Package gov.nih.mipav.model.file
Class FileInfoLSM
- java.lang.Object
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- gov.nih.mipav.model.structures.ModelSerialCloneable
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- gov.nih.mipav.model.file.FileInfoBase
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- gov.nih.mipav.model.file.FileInfoLSM
 
 
 
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- All Implemented Interfaces:
- java.io.Serializable,- java.lang.Cloneable
 
 public class FileInfoLSM extends FileInfoBase This structures contains the information that describes how a LSM image is stored on disk.- See Also:
- FileLSM, Serialized Form
 
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Nested Class Summary- 
Nested classes/interfaces inherited from class gov.nih.mipav.model.file.FileInfoBaseFileInfoBase.AxisOrientation, FileInfoBase.ImageOrientation, FileInfoBase.Modality, FileInfoBase.Unit, FileInfoBase.UnitType
 
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Field SummaryFields Modifier and Type Field Description private intbleachedROIShapeDOCUMENT ME!private int[]blueArrayDOCUMENT ME!private int[]channelDataTypesDOCUMENT ME!private java.lang.String[]channelNamesDOCUMENT ME!private intchannelsDOCUMENT ME!static intCIRCLEDOCUMENT ME!static intCLOSED_BEZIERDOCUMENT ME!static intCLOSED_POLYLINEDOCUMENT ME!private intdimensionMprivate intdimensionPprivate doubledisplayAspectTimeDOCUMENT ME!private doubledisplayAspectXDOCUMENT ME!private doubledisplayAspectYDOCUMENT ME!private doubledisplayAspectZDOCUMENT ME!static intELLIPSEDOCUMENT ME!private java.lang.String[]eventDescriptionDOCUMENT ME!private double[]eventTimeDOCUMENT ME!private int[]eventTypeDOCUMENT ME!private intfirstSliceAfterBleachDOCUMENT ME!private int[]greenArrayDOCUMENT ME!private java.lang.StringimageDescriptionprivate double[]knotXDOCUMENT ME!private double[]knotYDOCUMENT ME!private intlastSliceBeforeBleachDOCUMENT ME!private intLSMDataTypeDOCUMENT ME!private intLSMDataType2DOCUMENT ME!private intmonoDOCUMENT ME!private doubleobjectiveSphereCorrectionDOCUMENT ME!private doubleoriginXThe x-offset of the center of the image in meter relative to the optical axis.private doubleoriginYThe y-offset of the center of the image in meter relative to the optical axis.static intRECTANGLEBleached ROI shapes.private int[]redArrayDOCUMENT ME!private intscanTypeDOCUMENT ME!private static longserialVersionUIDUse serialVersionUID for interoperability.private intspectralScanDOCUMENT ME!private doubletimeDifferenceXprivate doubletimeDifferenceYprivate doubletimeDifferenceZprivate inttimeDimDOCUMENT ME!private doubletimeIntervalDOCUMENT ME!private double[]timeStampDOCUMENT ME!private double[]wavelengthsDOCUMENT ME!- 
Fields inherited from class gov.nih.mipav.model.file.FileInfoBaseANGSTROMS, ANGSTROMS_STRING, AXIAL, axisOrientation, axisOrientationStr, BIOMAGNETIC_IMAGING, cameraMake, cameraModel, CENTIMETERS, CENTIMETERS_STRING, COLOR_FLOW_DOPPLER, COMPRESSION_BZIP2, COMPRESSION_GZIP, COMPRESSION_NONE, COMPRESSION_ZIP, COMPUTED_RADIOGRAPHY, COMPUTED_TOMOGRAPHY, conversionSpaceTimeUnits, CORONAL, DEGREES, DEGREES_STRING, DIAPHANOGRAPHY, DIGITAL_RADIOGRAPHY, DUPLEX_DOPPLER, ENDOSCOPY, exposureTime, EXTERNAL_CAMERA_PHOTOGRAPHY, FA, fileName, fileSuffix, FNumber, focalLength, focalLength35, GENERAL_MICROSCOPY, HARDCOPY, HOURS, HOURS_STRING, HZ, HZ_STRING, ICG, imageOrientation, INCHES, INCHES_STRING, INTRAORAL_RADIOGRAPHY, ISOSpeedRating, KILOMETERS, KILOMETERS_STRING, LASER_SURFACE_SCAN, MAGNETIC_RESONANCE, MAGNETIC_RESONANCE_ANGIOGRAPHY, MAGNETIC_RESONANCE_SPECTROSCOPY, MAMMOGRAPHY, METERS, METERS_STRING, MICROMETERS, MICROMETERS_STRING, MICROSEC, MICROSEC_STRING, MILES, MILES_STRING, MILLIMETERS, MILLIMETERS_STRING, MILLISEC, MILLISEC_STRING, MILS, MILS_STRING, MINUTES, MINUTES_STRING, modality, NANOMETERS, NANOMETERS_STRING, NANOSEC, NANOSEC_STRING, NUCLEAR_MEDICINE, ORI_A2P_TYPE, ORI_I2S_TYPE, ORI_L2R_TYPE, ORI_P2A_TYPE, ORI_R2L_TYPE, ORI_S2I_TYPE, ORI_UNKNOWN_TYPE, origin, OTHER, PANORAMIC_XRAY, POSITRON_EMISSION_TOMOGRAPHY, PPM, PPM_STRING, RADIO_FLUOROSCOPY, RADIOGRAPHIC_IMAGING, RADIOTHERAPY_DOSE, RADIOTHERAPY_IMAGE, RADIOTHERAPY_PLAN, RADIOTHERAPY_RECORD, RADIOTHERAPY_STRUCTURE_SET, RADS, RADS_STRING, RED_FREE, SAGITTAL, SECONDS, SECONDS_STRING, SINGLE_PHOTON_EMISSION_COMPUTED_TOMOGRAPHY, SLIDE_MICROSCOPY, sUnits, tagDescription, tagName, THERMOGRAPHY, TRANSFORM_ANOTHER_DATASET, TRANSFORM_MNI_152, TRANSFORM_SCANNER_ANATOMICAL, TRANSFORM_TALAIRACH_TOURNOUX, TRANSFORM_UNKNOWN, tUnits, ULTRASOUND, unitsOfMeasure, UNKNOWN_MEASURE, UNKNOWN_MODALITY, UNKNOWN_ORIENT, UNKNOWN_STRING, XRAY_ANGIOGRAPHY
 
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Constructor SummaryConstructors Constructor Description FileInfoLSM(java.lang.String name, java.lang.String directory, int format)FileInfoLSM - file info storage constructor.
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Method SummaryAll Methods Instance Methods Concrete Methods Modifier and Type Method Description voiddisplayAboutInfo(JDialogBase dlog, TransMatrix matrix)displayAboutInfo - displays the file information.intgetBleachedROIShape()DOCUMENT ME!int[]getEventType()DOCUMENT ME!intgetFirstSliceAfterBleach()DOCUMENT ME!double[]getKnotX()DOCUMENT ME!double[]getKnotY()DOCUMENT ME!intgetLastSliceBeforeBleach()DOCUMENT ME!double[]getTimeStamp()DOCUMENT ME!voidsetBleachedROIShape(int bleachedROIShape)DOCUMENT ME!voidsetBlueArray(int[] blueArray)DOCUMENT ME!voidsetChannelDataTypes(int[] channelDataTypes)DOCUMENT ME!voidsetChannelNames(java.lang.String[] channelNames)DOCUMENT ME!voidsetChannels(int channels)DOCUMENT ME!voidsetDimensionM(int dimensionM)voidsetDimensionP(int dimensionP)voidsetDisplayAspectTime(double displayAspectTime)DOCUMENT ME!voidsetDisplayAspectX(double displayAspectX)DOCUMENT ME!voidsetDisplayAspectY(double displayAspectY)DOCUMENT ME!voidsetDisplayAspectZ(double displayAspectZ)DOCUMENT ME!voidsetEventDescription(java.lang.String[] eventDescription)DOCUMENT ME!voidsetEventTime(double[] eventTime)DOCUMENT ME!voidsetEventType(int[] eventType)DOCUMENT ME!voidsetFirstSliceAfterBleach(int firstSliceAfterBleach)DOCUMENT ME!voidsetGreenArray(int[] greenArray)DOCUMENT ME!voidsetImageDescription(java.lang.String imageDescription)DOCUMENT ME!voidsetKnotX(double[] knotX)DOCUMENT ME!voidsetKnotY(double[] knotY)DOCUMENT ME!voidsetLastSliceBeforeBleach(int lastSliceBeforeBleach)DOCUMENT ME!voidsetLSMDataType(int LSMDataType)DOCUMENT ME!voidsetLSMDataType2(int LSMDataType2)DOCUMENT ME!voidsetMono(int mono)DOCUMENT ME!voidsetObjectiveSphereCorrection(double objectiveSphereCorrection)DOCUMENT ME!voidsetOriginX(double originX)voidsetOriginY(double originY)voidsetRedArray(int[] redArray)DOCUMENT ME!voidsetScanType(int scanType)DOCUMENT ME!voidsetSpectralScan(int spectralScan)DOCUMENT ME!voidsetTimeDifferenceX(double timeDifferenceX)voidsetTimeDifferenceY(double timeDifferenceY)voidsetTimeDifferenceZ(double timeDifferenceZ)voidsetTimeDim(int timeDim)DOCUMENT ME!voidsetTimeInterval(double timeInterval)DOCUMENT ME!voidsetTimeStamp(double[] timeStamp)DOCUMENT ME!voidsetWavelengths(double[] wavelengths)DOCUMENT ME!- 
Methods inherited from class gov.nih.mipav.model.file.FileInfoBasecopyCoreInfo, copyCoreInfo, displayAboutInfo, displayPrimaryInfo, finalize, getAboutInfo, getAllSameDimUnits, getAreaUnitsOfMeasureStr, getAxisDirection, getAxisOrientation, getAxisOrientation, getAxisOrientationFromStr, getAxisOrientationStr, getCameraMake, getCameraModel, getCompressionType, getDataType, getDataTypeFromStr, getEndianess, getEndianessFromStr, getExposureTime, getExtents, getFileDirectory, getFileFormat, getFileName, getFileSuffix, getFNumber, getFocalLength, getFocalLength35, getImageOrientation, getImageOrientationFromStr, getImageOrientationStr, getIs2_5D, getISOSpeedRating, getLPSOrigin, getLUT, getMax, getMaxB, getMaxG, getMaxR, getMin, getMinB, getMinG, getMinR, getModality, getModalityFromStr, getModalityStr, getModalityStr, getMultiFile, getNumOfBytesPerPixel, getOffset, getOrigin, getOrigin, getOriginalEndianess, getOriginAtSlice, getPhotometric, getPixelPadValue, getPrimaryInfo, getRescaleIntercept, getRescaleSlope, getResolution, getResolutions, getSize, getSliceThickness, getUnitsOfMeasure, getUnitsOfMeasure, getUnitsOfMeasureAbbrevStr, getUnitsOfMeasureAbbrevStr, getUnitsOfMeasureFromStr, getUnitsOfMeasureStr, getUnitsOfMeasureStr, getVolumeUnitsOfMeasureStr, isDicomOrdered, oppositeOrient, sameAxis, setAxisOrientation, setAxisOrientation, setCameraMake, setCameraModel, setCompressionType, setDataType, setEndianess, setExposureTime, setExtents, setExtents, setFileDirectory, setFileFormat, setFileName, setFileSuffix, setFNumber, setFocalLength, setFocalLength35, setImageOrientation, setISOSpeedRating, setLUT, setMax, setMaxB, setMaxG, setMaxR, setMin, setMinB, setMinG, setMinR, setModality, setMultiFile, setOffset, setOrigin, setOrigin, setOriginalEndianess, setPhotometric, setPixelPadValue, setRescaleIntercept, setRescaleSlope, setResolutions, setResolutions, setSliceThickness, setTagDescription, setTagName, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, toString
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Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneableclone, nativeClone
 
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Field Detail- 
serialVersionUIDprivate static final long serialVersionUID Use serialVersionUID for interoperability.- See Also:
- Constant Field Values
 
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RECTANGLEpublic static final int RECTANGLE Bleached ROI shapes.- See Also:
- Constant Field Values
 
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ELLIPSEpublic static final int ELLIPSE DOCUMENT ME!- See Also:
- Constant Field Values
 
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CLOSED_POLYLINEpublic static final int CLOSED_POLYLINE DOCUMENT ME!- See Also:
- Constant Field Values
 
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CLOSED_BEZIERpublic static final int CLOSED_BEZIER DOCUMENT ME!- See Also:
- Constant Field Values
 
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CIRCLEpublic static final int CIRCLE DOCUMENT ME!- See Also:
- Constant Field Values
 
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bleachedROIShapeprivate int bleachedROIShape DOCUMENT ME!
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blueArrayprivate int[] blueArray DOCUMENT ME!
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channelDataTypesprivate int[] channelDataTypes DOCUMENT ME!
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channelNamesprivate java.lang.String[] channelNames DOCUMENT ME!
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channelsprivate int channels DOCUMENT ME!
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dimensionMprivate int dimensionM 
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dimensionPprivate int dimensionP 
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displayAspectTimeprivate double displayAspectTime DOCUMENT ME!
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displayAspectXprivate double displayAspectX DOCUMENT ME!
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displayAspectYprivate double displayAspectY DOCUMENT ME!
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displayAspectZprivate double displayAspectZ DOCUMENT ME!
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eventDescriptionprivate java.lang.String[] eventDescription DOCUMENT ME!
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eventTimeprivate double[] eventTime DOCUMENT ME!
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eventTypeprivate int[] eventType DOCUMENT ME!
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firstSliceAfterBleachprivate int firstSliceAfterBleach DOCUMENT ME!
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greenArrayprivate int[] greenArray DOCUMENT ME!
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imageDescriptionprivate java.lang.String imageDescription 
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knotXprivate double[] knotX DOCUMENT ME!
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knotYprivate double[] knotY DOCUMENT ME!
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lastSliceBeforeBleachprivate int lastSliceBeforeBleach DOCUMENT ME!
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LSMDataTypeprivate int LSMDataType DOCUMENT ME!
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LSMDataType2private int LSMDataType2 DOCUMENT ME!
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monoprivate int mono DOCUMENT ME!
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objectiveSphereCorrectionprivate double objectiveSphereCorrection DOCUMENT ME!
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originXprivate double originX The x-offset of the center of the image in meter relative to the optical axis. For LSM images the x-direction is the direction of the x-scanner. In releases prior to 4.0 the entry was not used and the value 0 was written instead.
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originYprivate double originY The y-offset of the center of the image in meter relative to the optical axis. For LSM images the y-direction is the direction of the y-scanner. In releases prior to 4.0 the entry was not used and the value 0 was written instead.
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redArrayprivate int[] redArray DOCUMENT ME!
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scanTypeprivate int scanType DOCUMENT ME!
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spectralScanprivate int spectralScan DOCUMENT ME!
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timeDifferenceXprivate double timeDifferenceX 
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timeDifferenceYprivate double timeDifferenceY 
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timeDifferenceZprivate double timeDifferenceZ 
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timeDimprivate int timeDim DOCUMENT ME!
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timeIntervalprivate double timeInterval DOCUMENT ME!
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timeStampprivate double[] timeStamp DOCUMENT ME!
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wavelengthsprivate double[] wavelengths DOCUMENT ME!
 
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Method Detail- 
displayAboutInfopublic void displayAboutInfo(JDialogBase dlog, TransMatrix matrix) displayAboutInfo - displays the file information.- Specified by:
- displayAboutInfoin class- FileInfoBase
- Parameters:
- dlog- dialog box that is written to
- matrix- transformation matrix
 
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getBleachedROIShapepublic int getBleachedROIShape() DOCUMENT ME!- Returns:
- DOCUMENT ME!
 
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getEventTypepublic int[] getEventType() DOCUMENT ME!- Returns:
- DOCUMENT ME!
 
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getFirstSliceAfterBleachpublic int getFirstSliceAfterBleach() DOCUMENT ME!- Returns:
- DOCUMENT ME!
 
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getKnotXpublic double[] getKnotX() DOCUMENT ME!- Returns:
- DOCUMENT ME!
 
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getKnotYpublic double[] getKnotY() DOCUMENT ME!- Returns:
- DOCUMENT ME!
 
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getLastSliceBeforeBleachpublic int getLastSliceBeforeBleach() DOCUMENT ME!- Returns:
- DOCUMENT ME!
 
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getTimeStamppublic double[] getTimeStamp() DOCUMENT ME!- Returns:
- DOCUMENT ME!
 
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setBleachedROIShapepublic void setBleachedROIShape(int bleachedROIShape) DOCUMENT ME!- Parameters:
- bleachedROIShape- DOCUMENT ME!
 
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setBlueArraypublic void setBlueArray(int[] blueArray) DOCUMENT ME!- Parameters:
- blueArray- DOCUMENT ME!
 
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setChannelDataTypespublic void setChannelDataTypes(int[] channelDataTypes) DOCUMENT ME!- Parameters:
- channelDataTypes- DOCUMENT ME!
 
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setChannelNamespublic void setChannelNames(java.lang.String[] channelNames) DOCUMENT ME!- Parameters:
- channelNames- DOCUMENT ME!
 
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setChannelspublic void setChannels(int channels) DOCUMENT ME!- Parameters:
- channels- DOCUMENT ME!
 
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setDimensionMpublic void setDimensionM(int dimensionM) 
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setDimensionPpublic void setDimensionP(int dimensionP) 
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setDisplayAspectTimepublic void setDisplayAspectTime(double displayAspectTime) DOCUMENT ME!- Parameters:
- displayAspectTime- DOCUMENT ME!
 
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setDisplayAspectXpublic void setDisplayAspectX(double displayAspectX) DOCUMENT ME!- Parameters:
- displayAspectX- DOCUMENT ME!
 
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setDisplayAspectYpublic void setDisplayAspectY(double displayAspectY) DOCUMENT ME!- Parameters:
- displayAspectY- DOCUMENT ME!
 
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setDisplayAspectZpublic void setDisplayAspectZ(double displayAspectZ) DOCUMENT ME!- Parameters:
- displayAspectZ- DOCUMENT ME!
 
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setEventDescriptionpublic void setEventDescription(java.lang.String[] eventDescription) DOCUMENT ME!- Parameters:
- eventDescription- DOCUMENT ME!
 
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setEventTimepublic void setEventTime(double[] eventTime) DOCUMENT ME!- Parameters:
- eventTime- DOCUMENT ME!
 
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setEventTypepublic void setEventType(int[] eventType) DOCUMENT ME!- Parameters:
- eventType- DOCUMENT ME!
 
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setFirstSliceAfterBleachpublic void setFirstSliceAfterBleach(int firstSliceAfterBleach) DOCUMENT ME!- Parameters:
- firstSliceAfterBleach- DOCUMENT ME!
 
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setGreenArraypublic void setGreenArray(int[] greenArray) DOCUMENT ME!- Parameters:
- greenArray- DOCUMENT ME!
 
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setImageDescriptionpublic void setImageDescription(java.lang.String imageDescription) DOCUMENT ME!- Parameters:
- imageDescription- DOCUMENT ME!
 
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setKnotXpublic void setKnotX(double[] knotX) DOCUMENT ME!- Parameters:
- knotX- DOCUMENT ME!
 
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setKnotYpublic void setKnotY(double[] knotY) DOCUMENT ME!- Parameters:
- knotY- DOCUMENT ME!
 
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setLastSliceBeforeBleachpublic void setLastSliceBeforeBleach(int lastSliceBeforeBleach) DOCUMENT ME!- Parameters:
- lastSliceBeforeBleach- DOCUMENT ME!
 
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setLSMDataTypepublic void setLSMDataType(int LSMDataType) DOCUMENT ME!- Parameters:
- LSMDataType- DOCUMENT ME!
 
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setLSMDataType2public void setLSMDataType2(int LSMDataType2) DOCUMENT ME!- Parameters:
- LSMDataType2- DOCUMENT ME!
 
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setMonopublic void setMono(int mono) DOCUMENT ME!- Parameters:
- mono- DOCUMENT ME!
 
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setObjectiveSphereCorrectionpublic void setObjectiveSphereCorrection(double objectiveSphereCorrection) DOCUMENT ME!- Parameters:
- objectiveSphereCorrection- DOCUMENT ME!
 
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setOriginXpublic void setOriginX(double originX) 
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setOriginYpublic void setOriginY(double originY) 
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setRedArraypublic void setRedArray(int[] redArray) DOCUMENT ME!- Parameters:
- redArray- DOCUMENT ME!
 
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setScanTypepublic void setScanType(int scanType) DOCUMENT ME!- Parameters:
- scanType- DOCUMENT ME!
 
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setSpectralScanpublic void setSpectralScan(int spectralScan) DOCUMENT ME!- Parameters:
- spectralScan- DOCUMENT ME!
 
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setTimeDifferenceXpublic void setTimeDifferenceX(double timeDifferenceX) 
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setTimeDifferenceYpublic void setTimeDifferenceY(double timeDifferenceY) 
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setTimeDifferenceZpublic void setTimeDifferenceZ(double timeDifferenceZ) 
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setTimeDimpublic void setTimeDim(int timeDim) DOCUMENT ME!- Parameters:
- timeDim- DOCUMENT ME!
 
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setTimeIntervalpublic void setTimeInterval(double timeInterval) DOCUMENT ME!- Parameters:
- timeInterval- DOCUMENT ME!
 
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setTimeStamppublic void setTimeStamp(double[] timeStamp) DOCUMENT ME!- Parameters:
- timeStamp- DOCUMENT ME!
 
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setWavelengthspublic void setWavelengths(double[] wavelengths) DOCUMENT ME!- Parameters:
- wavelengths- DOCUMENT ME!
 
 
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