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
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Nested classes/interfaces inherited from class gov.nih.mipav.model.file.FileInfoBase
FileInfoBase.AxisOrientation, FileInfoBase.ImageOrientation, FileInfoBase.Modality, FileInfoBase.Unit, FileInfoBase.UnitType
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Field Summary
Fields Modifier and Type Field Description private int
bleachedROIShape
DOCUMENT ME!private int[]
blueArray
DOCUMENT ME!private int[]
channelDataTypes
DOCUMENT ME!private java.lang.String[]
channelNames
DOCUMENT ME!private int
channels
DOCUMENT ME!static int
CIRCLE
DOCUMENT ME!static int
CLOSED_BEZIER
DOCUMENT ME!static int
CLOSED_POLYLINE
DOCUMENT ME!private int
dimensionM
private int
dimensionP
private double
displayAspectTime
DOCUMENT ME!private double
displayAspectX
DOCUMENT ME!private double
displayAspectY
DOCUMENT ME!private double
displayAspectZ
DOCUMENT ME!static int
ELLIPSE
DOCUMENT ME!private java.lang.String[]
eventDescription
DOCUMENT ME!private double[]
eventTime
DOCUMENT ME!private int[]
eventType
DOCUMENT ME!private int
firstSliceAfterBleach
DOCUMENT ME!private int[]
greenArray
DOCUMENT ME!private java.lang.String
imageDescription
private double[]
knotX
DOCUMENT ME!private double[]
knotY
DOCUMENT ME!private int
lastSliceBeforeBleach
DOCUMENT ME!private int
LSMDataType
DOCUMENT ME!private int
LSMDataType2
DOCUMENT ME!private int
mono
DOCUMENT ME!private double
objectiveSphereCorrection
DOCUMENT ME!private double
originX
The x-offset of the center of the image in meter relative to the optical axis.private double
originY
The y-offset of the center of the image in meter relative to the optical axis.static int
RECTANGLE
Bleached ROI shapes.private int[]
redArray
DOCUMENT ME!private int
scanType
DOCUMENT ME!private static long
serialVersionUID
Use serialVersionUID for interoperability.private int
spectralScan
DOCUMENT ME!private double
timeDifferenceX
private double
timeDifferenceY
private double
timeDifferenceZ
private int
timeDim
DOCUMENT ME!private double
timeInterval
DOCUMENT ME!private double[]
timeStamp
DOCUMENT ME!private double[]
wavelengths
DOCUMENT ME!-
Fields inherited from class gov.nih.mipav.model.file.FileInfoBase
ANGSTROMS, 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 Summary
Constructors Constructor Description FileInfoLSM(java.lang.String name, java.lang.String directory, int format)
FileInfoLSM - file info storage constructor.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
displayAboutInfo(JDialogBase dlog, TransMatrix matrix)
displayAboutInfo - displays the file information.int
getBleachedROIShape()
DOCUMENT ME!int[]
getEventType()
DOCUMENT ME!int
getFirstSliceAfterBleach()
DOCUMENT ME!double[]
getKnotX()
DOCUMENT ME!double[]
getKnotY()
DOCUMENT ME!int
getLastSliceBeforeBleach()
DOCUMENT ME!double[]
getTimeStamp()
DOCUMENT ME!void
setBleachedROIShape(int bleachedROIShape)
DOCUMENT ME!void
setBlueArray(int[] blueArray)
DOCUMENT ME!void
setChannelDataTypes(int[] channelDataTypes)
DOCUMENT ME!void
setChannelNames(java.lang.String[] channelNames)
DOCUMENT ME!void
setChannels(int channels)
DOCUMENT ME!void
setDimensionM(int dimensionM)
void
setDimensionP(int dimensionP)
void
setDisplayAspectTime(double displayAspectTime)
DOCUMENT ME!void
setDisplayAspectX(double displayAspectX)
DOCUMENT ME!void
setDisplayAspectY(double displayAspectY)
DOCUMENT ME!void
setDisplayAspectZ(double displayAspectZ)
DOCUMENT ME!void
setEventDescription(java.lang.String[] eventDescription)
DOCUMENT ME!void
setEventTime(double[] eventTime)
DOCUMENT ME!void
setEventType(int[] eventType)
DOCUMENT ME!void
setFirstSliceAfterBleach(int firstSliceAfterBleach)
DOCUMENT ME!void
setGreenArray(int[] greenArray)
DOCUMENT ME!void
setImageDescription(java.lang.String imageDescription)
DOCUMENT ME!void
setKnotX(double[] knotX)
DOCUMENT ME!void
setKnotY(double[] knotY)
DOCUMENT ME!void
setLastSliceBeforeBleach(int lastSliceBeforeBleach)
DOCUMENT ME!void
setLSMDataType(int LSMDataType)
DOCUMENT ME!void
setLSMDataType2(int LSMDataType2)
DOCUMENT ME!void
setMono(int mono)
DOCUMENT ME!void
setObjectiveSphereCorrection(double objectiveSphereCorrection)
DOCUMENT ME!void
setOriginX(double originX)
void
setOriginY(double originY)
void
setRedArray(int[] redArray)
DOCUMENT ME!void
setScanType(int scanType)
DOCUMENT ME!void
setSpectralScan(int spectralScan)
DOCUMENT ME!void
setTimeDifferenceX(double timeDifferenceX)
void
setTimeDifferenceY(double timeDifferenceY)
void
setTimeDifferenceZ(double timeDifferenceZ)
void
setTimeDim(int timeDim)
DOCUMENT ME!void
setTimeInterval(double timeInterval)
DOCUMENT ME!void
setTimeStamp(double[] timeStamp)
DOCUMENT ME!void
setWavelengths(double[] wavelengths)
DOCUMENT ME!-
Methods inherited from class gov.nih.mipav.model.file.FileInfoBase
copyCoreInfo, 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.ModelSerialCloneable
clone, nativeClone
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Field Detail
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serialVersionUID
private static final long serialVersionUID
Use serialVersionUID for interoperability.- See Also:
- Constant Field Values
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RECTANGLE
public static final int RECTANGLE
Bleached ROI shapes.- See Also:
- Constant Field Values
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ELLIPSE
public static final int ELLIPSE
DOCUMENT ME!- See Also:
- Constant Field Values
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CLOSED_POLYLINE
public static final int CLOSED_POLYLINE
DOCUMENT ME!- See Also:
- Constant Field Values
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CLOSED_BEZIER
public static final int CLOSED_BEZIER
DOCUMENT ME!- See Also:
- Constant Field Values
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CIRCLE
public static final int CIRCLE
DOCUMENT ME!- See Also:
- Constant Field Values
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bleachedROIShape
private int bleachedROIShape
DOCUMENT ME!
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blueArray
private int[] blueArray
DOCUMENT ME!
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channelDataTypes
private int[] channelDataTypes
DOCUMENT ME!
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channelNames
private java.lang.String[] channelNames
DOCUMENT ME!
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channels
private int channels
DOCUMENT ME!
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dimensionM
private int dimensionM
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dimensionP
private int dimensionP
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displayAspectTime
private double displayAspectTime
DOCUMENT ME!
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displayAspectX
private double displayAspectX
DOCUMENT ME!
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displayAspectY
private double displayAspectY
DOCUMENT ME!
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displayAspectZ
private double displayAspectZ
DOCUMENT ME!
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eventDescription
private java.lang.String[] eventDescription
DOCUMENT ME!
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eventTime
private double[] eventTime
DOCUMENT ME!
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eventType
private int[] eventType
DOCUMENT ME!
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firstSliceAfterBleach
private int firstSliceAfterBleach
DOCUMENT ME!
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greenArray
private int[] greenArray
DOCUMENT ME!
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imageDescription
private java.lang.String imageDescription
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knotX
private double[] knotX
DOCUMENT ME!
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knotY
private double[] knotY
DOCUMENT ME!
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lastSliceBeforeBleach
private int lastSliceBeforeBleach
DOCUMENT ME!
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LSMDataType
private int LSMDataType
DOCUMENT ME!
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LSMDataType2
private int LSMDataType2
DOCUMENT ME!
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mono
private int mono
DOCUMENT ME!
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objectiveSphereCorrection
private double objectiveSphereCorrection
DOCUMENT ME!
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originX
private 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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originY
private 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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redArray
private int[] redArray
DOCUMENT ME!
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scanType
private int scanType
DOCUMENT ME!
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spectralScan
private int spectralScan
DOCUMENT ME!
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timeDifferenceX
private double timeDifferenceX
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timeDifferenceY
private double timeDifferenceY
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timeDifferenceZ
private double timeDifferenceZ
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timeDim
private int timeDim
DOCUMENT ME!
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timeInterval
private double timeInterval
DOCUMENT ME!
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timeStamp
private double[] timeStamp
DOCUMENT ME!
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wavelengths
private double[] wavelengths
DOCUMENT ME!
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Method Detail
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displayAboutInfo
public void displayAboutInfo(JDialogBase dlog, TransMatrix matrix)
displayAboutInfo - displays the file information.- Specified by:
displayAboutInfo
in classFileInfoBase
- Parameters:
dlog
- dialog box that is written tomatrix
- transformation matrix
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getBleachedROIShape
public int getBleachedROIShape()
DOCUMENT ME!- Returns:
- DOCUMENT ME!
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getEventType
public int[] getEventType()
DOCUMENT ME!- Returns:
- DOCUMENT ME!
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getFirstSliceAfterBleach
public int getFirstSliceAfterBleach()
DOCUMENT ME!- Returns:
- DOCUMENT ME!
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getKnotX
public double[] getKnotX()
DOCUMENT ME!- Returns:
- DOCUMENT ME!
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getKnotY
public double[] getKnotY()
DOCUMENT ME!- Returns:
- DOCUMENT ME!
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getLastSliceBeforeBleach
public int getLastSliceBeforeBleach()
DOCUMENT ME!- Returns:
- DOCUMENT ME!
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getTimeStamp
public double[] getTimeStamp()
DOCUMENT ME!- Returns:
- DOCUMENT ME!
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setBleachedROIShape
public void setBleachedROIShape(int bleachedROIShape)
DOCUMENT ME!- Parameters:
bleachedROIShape
- DOCUMENT ME!
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setBlueArray
public void setBlueArray(int[] blueArray)
DOCUMENT ME!- Parameters:
blueArray
- DOCUMENT ME!
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setChannelDataTypes
public void setChannelDataTypes(int[] channelDataTypes)
DOCUMENT ME!- Parameters:
channelDataTypes
- DOCUMENT ME!
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setChannelNames
public void setChannelNames(java.lang.String[] channelNames)
DOCUMENT ME!- Parameters:
channelNames
- DOCUMENT ME!
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setChannels
public void setChannels(int channels)
DOCUMENT ME!- Parameters:
channels
- DOCUMENT ME!
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setDimensionM
public void setDimensionM(int dimensionM)
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setDimensionP
public void setDimensionP(int dimensionP)
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setDisplayAspectTime
public void setDisplayAspectTime(double displayAspectTime)
DOCUMENT ME!- Parameters:
displayAspectTime
- DOCUMENT ME!
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setDisplayAspectX
public void setDisplayAspectX(double displayAspectX)
DOCUMENT ME!- Parameters:
displayAspectX
- DOCUMENT ME!
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setDisplayAspectY
public void setDisplayAspectY(double displayAspectY)
DOCUMENT ME!- Parameters:
displayAspectY
- DOCUMENT ME!
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setDisplayAspectZ
public void setDisplayAspectZ(double displayAspectZ)
DOCUMENT ME!- Parameters:
displayAspectZ
- DOCUMENT ME!
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setEventDescription
public void setEventDescription(java.lang.String[] eventDescription)
DOCUMENT ME!- Parameters:
eventDescription
- DOCUMENT ME!
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setEventTime
public void setEventTime(double[] eventTime)
DOCUMENT ME!- Parameters:
eventTime
- DOCUMENT ME!
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setEventType
public void setEventType(int[] eventType)
DOCUMENT ME!- Parameters:
eventType
- DOCUMENT ME!
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setFirstSliceAfterBleach
public void setFirstSliceAfterBleach(int firstSliceAfterBleach)
DOCUMENT ME!- Parameters:
firstSliceAfterBleach
- DOCUMENT ME!
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setGreenArray
public void setGreenArray(int[] greenArray)
DOCUMENT ME!- Parameters:
greenArray
- DOCUMENT ME!
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setImageDescription
public void setImageDescription(java.lang.String imageDescription)
DOCUMENT ME!- Parameters:
imageDescription
- DOCUMENT ME!
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setKnotX
public void setKnotX(double[] knotX)
DOCUMENT ME!- Parameters:
knotX
- DOCUMENT ME!
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setKnotY
public void setKnotY(double[] knotY)
DOCUMENT ME!- Parameters:
knotY
- DOCUMENT ME!
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setLastSliceBeforeBleach
public void setLastSliceBeforeBleach(int lastSliceBeforeBleach)
DOCUMENT ME!- Parameters:
lastSliceBeforeBleach
- DOCUMENT ME!
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setLSMDataType
public void setLSMDataType(int LSMDataType)
DOCUMENT ME!- Parameters:
LSMDataType
- DOCUMENT ME!
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setLSMDataType2
public void setLSMDataType2(int LSMDataType2)
DOCUMENT ME!- Parameters:
LSMDataType2
- DOCUMENT ME!
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setMono
public void setMono(int mono)
DOCUMENT ME!- Parameters:
mono
- DOCUMENT ME!
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setObjectiveSphereCorrection
public void setObjectiveSphereCorrection(double objectiveSphereCorrection)
DOCUMENT ME!- Parameters:
objectiveSphereCorrection
- DOCUMENT ME!
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setOriginX
public void setOriginX(double originX)
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setOriginY
public void setOriginY(double originY)
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setRedArray
public void setRedArray(int[] redArray)
DOCUMENT ME!- Parameters:
redArray
- DOCUMENT ME!
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setScanType
public void setScanType(int scanType)
DOCUMENT ME!- Parameters:
scanType
- DOCUMENT ME!
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setSpectralScan
public void setSpectralScan(int spectralScan)
DOCUMENT ME!- Parameters:
spectralScan
- DOCUMENT ME!
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setTimeDifferenceX
public void setTimeDifferenceX(double timeDifferenceX)
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setTimeDifferenceY
public void setTimeDifferenceY(double timeDifferenceY)
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setTimeDifferenceZ
public void setTimeDifferenceZ(double timeDifferenceZ)
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setTimeDim
public void setTimeDim(int timeDim)
DOCUMENT ME!- Parameters:
timeDim
- DOCUMENT ME!
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setTimeInterval
public void setTimeInterval(double timeInterval)
DOCUMENT ME!- Parameters:
timeInterval
- DOCUMENT ME!
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setTimeStamp
public void setTimeStamp(double[] timeStamp)
DOCUMENT ME!- Parameters:
timeStamp
- DOCUMENT ME!
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setWavelengths
public void setWavelengths(double[] wavelengths)
DOCUMENT ME!- Parameters:
wavelengths
- DOCUMENT ME!
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