Constructor Detail

• WriteSequenceToHdf5

  public WriteSequenceToHdf5()

Method Detail

• writeHdf5File

  public static void writeHdf5File(AbstractSequenceDescription<?,?,?> seq,
                                   Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
                                   boolean deflate,
                                   File hdf5File,
                                   ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
                                   ExportScalePyramid.AfterEachPlane afterEachPlane,
                                   int numCellCreatorThreads,
                                   ProgressWriter progressWriter)

  Create a hdf5 file containing image data from all views and all timepoints in a chunked, mipmaped representation.

  Parameters:

  seq - description of the sequence to be stored as hdf5. (The AbstractSequenceDescription contains the number of setups and timepoints as well as an BasicImgLoader that provides the image data, Registration information is not needed here, that will go into the accompanying xml).

  perSetupMipmapInfo - this maps from setup id to ExportMipmapInfo for that setup. The ExportMipmapInfo contains for each mipmap level, the subsampling factors and subdivision block sizes.

  deflate - whether to compress the data with the HDF5 DEFLATE filter.

  hdf5File - hdf5 file to which the image data is written.

  loopbackHeuristic - heuristic to decide whether to create each resolution level by reading pixels from the original image or by reading back a finer resolution level already written to the hdf5. may be null (in this case always use the original image).

  afterEachPlane - this is called after each "plane of chunks" is written, giving the opportunity to clear caches, etc.

  numCellCreatorThreads - The number of threads that will be instantiated to generate cell data. Must be at least 1. (In addition the cell creator threads there is one writer thread that saves the generated data to HDF5.)

  progressWriter - completion ratio and status output will be directed here.

• writeHdf5File

  public static void writeHdf5File(AbstractSequenceDescription<?,?,?> seq,
                                   int[][] resolutions,
                                   int[][] subdivisions,
                                   boolean deflate,
                                   File hdf5File,
                                   ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
                                   ExportScalePyramid.AfterEachPlane afterEachPlane,
                                   int numCellCreatorThreads,
                                   ProgressWriter progressWriter)

  Create a hdf5 file containing image data from all views and all timepoints in a chunked, mipmaped representation. This is the same as WriteSequenceToHdf5#writeHdf5File(AbstractSequenceDescription, Map, boolean, File, LoopbackHeuristic, AfterEachPlane, int, ProgressWriter) except that only one set of supsampling factors and and subdivision blocksizes is given, which is used for all views.

  Parameters:

  seq - description of the sequence to be stored as hdf5. (The AbstractSequenceDescription contains the number of setups and timepoints as well as an BasicImgLoader that provides the image data, Registration information is not needed here, that will go into the accompanying xml).

  resolutions - this nested arrays contains per mipmap level, the subsampling factors.

  subdivisions - this nested arrays contains per mipmap level, the subdivision block sizes.

  deflate - whether to compress the data with the HDF5 DEFLATE filter.

  hdf5File - hdf5 file to which the image data is written.

  loopbackHeuristic - heuristic to decide whether to create each resolution level by reading pixels from the original image or by reading back a finer resolution level already written to the hdf5. may be null (in this case always use the original image).

  afterEachPlane - this is called after each "plane of chunks" is written, giving the opportunity to clear caches, etc.

  numCellCreatorThreads - The number of threads that will be instantiated to generate cell data. Must be at least 1. (In addition the cell creator threads there is one writer thread that saves the generated data to HDF5.)

  progressWriter - completion ratio and status output will be directed here.

• writeHdf5PartitionLinkFile

  public static void writeHdf5PartitionLinkFile(AbstractSequenceDescription<?,?,?> seq,
                                                Map<Integer,ExportMipmapInfo> perSetupMipmapInfo)

  Create a hdf5 master file linking to image data from all views and all timepoints. This is the same as writeHdf5PartitionLinkFile(AbstractSequenceDescription, Map, ArrayList, File), except that the information about the partition files as well as the path of the master file to be written is obtained from the BasicImgLoader of the sequence, which must be a Hdf5ImageLoader.

  Parameters:

  seq - description of the sequence to be stored as hdf5. (The AbstractSequenceDescription contains the number of setups and timepoints as well as an BasicImgLoader that provides the image data, Registration information is not needed here, that will go into the accompanying xml).

  perSetupMipmapInfo - this maps from setup id to ExportMipmapInfo for that setup. The ExportMipmapInfo contains for each mipmap level, the subsampling factors and subdivision block sizes.

• writeHdf5PartitionLinkFile

  public static void writeHdf5PartitionLinkFile(AbstractSequenceDescription<?,?,?> seq,
                                                Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
                                                ArrayList<Partition> partitions,
                                                File hdf5File)

  Create a hdf5 master file linking to image data from all views and all timepoints. Which hdf5 files contain which part of the image data is specified in the portitions parameter. Note that this method only writes the master file containing links. The individual partitions need to be written with #writeHdf5PartitionFile(AbstractSequenceDescription, Map, boolean, Partition, LoopbackHeuristic, AfterEachPlane, int, ProgressWriter).

  Parameters:

  seq - description of the sequence to be stored as hdf5. (The AbstractSequenceDescription contains the number of setups and timepoints as well as an BasicImgLoader that provides the image data, Registration information is not needed here, that will go into the accompanying xml).

  perSetupMipmapInfo - this maps from setup id to ExportMipmapInfo for that setup. The ExportMipmapInfo contains for each mipmap level, the subsampling factors and subdivision block sizes.

  partitions - which parts of the dataset are stored in which files.

  hdf5File - hdf5 master file to which the image data from the partition files is linked.

• writeHdf5PartitionFile

  public static void writeHdf5PartitionFile(AbstractSequenceDescription<?,?,?> seq,
                                            Map<Integer,ExportMipmapInfo> perSetupMipmapInfo,
                                            boolean deflate,
                                            Partition partition,
                                            ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
                                            ExportScalePyramid.AfterEachPlane afterEachPlane,
                                            int numCellCreatorThreads,
                                            ProgressWriter progressWriter)

  Create a hdf5 partition file containing image data for a subset of views and timepoints in a chunked, mipmaped representation. Please note that the description of the full dataset must be given in the seq, perSetupResolutions, and perSetupSubdivisions parameters. Then only the part described by partition will be written.

  Parameters:

  seq - description of the sequence to be stored as hdf5. (The AbstractSequenceDescription contains the number of setups and timepoints as well as an BasicImgLoader that provides the image data, Registration information is not needed here, that will go into the accompanying xml).

  perSetupMipmapInfo - this maps from setup id to ExportMipmapInfo for that setup. The ExportMipmapInfo contains for each mipmap level, the subsampling factors and subdivision block sizes.

  deflate - whether to compress the data with the HDF5 DEFLATE filter.

  partition - which part of the dataset to write, and to which file.

  loopbackHeuristic - heuristic to decide whether to create each resolution level by reading pixels from the original image or by reading back a finer resolution level already written to the hdf5. may be null (in this case always use the original image).

  afterEachPlane - this is called after each "plane of chunks" is written, giving the opportunity to clear caches, etc.

  numCellCreatorThreads - The number of threads that will be instantiated to generate cell data. Must be at least 1. (In addition the cell creator threads there is one writer thread that saves the generated data to HDF5.)

  progressWriter - completion ratio and status output will be directed here.

• writeViewToHdf5PartitionFile

  public static void writeViewToHdf5PartitionFile(RandomAccessibleInterval<UnsignedShortType> img,
                                                  Partition partition,
                                                  int timepointIdPartition,
                                                  int setupIdPartition,
                                                  ExportMipmapInfo mipmapInfo,
                                                  boolean writeMipmapInfo,
                                                  boolean deflate,
                                                  ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
                                                  ExportScalePyramid.AfterEachPlane afterEachPlane,
                                                  int numCellCreatorThreads,
                                                  ProgressWriter progressWriter)

  Write a single view to a hdf5 partition file, in a chunked, mipmaped representation. Note that the specified view must not already exist in the partition file!

  Parameters:

  img - the view to be written.

  partition - describes which part of the full sequence is contained in this partition, and to which file this partition is written.

  timepointIdPartition - the timepoint id wrt the partition of the view to be written. The information in partition relates this to timepoint id in the full sequence.

  setupIdPartition - the setup id wrt the partition of the view to be written. The information in partition relates this to setup id in the full sequence.

  mipmapInfo - contains for each mipmap level of the setup, the subsampling factors and subdivision block sizes.

  writeMipmapInfo - whether to write mipmap description for the setup. must be done (at least) once for each setup in the partition.

  deflate - whether to compress the data with the HDF5 DEFLATE filter.

  loopbackHeuristic - heuristic to decide whether to create each resolution level by reading pixels from the original image or by reading back a finer resolution level already written to the hdf5. may be null (in this case always use the original image).

  afterEachPlane - this is called after each "plane of chunks" is written, giving the opportunity to clear caches, etc.

  numCellCreatorThreads - The number of threads that will be instantiated to generate cell data. Must be at least 1. (In addition the cell creator threads there is one writer thread that saves the generated data to HDF5.)

  progressWriter - completion ratio and status output will be directed here. may be null.

• writeViewToHdf5PartitionFile

  public static void writeViewToHdf5PartitionFile(RandomAccessibleInterval<UnsignedShortType> img,
                                                  int timepointIdPartition,
                                                  int setupIdPartition,
                                                  ExportMipmapInfo mipmapInfo,
                                                  boolean writeMipmapInfo,
                                                  boolean deflate,
                                                  bdv.export.IHDF5Access writerQueue,
                                                  ExecutorService executorService,
                                                  int numThreads,
                                                  ExportScalePyramid.LoopbackHeuristic loopbackHeuristic,
                                                  ExportScalePyramid.AfterEachPlane afterEachPlane,
                                                  ProgressWriter progressWriter)

  Write a single view to a hdf5 partition file, in a chunked, mipmaped representation. Note that the specified view must not already exist in the partition file!

  Parameters:

  img - the view to be written.

  timepointIdPartition - the timepoint id wrt the partition of the view to be written. The information in partition relates this to timepoint id in the full sequence.

  setupIdPartition - the setup id wrt the partition of the view to be written. The information in partition relates this to setup id in the full sequence.

  mipmapInfo - contains for each mipmap level of the setup, the subsampling factors and subdivision block sizes.

  writeMipmapInfo - whether to write mipmap description for the setup. must be done (at least) once for each setup in the partition.

  deflate - whether to compress the data with the HDF5 DEFLATE filter.

  writerQueue - block writing tasks are enqueued here.

  executorService - executor used for creating (possibly down-sampled) blocks of the view to be written.

  numThreads -

  loopbackHeuristic - heuristic to decide whether to create each resolution level by reading pixels from the original image or by reading back a finer resolution level already written to the hdf5. may be null (in this case always use the original image).

  afterEachPlane - this is called after each "plane of chunks" is written, giving the opportunity to clear caches, etc.

  progressWriter - completion ratio and status output will be directed here. may be null.