bactimas.datamodel

Class CurrentExperiment

java.lang.Object

bactimas.datamodel.CurrentExperiment

public class CurrentExperiment
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
CurrentExperiment()

Method Summary

Methods

Modifier and Type	Method and Description
static Bacteria	addBacteria(int frameNo)
static void	beginExperiment(java.lang.String expName, java.lang.String redFolder, java.lang.String greenFolder, java.lang.String blueFolder, int spf, java.math.BigDecimal pixelWidth, java.math.BigDecimal pixelHeight, java.math.BigDecimal pictureScale) Loads the experiment with the given name or creates a new one.
static void	closeResultsWindow()
static void	deleteAllMeasurementsToBeMeasured()
static boolean	deleteExperiment(int idExperiment)
static void	dumpCSV(java.io.File csvFile)
static ITrackingAlgorithm	getAlgorithm(java.lang.String algorithmClassName)
static ITrackingAlgorithm	getAlgorithmForFrame(int frameNo)
static AlgorithmDesc[]	getAllAlgorithms()
static BacteriaStateChange[]	getAllBacteriaStateChanges()
static BacteriaState[]	getAllBacteriaStates()
static ExperimentEvent[]	getAllEvents()
static java.util.LinkedList<BTreeElement>	getBacteriaBTreeElements(Bacteria root, java.lang.String onWidthSQL, java.lang.String onColorSQL)
static java.util.LinkedList<BacteriaSplit>	getBacteriaFamilySplits(Bacteria root)
static java.util.LinkedList<Bacteria>	getBacteriasForFrame(int frameNo)
static java.lang.String	getBacteriaStateAt(Bacteria b, int frameNo)
static java.lang.String	getBlueFrameAbsFilename(int frameNo, java.lang.String altFormat)
static ij.ImagePlus	getBlueImagePlus(int frameNo, java.lang.String altFormat)
static ij.gui.Roi	getComputerRoiForBacteria(int idBacteria, int frameNo)
static ITrackingAlgorithm	getDefaultAlgorithm()
static Experiment	getExperiment()
static java.util.Hashtable<java.lang.String,ExperimentMeasurements>	getExperimentMeasures()
static Frame	getFrame(int frameNo) Returns a frame for the five frameNo (STARTING WITH 1)!!
static java.lang.String	getFrameAbsFilename(ImageStrip.ImageStripType channel, int frameNo, java.lang.String altFormat)
static int	getFrameCount()
static java.lang.String	getGreenFrameAbsFilename(int frameNo, java.lang.String altFormat)
static ij.ImagePlus	getGreenImagePlus(int frameNo, java.lang.String altFormat)
static ij.gui.Roi	getHumanRoiForBacteria(int idBacteria, int frameNo)
static int	getIdExperiment()
static ij.ImagePlus	getImagePlus(ImageStrip.ImageStripType channel, int frameNo, java.lang.String altFormat)
static java.util.Hashtable<java.lang.String,BacteriaKeyValue>	getMeasurements(int idBacteria, int frameNo, int roiType)
static ij.ImagePlus	getNewColorImagePlusWindow(int frameNo)
static java.util.LinkedList<java.awt.Color>	getPalette(int idPalette)
static int	getPrevFrameNo(int frameNo)
static java.lang.String	getRedFrameAbsFilename(int frameNo, java.lang.String altFormat)
static ij.ImagePlus	getRedImagePlus(int frameNo, java.lang.String altFormat)
static int	getSecondsPerFrame()
static java.util.LinkedList<Bacteria>	getSplitBacteriasForFrame(int frameNo)
static boolean	hasData()
static boolean	hasHumanRoi(int frameNo, int idBacteria)
static void	reloadFrames()
static void	saveMeasurements(java.util.LinkedList<BacteriaMeasurement> measurements)
static boolean	saveROI(ij.gui.Roi roi, int frameNo, Bacteria b, int roiType)
static boolean	setExperimentEvent(int frameNo, java.lang.String eventAbbr, java.lang.String eventDesc)
static boolean	setStateChange(int idBacteria, int frameNo, int idState)
static void	toggleIgnoreFrame(int frameNo)
static void	updateCurrentExperiment(java.lang.String expName, java.lang.String redFolder, java.lang.String greenFolder, java.lang.String blueFolder, int spf, java.math.BigDecimal pixelWidth, java.math.BigDecimal pixelHeight, java.math.BigDecimal pictureScale)
static void	updateExperimentMeasures(java.util.Hashtable<java.lang.String,ExperimentMeasurements> measures)
static boolean	updateFrameAlgorithm(int frameFrom, int frameTo, java.lang.String algorithmName)
static boolean	updateFrameBackgroundGreenMean(int frameNo, double mean)
static boolean	updateFrameBackgroundRedMean(int frameNo, double mean)
static boolean	updateFrameBackgroundRGBMean(int frameNo, double redMean, double greenMean, double blueMean)

Methods inherited from class java.lang.Object

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

Constructor Detail

CurrentExperiment

public CurrentExperiment()

Method Detail

getDefaultAlgorithm

public static ITrackingAlgorithm getDefaultAlgorithm()

getAlgorithmForFrame

public static ITrackingAlgorithm getAlgorithmForFrame(int frameNo)

getAlgorithm

public static ITrackingAlgorithm getAlgorithm(java.lang.String algorithmClassName)

getAllAlgorithms

public static AlgorithmDesc[] getAllAlgorithms()

getIdExperiment

public static int getIdExperiment()

getExperiment

public static Experiment getExperiment()

hasData

public static boolean hasData()

dumpCSV

public static void dumpCSV(java.io.File csvFile)

setExperimentEvent

public static boolean setExperimentEvent(int frameNo,
                         java.lang.String eventAbbr,
                         java.lang.String eventDesc)

getAllBacteriaStates

public static BacteriaState[] getAllBacteriaStates()

setStateChange

public static boolean setStateChange(int idBacteria,
                     int frameNo,
                     int idState)

beginExperiment

public static void beginExperiment(java.lang.String expName,
                   java.lang.String redFolder,
                   java.lang.String greenFolder,
                   java.lang.String blueFolder,
                   int spf,
                   java.math.BigDecimal pixelWidth,
                   java.math.BigDecimal pixelHeight,
                   java.math.BigDecimal pictureScale)
                            throws java.lang.Exception

Loads the experiment with the given name or creates a new one.

Parameters:

expName -

redFolder -

greenFolder -

blueFolder -

spf -

pixelWidth -

pixelHeight -

pictureScale -

Throws:

java.lang.Exception

updateCurrentExperiment

public static void updateCurrentExperiment(java.lang.String expName,
                           java.lang.String redFolder,
                           java.lang.String greenFolder,
                           java.lang.String blueFolder,
                           int spf,
                           java.math.BigDecimal pixelWidth,
                           java.math.BigDecimal pixelHeight,
                           java.math.BigDecimal pictureScale)
                                    throws java.lang.Exception

Throws:

java.lang.Exception

deleteExperiment

public static boolean deleteExperiment(int idExperiment)

reloadFrames

public static void reloadFrames()
                         throws java.lang.Exception

Throws:

java.lang.Exception

getFrameCount

public static int getFrameCount()

getFrame

public static Frame getFrame(int frameNo)

Returns a frame for the five frameNo (STARTING WITH 1)!!

Parameters:

frameNo -

Returns:

the frame

getBacteriasForFrame

public static java.util.LinkedList<Bacteria> getBacteriasForFrame(int frameNo)

getPrevFrameNo

public static int getPrevFrameNo(int frameNo)

getSecondsPerFrame

public static int getSecondsPerFrame()

getSplitBacteriasForFrame

public static java.util.LinkedList<Bacteria> getSplitBacteriasForFrame(int frameNo)

hasHumanRoi

public static boolean hasHumanRoi(int frameNo,
                  int idBacteria)

getMeasurements

public static java.util.Hashtable<java.lang.String,BacteriaKeyValue> getMeasurements(int idBacteria,
                                                                     int frameNo,
                                                                     int roiType)

saveROI

public static boolean saveROI(ij.gui.Roi roi,
              int frameNo,
              Bacteria b,
              int roiType)

closeResultsWindow

public static void closeResultsWindow()

updateFrameAlgorithm

public static boolean updateFrameAlgorithm(int frameFrom,
                           int frameTo,
                           java.lang.String algorithmName)

updateFrameBackgroundGreenMean

public static boolean updateFrameBackgroundGreenMean(int frameNo,
                                     double mean)

updateFrameBackgroundRedMean

public static boolean updateFrameBackgroundRedMean(int frameNo,
                                   double mean)

updateFrameBackgroundRGBMean

public static boolean updateFrameBackgroundRGBMean(int frameNo,
                                   double redMean,
                                   double greenMean,
                                   double blueMean)

updateExperimentMeasures

public static void updateExperimentMeasures(java.util.Hashtable<java.lang.String,ExperimentMeasurements> measures)

getExperimentMeasures

public static java.util.Hashtable<java.lang.String,ExperimentMeasurements> getExperimentMeasures()

getAllEvents

public static ExperimentEvent[] getAllEvents()

getAllBacteriaStateChanges

public static BacteriaStateChange[] getAllBacteriaStateChanges()

saveMeasurements

public static void saveMeasurements(java.util.LinkedList<BacteriaMeasurement> measurements)

getBacteriaStateAt

public static java.lang.String getBacteriaStateAt(Bacteria b,
                                  int frameNo)

toggleIgnoreFrame

public static void toggleIgnoreFrame(int frameNo)

deleteAllMeasurementsToBeMeasured

public static void deleteAllMeasurementsToBeMeasured()

getPalette

public static java.util.LinkedList<java.awt.Color> getPalette(int idPalette)

getBacteriaFamilySplits

public static java.util.LinkedList<BacteriaSplit> getBacteriaFamilySplits(Bacteria root)

getBacteriaBTreeElements

public static java.util.LinkedList<BTreeElement> getBacteriaBTreeElements(Bacteria root,
                                                          java.lang.String onWidthSQL,
                                                          java.lang.String onColorSQL)

getRedImagePlus

public static ij.ImagePlus getRedImagePlus(int frameNo,
                           java.lang.String altFormat)

getGreenImagePlus

public static ij.ImagePlus getGreenImagePlus(int frameNo,
                             java.lang.String altFormat)

getBlueImagePlus

public static ij.ImagePlus getBlueImagePlus(int frameNo,
                            java.lang.String altFormat)

getImagePlus

public static ij.ImagePlus getImagePlus(ImageStrip.ImageStripType channel,
                        int frameNo,
                        java.lang.String altFormat)

getBlueFrameAbsFilename

public static java.lang.String getBlueFrameAbsFilename(int frameNo,
                                       java.lang.String altFormat)

getGreenFrameAbsFilename

public static java.lang.String getGreenFrameAbsFilename(int frameNo,
                                        java.lang.String altFormat)

getRedFrameAbsFilename

public static java.lang.String getRedFrameAbsFilename(int frameNo,
                                      java.lang.String altFormat)

getFrameAbsFilename

public static java.lang.String getFrameAbsFilename(ImageStrip.ImageStripType channel,
                                   int frameNo,
                                   java.lang.String altFormat)

getNewColorImagePlusWindow

public static ij.ImagePlus getNewColorImagePlusWindow(int frameNo)

getComputerRoiForBacteria

public static ij.gui.Roi getComputerRoiForBacteria(int idBacteria,
                                   int frameNo)

getHumanRoiForBacteria

public static ij.gui.Roi getHumanRoiForBacteria(int idBacteria,
                                int frameNo)

addBacteria

public static Bacteria addBacteria(int frameNo)