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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectloci.formats.DummyMetadata
public class DummyMetadata
A dummy implementation for MetadataStore
and
MetadataRetrieve
that is used when no other
metadata implementations are available.
Constructor Summary | |
---|---|
DummyMetadata()
|
Method Summary | |
---|---|
void |
createRoot()
Creates a new root object to be used by the metadata store and resets the internal state of the metadata store. |
Float |
getAirPressure(Integer n)
Gets the air pressure associated with the given image. |
Float |
getArcPower(Integer arc)
Gets the power (in watts) of the given arc. |
String |
getArcType(Integer arc)
Gets the type of the given arc. |
Boolean |
getBigEndian(Integer image)
Gets the BigEndian attribute of the given pixels in the given image. |
Double |
getBlackLevel(Integer pixels,
Integer channel)
Gets the black level of the given channel in the given set of pixels. |
int |
getChannelCount(Integer n)
Returns the number of channels for the given pixels element. |
String |
getChannelName(Integer pixels,
Integer channel)
Gets the name of the given channel in the given set of pixels. |
Float |
getChannelNDFilter(Integer pixels,
Integer channel)
Gets the ND filter value for the given channel in the given set of pixels. |
Float |
getCO2Percent(Integer n)
Gets the CO2 percentage associated with the given image. |
String |
getColorMap(Integer image)
Gets the color map associated with the given pixels. |
Object |
getContact(Integer n)
Get the contact of the nth group. |
String |
getCreationDate(Integer n)
Gets the nth image's creation date. |
String |
getDataDirectory(Integer n)
Gets the data directory of the nth experimenter. |
String |
getDescription(Integer n)
Gets the nth image's description. |
Float |
getDetectorGain(Integer detector)
Gets the gain value of the given detector. |
String |
getDetectorManufacturer(Integer detector)
Gets the manufacturer of the given detector. |
String |
getDetectorModel(Integer detector)
Gets the model of the given detector. |
Float |
getDetectorOffset(Integer detector)
Gets the offset of the given detector. |
String |
getDetectorSerial(Integer detector)
Gets the serial number of the given detector. |
String |
getDetectorType(Integer detector)
Gets the type of the given detector. |
Float |
getDetectorVoltage(Integer detector)
Gets the voltage of the given detector. |
String |
getDichroicLotNumber(Integer dichroic)
Gets the lot number of the given dichroic. |
String |
getDichroicManufacturer(Integer dichroic)
Gets the manufacturer of the given dichroic. |
String |
getDichroicModel(Integer dichroic)
Gets the model of the given dichroic. |
String |
getDimensionOrder(Integer image)
Gets the DimensionOrder attribute of the given pixels in the given image. |
Object |
getDisplayOptions(Integer n)
Get the display options of the nth ROI. |
int |
getDisplayROICount()
Returns the number of DisplayROIs. |
String |
getEmail(Integer n)
Gets the email address of the nth experimenter. |
String |
getEmissionLotNumber(Integer filter)
Gets the lot number of the given emission filter. |
String |
getEmissionManufacturer(Integer filter)
Gets the manufacturer of the given emission filter. |
String |
getEmissionModel(Integer filter)
Gets the model of the given emission filter. |
String |
getEmissionType(Integer filter)
Gets the type of the given emission filter. |
Integer |
getEmWave(Integer pixels,
Integer channel)
Gets the emission wavelength of the given channel in the given set of pixels. |
String |
getExcitationLotNumber(Integer filter)
Gets the lot number of the given excitation filter. |
String |
getExcitationManufacturer(Integer filter)
Gets the manufacturer of the given excitation filter. |
String |
getExcitationModel(Integer filter)
Gets the model of the given excitation filter. |
String |
getExcitationType(Integer filter)
Gets the type of the given excitation filter. |
int |
getExperimenterCount()
Returns the number of experimenters. |
Float |
getExposureTime(Integer pixels,
Integer z,
Integer c,
Integer t)
Gets the exposure time of the plane with the given Z, C and T coordinates in the given set of pixels. |
Integer |
getExWave(Integer pixels,
Integer channel)
Gets the excitation wavelength of the given channel in the given set of pixels. |
Float |
getFilamentPower(Integer filament)
Gets the power (in watts) of the given filament. |
String |
getFilamentType(Integer filament)
Gets the type of the given filament. |
String |
getFilterSetLotNumber(Integer filterSet)
Gets the manufacturer of the given filter set. |
String |
getFilterSetManufacturer(Integer filterSet)
Gets the manufacturer of the given filter set. |
String |
getFilterSetModel(Integer filterSet)
Gets the manufacturer of the given filter set. |
String |
getFirstName(Integer n)
Gets the first name of the nth experimenter. |
Float |
getGamma(Integer pixels,
Integer channel)
Gets the gamma value of the given channel in the given set of pixels. |
Double |
getGlobalMax(Integer pixels,
Integer channel)
Gets the maximum pixel value within the given channel in the given set of pixels. |
Double |
getGlobalMin(Integer pixels,
Integer channel)
Gets the minimum pixel value within the given channel in the given set of pixels. |
Object |
getGroup(Integer n)
Gets the group of the nth experimenter. |
int |
getGroupCount()
Returns the number of groups. |
String |
getGroupName(Integer n)
Get the name of the nth group. |
Float |
getHumidity(Integer n)
Gets the humidity associated with the given image. |
int |
getImageCount()
Returns the number of images. |
String |
getImageName(Integer n)
Gets the nth image's name. |
String |
getInstitution(Integer n)
Gets the institution of the nth experimenter. |
int |
getInstrumentCount()
Returns the number of instruments. |
String |
getLaserMedium(Integer laser)
Gets the medium of the given laser. |
String |
getLaserType(Integer laser)
Gets the type of the given laser. |
Integer |
getLaserWavelength(Integer laser)
Gets the wavelength of the given laser. |
String |
getLastName(Integer n)
Gets the last name of the nth experimenter. |
Object |
getLeader(Integer n)
Get the leader of the nth group. |
Float |
getLensNA(Integer objective)
Gets the lens NA of the given objective. |
String |
getLightManufacturer(Integer light)
Gets the manufacturer of the given light source. |
String |
getLightModel(Integer light)
Gets the model of the given light source. |
String |
getLightSerial(Integer light)
Gets the serial number of the given light source. |
String |
getManufacturer(Integer n)
Get the manufacturer of the nth instrument. |
String |
getMode(Integer pixels,
Integer channel)
Gets the mode of the given channel in the given set of pixels. |
String |
getModel(Integer n)
Get the model of the nth instrument. |
Float |
getObjectiveMagnification(Integer objective)
Gets the magnification value of the given objective. |
String |
getObjectiveManufacturer(Integer objective)
Gets the manufacturer of the given objective. |
String |
getObjectiveModel(Integer objective)
Gets the model of the given objective. |
String |
getObjectiveSerial(Integer objective)
Gets the serial number of the given objective. |
Boolean |
getOTFOpticalAxisAverage(Integer otf)
Gets whether or not optical axis averaging is used for the given OTF. |
String |
getOTFPath(Integer otf)
Gets the path to the given OTF. |
String |
getOTFPixelType(Integer otf)
Gets the pixel type of the given OTF. |
Integer |
getOTFSizeX(Integer otf)
Gets the width of the given OTF. |
Integer |
getOTFSizeY(Integer otf)
Gets the height of the given OTF. |
String |
getPhotometricInterpretation(Integer pixels,
Integer channel)
Gets the photometric interpretation of the given channel in the given set of pixels. |
int |
getPixelsCount(Integer n)
Returns the number of pixels elements for the given image. |
Float |
getPixelSizeC(Integer n)
Gets the nth image's PixelSizeC attribute. |
Float |
getPixelSizeT(Integer n)
Gets the nth image's PixelSizeT attribute. |
Float |
getPixelSizeX(Integer n)
Gets the nth image's PixelSizeX attribute. |
Float |
getPixelSizeY(Integer n)
Gets the nth image's PixelSizeY attribute. |
Float |
getPixelSizeZ(Integer n)
Gets the nth image's PixelSizeZ attribute. |
String |
getPixelType(Integer image)
Gets the PixelType attribute of the given pixels in the given image. |
Float |
getPower(Integer laser)
Gets the power (in watts) of the given laser. |
String |
getPulse(Integer laser)
Gets the pulse of the given laser. |
Object |
getRoot()
Retrieves the root object of the metadata store. |
String |
getSerialNumber(Integer n)
Get the serial number of the nth instrument. |
Integer |
getSizeC(Integer image)
Gets the SizeC attribute of the given pixels in the given image. |
Integer |
getSizeT(Integer image)
Gets the SizeT attribute of the given pixels in the given image. |
Integer |
getSizeX(Integer image)
Gets the SizeX attribute of the given pixels in the given image. |
Integer |
getSizeY(Integer image)
Gets the SizeY attribute of the given pixels in the given image. |
Integer |
getSizeZ(Integer image)
Gets the SizeZ attribute of the given pixels in the given image. |
int |
getStageLabelCount()
Returns the number of stage labels. |
String |
getStageName(Integer n)
Gets the name of the nth stage label. |
Float |
getStageX(Integer n)
Gets the X coordinate of the nth stage label. |
Float |
getStageY(Integer n)
Gets the Y coordinate of the nth stage label. |
Float |
getStageZ(Integer n)
Gets the Z coordinate of the nth stage label. |
Integer |
getT0(Integer n)
Get the lower T bound of the nth ROI. |
Integer |
getT1(Integer n)
Get the upper T bound of the nth ROI. |
Float |
getTemperature(Integer n)
Gets the temperature associated with the given image. |
Float |
getTimestamp(Integer pixels,
Integer z,
Integer c,
Integer t)
Gets the timestamp of the plane with the given Z, C and T coordinates in the given set of pixels. |
Integer |
getTStart(Integer image)
Gets the minimum T coordinate for which the display settings apply. |
Integer |
getTStop(Integer image)
Gets the maximum T coordinate for which the display settings apply. |
String |
getType(Integer n)
Get the type of the nth instrument. |
Double |
getWhiteLevel(Integer pixels,
Integer channel)
Gets the white level of the given channel in the given set of pixels. |
Integer |
getX0(Integer n)
Get the lower X bound of the nth ROI. |
Integer |
getX1(Integer n)
Get the upper X bound of the nth ROI. |
Integer |
getY0(Integer n)
Get the lower Y bound of the nth ROI. |
Integer |
getY1(Integer n)
Get the upper Y bound of the nth ROI. |
Integer |
getZ0(Integer n)
Get the lower Z bound of the nth ROI. |
Integer |
getZ1(Integer n)
Get the upper Z bound of the nth ROI. |
Float |
getZoom(Integer image)
Gets the zoom value associated with the given pixels in the given image. |
Integer |
getZStart(Integer image)
Gets the minimum Z coordinate for which the display settings apply. |
Integer |
getZStop(Integer image)
Gets the maximum Z coordinate for which the display settings apply. |
Boolean |
isBlueChannelOn(Integer image)
Gets whether or not the blue channel is activated. |
Boolean |
isDisplayRGB(Integer image)
Gets whether or not the given pixels are displayed as an RGB image. |
Boolean |
isFrequencyDoubled(Integer laser)
Gets whether or not the frequency is doubled for the given laser. |
Boolean |
isGreenChannelOn(Integer image)
Gets whether or not the green channel is activated. |
Boolean |
isRedChannelOn(Integer image)
Gets whether or not the red channel is activated. |
Boolean |
isTunable(Integer laser)
Gets whether or not the given laser is tunable. |
void |
setArc(String type,
Float power,
Integer lightNdx,
Integer arcNdx)
Sets an arc for a particular instrument. |
void |
setChannelGlobalMinMax(int channel,
Double globalMin,
Double globalMax,
Integer i)
Sets a channel's global min and global max in the metadata store for a particular pixels set. |
void |
setDefaultDisplaySettings(Integer i)
Instructs the metadata store to set the default display settings for a particular pixels set. |
void |
setDetector(String manufacturer,
String model,
String serialNumber,
String type,
Float gain,
Float voltage,
Float offset,
Integer instrumentNdx,
Integer detectorNdx)
Sets a detector for a particular instrument. |
void |
setDichroic(String manufacturer,
String model,
String lotNumber,
Integer dichroicNdx)
Sets a dichroic for a particular instrument. |
void |
setDimensions(Float pixelSizeX,
Float pixelSizeY,
Float pixelSizeZ,
Float pixelSizeC,
Float pixelSizeT,
Integer i)
Creates a set of pixel dimensions in the metadata store with a particular index. |
void |
setDisplayChannel(Integer channelNumber,
Double blackLevel,
Double whiteLevel,
Float gamma,
Integer i)
Sets information about the specified channel for a particular image. |
void |
setDisplayOptions(Float zoom,
Boolean redChannelOn,
Boolean greenChannelOn,
Boolean blueChannelOn,
Boolean displayRGB,
String colorMap,
Integer zstart,
Integer zstop,
Integer tstart,
Integer tstop,
Integer imageNdx,
Integer pixelNdx,
Integer redChannel,
Integer greenChannel,
Integer blueChannel,
Integer grayChannel)
Sets various display options for a particular pixels set. |
void |
setDisplayROI(Integer x0,
Integer y0,
Integer z0,
Integer x1,
Integer y1,
Integer z1,
Integer t0,
Integer t1,
Object displayOptions,
Integer i)
Creates a 5D bounding box region of interest and a set of display options in the metadata store with a particular index. |
void |
setEmissionFilter(String manufacturer,
String model,
String lotNumber,
String type,
Integer filterNdx)
Sets an emission filter for a particular instrument. |
void |
setExcitationFilter(String manufacturer,
String model,
String lotNumber,
String type,
Integer filterNdx)
Sets an excitation filter for a particular instrument. |
void |
setExperimenter(String firstName,
String lastName,
String email,
String institution,
String dataDirectory,
Object group,
Integer i)
Creates an experimenter in the metadata store with a particular index. |
void |
setFilament(String type,
Float power,
Integer lightNdx,
Integer filamentNdx)
Sets a filament for a particular instrument. |
void |
setFilterSet(String manufacturer,
String model,
String lotNumber,
Integer filterSetNdx,
Integer filterNdx)
Sets a filter set for a particular instrument. |
void |
setGroup(String name,
Object leader,
Object contact,
Integer i)
Creates a group in the metadata store with a particular index. |
void |
setImage(String name,
String creationDate,
String description,
Integer i)
Creates an image in the metadata store with a particular index. |
void |
setImagingEnvironment(Float temperature,
Float airPressure,
Float humidity,
Float co2Percent,
Integer i)
Sets the imaging environment for a particular image. |
void |
setInstrument(String manufacturer,
String model,
String serialNumber,
String type,
Integer i)
Creates an instrument in the metadata store with a particular index. |
void |
setLaser(String type,
String medium,
Integer wavelength,
Boolean frequencyDoubled,
Boolean tunable,
String pulse,
Float power,
Integer instrumentNdx,
Integer lightNdx,
Integer pumpNdx,
Integer laserNdx)
Sets a laser for a particular instrument. |
void |
setLightSource(String manufacturer,
String model,
String serialNumber,
Integer instrumentNdx,
Integer lightNdx)
Sets a light source for a particular instrument. |
void |
setLogicalChannel(int channelIdx,
String name,
Integer samplesPerPixel,
Integer filter,
Integer lightSource,
Float lightAttenuation,
Integer lightWavelength,
Integer otf,
Integer detector,
Float detectorOffset,
Float detectorGain,
String illuminationType,
Integer pinholeSize,
String photometricInterpretation,
String mode,
String contrastMethod,
Integer auxLightSource,
Float auxLightAttenuation,
String auxTechnique,
Integer auxLightWavelength,
Integer emWave,
Integer exWave,
String fluor,
Float ndFilter,
Integer i)
Creates a logical channel and physical channel in the metadata store for a particular pixels. |
void |
setObjective(String manufacturer,
String model,
String serialNumber,
Float lensNA,
Float magnification,
Integer instrumentNdx,
Integer objectiveNdx)
Sets an objective for a particular instrument. |
void |
setOTF(Integer sizeX,
Integer sizeY,
String pixelType,
String path,
Boolean opticalAxisAverage,
Integer instrumentNdx,
Integer otfNdx,
Integer filterNdx,
Integer objectiveNdx)
Sets an OTF for a particular instrument. |
void |
setPixels(Integer sizeX,
Integer sizeY,
Integer sizeZ,
Integer sizeC,
Integer sizeT,
Integer pixelType,
Boolean bigEndian,
String dimensionOrder,
Integer imageNo,
Integer pixelsNo)
Creates a pixels set in the metadata store with a particular image and pixels index. |
void |
setPlaneInfo(int theZ,
int theC,
int theT,
Float timestamp,
Float exposureTime,
Integer i)
Sets the plane information for a particular X-Y plane (section) within a particular pixels set. |
void |
setRoot(Object root)
Sets the root object of the metadata store. |
void |
setStageLabel(String name,
Float x,
Float y,
Float z,
Integer i)
Creates a stage label in the metadata store with a particular index. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DummyMetadata()
Method Detail |
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public int getImageCount()
MetadataRetrieve
getImageCount
in interface MetadataRetrieve
public String getImageName(Integer n)
MetadataRetrieve
getImageName
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public String getCreationDate(Integer n)
MetadataRetrieve
getCreationDate
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public String getDescription(Integer n)
MetadataRetrieve
getDescription
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public int getExperimenterCount()
MetadataRetrieve
getExperimenterCount
in interface MetadataRetrieve
public String getFirstName(Integer n)
MetadataRetrieve
getFirstName
in interface MetadataRetrieve
n
- the index of the experimenter. If null
the default
index of 0 will be used.public String getLastName(Integer n)
MetadataRetrieve
getLastName
in interface MetadataRetrieve
n
- the index of the experimenter. If null
the default
index of 0 will be used.public String getEmail(Integer n)
MetadataRetrieve
getEmail
in interface MetadataRetrieve
n
- the index of the experimenter. If null
the default
index of 0 will be used.public String getInstitution(Integer n)
MetadataRetrieve
getInstitution
in interface MetadataRetrieve
n
- the index of the experimenter. If null
the default
index of 0 will be used.public String getDataDirectory(Integer n)
MetadataRetrieve
getDataDirectory
in interface MetadataRetrieve
n
- the index of the experimenter. If null
the default
index of 0 will be used.public Object getGroup(Integer n)
MetadataRetrieve
getGroup
in interface MetadataRetrieve
n
- the index of the experimenter. If null
the default
index of 0 will be used.public int getGroupCount()
MetadataRetrieve
getGroupCount
in interface MetadataRetrieve
public String getGroupName(Integer n)
MetadataRetrieve
getGroupName
in interface MetadataRetrieve
n
- the index of the group. If null
the default
index of 0 will be used.public Object getLeader(Integer n)
MetadataRetrieve
getLeader
in interface MetadataRetrieve
n
- the index of the group. If null
the default
index of 0 will be used.public Object getContact(Integer n)
MetadataRetrieve
getContact
in interface MetadataRetrieve
n
- the index of the group. If null
the default
index of 0 will be used.public int getInstrumentCount()
MetadataRetrieve
getInstrumentCount
in interface MetadataRetrieve
public String getManufacturer(Integer n)
MetadataRetrieve
getManufacturer
in interface MetadataRetrieve
n
- the index of the instrument. If null
the default
index of 0 will be used.public String getModel(Integer n)
MetadataRetrieve
getModel
in interface MetadataRetrieve
n
- the index of the instrument. If null
the default
index of 0 will be used.public String getSerialNumber(Integer n)
MetadataRetrieve
getSerialNumber
in interface MetadataRetrieve
n
- the index of the instrument. If null
the default
index of 0 will be used.public String getType(Integer n)
MetadataRetrieve
getType
in interface MetadataRetrieve
n
- the index of the instrument. If null
the default
index of 0 will be used.public Float getPixelSizeX(Integer n)
MetadataRetrieve
getPixelSizeX
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Float getPixelSizeY(Integer n)
MetadataRetrieve
getPixelSizeY
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Float getPixelSizeZ(Integer n)
MetadataRetrieve
getPixelSizeZ
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Float getPixelSizeC(Integer n)
MetadataRetrieve
getPixelSizeC
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Float getPixelSizeT(Integer n)
MetadataRetrieve
getPixelSizeT
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public int getDisplayROICount()
MetadataRetrieve
getDisplayROICount
in interface MetadataRetrieve
public Integer getX0(Integer n)
MetadataRetrieve
getX0
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Integer getY0(Integer n)
MetadataRetrieve
getY0
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Integer getZ0(Integer n)
MetadataRetrieve
getZ0
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Integer getT0(Integer n)
MetadataRetrieve
getT0
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Integer getX1(Integer n)
MetadataRetrieve
getX1
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Integer getY1(Integer n)
MetadataRetrieve
getY1
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Integer getZ1(Integer n)
MetadataRetrieve
getZ1
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Integer getT1(Integer n)
MetadataRetrieve
getT1
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public Object getDisplayOptions(Integer n)
MetadataRetrieve
getDisplayOptions
in interface MetadataRetrieve
n
- the index of the ROI. If null
the default
index of 0 will be used.public int getPixelsCount(Integer n)
MetadataRetrieve
getPixelsCount
in interface MetadataRetrieve
public Integer getSizeX(Integer image)
MetadataRetrieve
getSizeX
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getSizeY(Integer image)
MetadataRetrieve
getSizeY
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getSizeZ(Integer image)
MetadataRetrieve
getSizeZ
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getSizeC(Integer image)
MetadataRetrieve
getSizeC
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getSizeT(Integer image)
MetadataRetrieve
getSizeT
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public String getPixelType(Integer image)
MetadataRetrieve
getPixelType
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Boolean getBigEndian(Integer image)
MetadataRetrieve
getBigEndian
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public String getDimensionOrder(Integer image)
MetadataRetrieve
getDimensionOrder
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public int getStageLabelCount()
MetadataRetrieve
getStageLabelCount
in interface MetadataRetrieve
public String getStageName(Integer n)
MetadataRetrieve
getStageName
in interface MetadataRetrieve
n
- the index of the stage label. If null
the default
index of 0 will be used.public Float getStageX(Integer n)
MetadataRetrieve
getStageX
in interface MetadataRetrieve
n
- the index of the stage label. If null
the default
index of 0 will be used.public Float getStageY(Integer n)
MetadataRetrieve
getStageY
in interface MetadataRetrieve
n
- the index of the stage label. If null
the default
index of 0 will be used.public Float getStageZ(Integer n)
MetadataRetrieve
getStageZ
in interface MetadataRetrieve
n
- the index of the stage label. If null
the default
index of 0 will be used.public int getChannelCount(Integer n)
MetadataRetrieve
getChannelCount
in interface MetadataRetrieve
public String getChannelName(Integer pixels, Integer channel)
MetadataRetrieve
getChannelName
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Float getChannelNDFilter(Integer pixels, Integer channel)
MetadataRetrieve
getChannelNDFilter
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Integer getEmWave(Integer pixels, Integer channel)
MetadataRetrieve
getEmWave
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Integer getExWave(Integer pixels, Integer channel)
MetadataRetrieve
getExWave
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public String getPhotometricInterpretation(Integer pixels, Integer channel)
MetadataRetrieve
getPhotometricInterpretation
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public String getMode(Integer pixels, Integer channel)
MetadataRetrieve
getMode
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Double getGlobalMin(Integer pixels, Integer channel)
MetadataRetrieve
getGlobalMin
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Double getGlobalMax(Integer pixels, Integer channel)
MetadataRetrieve
getGlobalMax
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Float getTimestamp(Integer pixels, Integer z, Integer c, Integer t)
MetadataRetrieve
getTimestamp
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.z
- the Z coordinate of the plane. If null
the default
index of 0 will be used.c
- the C coordinate of the plane. If null
the default
index of 0 will be used.t
- the T coordinate of the plane. If null
the default
index of 0 will be used.public Float getExposureTime(Integer pixels, Integer z, Integer c, Integer t)
MetadataRetrieve
getExposureTime
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.z
- the Z coordinate of the plane. If null
the default
index of 0 will be used.c
- the C coordinate of the plane. If null
the default
index of 0 will be used.t
- the T coordinate of the plane. If null
the default
index of 0 will be used.public Float getTemperature(Integer n)
MetadataRetrieve
getTemperature
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Float getAirPressure(Integer n)
MetadataRetrieve
getAirPressure
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Float getHumidity(Integer n)
MetadataRetrieve
getHumidity
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Float getCO2Percent(Integer n)
MetadataRetrieve
getCO2Percent
in interface MetadataRetrieve
n
- the index of the image. If null
the default index
of 0 will be used.public Double getBlackLevel(Integer pixels, Integer channel)
MetadataRetrieve
getBlackLevel
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Double getWhiteLevel(Integer pixels, Integer channel)
MetadataRetrieve
getWhiteLevel
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Float getGamma(Integer pixels, Integer channel)
MetadataRetrieve
getGamma
in interface MetadataRetrieve
pixels
- the index of the pixels. If null
the default
index of 0 will be used.channel
- the index of the channel. If null
the default
index of 0 will be used.public Float getZoom(Integer image)
MetadataRetrieve
getZoom
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Boolean isRedChannelOn(Integer image)
MetadataRetrieve
isRedChannelOn
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Boolean isGreenChannelOn(Integer image)
MetadataRetrieve
isGreenChannelOn
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Boolean isBlueChannelOn(Integer image)
MetadataRetrieve
isBlueChannelOn
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Boolean isDisplayRGB(Integer image)
MetadataRetrieve
isDisplayRGB
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public String getColorMap(Integer image)
MetadataRetrieve
getColorMap
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getZStart(Integer image)
MetadataRetrieve
getZStart
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getZStop(Integer image)
MetadataRetrieve
getZStop
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getTStart(Integer image)
MetadataRetrieve
getTStart
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public Integer getTStop(Integer image)
MetadataRetrieve
getTStop
in interface MetadataRetrieve
image
- the index of the image. If null
the default
index of 0 will be used.public String getLightManufacturer(Integer light)
MetadataRetrieve
getLightManufacturer
in interface MetadataRetrieve
light
- the index of the light. If null
the default
index of 0 will be used.public String getLightModel(Integer light)
MetadataRetrieve
getLightModel
in interface MetadataRetrieve
light
- the index of the light. If null
the default
index of 0 will be used.public String getLightSerial(Integer light)
MetadataRetrieve
getLightSerial
in interface MetadataRetrieve
light
- the index of the light. If null
the default
index of 0 will be used.public String getLaserType(Integer laser)
MetadataRetrieve
getLaserType
in interface MetadataRetrieve
laser
- the index of the laser. If null
the default
index of 0 will be used.public String getLaserMedium(Integer laser)
MetadataRetrieve
getLaserMedium
in interface MetadataRetrieve
laser
- the index of the laser. If null
the default
index of 0 will be used.public Integer getLaserWavelength(Integer laser)
MetadataRetrieve
getLaserWavelength
in interface MetadataRetrieve
laser
- the index of the laser. If null
the default
index of 0 will be used.public Boolean isFrequencyDoubled(Integer laser)
MetadataRetrieve
isFrequencyDoubled
in interface MetadataRetrieve
laser
- the index of the laser. If null
the default
index of 0 will be used.public Boolean isTunable(Integer laser)
MetadataRetrieve
isTunable
in interface MetadataRetrieve
laser
- the index of the laser. If null
the default
index of 0 will be used.public String getPulse(Integer laser)
MetadataRetrieve
getPulse
in interface MetadataRetrieve
laser
- the index of the laser. If null
the default
index of 0 will be used.public Float getPower(Integer laser)
MetadataRetrieve
getPower
in interface MetadataRetrieve
laser
- the index of the laser. If null
the default
index of 0 will be used.public String getFilamentType(Integer filament)
MetadataRetrieve
getFilamentType
in interface MetadataRetrieve
filament
- the index of the filament. If null
the
default index of 0 will be used.public Float getFilamentPower(Integer filament)
MetadataRetrieve
getFilamentPower
in interface MetadataRetrieve
filament
- the index of the filament. If null
the
default index of 0 will be used.public String getArcType(Integer arc)
MetadataRetrieve
getArcType
in interface MetadataRetrieve
arc
- the index of the arc. If null
the default
index of 0 will be used.public Float getArcPower(Integer arc)
MetadataRetrieve
getArcPower
in interface MetadataRetrieve
arc
- the index of the arc. If null
the default
index of 0 will be used.public String getDetectorManufacturer(Integer detector)
MetadataRetrieve
getDetectorManufacturer
in interface MetadataRetrieve
detector
- the index of the detector. If null
the
default index of 0 will be used.public String getDetectorModel(Integer detector)
MetadataRetrieve
getDetectorModel
in interface MetadataRetrieve
detector
- the index of the detector. If null
the
default index of 0 will be used.public String getDetectorSerial(Integer detector)
MetadataRetrieve
getDetectorSerial
in interface MetadataRetrieve
detector
- the index of the detector. If null
the
default index of 0 will be used.public String getDetectorType(Integer detector)
MetadataRetrieve
getDetectorType
in interface MetadataRetrieve
detector
- the index of the detector. If null
the
default index of 0 will be used.public Float getDetectorGain(Integer detector)
MetadataRetrieve
getDetectorGain
in interface MetadataRetrieve
detector
- the index of the detector. If null
the
default index of 0 will be used.public Float getDetectorVoltage(Integer detector)
MetadataRetrieve
getDetectorVoltage
in interface MetadataRetrieve
detector
- the index of the detector. If null
the
default index of 0 will be used.public Float getDetectorOffset(Integer detector)
MetadataRetrieve
getDetectorOffset
in interface MetadataRetrieve
detector
- the index of the detector. If null
the
default index of 0 will be used.public String getObjectiveManufacturer(Integer objective)
MetadataRetrieve
getObjectiveManufacturer
in interface MetadataRetrieve
objective
- the index of the objective. If null
the
default index of 0 will be used.public String getObjectiveModel(Integer objective)
MetadataRetrieve
getObjectiveModel
in interface MetadataRetrieve
objective
- the index of the objective. If null
the
default index of 0 will be used.public String getObjectiveSerial(Integer objective)
MetadataRetrieve
getObjectiveSerial
in interface MetadataRetrieve
objective
- the index of the objective. If null
the
default index of 0 will be used.public Float getLensNA(Integer objective)
MetadataRetrieve
getLensNA
in interface MetadataRetrieve
objective
- the index of the objective. If null
the
default index of 0 will be used.public Float getObjectiveMagnification(Integer objective)
MetadataRetrieve
getObjectiveMagnification
in interface MetadataRetrieve
objective
- the index of the objective. If null
the
default index of 0 will be used.public String getExcitationManufacturer(Integer filter)
MetadataRetrieve
getExcitationManufacturer
in interface MetadataRetrieve
filter
- the index of the filter. If null
the
default index of 0 will be used.public String getExcitationModel(Integer filter)
MetadataRetrieve
getExcitationModel
in interface MetadataRetrieve
filter
- the index of the filter. If null
the
default index of 0 will be used.public String getExcitationLotNumber(Integer filter)
MetadataRetrieve
getExcitationLotNumber
in interface MetadataRetrieve
filter
- the index of the filter. If null
the
default index of 0 will be used.public String getExcitationType(Integer filter)
MetadataRetrieve
getExcitationType
in interface MetadataRetrieve
filter
- the index of the filter. If null
the
default index of 0 will be used.public String getDichroicManufacturer(Integer dichroic)
MetadataRetrieve
getDichroicManufacturer
in interface MetadataRetrieve
dichroic
- the index of the dichroic. If null
the
default index of 0 will be used.public String getDichroicModel(Integer dichroic)
MetadataRetrieve
getDichroicModel
in interface MetadataRetrieve
dichroic
- the index of the dichroic. If null
the
default index of 0 will be used.public String getDichroicLotNumber(Integer dichroic)
MetadataRetrieve
getDichroicLotNumber
in interface MetadataRetrieve
dichroic
- the index of the dichroic. If null
the
default index of 0 will be used.public String getEmissionManufacturer(Integer filter)
MetadataRetrieve
getEmissionManufacturer
in interface MetadataRetrieve
filter
- the index of the emission filter. If null
the
default index of 0 will be used.public String getEmissionModel(Integer filter)
MetadataRetrieve
getEmissionModel
in interface MetadataRetrieve
filter
- the index of the emission filter. If null
the
default index of 0 will be used.public String getEmissionLotNumber(Integer filter)
MetadataRetrieve
getEmissionLotNumber
in interface MetadataRetrieve
filter
- the index of the emission filter. If null
the
default index of 0 will be used.public String getEmissionType(Integer filter)
MetadataRetrieve
getEmissionType
in interface MetadataRetrieve
filter
- the index of the emission filter. If null
the
default index of 0 will be used.public String getFilterSetManufacturer(Integer filterSet)
MetadataRetrieve
getFilterSetManufacturer
in interface MetadataRetrieve
filterSet
- the index of the filter set. If null
the
default index of 0 will be used.public String getFilterSetModel(Integer filterSet)
MetadataRetrieve
getFilterSetModel
in interface MetadataRetrieve
filterSet
- the index of the filter set. If null
the
default index of 0 will be used.public String getFilterSetLotNumber(Integer filterSet)
MetadataRetrieve
getFilterSetLotNumber
in interface MetadataRetrieve
filterSet
- the index of the filter set. If null
the
default index of 0 will be used.public Integer getOTFSizeX(Integer otf)
MetadataRetrieve
getOTFSizeX
in interface MetadataRetrieve
otf
- the index of the OTF. If null
the
default index of 0 will be used.public Integer getOTFSizeY(Integer otf)
MetadataRetrieve
getOTFSizeY
in interface MetadataRetrieve
otf
- the index of the OTF. If null
the
default index of 0 will be used.public String getOTFPixelType(Integer otf)
MetadataRetrieve
getOTFPixelType
in interface MetadataRetrieve
otf
- the index of the OTF. If null
the
default index of 0 will be used.public String getOTFPath(Integer otf)
MetadataRetrieve
getOTFPath
in interface MetadataRetrieve
otf
- the index of the OTF. If null
the
default index of 0 will be used.public Boolean getOTFOpticalAxisAverage(Integer otf)
MetadataRetrieve
getOTFOpticalAxisAverage
in interface MetadataRetrieve
otf
- the index of the OTF. If null
the
default index of 0 will be used.public void createRoot()
MetadataStore
createRoot
in interface MetadataStore
public Object getRoot()
MetadataStore
getRoot
in interface MetadataStore
public void setChannelGlobalMinMax(int channel, Double globalMin, Double globalMax, Integer i)
MetadataStore
setChannelGlobalMinMax
in interface MetadataStore
channel
- the index of the channel within the pixels set.globalMin
- the global minimum pixel value for the channel.globalMax
- the global maximum pixel value for the channel.i
- the index of the pixels set within the metadata store.public void setDefaultDisplaySettings(Integer i)
MetadataStore
setDefaultDisplaySettings
in interface MetadataStore
i
- the index of the pixels set within the metadata store.public void setDimensions(Float pixelSizeX, Float pixelSizeY, Float pixelSizeZ, Float pixelSizeC, Float pixelSizeT, Integer i)
MetadataStore
setDimensions
in interface MetadataStore
pixelSizeX
- size of an individual pixel's X axis in microns.pixelSizeY
- size of an individual pixel's Y axis in microns.pixelSizeZ
- size of an individual pixel's Z axis in microns.pixelSizeC
- FIXME: UnknownpixelSizeT
- FIXME: Unknowni
- the index to use in the store. If null
the default
index of 0 will be used.public void setDisplayROI(Integer x0, Integer y0, Integer z0, Integer x1, Integer y1, Integer z1, Integer t0, Integer t1, Object displayOptions, Integer i)
MetadataStore
setDisplayROI
in interface MetadataStore
x0
- the starting X coordinate.y0
- the starting Y coordinate.z0
- the starting Z coordinate.x1
- the ending X coordinate.y1
- the ending Y coordinate.z1
- the ending Z coordinate.t0
- the starting timepoint.t1
- the ending timepoint.displayOptions
- the display options to attach to this region of
interest.i
- the index to use in the store. If null
the default
index of 0 will be used.public void setExperimenter(String firstName, String lastName, String email, String institution, String dataDirectory, Object group, Integer i)
MetadataStore
setExperimenter
in interface MetadataStore
firstName
- the first name of the experimenterlastName
- the last name of the experimenteremail
- the e-mail address of the experimenterinstitution
- the institution for which the experimenter belongsdataDirectory
- the fully qualified path to the experimenter's datagroup
- the group to which the experimenter belongsi
- the index to use in the store. If null
the default
index of 0 will be used.public void setGroup(String name, Object leader, Object contact, Integer i)
MetadataStore
setGroup
in interface MetadataStore
name
- the name of the group.leader
- the leader of the group.contact
- the contact for the group.i
- the index to use in the store. If null
the default
index of 0 will be used.public void setImage(String name, String creationDate, String description, Integer i)
MetadataStore
setImage
in interface MetadataStore
name
- the full name of the image.creationDate
- the creation date of the image.description
- the full description of the image.i
- the index to use in the store. If null
the default
index of 0 will be used.public void setInstrument(String manufacturer, String model, String serialNumber, String type, Integer i)
MetadataStore
setInstrument
in interface MetadataStore
manufacturer
- the name of the manufacturer.model
- the model number of the instrument.serialNumber
- the serial number of the instrument.type
- the type of the instrument.i
- the index to use in the store. If null
the default
index of 0 will be used.public void setLogicalChannel(int channelIdx, String name, Integer samplesPerPixel, Integer filter, Integer lightSource, Float lightAttenuation, Integer lightWavelength, Integer otf, Integer detector, Float detectorOffset, Float detectorGain, String illuminationType, Integer pinholeSize, String photometricInterpretation, String mode, String contrastMethod, Integer auxLightSource, Float auxLightAttenuation, String auxTechnique, Integer auxLightWavelength, Integer emWave, Integer exWave, String fluor, Float ndFilter, Integer i)
MetadataStore
setLogicalChannel
in interface MetadataStore
channelIdx
- the index of the channel within the pixels set.name
- the logical channel's name.filter
- index of the filter associated with this channel.lightSource
- index of the primary light source.lightAttenuation
- the primary light source attenuation.lightWavelength
- the primary light source wavelength.otf
- the index of the OTF associated with this channel.detector
- the index of the detector associated with this channel.detectorOffset
- the detector offset.detectorGain
- the detector gain.illuminationType
- the illumination type.pinholeSize
- the size of the pinhole.photometricInterpretation
- the photometric interpretation type.mode
- the acquisition mode.contrastMethod
- the constrast method name.auxLightSource
- index of the auxiliary light source.auxLightAttenuation
- the auxiliary light source attenuation.auxTechnique
- the auxiliary technique type.auxLightWavelength
- the auxiliary light source wavelength.emWave
- the emission wavelength.exWave
- the excitation wavelength.fluor
- the fluorescence type.ndFilter
- the neutral-density filter value.i
- the index of the pixels set within the metadata store.public void setPixels(Integer sizeX, Integer sizeY, Integer sizeZ, Integer sizeC, Integer sizeT, Integer pixelType, Boolean bigEndian, String dimensionOrder, Integer imageNo, Integer pixelsNo)
MetadataStore
setPixels
in interface MetadataStore
sizeX
- size of an individual plane or section's X axis (width)sizeY
- size of an individual plane of section's Y axis (height)sizeZ
- number of optical sections per channel, per timepoint
(per stack)sizeC
- number of channels per timepoint.sizeT
- number of timepoints.pixelType
- the pixel type. One of the enumerated static values
present in FormatReader
.bigEndian
- if the pixels set is big endian or not.dimensionOrder
- the dimension order of the pixels set.imageNo
- the image index to use in the store.
If null
the default index of 0 will be used.pixelsNo
- the pixels index to use in the store.
If null
the default index of 0 will be used.public void setPlaneInfo(int theZ, int theC, int theT, Float timestamp, Float exposureTime, Integer i)
MetadataStore
setPlaneInfo
in interface MetadataStore
theZ
- the optical section index.theC
- the channel index.theT
- the timepoint.timestamp
- the time of acquisition in seconds of the plane (section)
with zero being the start of acquistion.exposureTime
- exposure time in seconds.i
- the index of the pixels set within the metadata store.public void setRoot(Object root)
MetadataStore
setRoot
in interface MetadataStore
root
- object that the store can use as its root.public void setStageLabel(String name, Float x, Float y, Float z, Integer i)
MetadataStore
setStageLabel
in interface MetadataStore
name
- a name for the stage label.x
- coordinate of the stage.y
- coordinate of the stage.z
- coordinate of the stage.i
- the index to use in the store. If null
the default
index of 0 will be used.public void setImagingEnvironment(Float temperature, Float airPressure, Float humidity, Float co2Percent, Integer i)
MetadataStore
setImagingEnvironment
in interface MetadataStore
public void setDisplayChannel(Integer channelNumber, Double blackLevel, Double whiteLevel, Float gamma, Integer i)
MetadataStore
setDisplayChannel
in interface MetadataStore
public void setDisplayOptions(Float zoom, Boolean redChannelOn, Boolean greenChannelOn, Boolean blueChannelOn, Boolean displayRGB, String colorMap, Integer zstart, Integer zstop, Integer tstart, Integer tstop, Integer imageNdx, Integer pixelNdx, Integer redChannel, Integer greenChannel, Integer blueChannel, Integer grayChannel)
MetadataStore
setDisplayOptions
in interface MetadataStore
public void setLightSource(String manufacturer, String model, String serialNumber, Integer instrumentNdx, Integer lightNdx)
MetadataStore
setLightSource
in interface MetadataStore
public void setLaser(String type, String medium, Integer wavelength, Boolean frequencyDoubled, Boolean tunable, String pulse, Float power, Integer instrumentNdx, Integer lightNdx, Integer pumpNdx, Integer laserNdx)
MetadataStore
setLaser
in interface MetadataStore
public void setFilament(String type, Float power, Integer lightNdx, Integer filamentNdx)
MetadataStore
setFilament
in interface MetadataStore
public void setArc(String type, Float power, Integer lightNdx, Integer arcNdx)
MetadataStore
setArc
in interface MetadataStore
public void setDetector(String manufacturer, String model, String serialNumber, String type, Float gain, Float voltage, Float offset, Integer instrumentNdx, Integer detectorNdx)
MetadataStore
setDetector
in interface MetadataStore
public void setObjective(String manufacturer, String model, String serialNumber, Float lensNA, Float magnification, Integer instrumentNdx, Integer objectiveNdx)
MetadataStore
setObjective
in interface MetadataStore
public void setExcitationFilter(String manufacturer, String model, String lotNumber, String type, Integer filterNdx)
MetadataStore
setExcitationFilter
in interface MetadataStore
public void setDichroic(String manufacturer, String model, String lotNumber, Integer dichroicNdx)
MetadataStore
setDichroic
in interface MetadataStore
public void setEmissionFilter(String manufacturer, String model, String lotNumber, String type, Integer filterNdx)
MetadataStore
setEmissionFilter
in interface MetadataStore
public void setFilterSet(String manufacturer, String model, String lotNumber, Integer filterSetNdx, Integer filterNdx)
MetadataStore
setFilterSet
in interface MetadataStore
public void setOTF(Integer sizeX, Integer sizeY, String pixelType, String path, Boolean opticalAxisAverage, Integer instrumentNdx, Integer otfNdx, Integer filterNdx, Integer objectiveNdx)
MetadataStore
setOTF
in interface MetadataStore
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