Index

A

acceptRootGroup(Consumer<H5Group>) - Method in class nz.org.riskscape.hdf5.H5File

Convenience version of getRootGroup that handles closing the root group object for you.

ALLOWED_READ_SIZE_MB - Static variable in class nz.org.riskscape.hdf5.Hdf5Resolver

 

applyRootGroup(Function<H5Group, T>) - Method in class nz.org.riskscape.hdf5.H5File

Convenience version of getRootGroup that handles closing the root group object for you.

B

build(long) - Static method in class nz.org.riskscape.hdf5.types.H5Type

 

build(Hdf5Resolver.Parameters) - Method in class nz.org.riskscape.hdf5.Hdf5Resolver

 

byteOffset - Variable in class nz.org.riskscape.hdf5.H5CompoundMember

 

C

canEqual(Object) - Method in class nz.org.riskscape.hdf5.H5Attribute

 

canEqual(Object) - Method in class nz.org.riskscape.hdf5.H5DatasetPath

 

canEqual(Object) - Method in class nz.org.riskscape.hdf5.types.H5Type

 

clone(BaseRelation.Fields) - Method in class nz.org.riskscape.hdf5.relation.H5Relation

 

close() - Method in class nz.org.riskscape.hdf5.H5Attribute

 

close() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

close() - Method in class nz.org.riskscape.hdf5.H5DataSpace

 

close() - Method in class nz.org.riskscape.hdf5.H5File

 

close() - Method in class nz.org.riskscape.hdf5.H5Group

 

close() - Method in class nz.org.riskscape.hdf5.H5Object

 

close() - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

close() - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

close() - Method in class nz.org.riskscape.hdf5.types.H5EnumType

 

close() - Method in class nz.org.riskscape.hdf5.types.H5Type

 

close() - Method in class nz.org.riskscape.hdf5.types.H5VlenType

 

createMemSpace(long) - Static method in class nz.org.riskscape.hdf5.H5DataSpace

Returns a memory space suitable to use for reading the numElements specified from a one-dimensional dataset.

createMemSpace(long[]) - Static method in class nz.org.riskscape.hdf5.H5DataSpace

Creates a dataspace handle suitable to use as a 'memory space' in other HDF5 library calls.

createRawRelationFromBookmark(Hdf5Resolver.Parameters) - Method in class nz.org.riskscape.hdf5.Hdf5Resolver

Builds a relation for the desired dataset.

D

dataset - Variable in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

dataset - Variable in class nz.org.riskscape.hdf5.Hdf5Resolver.Parameters

 

datasetName - Variable in class nz.org.riskscape.hdf5.H5DatasetPath

 

dataspace - Variable in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

doCommand(Engine) - Method in class nz.org.riskscape.hdf5.Hdf5Command.LsCommand

 

E

equals(Object) - Method in class nz.org.riskscape.hdf5.H5Attribute

 

equals(Object) - Method in class nz.org.riskscape.hdf5.H5DatasetPath

 

equals(Object) - Method in class nz.org.riskscape.hdf5.types.H5Type

 

F

findIndex(String) - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

findMember(String) - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

G

getByteBuffer() - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

getByteOffsetFor(int) - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

getClassName() - Method in class nz.org.riskscape.hdf5.types.H5Type

 

getCurrentIndex() - Method in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

Gets the current position of the cursor within the dataset elements.

getCurrentIndex() - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

getDatasetName() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

getDatasetName() - Method in class nz.org.riskscape.hdf5.H5DatasetPath

 

getDataSize() - Method in class nz.org.riskscape.hdf5.types.H5Type

The size in bytes of any element of this type.

getDataSpace() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

getDataType() - Method in class nz.org.riskscape.hdf5.H5Attribute

 

getDataType() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

getDataType() - Method in enum class nz.org.riskscape.hdf5.Hdf5Resolver.DatasetMode

 

getDataType() - Method in class nz.org.riskscape.hdf5.Hdf5Resolver.Parameters

 

getDimensions() - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

getDimensionsSum() - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

getElementsAsDouble() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

getExtensionsToFormats() - Method in class nz.org.riskscape.hdf5.Hdf5Resolver

 

getExtent() - Method in class nz.org.riskscape.hdf5.H5DataSpace

 

getFeatures() - Method in class nz.org.riskscape.hdf5.Hdf5Plugin

 

getGroupName() - Method in class nz.org.riskscape.hdf5.H5DatasetPath

 

getGroupName() - Method in class nz.org.riskscape.hdf5.H5Group

 

getMembers() - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

getMembersArray() - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

getMemberType() - Method in class nz.org.riskscape.hdf5.types.H5VlenType

 

getName() - Method in class nz.org.riskscape.hdf5.H5Attribute

 

getName(H5Object) - Method in class nz.org.riskscape.hdf5.Hdf5Command.LsCommand

 

getParent() - Method in class nz.org.riskscape.hdf5.H5Group

The group above this one.

getPath() - Method in class nz.org.riskscape.hdf5.H5DatasetPath

 

getPointer() - Method in class nz.org.riskscape.hdf5.H5Object

 

getRootGroup() - Method in class nz.org.riskscape.hdf5.H5File

 

getSourceInformation() - Method in class nz.org.riskscape.hdf5.relation.H5Relation

 

getSuperType() - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

groupName - Variable in class nz.org.riskscape.hdf5.H5DatasetPath

 

H

H5ArrayType - Class in nz.org.riskscape.hdf5.types

 

H5ArrayType(long) - Constructor for class nz.org.riskscape.hdf5.types.H5ArrayType

 

H5Attribute - Class in nz.org.riskscape.hdf5

A metadata attribute for a dataset

H5Attribute(H5Object, String) - Constructor for class nz.org.riskscape.hdf5.H5Attribute

 

H5CompoundMember - Class in nz.org.riskscape.hdf5

 

H5CompoundMember(int, String, H5Type, H5CompoundType, int) - Constructor for class nz.org.riskscape.hdf5.H5CompoundMember

 

H5CompoundType - Class in nz.org.riskscape.hdf5.types

 

H5CompoundType(long) - Constructor for class nz.org.riskscape.hdf5.types.H5CompoundType

 

H5Dataset - Class in nz.org.riskscape.hdf5

Supports reading a one-dimensional dataset from an h5 file.

H5DatasetCursor - Class in nz.org.riskscape.hdf5.cursor

Iterates over elements of an H5Dataset.

H5DatasetCursor(H5Dataset, H5DataSpace, H5Type) - Constructor for class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

H5DatasetCursor.LocalProblems - Interface in nz.org.riskscape.hdf5.cursor

 

H5DatasetPath - Class in nz.org.riskscape.hdf5

Convenience for representing a complete path to a dataset.

H5DatasetPath(String, String) - Constructor for class nz.org.riskscape.hdf5.H5DatasetPath

 

H5DataSpace - Class in nz.org.riskscape.hdf5

A dataspace is a handle used to either read from or to a dataset.

H5DataSpace(long, H5Dataset) - Constructor for class nz.org.riskscape.hdf5.H5DataSpace

 

H5DataSpace(long, H5Dataset, long[]) - Constructor for class nz.org.riskscape.hdf5.H5DataSpace

 

H5EnumType - Class in nz.org.riskscape.hdf5.types

 

H5EnumType(long) - Constructor for class nz.org.riskscape.hdf5.types.H5EnumType

 

h5File - Variable in class nz.org.riskscape.hdf5.Hdf5Resolver.Parameters

 

H5File - Class in nz.org.riskscape.hdf5

Gives access to datasets stored within an hdf5 file on the filesystem.

H5File(String) - Constructor for class nz.org.riskscape.hdf5.H5File

 

H5File(Path) - Constructor for class nz.org.riskscape.hdf5.H5File

 

H5FixedSizeCursor - Class in nz.org.riskscape.hdf5.cursor

Iterates over elements of an H5Dataset

H5FixedSizeCursor(H5Dataset, H5DataSpace, H5Type, int) - Constructor for class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

H5FloatType - Class in nz.org.riskscape.hdf5.types

 

H5FloatType(long) - Constructor for class nz.org.riskscape.hdf5.types.H5FloatType

 

H5Group - Class in nz.org.riskscape.hdf5

Methods for inspecting and accessing elements within an H5Group.

H5GroupVisitor - Interface in nz.org.riskscape.hdf5

Interface for doing directory-style visiting of groups.

H5IntegerType - Class in nz.org.riskscape.hdf5.types

 

H5IntegerType(long) - Constructor for class nz.org.riskscape.hdf5.types.H5IntegerType

 

H5IntegerType(long, boolean) - Constructor for class nz.org.riskscape.hdf5.types.H5IntegerType

 

H5Object - Class in nz.org.riskscape.hdf5

Base class for any object that wraps the anonymous IDs that are returned from the H5 library.

H5Object(long) - Constructor for class nz.org.riskscape.hdf5.H5Object

 

H5Relation - Class in nz.org.riskscape.hdf5.relation

A relation that emits tuples formed from values in a one dimensional hdf5 dataset.

H5Relation(H5Dataset, Struct, Function<H5DatasetCursor, Tuple>, int) - Constructor for class nz.org.riskscape.hdf5.relation.H5Relation

Creates a relation from a HDF5 dataset.

H5StringType - Class in nz.org.riskscape.hdf5.types

 

H5StringType(long) - Constructor for class nz.org.riskscape.hdf5.types.H5StringType

 

H5Type - Class in nz.org.riskscape.hdf5.types

Represents an H5 data type, with some conveniences for mapping these to Riskscape types.

H5Type(long) - Constructor for class nz.org.riskscape.hdf5.types.H5Type

 

H5VlenType - Class in nz.org.riskscape.hdf5.types

 

H5VlenType(long) - Constructor for class nz.org.riskscape.hdf5.types.H5VlenType

 

hashCode() - Method in class nz.org.riskscape.hdf5.H5Attribute

 

hashCode() - Method in class nz.org.riskscape.hdf5.H5DatasetPath

 

hashCode() - Method in class nz.org.riskscape.hdf5.types.H5Type

 

hasNext() - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

Hdf5Command - Class in nz.org.riskscape.hdf5

 

Hdf5Command() - Constructor for class nz.org.riskscape.hdf5.Hdf5Command

 

Hdf5Command.LsCommand - Class in nz.org.riskscape.hdf5

 

hdf5File - Variable in class nz.org.riskscape.hdf5.Hdf5Command.LsCommand

 

Hdf5Plugin - Class in nz.org.riskscape.hdf5

 

Hdf5Plugin(PluginDescriptor) - Constructor for class nz.org.riskscape.hdf5.Hdf5Plugin

 

Hdf5Resolver - Class in nz.org.riskscape.hdf5

A general purpose resolver to open HDF5 files (or rather datasets within them) in a variety of ways.

Hdf5Resolver(Engine) - Constructor for class nz.org.riskscape.hdf5.Hdf5Resolver

 

Hdf5Resolver.DatasetMode - Enum Class in nz.org.riskscape.hdf5

 

Hdf5Resolver.Parameters - Class in nz.org.riskscape.hdf5

 

I

includeAttributes - Variable in class nz.org.riskscape.hdf5.Hdf5Resolver.Parameters

 

index - Variable in class nz.org.riskscape.hdf5.H5CompoundMember

 

initializeEngine(Engine) - Method in class nz.org.riskscape.hdf5.Hdf5Plugin

 

intToBytes(long) - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

 

isOpaqueUnsignedLongs() - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

As a performance optimisation, we can read a 64 bit unsigned long as a signed long, to avoid having to use BigIntegers.

isRoot() - Method in class nz.org.riskscape.hdf5.H5Group

 

isUnsigned() - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5EnumType

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5FloatType

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5StringType

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5Type

 

isVariableLength() - Method in class nz.org.riskscape.hdf5.types.H5VlenType

 

L

location - Variable in class nz.org.riskscape.hdf5.Hdf5Command.LsCommand

 

LsCommand() - Constructor for class nz.org.riskscape.hdf5.Hdf5Command.LsCommand

 

M

mode - Variable in class nz.org.riskscape.hdf5.Hdf5Resolver.Parameters

 

N

name - Variable in class nz.org.riskscape.hdf5.H5CompoundMember

 

newDataSpace() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

next() - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

numDimensions() - Method in class nz.org.riskscape.hdf5.H5DataSpace

 

numElements - Variable in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

numElements() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

numElements() - Method in class nz.org.riskscape.hdf5.H5DataSpace

 

numElementsAsInt() - Method in class nz.org.riskscape.hdf5.H5DataSpace

Same as numElements() but should only be used when you're certain that the number of elements in the dataset will not overflow an integer value.

nz.org.riskscape.hdf5 - package nz.org.riskscape.hdf5

 

nz.org.riskscape.hdf5.cursor - package nz.org.riskscape.hdf5.cursor

 

nz.org.riskscape.hdf5.relation - package nz.org.riskscape.hdf5.relation

 

nz.org.riskscape.hdf5.types - package nz.org.riskscape.hdf5.types

 

O

openChild(String) - Method in class nz.org.riskscape.hdf5.H5Group

Opens either a group or dataset, which is a member of this group, by its name

openCursor() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

openCursor(int) - Method in class nz.org.riskscape.hdf5.H5Dataset

 

openDataset(String, String) - Method in class nz.org.riskscape.hdf5.H5File

 

openDataset(H5DatasetPath) - Method in class nz.org.riskscape.hdf5.H5File

 

openObject(String) - Method in class nz.org.riskscape.hdf5.H5File

 

owner - Variable in class nz.org.riskscape.hdf5.H5CompoundMember

 

P

Parameters() - Constructor for class nz.org.riskscape.hdf5.Hdf5Resolver.Parameters

 

parse(String) - Static method in class nz.org.riskscape.hdf5.H5DatasetPath

 

peek() - Method in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

Same as Iterator.next() but the cursor position is not changed.

peek() - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

peek(H5CompoundMember) - Method in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

Read the data for member only.

peek(H5CompoundMember) - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

PROBLEMS - Static variable in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

ptr - Variable in class nz.org.riskscape.hdf5.H5Object

 

R

rawIterator() - Method in class nz.org.riskscape.hdf5.relation.H5Relation

 

read() - Method in class nz.org.riskscape.hdf5.H5Attribute

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.H5CompoundMember

Shortcut to replace member.type.read(buffer, member.getByteOffset() + offset)

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5EnumType

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5FloatType

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5StringType

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5Type

 

read(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5VlenType

 

readElements(long[], long[]) - Method in class nz.org.riskscape.hdf5.H5DataSpace

Reads the specified elements from a dataset.

readElements(long, long) - Method in class nz.org.riskscape.hdf5.H5DataSpace

Reads the specified elements from a one-dimensional dataset.

readFloats(ByteBuffer, int) - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

Efficient alternative to read for returning whatever numeric value is held in in the super type in to an array of floats.

readSizeMb - Variable in class nz.org.riskscape.hdf5.Hdf5Resolver.Parameters

 

readSizeTooSmallForMultiDimensionedData(long, long) - Method in interface nz.org.riskscape.hdf5.cursor.H5DatasetCursor.LocalProblems

When the user defined read size is not big enough to fit all of a multi-dimensioned dataset.

readValue(H5Object, String, Class<T>) - Static method in class nz.org.riskscape.hdf5.H5Attribute

Helper to read an attribute's value from a given HDF5 object (e.g.

readVlen(byte[]) - Method in class nz.org.riskscape.hdf5.types.H5Type

Special case read method for reading variable length data from the result of a call to H5.h5d_readVL.

readVlenElements(H5DataSpace, H5DataSpace, int) - Method in class nz.org.riskscape.hdf5.H5Dataset

Read n variable length (vlen) elements and return them as a 2d array of bytes, where the 1st dimension contains the bytes of each element.

RELATION - Enum constant in enum class nz.org.riskscape.hdf5.Hdf5Resolver.DatasetMode

 

rewind() - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

S

selectElements(long[], long[]) - Method in class nz.org.riskscape.hdf5.H5DataSpace

Selects a hyperslab of elements within the dataspace, using the starting position and number of elements specified.

selectElementsAt(long[][]) - Method in class nz.org.riskscape.hdf5.H5DataSpace

Select specific elements from arbitrary locations from the dataset by specifying them as points within the n dimensional dataset.

setCurrentIndex(long) - Method in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

Resets the position of the cursor to the given element index.

setCurrentIndex(long) - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

setOpaqueUnsignedLongs(boolean) - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

As a performance optimisation, we can read a 64 bit unsigned long as a signed long, to avoid having to use BigIntegers.

SETTING_LIB_PATH - Static variable in class nz.org.riskscape.hdf5.Hdf5Plugin

 

size() - Method in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

size() - Method in class nz.org.riskscape.hdf5.relation.H5Relation

 

sizeAsInt() - Method in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

skip() - Method in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

Advances the cursor index one step.

skip() - Method in class nz.org.riskscape.hdf5.cursor.H5FixedSizeCursor

 

startUp(Map<String, List<String>>) - Method in class nz.org.riskscape.hdf5.Hdf5Plugin

 

T

toString() - Method in class nz.org.riskscape.hdf5.H5Attribute

 

toString() - Method in class nz.org.riskscape.hdf5.H5CompoundMember

 

toString() - Method in class nz.org.riskscape.hdf5.H5Dataset

 

toString() - Method in class nz.org.riskscape.hdf5.H5DatasetPath

 

toString() - Method in class nz.org.riskscape.hdf5.H5Group

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5EnumType

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5FloatType

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5StringType

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5Type

 

toString() - Method in class nz.org.riskscape.hdf5.types.H5VlenType

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5ArrayType

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5CompoundType

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5EnumType

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5FloatType

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5IntegerType

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5StringType

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5Type

 

toType() - Method in class nz.org.riskscape.hdf5.types.H5VlenType

 

type - Variable in class nz.org.riskscape.hdf5.cursor.H5DatasetCursor

 

type - Variable in class nz.org.riskscape.hdf5.H5CompoundMember

 

V

validateParameters(Hdf5Resolver.Parameters, BindingContext) - Method in class nz.org.riskscape.hdf5.Hdf5Resolver

 

valueOf(String) - Static method in enum class nz.org.riskscape.hdf5.Hdf5Resolver.DatasetMode

Returns the enum constant of this class with the specified name.

values() - Static method in enum class nz.org.riskscape.hdf5.Hdf5Resolver.DatasetMode

Returns an array containing the constants of this enum class, in the order they are declared.

visit(H5Group, String, Supplier<H5Object>) - Method in interface nz.org.riskscape.hdf5.H5GroupVisitor

 

visit(H5GroupVisitor) - Method in class nz.org.riskscape.hdf5.H5Group

Visit all the child objects (other groups and datasets) of this group using a callback