Package org.anchoranalysis.mpp.mark.voxelized

Interface VoxelizedMark

public interface VoxelizedMark
A voxelized representation of a Mark i.e. a mark turned into voxels.
Author:
Owen Feehan

  • Method Summary

    Modifier and Type Method Description
    org.anchoranalysis.spatial.box.BoundingBox boundingBox()
    Gets the bounding-box enclosing the voxelized representation of the mark.
    org.anchoranalysis.spatial.box.BoundingBox boundingBoxFlattened()
    Gets the bounding-box flattened in z dimension.
    void cleanUp()
    Cleans up any resources associated with this voxelized mark.
    VoxelizedMark duplicate()
    Creates a duplicate of this voxelized mark.
    org.anchoranalysis.image.voxel.statistics.VoxelStatistics statisticsFor​(int channelID, int regionID, int sliceID)
    Calculates statistics for a specific slice in a specific channel and region.
    org.anchoranalysis.image.voxel.statistics.VoxelStatistics statisticsForAllSlices​(int channelID, int regionID)
    Calculates statistics for all slices in a specific channel and region.
    org.anchoranalysis.image.voxel.statistics.VoxelStatistics statisticsForAllSlicesMaskSlice​(int channelID, int regionID, int maskChannelID)
    Calculates statistics for all slices in a specific channel and region, using a mask from another channel.
    org.anchoranalysis.image.voxel.BoundedVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> voxels()
    Gets the voxel representation of the mark.
    org.anchoranalysis.image.voxel.BoundedVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> voxelsMaximumIntensityProjection()
    Gets the maximum intensity projection of the voxelized mark.

  • Method Details

    • voxels

      org.anchoranalysis.image.voxel.BoundedVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> voxels()
      Gets the voxel representation of the mark.
      Returns:
      the BoundedVoxels representing the mark

    • voxelsMaximumIntensityProjection

      org.anchoranalysis.image.voxel.BoundedVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> voxelsMaximumIntensityProjection()
      Gets the maximum intensity projection of the voxelized mark.
      Returns:
      the BoundedVoxels representing the maximum intensity projection

    • boundingBox

      org.anchoranalysis.spatial.box.BoundingBox boundingBox()
      Gets the bounding-box enclosing the voxelized representation of the mark.
      Returns:
      the BoundingBox enclosing the mark

    • boundingBoxFlattened

      org.anchoranalysis.spatial.box.BoundingBox boundingBoxFlattened()
      Gets the bounding-box flattened in z dimension.
      Returns:
      the flattened BoundingBox

    • duplicate

      VoxelizedMark duplicate()
      Creates a duplicate of this voxelized mark.
      Returns:
      a new VoxelizedMark instance that is a copy of this one

    • statisticsForAllSlices

      org.anchoranalysis.image.voxel.statistics.VoxelStatistics statisticsForAllSlices​(int channelID, int regionID)
      Calculates statistics for all slices in a specific channel and region.
      Parameters:
      channelID - the ID of the channel
      regionID - the ID of the region
      Returns:
      the VoxelStatistics for the specified channel and region

    • statisticsForAllSlicesMaskSlice

      org.anchoranalysis.image.voxel.statistics.VoxelStatistics statisticsForAllSlicesMaskSlice​(int channelID, int regionID, int maskChannelID)
      Calculates statistics for all slices in a specific channel and region, using a mask from another channel.
      Parameters:
      channelID - the ID of the channel for statistics
      regionID - the ID of the region
      maskChannelID - the ID of the channel to use as a mask
      Returns:
      the VoxelStatistics for the specified channel and region, masked by another channel

    • statisticsFor

      org.anchoranalysis.image.voxel.statistics.VoxelStatistics statisticsFor​(int channelID, int regionID, int sliceID)
      Calculates statistics for a specific slice in a specific channel and region.
      Parameters:
      channelID - the ID of the channel
      regionID - the ID of the region
      sliceID - the ID of the slice
      Returns:
      the VoxelStatistics for the specified channel, region, and slice

    • cleanUp

      void cleanUp()
      Cleans up any resources associated with this voxelized mark.