Class OMEZarrWriter.Builder

java.lang.Object
qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Enclosing class:
OMEZarrWriter
public static class OMEZarrWriter.Builder extends Object
Builder to create an instance of a OMEZarrWriter.

  • Constructor Details

  • Method Details

    • compression

      public OMEZarrWriter.Builder compression(com.bc.zarr.Compressor compressor)
      Set the compressor to use when writing tiles. By default, the blocs compression is used.
      Parameters:
      compressor - the compressor to use when writing tiles
      Returns:
      this builder
      Throws:
      NullPointerException - if the provided compressor is null

    • parallelize

      public OMEZarrWriter.Builder parallelize(int numberOfThreads)
      Tiles will be written from a pool of thread. This function specifies the number of threads to use. By default, ThreadTools.getParallelism() threads are used.
      Parameters:
      numberOfThreads - the number of threads to use when writing tiles
      Returns:
      this builder
      Throws:
      IllegalArgumentException - if the provided number of threads is less than 1

    • downsamples

      public OMEZarrWriter.Builder downsamples(double... downsamples)
      Enable the creation of a pyramidal image with the provided downsamples. The levels corresponding to the provided downsamples will be automatically generated.

      If this function is not called (or if it is called with no parameters), the downsamples of the provided image server will be used instead.

      Parameters:
      downsamples - the downsamples of the pyramid to generate
      Returns:
      this builder

    • setMaxNumberOfChunksOnEachSpatialDimension

      public OMEZarrWriter.Builder setMaxNumberOfChunksOnEachSpatialDimension(int maxNumberOfChunks)
      In Zarr images, data is stored in chunks. This parameter defines the maximum number of chunks on the x,y, and z dimensions. By default, this value is set to -1.

      Use a negative value to not define any maximum number of chunks.

      Parameters:
      maxNumberOfChunks - the maximum number of chunks on the x,y, and z dimensions
      Returns:
      this builder

    • tileSize

      public OMEZarrWriter.Builder tileSize(int tileSize)
      In Zarr images, data is stored in chunks. This parameter defines the size of chunks on the x and y dimensions. By default, these values are set to -1.

      Use a negative value to use the tile width/height of the provided image server.

      The provided tile width/height may not be used if this implies creating more chunks than the value given in setMaxNumberOfChunksOnEachSpatialDimension(int).

      Parameters:
      tileSize - the width/height each chunk should have
      Returns:
      this builder

    • tileSize

      public OMEZarrWriter.Builder tileSize(int tileWidth, int tileHeight)
      In Zarr images, data is stored in chunks. This parameter defines the size of chunks on the x and y dimensions. By default, these values are set to -1.

      Use a negative value to use the tile width/height of the provided image server.

      The provided tile width/height may not be used if this implies creating more chunks than the value given in setMaxNumberOfChunksOnEachSpatialDimension(int).

      Parameters:
      tileWidth - the width each chunk should have
      tileHeight - the height each chunk should have
      Returns:
      this builder

    • region

      public OMEZarrWriter.Builder region(ImageRegion boundingBox)
      Define a region (on the x-axis and y-axis) of the input image to consider.
      Parameters:
      boundingBox - the region to consider. Only the x, y, width, and height of this region are taken into account. Can be null to use the entire image. Null by default
      Returns:
      this builder

    • zSlices

      public OMEZarrWriter.Builder zSlices(int zStart, int zEnd)
      Define the z-slices of the input image to consider.
      Parameters:
      zStart - the 0-based inclusive index of the first z-slice to consider. 0 by default
      zEnd - the 0-based exclusive index of the last z-slice to consider. Equal to the number of z-slices of the image by default
      Returns:
      this builder
      Throws:
      IllegalArgumentException - if the min z-slice index is greater than the max z-slice index

    • timePoints

      public OMEZarrWriter.Builder timePoints(int tStart, int tEnd)
      Define the timepoints of the input image to consider.
      Parameters:
      tStart - the 0-based inclusive index of the first timepoint to consider. 0 by default
      tEnd - the 0-based exclusive index of the last timepoint to consider. Equal to the number of timepoints of the image by default
      Returns:
      this builder
      Throws:
      IllegalArgumentException - if the min timepoint index is greater than the max timepoint index

    • onTileWritten

      public OMEZarrWriter.Builder onTileWritten(Consumer<TileRequest> onTileWritten)
      Set a function that will be called each time a TileRequest is successfully or unsuccessfully written.

      This function may be called from any thread.

      Parameters:
      onTileWritten - a function that will be called each time a TileRequest is successfully or unsuccessfully written
      Returns:
      this builder
      Throws:
      NullPointerException - if the provided parameter is null

    • build

      public OMEZarrWriter build(String path) throws IOException
      Create a new instance of OMEZarrWriter. This will also create an empty image on the provided path.
      Parameters:
      path - the path where to write the image. It must end with ".ome.zarr" and shouldn't already exist
      Returns:
      the new OMEZarrWriter
      Throws:
      InvalidPathException - if a path object cannot be created from the provided path
      IOException - if the empty image cannot be created. This can happen if the provided path is incorrect or if the user doesn't have enough permissions
      IllegalArgumentException - if the provided path doesn't end with ".ome.zarr" or a file/directory already exists at this location