bdv.img.hdf5

Class Partition

java.lang.Object

bdv.img.hdf5.Partition

public class Partition
extends Object

Partition describes one partition file of a dataset that is split across multiple hdf5 files. An aggregating hdf5 linking the partition files can be created using the Partition information (without looking at the constituent files).

Author:

Tobias Pietzsch

Field Summary

Fields

Modifier and Type	Field and Description
protected String	path

Constructor Summary

Constructors

Constructor and Description
Partition(String path, int[] timepointIdsSequence, int[] setupIdsSequence, int[] timepointIdsPartition, int[] setupIdsPartition) Create a new Partition description.
Partition(String path, Map<Integer,Integer> timepointIdSequenceToPartition, Map<Integer,Integer> setupIdSequenceToPartition) Create a new Partition description.

Method Summary

Modifier and Type	Method and Description
boolean	contains(ViewId viewId) Does this partition contain the given view (timepoint-setup pair)?
String	getPath() Get the path to the hdf5 file for this partition.
Map<Integer,Integer>	getSetupIdSequenceToPartition() Get a map from setup ids of the full sequence to setup ids of this partition.
Map<Integer,Integer>	getTimepointIdSequenceToPartition() Get a map from timepoint ids of the full sequence to timepoint ids of this partition.
static ArrayList<Partition>	split(List<TimePoint> timepoints, List<? extends BasicViewSetup> setups, int timepointsPerPartition, int setupsPerPartition, String basename) Split a sequence into partitions, each containing a specified number of timepoints and setups.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

path

protected final String path

Constructor Detail

Partition

public Partition(String path,
                 int[] timepointIdsSequence,
                 int[] setupIdsSequence,
                 int[] timepointIdsPartition,
                 int[] setupIdsPartition)

Create a new Partition description.

Parameters:

path - path to the hdf5 file for this partition

timepointIdsSequence -

setupIdsSequence -

timepointIdsPartition -

setupIdsPartition -

Partition

public Partition(String path,
                 Map<Integer,Integer> timepointIdSequenceToPartition,
                 Map<Integer,Integer> setupIdSequenceToPartition)

Create a new Partition description.

Parameters:

path - path to the hdf5 file for this partition

timepointIdSequenceToPartition -

setupIdSequenceToPartition -

Method Detail

getPath

public String getPath()

Get the path to the hdf5 file for this partition.

Returns:

path to the hdf5 file for this partition.

getTimepointIdSequenceToPartition

public Map<Integer,Integer> getTimepointIdSequenceToPartition()

Get a map from timepoint ids of the full sequence to timepoint ids of this partition.

getSetupIdSequenceToPartition

public Map<Integer,Integer> getSetupIdSequenceToPartition()

Get a map from setup ids of the full sequence to setup ids of this partition.

contains

public boolean contains(ViewId viewId)

Does this partition contain the given view (timepoint-setup pair)?

Parameters:

viewId - view (timepoint and setup id wrt. the full sequence)

Returns:

whether this partition contains the given view.

split

public static ArrayList<Partition> split(List<TimePoint> timepoints,
                                         List<? extends BasicViewSetup> setups,
                                         int timepointsPerPartition,
                                         int setupsPerPartition,
                                         String basename)

Split a sequence into partitions, each containing a specified number of timepoints and setups.

Parameters:

timepoints - list of all TimePoints.

setups - list of all BasicViewSetups.

timepointsPerPartition - how many timepoints should each partition contain (if this is ≤0, put do not split timepoints across partitions).

setupsPerPartition - how many setups should each partition contain (if this is ≤0, put do not split setups across partitions).

basename - This is used to generate paths for the partitions. Partitions are named "basename-TT-SS.h5" where TT and SS are the index of the timepoint and setup batch, respectively.

Returns:

list of partitions.