ALICA AC Pack¶

Javadoc¶

ch.epfl.leb.alica.acpack.analyzers.autolase¶

AutoLase¶

public class AutoLase implements Analyzer¶

Wrapper for Thomas Pengo’s implementation of AutoLase algorithm.

Author:	Marcel Stefko

Constructors¶

AutoLase¶

public AutoLase(int threshold)¶

Initializes AutoLase with default threshold (120) and averaging (30) values.

Parameters:	threshold –

Methods¶

dispose¶

public void dispose()¶

getBatchOutput¶

public double getBatchOutput()¶

getIntermittentOutput¶

public double getIntermittentOutput()¶

getName¶

public String getName()¶

getShortReturnDescription¶

public String getShortReturnDescription()¶

getStatusPanel¶

public AnalyzerStatusPanel getStatusPanel()¶

processImage¶

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

setROI¶

public void setROI(Roi roi)¶

AutoLaseAnalyzer¶

class AutoLaseAnalyzer¶

This class estimates the density of activations. The density at a particular point relates to the maximum time a certain pixel is “on”, or above a certain threshold. The density is calculated as a moving average 30 frames. The code only works for 2 bytes per pixel cameras for now.

Author:	Thomas Pengo

Fields¶

currentDensity¶

double currentDensity¶

running¶

boolean running¶

stopping¶

boolean stopping¶

Constructors¶

AutoLaseAnalyzer¶

public AutoLaseAnalyzer(int threshold)¶

Methods¶

getCurrentValue¶

public double getCurrentValue()¶

Returns error signal value from AutoLase

Returns:	estimated averaged max emitter density

getRawCurrentValue¶

public double getRawCurrentValue()¶

Returns raw error signal value from AutoLase

Returns:	estimated max emitter density for most recent frame

nextImage¶

public void nextImage(ShortProcessor sp)¶

Analyzes next image and adjusts internal state.

Parameters:	image – image to be analyzed

setParameters¶

public void setParameters(int threshold)¶

setROI¶

public void setROI(Roi roi)¶

AutoLaseSetupPanel¶

public class AutoLaseSetupPanel extends AnalyzerSetupPanel¶

Setup panel for AutoLase, allows setup of thresholding and averaging.

Author:	Marcel Stefko

Constructors¶

AutoLaseSetupPanel¶

public AutoLaseSetupPanel()¶: Creates new form SetupPanel

Methods¶

getName¶

public String getName()¶

initAnalyzer¶

public Analyzer initAnalyzer()¶

toString¶

public String toString()¶

ch.epfl.leb.alica.acpack.analyzers.defcon¶

DEFCoNSetupPanel¶

public class DEFCoNSetupPanel extends AnalyzerSetupPanel¶

The DEFCoN analyzer setup panel.

Author:	Kyle M. Douglass

Constructors¶

DEFCoNSetupPanel¶

public DEFCoNSetupPanel()¶: Creates new form SetupPanel

Methods¶

getName¶

public String getName()¶

initAnalyzer¶

public Analyzer initAnalyzer()¶: Initializes the analyzer using the properties from the setup panel.

Defcon¶

public class Defcon implements Analyzer¶

A fluorescent spot counter derived from the DEFCoN package.

Author:	Kyle M. Douglass

See also: DEFCoN-ImageJ

Constructors¶

Defcon¶

public Defcon(String pathToModel)¶

Initializes the DEFCoN analyzer.

Parameters:	pathToModel – The path to the DEFCoN network model.

Methods¶

dispose¶

public void dispose()¶: Cleans up the analyzer when it’s finished.

finalize¶

protected void finalize()¶

Failsafe in case the predictor has not been closed at the point of garbage collection.

Throws:	java.lang.Throwable –

getBatchOutput¶

public double getBatchOutput()¶

Returns the averaged DEFCoN count value since the last call. Double.NaN is returned if there is no new count since the previous call.

Returns:	The averaged DEFCoN count.

getBoxSize¶

public int getBoxSize()¶

Returns the current square kernel size for maximum local counts.

Returns:	The kernel size for computing the maximum local count.

getIntermittentOutput¶

public double getIntermittentOutput()¶

Returns the intermittent output of the analyzer.

Returns:	The analyzer’s current output value.

getName¶

public String getName()¶

Returns the name of the DEFCoN analyzer.

Returns:	The name of the DEFCoN analyzer.

getShortReturnDescription¶

public String getShortReturnDescription()¶

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

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

isLiveModeOn¶

public boolean isLiveModeOn()¶

True if live mode is on, false otherwise.

Returns:	True if live mode is on, false otherwise

isMaxLocalCount¶

public boolean isMaxLocalCount()¶

True if the analyzer is computing the maximum local count.

Returns:	True if the analyzer is computing the maximum local count.

liveModeOff¶

public void liveModeOff()¶: Turns off the live view of the density map.

liveModeOn¶

public void liveModeOn()¶: Turns on the live view of the density map.

maxLocalCountOff¶

public void maxLocalCountOff()¶: Turns off the live view of the density map.

maxLocalCountOn¶

public void maxLocalCountOn()¶: Turns on the live view of the density map.

processImage¶

public void processImage(Object image, int width, int height, double pixelSizeUm, long timeMs)¶

Processes an image and adjusts 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.

Parameters:	image – The image to be processed as 1D raw pixel data. width – Image width in pixels. height – Image height in pixels. pixelSizeUm – Length of a side of a square pixel in micrometers. timeMs – Image acquisition time in milliseconds.

setBoxSize¶

public void setBoxSize(int boxSize)¶

Sets the square kernel size for computing the maximum local count.

Parameters:	boxSize – The kernel size for computing the maximum local count.

setROI¶

public void setROI(Roi roi)¶

updateLiveView¶

public void updateLiveView()¶: Updates the live viewer.

DefconStatusPanel¶

public class DefconStatusPanel extends AnalyzerStatusPanel¶

Status panel of the DEFCoN analyzer.

Author:	Kyle M. Douglass

Constructors¶

DefconStatusPanel¶

public DefconStatusPanel(Defcon defcon)¶: Creates new form DefconStatusPanel.

DefconTest¶

public class DefconTest¶

Unit tests for the Defcon class.

Author:	Kyle M. Douglass

Methods¶

setUp¶

public void setUp()¶

testGetSetBoxSize¶

public void testGetSetBoxSize()¶: Gets/sets the box size field for the maximum local count.

testMaxLocalCount¶

public void testMaxLocalCount()¶: Toggles the maximum local count feature.

testNegativeBoxSize¶

public void testNegativeBoxSize()¶: Ensures that the boxSize value is greater than 1.

testOddBoxSize¶

public void testOddBoxSize()¶: Ensures that the boxSize value is odd.

testProcessImage¶

public void testProcessImage()¶: Ensures that the processImage() method is called without errors.

testProcessMaxLocalCount¶

public void testProcessMaxLocalCount()¶: Analyzer predicts the maximum local count instead of the density map.

ch.epfl.leb.alica.acpack.analyzers.integrator¶

Integrator¶

public class Integrator implements Analyzer¶

Analyzer which outputs the average pixel value per frame. The average is taken over the area of the image (or ROI) in units of squared pixels.

Author:	Marcel Stefko

Constructors¶

Integrator¶

public Integrator()¶

Methods¶

dispose¶

public void dispose()¶

getBatchOutput¶

public double getBatchOutput()¶

getIntermittentOutput¶

public double getIntermittentOutput()¶

getName¶

public String getName()¶

getShortReturnDescription¶

public String getShortReturnDescription()¶

getStatusPanel¶

public AnalyzerStatusPanel getStatusPanel()¶

processImage¶

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

Computes the average of the pixel values taken over the image (or ROI).

Parameters:	image – image_width – image_height – pixel_size_um – time_ms –

setROI¶

public void setROI(Roi roi)¶

IntegratorSetupPanel¶

public class IntegratorSetupPanel extends AnalyzerSetupPanel¶

Empty panel

Author:	stefko

Constructors¶

IntegratorSetupPanel¶

public IntegratorSetupPanel()¶: Creates new form IntegratorSetupPanel

Methods¶

getName¶

public String getName()¶

initAnalyzer¶

public Analyzer initAnalyzer()¶

IntegratorTest¶

public class IntegratorTest¶

Author:	douglass

Methods¶

setUp¶

public void setUp()¶

testGetBatchOutput¶

public void testGetBatchOutput()¶: Test of getBatchOutput method, of class Integrator.

testProcessImage¶

public void testProcessImage()¶: Test of processImage method, of class Integrator.

ch.epfl.leb.alica.acpack.analyzers.quickpalm¶

MyDialogs¶

class MyDialogs¶

Fields¶

attach¶

boolean attach¶

buffer¶

int buffer¶

cal_z¶

double cal_z¶

calfile¶

java.lang.String calfile¶

fwhm¶

double fwhm¶

height¶

int height¶

imagedir¶

java.lang.String imagedir¶

imp¶

ImagePlus imp¶

imtitle¶

String imtitle¶

is3d¶

boolean is3d¶

magn¶

double magn¶

maxpart¶

int maxpart¶

maxsize¶

double maxsize¶

minsize¶

double minsize¶

model¶

java.lang.String model¶

models¶

java.lang.String[] models¶

nimchars¶

int nimchars¶

nimstart¶

int nimstart¶

nrois¶

int nrois¶

nslices¶

int nslices¶

part_divergence¶

boolean part_divergence¶

part_extrainfo¶

boolean part_extrainfo¶

pattern¶

java.lang.String pattern¶

pixelsize¶

double pixelsize¶

prefix¶

java.lang.String prefix¶

prefs¶

ij.Prefs prefs¶

ptablefile¶

java.lang.String ptablefile¶

pthrsh¶

double pthrsh¶

rmanager¶

RoiManager rmanager¶

rois¶

Roi[] rois¶

saturation¶

double saturation¶

smartsnr¶

boolean smartsnr¶

snr¶

int snr¶

sufix¶

java.lang.String sufix¶

symmetry¶

double symmetry¶

threads¶

int threads¶

view¶

boolean view¶

view_mode¶

java.lang.String view_mode¶

view_modes¶

java.lang.String[] view_modes¶

viewer_accumulate¶

int viewer_accumulate¶

viewer_do3d¶

boolean viewer_do3d¶

viewer_doConvolve¶

boolean viewer_doConvolve¶

viewer_doMovie¶

boolean viewer_doMovie¶

viewer_fwhm¶

double viewer_fwhm¶

viewer_is8bit¶

boolean viewer_is8bit¶

viewer_mergeabove¶

double viewer_mergeabove¶

viewer_mergebellow¶

double viewer_mergebellow¶

viewer_oheight¶

int viewer_oheight¶

viewer_owidth¶

int viewer_owidth¶

viewer_tpixelsize¶

double viewer_tpixelsize¶

viewer_update¶

int viewer_update¶

viewer_zstep¶

double viewer_zstep¶

waittime¶

int waittime¶

width¶

int width¶

window¶

int window¶

Methods¶

analyseParticles¶

public boolean analyseParticles(MyFunctions f)¶

MyFunctions¶

class MyFunctions¶

Fields¶

cal3d_center¶

int cal3d_center¶

cal3d_wmh¶

double[] cal3d_wmh¶

cal3d_z¶

double[] cal3d_z¶

caltable¶

ResultsTable caltable¶

debug¶

boolean debug¶

dtable¶

ResultsTable dtable¶

gblur¶

GaussianBlur gblur¶

live_view¶

ImagePlus live_view¶

ptable¶

ResultsTable ptable¶

ptable_lock¶

java.util.concurrent.locks.Lock ptable_lock¶

Constructors¶

MyFunctions¶

public MyFunctions(boolean live_view)¶

Methods¶

argmax¶

int argmax(double[] arr)¶

argmin¶

int argmin(double[] arr)¶

clearRegion¶

void clearRegion(double thrsh, ImageProcessor ip, boolean[][] mask, int xstart, int xend, int ystart, int yend)¶

detectParticles¶

int detectParticles(ImageProcessor ip, MyDialogs dg, int nframe)¶

Particle finding method, will search the image for particles.

Parameters:	ip – image to search for particles on dg – dialog manager nframe – the frame index corresponding to this image

dispose¶

public void dispose()¶

getClosest¶

int getClosest(double value, double[] arr, int center)¶

getMaxPositions¶

int[] getMaxPositions(ImageProcessor ip)¶

getNextImage¶

ImagePlus getNextImage(MyDialogs dg, int frame)¶

Grabs a new image on an observed folder on the case of the analysis being attached to the acquisition.

Parameters:	dg – dialog manager frame – frame index to search for on the folder
Returns:	found image

getParticle¶

boolean getParticle(ImageProcessor ip, boolean[][] mask, int[] maxs, MyDialogs dg, ResultsTable ptable, int nframe)¶

Particle analysis method, called for each particle candidate found by detectParticles.

Parameters:	ip – image to search for particles on dg – dialog manager nframe – the frame index corresponding to this image

getParticleForCalibration¶

double[] getParticleForCalibration(ImageProcessor ip, MyDialogs dg, int xstart, int xend, int ystart, int yend)¶

getZ¶

double getZ(double wmh)¶

Given a calculated width-minus-height (wmh) converts this value into the corresponding coordinate in Z by comparing against the loaded Z-calibration table. Only used it the particle is disturbed by astigmatism.

Parameters:	wmh – the width-minus-height of a particle
Returns:	corresponding z-position value, will return 9999 if wmh is out of limits

initialize3d¶

void initialize3d()¶: Loads values from the calibration table into the cal3d_* arrays.

log¶

void log(java.lang.String txt)¶

mean¶

double mean(double[] array, int start, int stop)¶

movingMean¶

double[] movingMean(double[] arr, int window)¶

showTable¶

void showTable()¶

QuickPalm¶

public class QuickPalm implements Analyzer¶

Produces a localization count per area using QuickPALM.

Author:	Marcel Stefko

Constructors¶

QuickPalm¶

public QuickPalm(boolean live_view)¶

Implementation of the QuickPALM algorithm as an analyzer, which produces particle count as output.

Parameters:	live_view – if true, live view of particle positions is shown

Methods¶

dispose¶

public void dispose()¶

getBatchOutput¶

public double getBatchOutput()¶

getIntermittentOutput¶

public double getIntermittentOutput()¶

getName¶

public String getName()¶

getShortReturnDescription¶

public String getShortReturnDescription()¶

getStatusPanel¶

public AnalyzerStatusPanel getStatusPanel()¶

processImage¶

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

setROI¶

public void setROI(Roi roi)¶

QuickPalmCore¶

public class QuickPalmCore¶

Wrapper for QuickPalm ImageJ plugin functionality developed by Ricardo Henriques @ Instituto de Medicina Molecular (PT) / Institut Pasteur (FR).

Author:	Marcel Stefko

Constructors¶

QuickPalmCore¶

public QuickPalmCore(boolean live_view)¶

Initializes the core and launches a dialog for parameter setup.

Parameters:	live_view – if true, live view of particle positions will be shown

Methods¶

dispose¶

public void dispose()¶: Close preview window if opened.

processImage¶

public int processImage(ImageProcessor ip, int frame)¶

Counts particles in the image.

Parameters:	ip – image to be processed frame – id of the image
Returns:	no. of detected particles

QuickPalmSetupPanel¶

public class QuickPalmSetupPanel extends AnalyzerSetupPanel¶

Author:	stefko

Constructors¶

QuickPalmSetupPanel¶

public QuickPalmSetupPanel()¶: Creates new form QuickPalmSetupPanel

Methods¶

getName¶

public String getName()¶

initAnalyzer¶

public Analyzer initAnalyzer()¶

ch.epfl.leb.alica.acpack.analyzers.spotcounter¶

FindLocalMaxima¶

public class FindLocalMaxima¶: Find local maxima in an Image (or ROI) using the algorithm described in Neubeck and Van Gool. Efficient non-maximum suppression. Pattern Recognition (2006) vol. 3 pp. 850-855 Jonas Ries brought this to my attention and send me C code implementing one of the described algorithms

Methods¶

FindMax¶

public static Polygon FindMax(ImageProcessor iProc, Roi roi, int n, int threshold, FilterType filterType)¶

Static utility function to find local maxima in an Image

Parameters:	iProc – ImageProcessor object in which to look for local maxima roi – region of interest to which the analysis is constrained n – minimum distance to other local maximum threshold – value below which a maximum will be rejected filterType – Prefilter the image. Either none or Gaussian1_5
Returns:	Polygon with maxima

noiseFilter¶

public static Polygon noiseFilter(ImageProcessor iProc, Polygon inputPoints, int threshold)¶

Parameters:	iProc – inputPoints – threshold –

FindLocalMaxima.FilterType¶

public enum FilterType¶: Different filters for image preprocessing.

Enum Constants¶

GAUSSIAN1_5¶

public static final FindLocalMaxima.FilterType GAUSSIAN1_5¶

NONE¶

public static final FindLocalMaxima.FilterType NONE¶: No preprocessing.

SpotCounter¶

public class SpotCounter implements Analyzer¶

Author:	stefko

Constructors¶

SpotCounter¶

public SpotCounter(int noise_tolerance, int box_size, boolean live_view)¶

Initialize the analyzer

Parameters:	noise_tolerance – required height of peak around surroundings box_size – size of the scanning box in pixels live_view – if true, live preview is shown

Methods¶

dispose¶

public void dispose()¶

getBatchOutput¶

public double getBatchOutput()¶

getIntermittentOutput¶

public double getIntermittentOutput()¶

getName¶

public String getName()¶

getShortReturnDescription¶

public String getShortReturnDescription()¶

getStatusPanel¶

public AnalyzerStatusPanel getStatusPanel()¶

processImage¶

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

setROI¶

public void setROI(Roi roi)¶

SpotCounterCore¶

public class SpotCounterCore¶

Core of the SpotCounter algorithm

Author:	Nico Stuurman

Constructors¶

SpotCounterCore¶

public SpotCounterCore(int noiseTolerance, int boxSize, boolean live_mode)¶

Parameters:	noiseTolerance – minimum peak value boxSize – size of scanning box live_mode – if true, live preview is shown

Methods¶

analyze¶

public HashMap<String, Double> analyze(ImageProcessor ip)¶

Analyzes the image and returns information about current state.

Parameters:	ip – image to be analyzed
Returns:	ResultsTable which contains information about analysis results.

dispose¶

public void dispose()¶: Hide live view window if it exists.

getBoxSize¶

public int getBoxSize()¶

getNoiseTolerance¶

public int getNoiseTolerance()¶

isLiveModeOn¶

public boolean isLiveModeOn()¶

Returns:	true if live mode is on, false otherwise

liveModeOff¶

public void liveModeOff()¶: Turns off live viewing of SpotCounter analysis.

liveModeOn¶

public void liveModeOn()¶: Turns on live viewing of SpotCounter analysis.

setParams¶

public void setParams(int noiseTolerance, int boxSize)¶

Set new parameters for the analysis

Parameters:	noiseTolerance – minimum peak value boxSize – size of scanning box

setROI¶

public void setROI(Roi roi)¶

Constrain analysis to given ROI.

Parameters:	roi – ROI to constrain analysis to

SpotCounterSetupPanel¶

public class SpotCounterSetupPanel extends AnalyzerSetupPanel¶

Setup panel to initialize the SpotCounter

Author:	Marcel Stefko

Constructors¶

SpotCounterSetupPanel¶

public SpotCounterSetupPanel()¶: Creates new form SetupPanel

Methods¶

getName¶

public String getName()¶

initAnalyzer¶

public Analyzer initAnalyzer()¶

SpotCounterStatusPanel¶

public class SpotCounterStatusPanel extends AnalyzerStatusPanel¶

Status panel of SpotCounter, enables modification of threshold in real time.

Author:	Marcel Stefko

Constructors¶

SpotCounterStatusPanel¶

public SpotCounterStatusPanel(SpotCounterCore core)¶

Creates new form SpotCounterStatusPanel

Parameters:	core – SpotCounterCore

ch.epfl.leb.alica.acpack.controllers.inverter¶

InvertController¶

public class InvertController implements Controller¶

Controller which inverts and scales the input using 1/x function. (high input -> low output, low input -> high output)

Author:	Marcel Stefko

Fields¶

maximum¶

protected double maximum¶: Maximal possible output value.

Constructors¶

InvertController¶

public InvertController(double maximum, double value_at_1_mw)¶

Initializes the InvertController

Parameters:	maximum – max output value value_at_1_mw – what is the value of input that you want to cause an output value of 1.0 (scaling constant)

Methods¶

getCurrentOutput¶

public double getCurrentOutput()¶

getName¶

public String getName()¶

getSetpoint¶

public double getSetpoint()¶

getStatusPanel¶

public ControllerStatusPanel getStatusPanel()¶

nextValue¶

public double nextValue(double value)¶

setSetpoint¶

public void setSetpoint(double value)¶

Sets the scaling constant, since it basically fulfills the role of setpoint for this controller.

Parameters:	value – new scaling constant

InverterSetupPanel¶

public class InverterSetupPanel extends ControllerSetupPanel¶

Setup panel for the InvertController

Author:	Marcel Stefko

Constructors¶

InverterSetupPanel¶

public InverterSetupPanel()¶: Creates new form InverterSetupPanel

Methods¶

getName¶

public String getName()¶

initController¶

public Controller initController(double max_controller_output, double tick_rate_ms)¶

ch.epfl.leb.alica.acpack.controllers.manual¶

ManualController¶

public class ManualController implements Controller¶

Manual controller. Output is equal to setpoint value, any input is ignored.

Author:	Marcel Stefko

Fields¶

maximum¶

protected double maximum¶: Maximal possible output value.

setpoint¶

protected double setpoint¶: Output value

Constructors¶

ManualController¶

public ManualController(double maximum, double initial_output)¶

Initialize with maximal output value

Parameters:	maximum – max output value initial_output – starting value of output

Methods¶

getCurrentOutput¶

public double getCurrentOutput()¶

getName¶

public String getName()¶

getSetpoint¶

public double getSetpoint()¶

getStatusPanel¶

public ControllerStatusPanel getStatusPanel()¶

nextValue¶

public double nextValue(double value)¶

setSetpoint¶

public void setSetpoint(double new_setpoint)¶

ManualSetupPanel¶

public class ManualSetupPanel extends ControllerSetupPanel¶

Author:	stefko

Constructors¶

ManualSetupPanel¶

public ManualSetupPanel()¶: Creates new form ManualSetupPanel

Methods¶

getName¶

public String getName()¶

initController¶

public Controller initController(double max_controller_output, double tick_rate_ms)¶

ch.epfl.leb.alica.acpack.controllers.pi¶

PI_SetupPanel¶

public class PI_SetupPanel extends ControllerSetupPanel¶

Author:	stefko

Constructors¶

PI_SetupPanel¶

public PI_SetupPanel()¶: Creates new form PI_SetupPanel

Methods¶

getName¶

public String getName()¶

initController¶

public Controller initController(double max_controller_output, double tick_rate_ms)¶

PI_StatusPanel¶

public class PI_StatusPanel extends ControllerStatusPanel¶

Author:	stefko

Constructors¶

PI_StatusPanel¶

public PI_StatusPanel(PI_controller controller)¶: Creates new form PI_StatusPanel

Methods¶

setValuesDisplay¶

public void setValuesDisplay(double P, double I)¶

PI_controller¶

public class PI_controller implements Controller¶

Simple implementation of PI controller with output constraining and windup prevention.

Author:	Marcel Stefko

Fields¶

I¶

protected double I¶: Integral component

P¶

protected double P¶: Proportional component

current_output¶

protected double current_output¶: Last calculated output of the controller

is_blocked¶

protected boolean is_blocked¶

Constructors¶

PI_controller¶

public PI_controller(double P, double I_per_second, double max_output, double sampling_period_s)¶

Initialize the PI controller.

Parameters:	P – proportional component I_per_second – integral component (per second) max_output – maximal output value sampling_period_s – controller tick rate in seconds

Methods¶

block¶

public void block()¶: Temporarily stops the controller from taking in input, and forces output to be 0.

getCurrentOutput¶

public double getCurrentOutput()¶

getName¶

public String getName()¶

getSetpoint¶

public double getSetpoint()¶

getStatusPanel¶

public ControllerStatusPanel getStatusPanel()¶

nextValue¶

public double nextValue(double value)¶

setSetpoint¶

public void setSetpoint(double new_setpoint)¶

unblock¶

public void unblock()¶: Resets integral before unblocking the output

ch.epfl.leb.alica.acpack.controllers.selftuningpi¶

SelfTuningController¶

public class SelfTuningController extends PI_controller ¶

A self-tuning implementation of the PI controller. It waits for 10 cycles, and over next 20 cycles generates a step pulse and measures response. From this response it estimates the P and I components of the PID controller.

Author:	Marcel Stefko

Constructors¶

SelfTuningController¶

public SelfTuningController(double max_output, double sampling_period_s)¶

Initialize a new SelfTuningController

Parameters:	max_output – max output sampling_period_s – tick rate of controller in seconds step_height – how big step pulse should be generated p_factor – scaling factor for P in tuning i_factor – scaling factor for I in tuning

Methods¶

getName¶

public String getName()¶

getStatusPanel¶

public ControllerStatusPanel getStatusPanel()¶

nextValue¶

public double nextValue(double value)¶

recalibrate¶

public final void recalibrate(double step_height, double p_factor, double i_factor)¶

SelfTuningSetupPanel¶

public class SelfTuningSetupPanel extends ControllerSetupPanel¶

Author:	stefko

Constructors¶

SelfTuningSetupPanel¶

public SelfTuningSetupPanel()¶: Creates new form SelfTuningSetupPanel

Methods¶

getName¶

public String getName()¶

initController¶

public Controller initController(double max_controller_output, double tick_rate_ms)¶

SelfTuningStatusPanel¶

public class SelfTuningStatusPanel extends ControllerStatusPanel¶

Author:	stefko

Constructors¶

SelfTuningStatusPanel¶

public SelfTuningStatusPanel(SelfTuningController controller)¶: Creates new form SeltTuningStatusPanel

Methods¶

setCalibrationStatusDisplay¶

public void setCalibrationStatusDisplay(String text)¶

setValuesDisplay¶

public void setValuesDisplay(double P, double I)¶

This package contains the implementations for the analyzers and controllers in ALICA, the automatic illumination control package for light microscopy. It is a run-time dependency of ALICA. These implementations are maintained separately of ALICA because they are used in SASS as well.

Relationship with ALICA and SASS¶

Relationships between the modules of ALICA and SASS.

Authors¶

Indices and tables¶

Index