Package org.anchoranalysis.io.bioformats.bean.options

Class ReadOptions

Object
AnchorBean<ReadOptions>
ReadOptions
Direct Known Subclasses:
Default, ReadOptionsDelegate
public abstract class ReadOptions extends AnchorBean<ReadOptions>
Options that influence how stack is read in BioformatsReader.
Author:
Owen Feehan

  • Constructor Details

    • ReadOptions

      public ReadOptions()

  • Method Details

    • sizeC

      public abstract int sizeC(loci.formats.IFormatReader reader)
      Number of channels.
      Parameters:
      reader - the bioformats reader
      Returns:
      the number of channels

    • sizeT

      public abstract int sizeT(loci.formats.IFormatReader reader)
      Number of time-points (frames in a time series).
      Parameters:
      reader - the bioformats reader
      Returns:
      the number of channels

    • sizeZ

      public abstract int sizeZ(loci.formats.IFormatReader reader)
      Number of z-slices (slices in a 3D image).
      Parameters:
      reader - the bioformats reader
      Returns:
      the number of slices

    • effectiveBitsPerPixel

      public abstract int effectiveBitsPerPixel(loci.formats.IFormatReader reader)
      The number of bits used per pixel.

      This may be a smaller number than the size of the voxel's data-type e.g. a 16-bit format may be used to store only 12-bits of image data.

      Parameters:
      reader - the bioformats reader
      Returns:
      the number of bits used per pixel.

    • channelsPerByteArray

      public abstract int channelsPerByteArray(loci.formats.IFormatReader reader)
      The number of channels returned with each call to IFormatReader.openBytes(int).
      Parameters:
      reader - the bioformats reader
      Returns:
      the number of channels returned with each call to openBytes.

    • isRGB

      public abstract boolean isRGB(loci.formats.IFormatReader reader)
      Is it an image with three channels (red, green and blue)?
      Parameters:
      reader - the bioformats reader
      Returns:
      true iff its a RGB image

    • determineChannelNames

      public abstract Optional<List<String>> determineChannelNames(loci.formats.IFormatReader reader)
      A list of channel-names, if available.

      The order matches the channel indexing e.g. the first name in the list corresponds to the channel with index=0.

      Parameters:
      reader - the bioformats reader
      Returns:
      the channel-names, if available.