ImageJSimulator

public class ImageJSimulator extends DefaultSimulator

The default simulator that is run as, for example, the ImageJ plugin.

Author:Marcel Stefko

Fields

TIMEPERFRAME

protected final long TIMEPERFRAME

The time duration of each frame. This is here only for compatibility with ALICA’s analyzers, which require a time argument.

analyzer

protected final Analyzer analyzer

Analyzer which analyzes generated images

controller

protected final Controller controller

Takes the output of a single analyzer, processes it, and outputs a signal to the generator, for feedback loop control.

history

protected HashMap<Integer, JSONObject> history

Records of values of output of analyzer, controller.

image_count

protected int image_count

Number of already-generated images.

positionLogger

protected PositionLogger positionLogger

Logs the ground truth positions of the molecules.

stateLogger

protected StateLogger stateLogger

Logs the state transitions of the molecules.

Constructors

ImageJSimulator

public ImageJSimulator(Microscope microscope, Analyzer analyzer, Controller controller)

Initialize the simulator from user-specified components.

Parameters:
  • microscope – The microscope to be simulated.
  • analyzer – An analyzer for processing images from the microscope.
  • controller – A controller that adjusts the state of the microscope.

Methods

execute

public ImageS execute(int no_of_images, int controller_refresh_rate, String csv_save_path, String tiff_save_path)

An example simulation

Parameters:
  • no_of_images –
  • controller_refresh_rate –
  • csv_save_path –
  • tiff_save_path –

getImageCount

public int getImageCount()

Returns the number of generated images since simulation start.

Returns:number of generated images

getPositionLogger

public PositionLogger getPositionLogger()
Returns:The emitter position logger.

getStateLogger

public StateLogger getStateLogger()
Returns:The state transition logger.

incrementCounter

public void incrementCounter()

Increments image counter in case an image was generated outside of this class.

saveStack

public void saveStack(File tiff_file)

Save current ImageStack to TIFF file

Parameters:
  • tiff_file – file to save to

saveToCsv

public void saveToCsv(File file)

Saves the data for generator, analyzer and controller for each frame into a .csv file

Parameters:
  • file – destination csv file