ALICA Interfaces

Interfaces to the primary components of ALICA.

Javadoc

ch.epfl.leb.alica.interfaces

AbstractFactory

public abstract class AbstractFactory<ProductSetupPanel>

A template for factories that are set up using a JPanel. This template is currently used by the Analyzer and Controller interfaces.

Author:

Marcel Stefko

Parameters:

• <ProductSetupPanel> – A JPanel for setting up the parameters.

Fields

selected_name

String selected_name

The name of analyzer/controller.

Constructors

AbstractFactory

public AbstractFactory()

Initializes the map which stores different setup panels.

Methods

addSetupPanel

protected void addSetupPanel(String name, ProductSetupPanel panel)

Adds a new setup panel to the list.

Parameters:

• name – ID of the product belonging to the panel and displayed in the GUI.
• panel – The JPanel to setup the analyzer/controller.

getProductNameList

public Set<String> getProductNameList()

Returns a list of all possible analyzer/controller names.

Returns:A list of all possible product keys.

getProductSetupPanelCollection

public Collection<ProductSetupPanel> getProductSetupPanelCollection()

Returns a group of all the possible setup panels for the available analyzers/controllers.

Returns:A collection of all possible product setup panels.

getSelectedProductName

public String getSelectedProductName()

Returns the name of the selected analyzer/controller.

Returns:The name of currently selected product.

getSelectedSetupPanel

public ProductSetupPanel getSelectedSetupPanel()

Returns the setup panel of the currently selected analyzer/controller.

Returns:The setup panel of currently selected analyzer/product.

selectProduct

public void selectProduct(String name)

Selects a product from factory.

Parameters:

• name – The product identifier.

Analyzer

public interface Analyzer

Processes an image or series of images. Analyzers compute quantities from an image or series of images that are relevant for real-time control. These quantities can include, for example, the number of fluorescent molecules or the resolution.

Author:Marcel Stefko

Methods

dispose

public void dispose()

Close all windows that were opened and are owned by this analyzer.

getBatchOutput

public double getBatchOutput()

Returns the output of the analyzer for Controller input. If no output can be provided (such as when there are no new analyzed images), Double.NaN should be returned. This method can also modify the internal state of the analyzer (such as flushing the intermittent value cache).

Returns:The analyzer’s current output value for use by the controller

See also: ch.epfl.leb.alica.interfaces.Controller

getIntermittentOutput

public double getIntermittentOutput()

Returns the intermittent output of the analyzer. This is used to read the current output of the analyzer; its internal state is unchanged. getBatchOutput() should be used to obtain output that will be passed to the controller.

Returns:The analyzer’s current output value.

getName

public String getName()

Returns a unique name for the analyzer.

Returns:The analyzer’s name.

getShortReturnDescription

public String getShortReturnDescription()

Returns a short description of the values returned by the analyzer.

Returns:A short description of the values returned by the analyzer.

getStatusPanel

public AnalyzerStatusPanel getStatusPanel()

Returns the analyzer’s status panel that will be displayed in the GUI. If no panel is implemented, this method should return null. In this case, the corresponding space in the MonitorGUI will appear blank.

Returns:The status panel of the analyzer, or null.

processImage

public void processImage(Object image, int image_width, int image_height, double pixel_size_um, long time_ms)

Processes an image and adjust the analyzer’s internal state to reflect the results of the calculation. This method is called after each new image acquisition by the AnalysisWorker. You can use the synchronized(this) statement within the body of an implementation of an Analyzer to ensure that no output readout happens during code execution. When implementing new Analyzers, try to keep the computation time as short as possible.

Parameters:

• image – The image to be processed as 1D raw pixel data.
• image_width – Image width in pixels.
• image_height – Image height in pixels.
• pixel_size_um – Length of a side of a square pixel in micrometers.
• time_ms – Image acquisition time in milliseconds.

setROI

public void setROI(Roi roi)

Sets the region of interest in the image so that only a portion of the whole image is analyzed.

Parameters:

• roi – The Roi object corresponding to the region.

See also: ij.gui.Roi

Controller

public interface Controller

Adjusts control parameters in response to values provided by the analyzer. A controller receives the output of the analyzer as input, and then adjusts its internal state accordingly. It can be asked for its state at any time by the WorkerThread.

Author:Marcel Stefko

Methods

getCurrentOutput

public double getCurrentOutput()

Returns an output value derived from the controller’s internal state.

Returns:The controller’s new output value for the control signal.

getName

public String getName()

Returns a unique name for the controller.

Returns:A unique name for the controller.

getSetpoint

public double getSetpoint()

Returns the current value for the setpoint.

Returns:The current setpoint value.

getStatusPanel

public ControllerStatusPanel getStatusPanel()

Returns the controller’s status panel that will be displayed in the GUI. If no panel is implemented, this method should return null. In this case, the corresponding space in the MonitorGUI will appear blank.

Returns:The status panel of the controller, or null.

nextValue

public double nextValue(double value)

Receives next input from the WorkerThread (this the batched output of the analyzer). This method must be able to accept Double.NaN, which the analyzer will produce if if can not produce an output for some reason.

Parameters:

• value – The analyzer’s input value.

Returns:

The controller’s new output value for the control signal.

setSetpoint

public void setSetpoint(double new_setpoint)

Sets a new values for the controller’s setpoint.

Parameters:

• new_setpoint – The desired value for the process variable.

ch.epfl.leb.alica.interfaces.analyzers

AnalyzerFactory

public class AnalyzerFactory extends AbstractFactory<AnalyzerSetupPanel>

Analyzer factory.

Author:Marcel Stefko

Constructors

AnalyzerFactory

public AnalyzerFactory()

Adds the known algorithms to the list.

Methods

build

public Analyzer build()

Build the selected analyzer using current settings

Returns:initialized analyzer

AnalyzerSetupPanel

public abstract class AnalyzerSetupPanel extends javax.swing.JPanel

Sets up the analyzer, allows to customize settings.

Author:Marcel Stefko

Methods

getName

public abstract String getName()

initAnalyzer

public abstract Analyzer initAnalyzer()

Construct the analyzer from current settings.

Returns:initialized analyzer

AnalyzerSetupPanelLoader

class AnalyzerSetupPanelLoader

Methods

getAnalyzerSetupPanels

public static ArrayList<AnalyzerSetupPanel> getAnalyzerSetupPanels()

Dynamically loads AnalyzerSetupPanels from available jar files. The jar filename MUST begin with “ALICA_” for the jar to be recognized.

Returns:list of loaded setup panels

AnalyzerStatusPanel

public abstract class AnalyzerStatusPanel extends javax.swing.JPanel

A panel which will display status of the analyzer. Can be used to change settings during runtime (optional).

Author:Marcel Stefko

ch.epfl.leb.alica.interfaces.controllers

ControllerFactory

public class ControllerFactory extends AbstractFactory<ControllerSetupPanel>

Controller Factory

Author:Marcel Stefko

Constructors

ControllerFactory

public ControllerFactory()

Initialize the factory with known controllers

Methods

build

public Controller build()

Build the selected controller using current settings

Returns:initialized controller

setControllerTickRateMs

public void setControllerTickRateMs(double tick_rate_ms)

Set the tick rate at which the controller will operate.

Parameters:

• tick_rate_ms – tick rate in milliseconds

setMaxControllerOutput

public void setMaxControllerOutput(double max_controller_output)

Set maximal output value of the constructed controller

Parameters:

• max_controller_output –

ControllerSetupPanel

public abstract class ControllerSetupPanel extends javax.swing.JPanel

Makes sure that the added setup panels know how to initialize Controllers.

Author:Marcel Stefko

Methods

getName

public abstract String getName()

initController

public abstract Controller initController(double max_controller_output, double tick_rate_ms)

Initialize and return the controller based on GUI information.

Parameters:

• max_controller_output – maximal output value, this is passed from different part of the GUI
• tick_rate_ms – tick rate at which the controller will operate, passed from GUI

Returns:

initialized controller

ControllerSetupPanelLoader

class ControllerSetupPanelLoader

Methods

getControllerSetupPanels

public static ArrayList<ControllerSetupPanel> getControllerSetupPanels()

Dynamically loads ControllerSetupPanels from available jar files. The jar filename MUST begin with “ALICA_” for the jar to be recognized.

Returns:list of loaded setup panels

ControllerStatusPanel

public abstract class ControllerStatusPanel extends javax.swing.JPanel

A panel which will display status info of the controller. Can be used to change settings during runtime.

Author:Marcel Stefko

This package contains the interface definitions for the primary components of ALICA, the automatic illumination control package for light microscopy. It is a compile-time dependency of ALICA. These interfaces are maintained separately of ALICA and SASS because they are not expected to change frequently and should be quite stable.

Relationship with ALICA and SASS

Authors

• Marcel Štefko
• Kyle M. Douglass

See Also

• ALICA - Automated Laser Illumination Control Algorithm
• SASS - SMLM Acquistion Simulation Software

Indices and tables

• Index