Package loci.formats.in

Class PrairieMetadata.Frame

java.lang.Object
loci.formats.in.PrairieMetadata.Frame
Enclosing class:
PrairieMetadata
public class PrairieMetadata.Frame extends Object
A Prairie <Frame>, beneath a <Sequence>.

  • Field Details

    • sequence

      private PrairieMetadata.Sequence sequence
      The <Sequence> containing this <Frame>.

    • files

      private final HashMap<Integer,PrairieMetadata.PFile> files
      <File> elements beneath this <Frame>, keyed on each file's channel.

    • frameValues

      private final PrairieMetadata.ValueTable frameValues
      Table of key/value pairs for this <Frame>.

    • firstFile

      private PrairieMetadata.PFile firstFile
      The first actual <File> element for this <Frame>.

    • relativeTime

      private Double relativeTime
      relativeTime attribute of this <Frame>.

    • absoluteTime

      private Double absoluteTime
      absoluteTime attribute of this <Frame>.

    • index

      private Integer index
      index of this <Frame>.

  • Constructor Details

  • Method Details

    • getSequence

      public PrairieMetadata.Sequence getSequence()
      Gets the <Sequence> containing this <Frame>.

    • parse

      public void parse(Element frameElement)
      Parses metadata from the given Frame element.

    • getRelativeTime

      public double getRelativeTime()
      Gets the relativeTime associated with this Frame.

    • getAbsoluteTime

      public double getAbsoluteTime()
      Gets the absoluteTime associated with this Frame.

    • getIndex

      public int getIndex()
      Gets the index associated with this Frame.

    • getFirstFile

      public PrairieMetadata.PFile getFirstFile()
      Gets the first File of the Sequence.

    • getFile

      public PrairieMetadata.PFile getFile(int channel)
      Gets the File with the given channel.

    • getObjectiveLens

      public String getObjectiveLens()
      Gets the objective lens string for this Frame.

    • getObjectiveManufacturer

      public String getObjectiveManufacturer()
      Extracts the objective manufacturer from the objective lens string.

    • getMagnification

      public Double getMagnification()
      Extracts the magnification from the objective lens string.

    • getImmersion

      public String getImmersion()
      Extracts the immersion from the objective lens string.

    • getObjectiveLensNA

      public Double getObjectiveLensNA()
      Gets the numerical aperture of the lens for this Frame.

    • getPixelsPerLine

      public Integer getPixelsPerLine()
      Gets the pixels per line for this Frame.

    • getLinesPerFrame

      public Integer getLinesPerFrame()
      Gets the lines per frame for this Frame.

    • toLength

      private ome.units.quantity.Length toLength(Double position, boolean isInvert)
      Convert a position number to a length in the microscope reference frame.
      Parameters:
      position - a position number, may be null
      isInvert - if the number's sign should be flipped
      Returns:
      a length corresponding to the number, may be null

    • getPositionX

      public ome.units.quantity.Length getPositionX()
      Gets the X stage position associated with this Frame.

    • getPositionY

      public ome.units.quantity.Length getPositionY()
      Gets the Y stage position associated with this Frame.

    • getPositionZ

      public ome.units.quantity.Length getPositionZ()
      Gets the Z stage position associated with this Frame.

    • getOpticalZoom

      public Double getOpticalZoom()
      Gets the optical zoom associated with this Frame.

    • getMicronsPerPixelX

      public Double getMicronsPerPixelX()
      Gets the microns per pixel along X for this Frame.

    • getMicronsPerPixelY

      public Double getMicronsPerPixelY()
      Gets the microns per pixel along Y for this Frame.

    • getOffset

      public Double getOffset(int c)
      Gets the cth offset for this Frame.
      Parameters:
      c - The 0-based(!) channel index for which to obtain the offset.

    • getGain

      public Double getGain(int c)
      Gets the cth gain for this Frame.
      Parameters:
      c - The 0-based(!) channel index for which to obtain the gain.

    • getImagingDevice

      public String getImagingDevice()
      Gets the imaging device associated with this Frame.

    • getValue

      public PrairieMetadata.Value getValue(String key)
      Gets the value of the given key, beneath this Frame, inferring the value from the parent <Sequence> or grandparent <PVScan> section as needed.

    • getValues

      public PrairieMetadata.ValueTable getValues()
      Gets the table of Frame key/value pairs.