Serialized Form

Package ncsa.hdf.hdf5lib.exceptions

Class ncsa.hdf.hdf5lib.exceptions.HDF5AtomException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5AttributeException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5BtreeException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DataFiltersException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DatasetInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DataspaceInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DataStorageException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5Exception extends java.lang.Exception implements Serializable

Serialized Fields

detailMessage

java.lang.String detailMessage

Class ncsa.hdf.hdf5lib.exceptions.HDF5ExternalFileListException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5FileInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5FunctionArgumentException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5FunctionEntryExitException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5HeapException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5InternalErrorException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5JavaException extends HDF5Exception implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException extends HDF5Exception implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5LowLevelIOException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5MetaDataCacheException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5ObjectHeaderException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5PropertyListInterfaceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5ReferenceException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5ResourceUnavailableException extends HDF5LibraryException implements Serializable

Class ncsa.hdf.hdf5lib.exceptions.HDF5SymbolTableException extends HDF5LibraryException implements Serializable

Package ncsa.hdf.hdf5lib.structs

Class ncsa.hdf.hdf5lib.structs.H5_ih_info_t extends java.lang.Object implements Serializable

Serialized Fields

index_size

long index_size

heap_size

long heap_size

Class ncsa.hdf.hdf5lib.structs.H5A_info_t extends java.lang.Object implements Serializable

Serialized Fields

corder_valid

boolean corder_valid

corder

long corder

cset

int cset

data_size

long data_size

Class ncsa.hdf.hdf5lib.structs.H5G_info_t extends java.lang.Object implements Serializable

Serialized Fields

storage_type

int storage_type

nlinks

long nlinks

max_corder

long max_corder

mounted

boolean mounted

Class ncsa.hdf.hdf5lib.structs.H5L_info_t extends java.lang.Object implements Serializable

Serialized Fields

type

int type

corder_valid

boolean corder_valid

corder

long corder

cset

int cset

address_val_size

long address_val_size

Class ncsa.hdf.hdf5lib.structs.H5O_hdr_info_t extends java.lang.Object implements Serializable

Serialized Fields

version

int version

nmesgs

int nmesgs

nchunks

int nchunks

flags

int flags

space_total

long space_total

space_meta

long space_meta

space_mesg

long space_mesg

space_free

long space_free

mesg_present

long mesg_present

mesg_shared

long mesg_shared

Class ncsa.hdf.hdf5lib.structs.H5O_info_t extends java.lang.Object implements Serializable

Serialized Fields

fileno

long fileno

addr

long addr

type

int type

rc

int rc

atime

long atime

mtime

long mtime

ctime

long ctime

btime

long btime

num_attrs

long num_attrs

hdr

H5O_hdr_info_t hdr

meta_size_obj

H5_ih_info_t meta_size_obj

meta_size_attr

H5_ih_info_t meta_size_attr

Package ncsa.hdf.hdflib

Class ncsa.hdf.hdflib.HDFException extends java.lang.Exception implements Serializable

Serialized Fields

HDFerror

int HDFerror

msg

java.lang.String msg

Class ncsa.hdf.hdflib.HDFJavaException extends HDFException implements Serializable

Serialized Fields

msg

java.lang.String msg

Class ncsa.hdf.hdflib.HDFLibraryException extends HDFException implements Serializable

Serialized Fields

HDFerror

int HDFerror

msg

java.lang.String msg

Class ncsa.hdf.hdflib.HDFNotImplementedException extends HDFJavaException implements Serializable

Serialized Fields

msg

java.lang.String msg

Package ncsa.hdf.object

Class ncsa.hdf.object.Attribute extends java.lang.Object implements Serializable

serialVersionUID: 240L

Serialized Fields

name

java.lang.String name

The name of the attribute.

type

Datatype type

The datatype of the attribute.

rank

int rank

The rank of the data value of the attribute.

dims

long[] dims

The dimension sizes of the attribute.

value

java.lang.Object value

The value of the attribute.

isUnsigned

boolean isUnsigned

Flag to indicate if the datatype is an unsigned integer.

Class ncsa.hdf.object.CompoundDS extends Dataset implements Serializable

Serialized Fields

numberOfMembers

int numberOfMembers

The number of members of the compound dataset.

memberNames

java.lang.String[] memberNames

The names of members of the compound dataset.

memberOrders

int[] memberOrders

Returns array containing the total number of elements of the members of compound.

For example, a compound dataset COMP has members of A, B and C as

     COMP {
         int A;
         float B[5];
         double C[2][3];
     }
 

memberOrders is an integer array of {1, 5, 6} to indicate that member A has one element, member B has 5 elements, and member C has 6 elements.

memberDims

java.lang.Object[] memberDims

The dimension sizes of each member.

The i-th element of the Object[] is an integer array (int[]) that contains the dimension sizes of the i-th member.

memberTypes

Datatype[] memberTypes

The datatypes of compound members.

isMemberSelected

boolean[] isMemberSelected

The array to store flags to indicate if a member of compound dataset is selected for read/write.

If a member is selected, the read/write will perform on the member. Applications such as HDFView will only display the selected members of the compound dataset.

 For example, if a compound dataset has four members
     String[] memberNames = {"X", "Y", "Z", "TIME"};
 and
     boolean[] isMemberSelected = {true, false, false, true};
 members "X" and "TIME" are selected for read and write.
 

Class ncsa.hdf.object.Dataset extends HObject implements Serializable

Serialized Fields

data

java.lang.Object data

The memory buffer that holds the raw data of the dataset.

rank

int rank

The number of dimensions of the dataset.

dims

long[] dims

The current dimension sizes of the dataset

maxDims

long[] maxDims

The max dimension sizes of the dataset

selectedDims

long[] selectedDims

Array that contains the number of data points selected (for read/write) in each dimension.

The select size must be less than or equal to the current dimension size. A subset of a rectangle selection is defined by the starting position and selected sizes.

For example, a 4 X 5 dataset

     0,  1,  2,  3,  4
    10, 11, 12, 13, 14
    20, 21, 22, 23, 24
    30, 31, 32, 33, 34
 long[] dims = {4, 5};
 long[] startDims = {1, 2};
 long[] selectedDims = {3, 3};
 then the following subset is selected by the startDims and selectedDims above
     12, 13, 14
     22, 23, 24
 32, 33, 34

startDims

long[] startDims

The starting position of each dimension of a selected subset. With both the starting position and selected sizes, the subset of a rectangle selection is fully defined.

selectedIndex

int[] selectedIndex

Array that contains the indices of the dimensions selected for display.

selectedIndex[] is provied for two purpose:

1. selectedIndex[] is used to indicate the order of dimensions for display, i.e. selectedIndex[0] = row, selectedIndex[1] = column and selectedIndex[2] = depth. For example, for a four dimesion dataset, if selectedIndex[] is {1, 2, 3}, then dim[1] is selected as row index, dim[2] is selected as column index and dim[3] is selected as depth index.
2. selectedIndex[] is also used to select dimensions for display for datasets with three or more dimensions. We assume that applications such as HDFView can only display data up to three dimensions (a 2D spreadsheet/image with a third dimension that the 2D spreadsheet/image is cut from). For dataset with more than three dimensions, we need selectedIndex[] to store which three dimensions are chosen for display. For example, for a four dimesion dataset, if selectedIndex[] = {1, 2, 3}, then dim[1] is selected as row index, dim[2] is selected as column index and dim[3] is selected as depth index. dim[0] is not selected. Its location is fixed at 0 by default.

selectedStride

long[] selectedStride

The number of elements to move from the start location in each dimension. For example, if selectedStride[0] = 2, every other data point is selected along dim[0].

chunkSize

long[] chunkSize

The array of dimension sizes for a chunk.

compression

java.lang.String compression

The GZIP compression level.

datatype

Datatype datatype

The datatype object of the dataset.

dimNames

java.lang.String[] dimNames

Array of strings that represent the dimension names. It is null if dimension names do not exist.

convertByteToString

boolean convertByteToString

Flag to indicate if the byte[] array is converted to strings

isDataLoaded

boolean isDataLoaded

Flag to indicate if data values are loaded into memory.

nPoints

long nPoints

The number of data points in the memory buffer.

originalBuf

java.lang.Object originalBuf

The data buffer that contains the raw data directly reading from file (before any data conversion).

convertedBuf

java.lang.Object convertedBuf

The array that holds the converted data of unsigned C-type integers.

For example, Suppose that the original data is an array of unsigned 16-bit short integers. Since Java does not support unsigned integer, the data is converted to an array of 32-bit singed integer. In that case, the converted buffer is the array of 32-bit singed integer.

enumConverted

boolean enumConverted

Flag to indicate if the enum data is converted to strings.

Class ncsa.hdf.object.Datatype extends HObject implements Serializable

Serialized Fields

datatypeClass

int datatypeClass

The class of the datatype.

datatypeSize

int datatypeSize

The size (in bytes) of the datatype.

datatypeOrder

int datatypeOrder

The byte order of the datatype. Valid values are ORDER_LE, ORDER_BE, and ORDER_VAX.

datatypeSign

int datatypeSign

The sign of the datatype.

enumMembers

java.lang.String enumMembers

The (name, value) pairs of enum members

baseType

Datatype baseType

The base datatype of every element of the array (for CLASS_ARRAY datatype).

dims

long[] dims

Class ncsa.hdf.object.FileFormat extends java.io.File implements Serializable

Serialized Fields

max_members

int max_members

Current Java applications, such as HDFView, cannot handle files with large numbers of objects due to JVM memory limitations. For example, 1,000,000 objects is too many. max_members is defined so that applications such as HDFView will load up to max_members objects starting with the start_members -th object. The implementing class has freedom in its interpretation of how to "count" objects in the file.

start_members

int start_members

fid

int fid

File identifier. -1 indicates the file is not open.

fullFileName

java.lang.String fullFileName

The absolute pathname (path+name) of the file.

isReadOnly

boolean isReadOnly

Flag indicating if the file access is read-only.

Class ncsa.hdf.object.Group extends HObject implements Serializable

serialVersionUID: 1L

Serialized Fields

memberList

java.util.List<E> memberList

The list of members (Groups and Datasets) of this group in memory.

parent

Group parent

The parent group where this group is located. The parent of the root group is null.

nMembersInFile

int nMembersInFile

Total number of (Groups and Datasets) of this group in file.

Class ncsa.hdf.object.HObject extends java.lang.Object implements Serializable

serialVersionUID: 240L

Serialized Fields

filename

java.lang.String filename

The full path of the file that contains the object.

fileFormat

FileFormat fileFormat

The file which contains the object

name

java.lang.String name

The name of the data object. The root group has its default name, a slash. The name can be changed except the root group.

path

java.lang.String path

The full path of the data object. The full path always starts with the root, a slash. The path cannot be changed. Also, a path must ended with a slash. For example, /arrays/ints/

fullName

java.lang.String fullName

The full name of the data object, i.e. "path + name"

oid

long[] oid

Array of long integer storing unique identifier for the object.

HDF4 objects are uniquely identified by a (ref_id, tag_id) pair. i.e. oid[0]=tag, oid[1]=ref.
HDF5 objects are uniquely identified by an object reference.

linkTargetObjName

java.lang.String linkTargetObjName

The name of the Target Object that is being linked to.

Class ncsa.hdf.object.ScalarDS extends Dataset implements Serializable

Serialized Fields

interlace

int interlace

The interlace mode of the stored raster image data. Valid values are INTERLACE_PIXEL, INTERLACE_LINE and INTERLACE_PLANE.

imageDataRange

double[] imageDataRange

The min-max range of image data values. For example, [0, 255] indicates the min is 0, and the max is 255.

palette

byte[][] palette

The indexed RGB color model with 256 colors.

The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.

isImage

boolean isImage

True if this dataset is an image.

isTrueColor

boolean isTrueColor

True if this dataset is a true color image.

isText

boolean isText

True if this dataset is ASCII text.

isUnsigned

boolean isUnsigned

Flag to indicate if the original C data is unsigned integer.

unsignedConverted

boolean unsignedConverted

Flag to indicate is the original unsigned C data is converted.

fillValue

java.lang.Object fillValue

The fill value of the dataset.

isImageDisplay

boolean isImageDisplay

Flag to indicate if the dataset is displayed as an image

isDefaultImageOrder

boolean isDefaultImageOrder

Flag to indicate if the dataset is displayed as an image with default order of dimensions

isFillValueConverted

boolean isFillValueConverted

Flag to indicate if the FillValue is converted from unsigned C.

Package ncsa.hdf.object.h4

Class ncsa.hdf.object.h4.H4Datatype extends Datatype implements Serializable

serialVersionUID: 240L

Class ncsa.hdf.object.h4.H4File extends FileFormat implements Serializable

serialVersionUID: 240L

Serialized Fields

flag

int flag

the file access flag.

rootNode

javax.swing.tree.DefaultMutableTreeNode rootNode

The root node of the tree structure of this file.

objList

java.util.List<E> objList

The list of unique (tag, ref) pairs. It is used to avoid duplicate objects in memory.

grid

int grid

The GR interface identifier. The identifier is returned by GRstart(fid), which initializes the GR interface for the file specified by the parameter. GRstart(fid) is an expensive call. It should be called only once. Calling GRstart(fid) in a loop should be avoided.

isNetCDF

boolean isNetCDF

sdid

int sdid

The SDS interface identifier. The identifier is returned by SDstart(fname, flag), which initializes the SD interface for the file specified by the parameter. SDstart(fname, flag) is an expensive call. It should be called only once Calling SDstart(fname, flag) in a loop should be avoided.

showAll

boolean showAll

Class ncsa.hdf.object.h4.H4GRImage extends ScalarDS implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes of this data object. Members of the list are instance of Attribute.

grid

int grid

The GR interface identifier obtained from GRstart(fid)

ncomp

int ncomp

The number of components in the raster image

datatypeID

int datatypeID

the datatype identifier

nAttributes

int nAttributes

Class ncsa.hdf.object.h4.H4Group extends Group implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes of this data object. Members of the list are instance of Attribute.

nAttributes

int nAttributes

Class ncsa.hdf.object.h4.H4SDS extends ScalarDS implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes of this data object. Members of the list are instance of Attribute.

sdid

int sdid

The SDS interface identifier obtained from SDstart(filename, access)

datatypeID

int datatypeID

the datatype identifier

nAttributes

int nAttributes

Class ncsa.hdf.object.h4.H4Vdata extends CompoundDS implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes of this data object. Members of the list are instance of Attribute.

numberOfRecords

int numberOfRecords

Number of records of this Vdata table.

memberTIDs

int[] memberTIDs

The data types of the members of the compound dataset.

nAttributes

int nAttributes

Package ncsa.hdf.object.h5

Class ncsa.hdf.object.h5.H5CompoundDS extends CompoundDS implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes attached data object.

nAttributes

int nAttributes

obj_info

H5O_info_t obj_info

flatNameList

java.util.List<E> flatNameList

A list of names of all fields including nested fields.

The nested names are separated by CompoundDs.separator. For example, if compound dataset "A" has the following nested structure,

 A --> m01
 A --> m02
 A --> nest1 --> m11
 A --> nest1 --> m12
 A --> nest1 --> nest2 --> m21
 A --> nest1 --> nest2 --> m22
 i.e.
 A = { m01, m02, nest1{m11, m12, nest2{ m21, m22}}}
 

The flatNameList of compound dataset "A" will be {m01, m02, nest1[m11, nest1[m12, nest1[nest2[m21, nest1[nest2[m22}

flatTypeList

java.util.List<E> flatTypeList

A list of datatypes of all fields including nested fields.

isExternal

boolean isExternal

flag to indicate is the dataset is an external dataset

Class ncsa.hdf.object.h5.H5Datatype extends Datatype implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes of this data object.

isNamed

boolean isNamed

Flag to indicate if this datatype is a named datatype

nAttributes

int nAttributes

obj_info

H5O_info_t obj_info

isVLEN

boolean isVLEN

description

java.lang.String description

Class ncsa.hdf.object.h5.H5File extends FileFormat implements Serializable

serialVersionUID: 240L

Serialized Fields

flag

int flag

the file access flag. Valid values are HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5F_ACC_RDWR and HDF5Constants.H5F_ACC_CREAT.

indexType

int indexType

The index type. Valid values are HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_INDEX_CRT_ORDER.

rootNode

javax.swing.tree.DefaultMutableTreeNode rootNode

The root node of the file hierarchy.

libver

int[] libver

The library version bounds

attrFlag

boolean attrFlag

Class ncsa.hdf.object.h5.H5Group extends Group implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes of this data object. Members of the list are instance of Attribute.

nAttributes

int nAttributes

obj_info

H5O_info_t obj_info

Class ncsa.hdf.object.h5.H5Link extends HObject implements Serializable

serialVersionUID: 240L

Serialized Fields

obj_info

H5O_info_t obj_info

Class ncsa.hdf.object.h5.H5ScalarDS extends ScalarDS implements Serializable

serialVersionUID: 240L

Serialized Fields

attributeList

java.util.List<E> attributeList

The list of attributes of this data object. Members of the list are instance of Attribute.

paletteRefs

byte[] paletteRefs

The byte array containing references of palettes. Each reference requires eight bytes storage. Therefore, the array length is 8*numberOfPalettes.

isVLEN

boolean isVLEN

flag to indicate if the dataset is a variable length

isEnum

boolean isEnum

flag to indicate if the dataset is enum

isExternal

boolean isExternal

flag to indicate if the dataset is an external dataset

isNativeDatatype

boolean isNativeDatatype

flag to indicate if the datatype in file is the same as dataype in memory

isRegRef

boolean isRegRef

flag to indicate is the datatype is reg. ref.

nAttributes

int nAttributes

obj_info

H5O_info_t obj_info