bactimas.db

Class DALService

java.lang.Object

bactimas.db.DALService

public class DALService
extends java.lang.Object

Author:

igor

Constructor Summary

Constructors

Constructor and Description
DALService()

Method Summary

Methods

Modifier and Type	Method and Description
static Experiment	beginExperiment(java.lang.String expName, java.lang.String redPath, java.lang.String greenPath, java.lang.String bluePath, 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 boolean	deleteAllMeasurementsToBeMeasured(int idExperiment)
static boolean	deleteExperiment(int idExperiment)
static void	dumpCSV(int idExperiment, java.io.File csvFile)
static BacteriaStateChange[]	getAllBacteriaStateChanges(int idExperiment)
static BacteriaState[]	getAllBacteriaStates()
static ExperimentEvent[]	getAllEvents(int idExperiment)
static Experiment[]	getAllExperiments()
static java.util.LinkedList<BTreeElement>	getBacteriaBTreeElements(int idExperiment, Bacteria root, java.lang.String onWidthSQL, java.lang.String onColorSQL)
static java.util.LinkedList<BacteriaSplit>	getBacteriaFamilySplits(int idExperiment, Bacteria root)
static java.util.LinkedList<BacteriaMeasurement>	getBacteriaMeasurementsForFrame(int idBacteria, int frameNo, int idRoiType) Returns measurements for the given frame (from the DB).
static java.util.LinkedList<Bacteria>	getBacteriasForFrame(Frame f)
static java.lang.String	getBacteriaStateAt(Bacteria b, int frameNo)
static int	getChannelId(java.lang.String channelName)
static java.util.Hashtable<java.lang.String,ExperimentMeasurements>	getExperimentMeasures(int idExperiment)
static VPoint	getFrameTranslation(int frameNo)
static int	getMeasurementId(java.lang.String measurementName)
static Bacteria	getOrInsertBacteria(java.lang.String bactName)
static java.util.LinkedList<java.awt.Color>	getPalette(int idPalette)
static Roi	getRoiForBacteria(int bacteriaId, int frameNo, int idRoiType) Returns a computer/humean generated Roi that is stored in a DB.
static int	getSecondsPerFrame(int idExperiment)
static java.util.LinkedList<Bacteria>	getSplitBacteriasForFrame(Frame f)
static java.util.LinkedList<ExpMeasurement>	getUserMeasures(int idExperiment)
static boolean	hasHumanRoi(int bacteriaId, int frameNo)
static java.util.ArrayList<Frame>	initFrames(java.lang.String redFolder, java.lang.String greenFolder, java.lang.String blueFolder) Loads the frames for the active experiment or initializes (inserts) new ones.
static boolean	insertBacteriaMeasurements(java.util.LinkedList<BacteriaMeasurement> measurements)
static java.lang.String	moveBacteriaSplit(Bacteria someChild, int delta)
static boolean	setExperimentEvent(int idExperiment, int frameNo, java.lang.String eventAbbr, java.lang.String eventDesc)
static boolean	setStateChange(int idBacteria, int frameNo, int idState)
static Bacteria[]	splitBacteria(Bacteria b, int frameNo)
static boolean	toggleIgnoreFrame(int idExperiment, int frameNo)
static boolean	truncateFromFrame(int frameNo)
static Experiment	updateExperiment(java.lang.String expName, java.lang.String redPath, java.lang.String greenPath, java.lang.String bluePath, int spf, java.math.BigDecimal pixelWidth, java.math.BigDecimal pixelHeight, java.math.BigDecimal pictureScale, int idExperiment)
static void	updateExperimentMeasures(java.util.Hashtable<java.lang.String,ExperimentMeasurements> measures, int idExperiment)
static boolean	updateFrameAlgorithm(int idExperiment, int frameFrom, int frameTo, java.lang.String algorithmName)
static boolean	updateFrameBackgroundGreenMean(int idExperiment, int frameNo, double mean)
static boolean	updateFrameBackgroundRedMean(int idExperiment, int frameNo, double mean)
static boolean	updateFrameBackgroundRGBMean(int idExperiment, int frameNo, double redMean, double greenMean, double blueMean)
static boolean	updateFrameTranslation(int frameNo, VPoint trans)
static boolean	updateRoiForBacteria(Roi dbRoi)

Methods inherited from class java.lang.Object

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

Constructor Detail

DALService

public DALService()

Method Detail

deleteExperiment

public static boolean deleteExperiment(int idExperiment)

beginExperiment

public static Experiment beginExperiment(java.lang.String expName,
                         java.lang.String redPath,
                         java.lang.String greenPath,
                         java.lang.String bluePath,
                         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.

Parameters:

expName -

redPath -

greenPath -

bluePath -

spf -

pixelWidth -

pixelHeight -

pictureScale -

Returns:

Experiment object

updateExperiment

public static Experiment updateExperiment(java.lang.String expName,
                          java.lang.String redPath,
                          java.lang.String greenPath,
                          java.lang.String bluePath,
                          int spf,
                          java.math.BigDecimal pixelWidth,
                          java.math.BigDecimal pixelHeight,
                          java.math.BigDecimal pictureScale,
                          int idExperiment)

getAllExperiments

public static Experiment[] getAllExperiments()

dumpCSV

public static void dumpCSV(int idExperiment,
           java.io.File csvFile)

getUserMeasures

public static java.util.LinkedList<ExpMeasurement> getUserMeasures(int idExperiment)

initFrames

public static java.util.ArrayList<Frame> initFrames(java.lang.String redFolder,
                                    java.lang.String greenFolder,
                                    java.lang.String blueFolder)
                                             throws java.lang.Exception

Loads the frames for the active experiment or initializes (inserts) new ones.

Parameters:

redFolder -

greenFolder -

blueFolder -

Returns:

an ArrayList of Frames

Throws:

java.lang.Exception

getBacteriaMeasurementsForFrame

public static java.util.LinkedList<BacteriaMeasurement> getBacteriaMeasurementsForFrame(int idBacteria,
                                                                        int frameNo,
                                                                        int idRoiType)

Returns measurements for the given frame (from the DB).

Parameters:

idBacteria -

frameNo -

idRoiType -

Returns:

a list of BacteriaMeasurement objects

getBacteriasForFrame

public static java.util.LinkedList<Bacteria> getBacteriasForFrame(Frame f)

getSplitBacteriasForFrame

public static java.util.LinkedList<Bacteria> getSplitBacteriasForFrame(Frame f)

getBacteriaFamilySplits

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

getSecondsPerFrame

public static int getSecondsPerFrame(int idExperiment)

getPalette

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

getBacteriaBTreeElements

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

truncateFromFrame

public static boolean truncateFromFrame(int frameNo)

splitBacteria

public static Bacteria[] splitBacteria(Bacteria b,
                       int frameNo)

moveBacteriaSplit

public static java.lang.String moveBacteriaSplit(Bacteria someChild,
                                 int delta)

getOrInsertBacteria

public static Bacteria getOrInsertBacteria(java.lang.String bactName)

getRoiForBacteria

public static Roi getRoiForBacteria(int bacteriaId,
                    int frameNo,
                    int idRoiType)

Returns a computer/humean generated Roi that is stored in a DB.

Parameters:

bacteriaId -

frameNo -

idRoiType -

Returns:

ImageJ Roi object

hasHumanRoi

public static boolean hasHumanRoi(int bacteriaId,
                  int frameNo)

updateRoiForBacteria

public static boolean updateRoiForBacteria(Roi dbRoi)

deleteAllMeasurementsToBeMeasured

public static boolean deleteAllMeasurementsToBeMeasured(int idExperiment)

getAllBacteriaStateChanges

public static BacteriaStateChange[] getAllBacteriaStateChanges(int idExperiment)

getBacteriaStateAt

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

getAllEvents

public static ExperimentEvent[] getAllEvents(int idExperiment)

getAllBacteriaStates

public static BacteriaState[] getAllBacteriaStates()

setStateChange

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

setExperimentEvent

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

insertBacteriaMeasurements

public static boolean insertBacteriaMeasurements(java.util.LinkedList<BacteriaMeasurement> measurements)

updateFrameTranslation

public static boolean updateFrameTranslation(int frameNo,
                             VPoint trans)

updateFrameAlgorithm

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

updateFrameBackgroundGreenMean

public static boolean updateFrameBackgroundGreenMean(int idExperiment,
                                     int frameNo,
                                     double mean)

updateFrameBackgroundRedMean

public static boolean updateFrameBackgroundRedMean(int idExperiment,
                                   int frameNo,
                                   double mean)

updateFrameBackgroundRGBMean

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

toggleIgnoreFrame

public static boolean toggleIgnoreFrame(int idExperiment,
                        int frameNo)

getFrameTranslation

public static VPoint getFrameTranslation(int frameNo)

getChannelId

public static int getChannelId(java.lang.String channelName)

getExperimentMeasures

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

updateExperimentMeasures

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

getMeasurementId

public static int getMeasurementId(java.lang.String measurementName)