropertyValue(java.lang.String name)
                           throws java.lang.Exception

Gets the value of a named property.

Parameters:

name - named property

Returns:

value for the given property

Throws:

java.lang.Exception - Not sure what this may indicate

setPropertyValue

void setPropertyValue(java.lang.String name,
                      java.lang.String value)
               throws java.lang.Exception

Sets the value of a named property.

Parameters:

name - PropertyName

value - PropertyValue

Throws:

java.lang.Exception - by MMCore

getCurrentFocusScore

double getCurrentFocusScore()

Returns the current focus "score" (goodness of focus).

Returns:

focus score (goodness of focus)

enableContinuousFocus

void enableContinuousFocus(boolean enable)
                    throws java.lang.Exception

Turns on continuous autofocus. Typically used by hardware autofocus devices such as the Nikon Perfect Focus (PFS).

Parameters:

enable - Switch on when true, off otherwise.

Throws:

java.lang.Exception - Hardware may throw and exception

isContinuousFocusEnabled

boolean isContinuousFocusEnabled()
                          throws java.lang.Exception

Returns true if continuous autofocus has been enabled. Typically used by hardware autofocus devices such as the Nikon Perfect Focus (PFS).

Returns:

true if enabled, false otherwise

Throws:

java.lang.Exception - May be thrown by the hardware

isContinuousFocusLocked

boolean isContinuousFocusLocked()
                         throws java.lang.Exception

Returns true if continuous autofocus is currently locked (successfully following the specimen). Typically used by hardware autofocus devices such as the Nikon Perfect Focus (PFS).

Returns:

true if locked

Throws:

java.lang.Exception - thrown by MMCore

computeScore

double computeScore(ij.process.ImageProcessor impro)

Computes a focus score for the given image.

Parameters:

impro - ImageProcessor to be used in the calculation.

Returns:

calculated score