loci.formats
Class DummyMetadata

java.lang.Object
  extended by loci.formats.DummyMetadata
All Implemented Interfaces:
MetadataRetrieve, MetadataStore

public class DummyMetadata
extends Object
implements MetadataStore, MetadataRetrieve

A dummy implementation for MetadataStore and MetadataRetrieve that is used when no other metadata implementations are available.

Source code:
Trac, SVN

Author:
Chris Allan callan at blackcat.ca

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

DummyMetadata

public DummyMetadata()
Method Detail

getImageCount

public int getImageCount()
Description copied from interface: MetadataRetrieve
Returns the number of images.

Specified by:
getImageCount in interface MetadataRetrieve

getImageName

public String getImageName(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's name.

Specified by:
getImageName in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getCreationDate

public String getCreationDate(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's creation date.

Specified by:
getCreationDate in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getDescription

public String getDescription(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's description.

Specified by:
getDescription in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getExperimenterCount

public int getExperimenterCount()
Description copied from interface: MetadataRetrieve
Returns the number of experimenters.

Specified by:
getExperimenterCount in interface MetadataRetrieve

getFirstName

public String getFirstName(Integer n)
Description copied from interface: MetadataRetrieve
Gets the first name of the nth experimenter.

Specified by:
getFirstName in interface MetadataRetrieve
Parameters:
n - the index of the experimenter. If null the default index of 0 will be used.

getLastName

public String getLastName(Integer n)
Description copied from interface: MetadataRetrieve
Gets the last name of the nth experimenter.

Specified by:
getLastName in interface MetadataRetrieve
Parameters:
n - the index of the experimenter. If null the default index of 0 will be used.

getEmail

public String getEmail(Integer n)
Description copied from interface: MetadataRetrieve
Gets the email address of the nth experimenter.

Specified by:
getEmail in interface MetadataRetrieve
Parameters:
n - the index of the experimenter. If null the default index of 0 will be used.

getInstitution

public String getInstitution(Integer n)
Description copied from interface: MetadataRetrieve
Gets the institution of the nth experimenter.

Specified by:
getInstitution in interface MetadataRetrieve
Parameters:
n - the index of the experimenter. If null the default index of 0 will be used.

getDataDirectory

public String getDataDirectory(Integer n)
Description copied from interface: MetadataRetrieve
Gets the data directory of the nth experimenter.

Specified by:
getDataDirectory in interface MetadataRetrieve
Parameters:
n - the index of the experimenter. If null the default index of 0 will be used.

getGroup

public Object getGroup(Integer n)
Description copied from interface: MetadataRetrieve
Gets the group of the nth experimenter.

Specified by:
getGroup in interface MetadataRetrieve
Parameters:
n - the index of the experimenter. If null the default index of 0 will be used.

getGroupCount

public int getGroupCount()
Description copied from interface: MetadataRetrieve
Returns the number of groups.

Specified by:
getGroupCount in interface MetadataRetrieve

getGroupName

public String getGroupName(Integer n)
Description copied from interface: MetadataRetrieve
Get the name of the nth group.

Specified by:
getGroupName in interface MetadataRetrieve
Parameters:
n - the index of the group. If null the default index of 0 will be used.

getLeader

public Object getLeader(Integer n)
Description copied from interface: MetadataRetrieve
Get the leader of the nth group.

Specified by:
getLeader in interface MetadataRetrieve
Parameters:
n - the index of the group. If null the default index of 0 will be used.

getContact

public Object getContact(Integer n)
Description copied from interface: MetadataRetrieve
Get the contact of the nth group.

Specified by:
getContact in interface MetadataRetrieve
Parameters:
n - the index of the group. If null the default index of 0 will be used.

getInstrumentCount

public int getInstrumentCount()
Description copied from interface: MetadataRetrieve
Returns the number of instruments.

Specified by:
getInstrumentCount in interface MetadataRetrieve

getManufacturer

public String getManufacturer(Integer n)
Description copied from interface: MetadataRetrieve
Get the manufacturer of the nth instrument.

Specified by:
getManufacturer in interface MetadataRetrieve
Parameters:
n - the index of the instrument. If null the default index of 0 will be used.

getModel

public String getModel(Integer n)
Description copied from interface: MetadataRetrieve
Get the model of the nth instrument.

Specified by:
getModel in interface MetadataRetrieve
Parameters:
n - the index of the instrument. If null the default index of 0 will be used.

getSerialNumber

public String getSerialNumber(Integer n)
Description copied from interface: MetadataRetrieve
Get the serial number of the nth instrument.

Specified by:
getSerialNumber in interface MetadataRetrieve
Parameters:
n - the index of the instrument. If null the default index of 0 will be used.

getType

public String getType(Integer n)
Description copied from interface: MetadataRetrieve
Get the type of the nth instrument.

Specified by:
getType in interface MetadataRetrieve
Parameters:
n - the index of the instrument. If null the default index of 0 will be used.

getPixelSizeX

public Float getPixelSizeX(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's PixelSizeX attribute.

Specified by:
getPixelSizeX in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getPixelSizeY

public Float getPixelSizeY(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's PixelSizeY attribute.

Specified by:
getPixelSizeY in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getPixelSizeZ

public Float getPixelSizeZ(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's PixelSizeZ attribute.

Specified by:
getPixelSizeZ in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getPixelSizeC

public Float getPixelSizeC(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's PixelSizeC attribute.

Specified by:
getPixelSizeC in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getPixelSizeT

public Float getPixelSizeT(Integer n)
Description copied from interface: MetadataRetrieve
Gets the nth image's PixelSizeT attribute.

Specified by:
getPixelSizeT in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getDisplayROICount

public int getDisplayROICount()
Description copied from interface: MetadataRetrieve
Returns the number of DisplayROIs.

Specified by:
getDisplayROICount in interface MetadataRetrieve

getX0

public Integer getX0(Integer n)
Description copied from interface: MetadataRetrieve
Get the lower X bound of the nth ROI.

Specified by:
getX0 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getY0

public Integer getY0(Integer n)
Description copied from interface: MetadataRetrieve
Get the lower Y bound of the nth ROI.

Specified by:
getY0 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getZ0

public Integer getZ0(Integer n)
Description copied from interface: MetadataRetrieve
Get the lower Z bound of the nth ROI.

Specified by:
getZ0 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getT0

public Integer getT0(Integer n)
Description copied from interface: MetadataRetrieve
Get the lower T bound of the nth ROI.

Specified by:
getT0 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getX1

public Integer getX1(Integer n)
Description copied from interface: MetadataRetrieve
Get the upper X bound of the nth ROI.

Specified by:
getX1 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getY1

public Integer getY1(Integer n)
Description copied from interface: MetadataRetrieve
Get the upper Y bound of the nth ROI.

Specified by:
getY1 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getZ1

public Integer getZ1(Integer n)
Description copied from interface: MetadataRetrieve
Get the upper Z bound of the nth ROI.

Specified by:
getZ1 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getT1

public Integer getT1(Integer n)
Description copied from interface: MetadataRetrieve
Get the upper T bound of the nth ROI.

Specified by:
getT1 in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getDisplayOptions

public Object getDisplayOptions(Integer n)
Description copied from interface: MetadataRetrieve
Get the display options of the nth ROI.

Specified by:
getDisplayOptions in interface MetadataRetrieve
Parameters:
n - the index of the ROI. If null the default index of 0 will be used.

getPixelsCount

public int getPixelsCount(Integer n)
Description copied from interface: MetadataRetrieve
Returns the number of pixels elements for the given image.

Specified by:
getPixelsCount in interface MetadataRetrieve

getSizeX

public Integer getSizeX(Integer image)
Description copied from interface: MetadataRetrieve
Gets the SizeX attribute of the given pixels in the given image.

Specified by:
getSizeX in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getSizeY

public Integer getSizeY(Integer image)
Description copied from interface: MetadataRetrieve
Gets the SizeY attribute of the given pixels in the given image.

Specified by:
getSizeY in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getSizeZ

public Integer getSizeZ(Integer image)
Description copied from interface: MetadataRetrieve
Gets the SizeZ attribute of the given pixels in the given image.

Specified by:
getSizeZ in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getSizeC

public Integer getSizeC(Integer image)
Description copied from interface: MetadataRetrieve
Gets the SizeC attribute of the given pixels in the given image.

Specified by:
getSizeC in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getSizeT

public Integer getSizeT(Integer image)
Description copied from interface: MetadataRetrieve
Gets the SizeT attribute of the given pixels in the given image.

Specified by:
getSizeT in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getPixelType

public String getPixelType(Integer image)
Description copied from interface: MetadataRetrieve
Gets the PixelType attribute of the given pixels in the given image.

Specified by:
getPixelType in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getBigEndian

public Boolean getBigEndian(Integer image)
Description copied from interface: MetadataRetrieve
Gets the BigEndian attribute of the given pixels in the given image.

Specified by:
getBigEndian in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getDimensionOrder

public String getDimensionOrder(Integer image)
Description copied from interface: MetadataRetrieve
Gets the DimensionOrder attribute of the given pixels in the given image.

Specified by:
getDimensionOrder in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getStageLabelCount

public int getStageLabelCount()
Description copied from interface: MetadataRetrieve
Returns the number of stage labels.

Specified by:
getStageLabelCount in interface MetadataRetrieve

getStageName

public String getStageName(Integer n)
Description copied from interface: MetadataRetrieve
Gets the name of the nth stage label.

Specified by:
getStageName in interface MetadataRetrieve
Parameters:
n - the index of the stage label. If null the default index of 0 will be used.

getStageX

public Float getStageX(Integer n)
Description copied from interface: MetadataRetrieve
Gets the X coordinate of the nth stage label.

Specified by:
getStageX in interface MetadataRetrieve
Parameters:
n - the index of the stage label. If null the default index of 0 will be used.

getStageY

public Float getStageY(Integer n)
Description copied from interface: MetadataRetrieve
Gets the Y coordinate of the nth stage label.

Specified by:
getStageY in interface MetadataRetrieve
Parameters:
n - the index of the stage label. If null the default index of 0 will be used.

getStageZ

public Float getStageZ(Integer n)
Description copied from interface: MetadataRetrieve
Gets the Z coordinate of the nth stage label.

Specified by:
getStageZ in interface MetadataRetrieve
Parameters:
n - the index of the stage label. If null the default index of 0 will be used.

getChannelCount

public int getChannelCount(Integer n)
Description copied from interface: MetadataRetrieve
Returns the number of channels for the given pixels element.

Specified by:
getChannelCount in interface MetadataRetrieve

getChannelName

public String getChannelName(Integer pixels,
                             Integer channel)
Description copied from interface: MetadataRetrieve
Gets the name of the given channel in the given set of pixels.

Specified by:
getChannelName in interface MetadataRetrieve
Parameters:
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.

getChannelNDFilter

public Float getChannelNDFilter(Integer pixels,
                                Integer channel)
Description copied from interface: MetadataRetrieve
Gets the ND filter value for the given channel in the given set of pixels.

Specified by:
getChannelNDFilter in interface MetadataRetrieve
Parameters:
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.

getEmWave

public Integer getEmWave(Integer pixels,
                         Integer channel)
Description copied from interface: MetadataRetrieve
Gets the emission wavelength of the given channel in the given set of pixels.

Specified by:
getEmWave in interface MetadataRetrieve
Parameters:
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.

getExWave

public Integer getExWave(Integer pixels,
                         Integer channel)
Description copied from interface: MetadataRetrieve
Gets the excitation wavelength of the given channel in the given set of pixels.

Specified by:
getExWave in interface MetadataRetrieve
Parameters:
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.

getPhotometricInterpretation

public String getPhotometricInterpretation(Integer pixels,
                                           Integer channel)
Description copied from interface: MetadataRetrieve
Gets the photometric interpretation of the given channel in the given set of pixels.

Specified by:
getPhotometricInterpretation in interface MetadataRetrieve
Parameters:
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.

getMode

public String getMode(Integer pixels,
                      Integer channel)
Description copied from interface: MetadataRetrieve
Gets the mode of the given channel in the given set of pixels.

Specified by:
getMode in interface MetadataRetrieve
Parameters:
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.

getGlobalMin

public Double getGlobalMin(Integer pixels,
                           Integer channel)
Description copied from interface: MetadataRetrieve
Gets the minimum pixel value within the given channel in the given set of pixels.

Specified by:
getGlobalMin in interface MetadataRetrieve
Parameters:
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.

getGlobalMax

public Double getGlobalMax(Integer pixels,
                           Integer channel)
Description copied from interface: MetadataRetrieve
Gets the maximum pixel value within the given channel in the given set of pixels.

Specified by:
getGlobalMax in interface MetadataRetrieve
Parameters:
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.

getTimestamp

public Float getTimestamp(Integer pixels,
                          Integer z,
                          Integer c,
                          Integer t)
Description copied from interface: MetadataRetrieve
Gets the timestamp of the plane with the given Z, C and T coordinates in the given set of pixels.

Specified by:
getTimestamp in interface MetadataRetrieve
Parameters:
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.

getExposureTime

public Float getExposureTime(Integer pixels,
                             Integer z,
                             Integer c,
                             Integer t)
Description copied from interface: MetadataRetrieve
Gets the exposure time of the plane with the given Z, C and T coordinates in the given set of pixels.

Specified by:
getExposureTime in interface MetadataRetrieve
Parameters:
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.

getTemperature

public Float getTemperature(Integer n)
Description copied from interface: MetadataRetrieve
Gets the temperature associated with the given image.

Specified by:
getTemperature in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getAirPressure

public Float getAirPressure(Integer n)
Description copied from interface: MetadataRetrieve
Gets the air pressure associated with the given image.

Specified by:
getAirPressure in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getHumidity

public Float getHumidity(Integer n)
Description copied from interface: MetadataRetrieve
Gets the humidity associated with the given image.

Specified by:
getHumidity in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getCO2Percent

public Float getCO2Percent(Integer n)
Description copied from interface: MetadataRetrieve
Gets the CO2 percentage associated with the given image.

Specified by:
getCO2Percent in interface MetadataRetrieve
Parameters:
n - the index of the image. If null the default index of 0 will be used.

getBlackLevel

public Double getBlackLevel(Integer pixels,
                            Integer channel)
Description copied from interface: MetadataRetrieve
Gets the black level of the given channel in the given set of pixels.

Specified by:
getBlackLevel in interface MetadataRetrieve
Parameters:
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.

getWhiteLevel

public Double getWhiteLevel(Integer pixels,
                            Integer channel)
Description copied from interface: MetadataRetrieve
Gets the white level of the given channel in the given set of pixels.

Specified by:
getWhiteLevel in interface MetadataRetrieve
Parameters:
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.

getGamma

public Float getGamma(Integer pixels,
                      Integer channel)
Description copied from interface: MetadataRetrieve
Gets the gamma value of the given channel in the given set of pixels.

Specified by:
getGamma in interface MetadataRetrieve
Parameters:
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.

getZoom

public Float getZoom(Integer image)
Description copied from interface: MetadataRetrieve
Gets the zoom value associated with the given pixels in the given image.

Specified by:
getZoom in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

isRedChannelOn

public Boolean isRedChannelOn(Integer image)
Description copied from interface: MetadataRetrieve
Gets whether or not the red channel is activated.

Specified by:
isRedChannelOn in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

isGreenChannelOn

public Boolean isGreenChannelOn(Integer image)
Description copied from interface: MetadataRetrieve
Gets whether or not the green channel is activated.

Specified by:
isGreenChannelOn in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

isBlueChannelOn

public Boolean isBlueChannelOn(Integer image)
Description copied from interface: MetadataRetrieve
Gets whether or not the blue channel is activated.

Specified by:
isBlueChannelOn in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

isDisplayRGB

public Boolean isDisplayRGB(Integer image)
Description copied from interface: MetadataRetrieve
Gets whether or not the given pixels are displayed as an RGB image.

Specified by:
isDisplayRGB in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getColorMap

public String getColorMap(Integer image)
Description copied from interface: MetadataRetrieve
Gets the color map associated with the given pixels.

Specified by:
getColorMap in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getZStart

public Integer getZStart(Integer image)
Description copied from interface: MetadataRetrieve
Gets the minimum Z coordinate for which the display settings apply.

Specified by:
getZStart in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getZStop

public Integer getZStop(Integer image)
Description copied from interface: MetadataRetrieve
Gets the maximum Z coordinate for which the display settings apply.

Specified by:
getZStop in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getTStart

public Integer getTStart(Integer image)
Description copied from interface: MetadataRetrieve
Gets the minimum T coordinate for which the display settings apply.

Specified by:
getTStart in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getTStop

public Integer getTStop(Integer image)
Description copied from interface: MetadataRetrieve
Gets the maximum T coordinate for which the display settings apply.

Specified by:
getTStop in interface MetadataRetrieve
Parameters:
image - the index of the image. If null the default index of 0 will be used.

getLightManufacturer

public String getLightManufacturer(Integer light)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given light source.

Specified by:
getLightManufacturer in interface MetadataRetrieve
Parameters:
light - the index of the light. If null the default index of 0 will be used.

getLightModel

public String getLightModel(Integer light)
Description copied from interface: MetadataRetrieve
Gets the model of the given light source.

Specified by:
getLightModel in interface MetadataRetrieve
Parameters:
light - the index of the light. If null the default index of 0 will be used.

getLightSerial

public String getLightSerial(Integer light)
Description copied from interface: MetadataRetrieve
Gets the serial number of the given light source.

Specified by:
getLightSerial in interface MetadataRetrieve
Parameters:
light - the index of the light. If null the default index of 0 will be used.

getLaserType

public String getLaserType(Integer laser)
Description copied from interface: MetadataRetrieve
Gets the type of the given laser.

Specified by:
getLaserType in interface MetadataRetrieve
Parameters:
laser - the index of the laser. If null the default index of 0 will be used.

getLaserMedium

public String getLaserMedium(Integer laser)
Description copied from interface: MetadataRetrieve
Gets the medium of the given laser.

Specified by:
getLaserMedium in interface MetadataRetrieve
Parameters:
laser - the index of the laser. If null the default index of 0 will be used.

getLaserWavelength

public Integer getLaserWavelength(Integer laser)
Description copied from interface: MetadataRetrieve
Gets the wavelength of the given laser.

Specified by:
getLaserWavelength in interface MetadataRetrieve
Parameters:
laser - the index of the laser. If null the default index of 0 will be used.

isFrequencyDoubled

public Boolean isFrequencyDoubled(Integer laser)
Description copied from interface: MetadataRetrieve
Gets whether or not the frequency is doubled for the given laser.

Specified by:
isFrequencyDoubled in interface MetadataRetrieve
Parameters:
laser - the index of the laser. If null the default index of 0 will be used.

isTunable

public Boolean isTunable(Integer laser)
Description copied from interface: MetadataRetrieve
Gets whether or not the given laser is tunable.

Specified by:
isTunable in interface MetadataRetrieve
Parameters:
laser - the index of the laser. If null the default index of 0 will be used.

getPulse

public String getPulse(Integer laser)
Description copied from interface: MetadataRetrieve
Gets the pulse of the given laser.

Specified by:
getPulse in interface MetadataRetrieve
Parameters:
laser - the index of the laser. If null the default index of 0 will be used.

getPower

public Float getPower(Integer laser)
Description copied from interface: MetadataRetrieve
Gets the power (in watts) of the given laser.

Specified by:
getPower in interface MetadataRetrieve
Parameters:
laser - the index of the laser. If null the default index of 0 will be used.

getFilamentType

public String getFilamentType(Integer filament)
Description copied from interface: MetadataRetrieve
Gets the type of the given filament.

Specified by:
getFilamentType in interface MetadataRetrieve
Parameters:
filament - the index of the filament. If null the default index of 0 will be used.

getFilamentPower

public Float getFilamentPower(Integer filament)
Description copied from interface: MetadataRetrieve
Gets the power (in watts) of the given filament.

Specified by:
getFilamentPower in interface MetadataRetrieve
Parameters:
filament - the index of the filament. If null the default index of 0 will be used.

getArcType

public String getArcType(Integer arc)
Description copied from interface: MetadataRetrieve
Gets the type of the given arc.

Specified by:
getArcType in interface MetadataRetrieve
Parameters:
arc - the index of the arc. If null the default index of 0 will be used.

getArcPower

public Float getArcPower(Integer arc)
Description copied from interface: MetadataRetrieve
Gets the power (in watts) of the given arc.

Specified by:
getArcPower in interface MetadataRetrieve
Parameters:
arc - the index of the arc. If null the default index of 0 will be used.

getDetectorManufacturer

public String getDetectorManufacturer(Integer detector)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given detector.

Specified by:
getDetectorManufacturer in interface MetadataRetrieve
Parameters:
detector - the index of the detector. If null the default index of 0 will be used.

getDetectorModel

public String getDetectorModel(Integer detector)
Description copied from interface: MetadataRetrieve
Gets the model of the given detector.

Specified by:
getDetectorModel in interface MetadataRetrieve
Parameters:
detector - the index of the detector. If null the default index of 0 will be used.

getDetectorSerial

public String getDetectorSerial(Integer detector)
Description copied from interface: MetadataRetrieve
Gets the serial number of the given detector.

Specified by:
getDetectorSerial in interface MetadataRetrieve
Parameters:
detector - the index of the detector. If null the default index of 0 will be used.

getDetectorType

public String getDetectorType(Integer detector)
Description copied from interface: MetadataRetrieve
Gets the type of the given detector.

Specified by:
getDetectorType in interface MetadataRetrieve
Parameters:
detector - the index of the detector. If null the default index of 0 will be used.

getDetectorGain

public Float getDetectorGain(Integer detector)
Description copied from interface: MetadataRetrieve
Gets the gain value of the given detector.

Specified by:
getDetectorGain in interface MetadataRetrieve
Parameters:
detector - the index of the detector. If null the default index of 0 will be used.

getDetectorVoltage

public Float getDetectorVoltage(Integer detector)
Description copied from interface: MetadataRetrieve
Gets the voltage of the given detector.

Specified by:
getDetectorVoltage in interface MetadataRetrieve
Parameters:
detector - the index of the detector. If null the default index of 0 will be used.

getDetectorOffset

public Float getDetectorOffset(Integer detector)
Description copied from interface: MetadataRetrieve
Gets the offset of the given detector.

Specified by:
getDetectorOffset in interface MetadataRetrieve
Parameters:
detector - the index of the detector. If null the default index of 0 will be used.

getObjectiveManufacturer

public String getObjectiveManufacturer(Integer objective)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given objective.

Specified by:
getObjectiveManufacturer in interface MetadataRetrieve
Parameters:
objective - the index of the objective. If null the default index of 0 will be used.

getObjectiveModel

public String getObjectiveModel(Integer objective)
Description copied from interface: MetadataRetrieve
Gets the model of the given objective.

Specified by:
getObjectiveModel in interface MetadataRetrieve
Parameters:
objective - the index of the objective. If null the default index of 0 will be used.

getObjectiveSerial

public String getObjectiveSerial(Integer objective)
Description copied from interface: MetadataRetrieve
Gets the serial number of the given objective.

Specified by:
getObjectiveSerial in interface MetadataRetrieve
Parameters:
objective - the index of the objective. If null the default index of 0 will be used.

getLensNA

public Float getLensNA(Integer objective)
Description copied from interface: MetadataRetrieve
Gets the lens NA of the given objective.

Specified by:
getLensNA in interface MetadataRetrieve
Parameters:
objective - the index of the objective. If null the default index of 0 will be used.

getObjectiveMagnification

public Float getObjectiveMagnification(Integer objective)
Description copied from interface: MetadataRetrieve
Gets the magnification value of the given objective.

Specified by:
getObjectiveMagnification in interface MetadataRetrieve
Parameters:
objective - the index of the objective. If null the default index of 0 will be used.

getExcitationManufacturer

public String getExcitationManufacturer(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given excitation filter.

Specified by:
getExcitationManufacturer in interface MetadataRetrieve
Parameters:
filter - the index of the filter. If null the default index of 0 will be used.

getExcitationModel

public String getExcitationModel(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the model of the given excitation filter.

Specified by:
getExcitationModel in interface MetadataRetrieve
Parameters:
filter - the index of the filter. If null the default index of 0 will be used.

getExcitationLotNumber

public String getExcitationLotNumber(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the lot number of the given excitation filter.

Specified by:
getExcitationLotNumber in interface MetadataRetrieve
Parameters:
filter - the index of the filter. If null the default index of 0 will be used.

getExcitationType

public String getExcitationType(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the type of the given excitation filter.

Specified by:
getExcitationType in interface MetadataRetrieve
Parameters:
filter - the index of the filter. If null the default index of 0 will be used.

getDichroicManufacturer

public String getDichroicManufacturer(Integer dichroic)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given dichroic.

Specified by:
getDichroicManufacturer in interface MetadataRetrieve
Parameters:
dichroic - the index of the dichroic. If null the default index of 0 will be used.

getDichroicModel

public String getDichroicModel(Integer dichroic)
Description copied from interface: MetadataRetrieve
Gets the model of the given dichroic.

Specified by:
getDichroicModel in interface MetadataRetrieve
Parameters:
dichroic - the index of the dichroic. If null the default index of 0 will be used.

getDichroicLotNumber

public String getDichroicLotNumber(Integer dichroic)
Description copied from interface: MetadataRetrieve
Gets the lot number of the given dichroic.

Specified by:
getDichroicLotNumber in interface MetadataRetrieve
Parameters:
dichroic - the index of the dichroic. If null the default index of 0 will be used.

getEmissionManufacturer

public String getEmissionManufacturer(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given emission filter.

Specified by:
getEmissionManufacturer in interface MetadataRetrieve
Parameters:
filter - the index of the emission filter. If null the default index of 0 will be used.

getEmissionModel

public String getEmissionModel(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the model of the given emission filter.

Specified by:
getEmissionModel in interface MetadataRetrieve
Parameters:
filter - the index of the emission filter. If null the default index of 0 will be used.

getEmissionLotNumber

public String getEmissionLotNumber(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the lot number of the given emission filter.

Specified by:
getEmissionLotNumber in interface MetadataRetrieve
Parameters:
filter - the index of the emission filter. If null the default index of 0 will be used.

getEmissionType

public String getEmissionType(Integer filter)
Description copied from interface: MetadataRetrieve
Gets the type of the given emission filter.

Specified by:
getEmissionType in interface MetadataRetrieve
Parameters:
filter - the index of the emission filter. If null the default index of 0 will be used.

getFilterSetManufacturer

public String getFilterSetManufacturer(Integer filterSet)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given filter set.

Specified by:
getFilterSetManufacturer in interface MetadataRetrieve
Parameters:
filterSet - the index of the filter set. If null the default index of 0 will be used.

getFilterSetModel

public String getFilterSetModel(Integer filterSet)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given filter set.

Specified by:
getFilterSetModel in interface MetadataRetrieve
Parameters:
filterSet - the index of the filter set. If null the default index of 0 will be used.

getFilterSetLotNumber

public String getFilterSetLotNumber(Integer filterSet)
Description copied from interface: MetadataRetrieve
Gets the manufacturer of the given filter set.

Specified by:
getFilterSetLotNumber in interface MetadataRetrieve
Parameters:
filterSet - the index of the filter set. If null the default index of 0 will be used.

getOTFSizeX

public Integer getOTFSizeX(Integer otf)
Description copied from interface: MetadataRetrieve
Gets the width of the given OTF.

Specified by:
getOTFSizeX in interface MetadataRetrieve
Parameters:
otf - the index of the OTF. If null the default index of 0 will be used.

getOTFSizeY

public Integer getOTFSizeY(Integer otf)
Description copied from interface: MetadataRetrieve
Gets the height of the given OTF.

Specified by:
getOTFSizeY in interface MetadataRetrieve
Parameters:
otf - the index of the OTF. If null the default index of 0 will be used.

getOTFPixelType

public String getOTFPixelType(Integer otf)
Description copied from interface: MetadataRetrieve
Gets the pixel type of the given OTF.

Specified by:
getOTFPixelType in interface MetadataRetrieve
Parameters:
otf - the index of the OTF. If null the default index of 0 will be used.

getOTFPath

public String getOTFPath(Integer otf)
Description copied from interface: MetadataRetrieve
Gets the path to the given OTF.

Specified by:
getOTFPath in interface MetadataRetrieve
Parameters:
otf - the index of the OTF. If null the default index of 0 will be used.

getOTFOpticalAxisAverage

public Boolean getOTFOpticalAxisAverage(Integer otf)
Description copied from interface: MetadataRetrieve
Gets whether or not optical axis averaging is used for the given OTF.

Specified by:
getOTFOpticalAxisAverage in interface MetadataRetrieve
Parameters:
otf - the index of the OTF. If null the default index of 0 will be used.

createRoot

public void createRoot()
Description copied from interface: MetadataStore
Creates a new root object to be used by the metadata store and resets the internal state of the metadata store.

Specified by:
createRoot in interface MetadataStore

getRoot

public Object getRoot()
Description copied from interface: MetadataStore
Retrieves the root object of the metadata store.

Specified by:
getRoot in interface MetadataStore
Returns:
object that the store is using as its root.

setChannelGlobalMinMax

public void setChannelGlobalMinMax(int channel,
                                   Double globalMin,
                                   Double globalMax,
                                   Integer i)
Description copied from interface: MetadataStore
Sets a channel's global min and global max in the metadata store for a particular pixels set. NOTE: The implementation of this method is optional and can be purely a no-op. It is here to ensure compatability with certain stores which require this data to be specified explicitly.

Specified by:
setChannelGlobalMinMax in interface MetadataStore
Parameters:
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.

setDefaultDisplaySettings

public void setDefaultDisplaySettings(Integer i)
Description copied from interface: MetadataStore
Instructs the metadata store to set the default display settings for a particular pixels set.

Specified by:
setDefaultDisplaySettings in interface MetadataStore
Parameters:
i - the index of the pixels set within the metadata store.

setDimensions

public void setDimensions(Float pixelSizeX,
                          Float pixelSizeY,
                          Float pixelSizeZ,
                          Float pixelSizeC,
                          Float pixelSizeT,
                          Integer i)
Description copied from interface: MetadataStore
Creates a set of pixel dimensions in the metadata store with a particular index. Unless both values are non-null, the MetadataStore should assume pixelSizeX equals pixelSizeY (i.e., should populate the null field with the other field's value).

Specified by:
setDimensions in interface MetadataStore
Parameters:
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: Unknown
pixelSizeT - FIXME: Unknown
i - the index to use in the store. If null the default index of 0 will be used.

setDisplayROI

public void setDisplayROI(Integer x0,
                          Integer y0,
                          Integer z0,
                          Integer x1,
                          Integer y1,
                          Integer z1,
                          Integer t0,
                          Integer t1,
                          Object displayOptions,
                          Integer i)
Description copied from interface: MetadataStore
Creates a 5D bounding box region of interest and a set of display options in the metadata store with a particular index.

Specified by:
setDisplayROI in interface MetadataStore
Parameters:
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.

setExperimenter

public void setExperimenter(String firstName,
                            String lastName,
                            String email,
                            String institution,
                            String dataDirectory,
                            Object group,
                            Integer i)
Description copied from interface: MetadataStore
Creates an experimenter in the metadata store with a particular index.

Specified by:
setExperimenter in interface MetadataStore
Parameters:
firstName - the first name of the experimenter
lastName - the last name of the experimenter
email - the e-mail address of the experimenter
institution - the institution for which the experimenter belongs
dataDirectory - the fully qualified path to the experimenter's data
group - the group to which the experimenter belongs
i - the index to use in the store. If null the default index of 0 will be used.

setGroup

public void setGroup(String name,
                     Object leader,
                     Object contact,
                     Integer i)
Description copied from interface: MetadataStore
Creates a group in the metadata store with a particular index.

Specified by:
setGroup in interface MetadataStore
Parameters:
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.

setImage

public void setImage(String name,
                     String creationDate,
                     String description,
                     Integer i)
Description copied from interface: MetadataStore
Creates an image in the metadata store with a particular index.

Specified by:
setImage in interface MetadataStore
Parameters:
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.

setInstrument

public void setInstrument(String manufacturer,
                          String model,
                          String serialNumber,
                          String type,
                          Integer i)
Description copied from interface: MetadataStore
Creates an instrument in the metadata store with a particular index.

Specified by:
setInstrument in interface MetadataStore
Parameters:
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.

setLogicalChannel

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)
Description copied from interface: MetadataStore
Creates a logical channel and physical channel in the metadata store for a particular pixels.

Specified by:
setLogicalChannel in interface MetadataStore
Parameters:
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.

setPixels

public void setPixels(Integer sizeX,
                      Integer sizeY,
                      Integer sizeZ,
                      Integer sizeC,
                      Integer sizeT,
                      Integer pixelType,
                      Boolean bigEndian,
                      String dimensionOrder,
                      Integer imageNo,
                      Integer pixelsNo)
Description copied from interface: MetadataStore
Creates a pixels set in the metadata store with a particular image and pixels index.

Specified by:
setPixels in interface MetadataStore
Parameters:
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.

setPlaneInfo

public void setPlaneInfo(int theZ,
                         int theC,
                         int theT,
                         Float timestamp,
                         Float exposureTime,
                         Integer i)
Description copied from interface: MetadataStore
Sets the plane information for a particular X-Y plane (section) within a particular pixels set. NOTE: The implementation of this method is optional as this is a transitional type. More information about the PlaneInfo type can be found here.

Specified by:
setPlaneInfo in interface MetadataStore
Parameters:
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.

setRoot

public void setRoot(Object root)
Description copied from interface: MetadataStore
Sets the root object of the metadata store.

Specified by:
setRoot in interface MetadataStore
Parameters:
root - object that the store can use as its root.

setStageLabel

public void setStageLabel(String name,
                          Float x,
                          Float y,
                          Float z,
                          Integer i)
Description copied from interface: MetadataStore
Creates a stage label in the metadata store with a particular index.

Specified by:
setStageLabel in interface MetadataStore
Parameters:
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.

setImagingEnvironment

public void setImagingEnvironment(Float temperature,
                                  Float airPressure,
                                  Float humidity,
                                  Float co2Percent,
                                  Integer i)
Description copied from interface: MetadataStore
Sets the imaging environment for a particular image.

Specified by:
setImagingEnvironment in interface MetadataStore

setDisplayChannel

public void setDisplayChannel(Integer channelNumber,
                              Double blackLevel,
                              Double whiteLevel,
                              Float gamma,
                              Integer i)
Description copied from interface: MetadataStore
Sets information about the specified channel for a particular image.

Specified by:
setDisplayChannel in interface MetadataStore

setDisplayOptions

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)
Description copied from interface: MetadataStore
Sets various display options for a particular pixels set.

Specified by:
setDisplayOptions in interface MetadataStore

setLightSource

public void setLightSource(String manufacturer,
                           String model,
                           String serialNumber,
                           Integer instrumentNdx,
                           Integer lightNdx)
Description copied from interface: MetadataStore
Sets a light source for a particular instrument.

Specified by:
setLightSource in interface MetadataStore

setLaser

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)
Description copied from interface: MetadataStore
Sets a laser for a particular instrument.

Specified by:
setLaser in interface MetadataStore

setFilament

public void setFilament(String type,
                        Float power,
                        Integer lightNdx,
                        Integer filamentNdx)
Description copied from interface: MetadataStore
Sets a filament for a particular instrument.

Specified by:
setFilament in interface MetadataStore

setArc

public void setArc(String type,
                   Float power,
                   Integer lightNdx,
                   Integer arcNdx)
Description copied from interface: MetadataStore
Sets an arc for a particular instrument.

Specified by:
setArc in interface MetadataStore

setDetector

public void setDetector(String manufacturer,
                        String model,
                        String serialNumber,
                        String type,
                        Float gain,
                        Float voltage,
                        Float offset,
                        Integer instrumentNdx,
                        Integer detectorNdx)
Description copied from interface: MetadataStore
Sets a detector for a particular instrument.

Specified by:
setDetector in interface MetadataStore

setObjective

public void setObjective(String manufacturer,
                         String model,
                         String serialNumber,
                         Float lensNA,
                         Float magnification,
                         Integer instrumentNdx,
                         Integer objectiveNdx)
Description copied from interface: MetadataStore
Sets an objective for a particular instrument.

Specified by:
setObjective in interface MetadataStore

setExcitationFilter

public void setExcitationFilter(String manufacturer,
                                String model,
                                String lotNumber,
                                String type,
                                Integer filterNdx)
Description copied from interface: MetadataStore
Sets an excitation filter for a particular instrument.

Specified by:
setExcitationFilter in interface MetadataStore

setDichroic

public void setDichroic(String manufacturer,
                        String model,
                        String lotNumber,
                        Integer dichroicNdx)
Description copied from interface: MetadataStore
Sets a dichroic for a particular instrument.

Specified by:
setDichroic in interface MetadataStore

setEmissionFilter

public void setEmissionFilter(String manufacturer,
                              String model,
                              String lotNumber,
                              String type,
                              Integer filterNdx)
Description copied from interface: MetadataStore
Sets an emission filter for a particular instrument.

Specified by:
setEmissionFilter in interface MetadataStore

setFilterSet

public void setFilterSet(String manufacturer,
                         String model,
                         String lotNumber,
                         Integer filterSetNdx,
                         Integer filterNdx)
Description copied from interface: MetadataStore
Sets a filter set for a particular instrument.

Specified by:
setFilterSet in interface MetadataStore

setOTF

public void setOTF(Integer sizeX,
                   Integer sizeY,
                   String pixelType,
                   String path,
                   Boolean opticalAxisAverage,
                   Integer instrumentNdx,
                   Integer otfNdx,
                   Integer filterNdx,
                   Integer objectiveNdx)
Description copied from interface: MetadataStore
Sets an OTF for a particular instrument.

Specified by:
setOTF in interface MetadataStore