Serialized Form


Package ncsa.hdf.hdf5lib

Class ncsa.hdf.hdf5lib.H5 extends java.lang.Object implements Serializable

serialVersionUID: 6129888282117053288L


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

serialVersionUID: -142238015615462707L

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

serialVersionUID: 2791443594041667613L

Serialized Fields

corder_valid

boolean corder_valid

corder

long corder

cset

int cset

data_size

long data_size

Class ncsa.hdf.hdf5lib.structs.H5AC_cache_config_t extends java.lang.Object implements Serializable

serialVersionUID: -6748085696476149972L

Serialized Fields

version

int version

rpt_fcn_enabled

boolean rpt_fcn_enabled

open_trace_file

boolean open_trace_file

close_trace_file

boolean close_trace_file

trace_file_name

java.lang.String trace_file_name

evictions_enabled

boolean evictions_enabled

set_initial_size

boolean set_initial_size

initial_size

long initial_size

min_clean_fraction

double min_clean_fraction

max_size

long max_size

min_size

long min_size

epoch_length

long epoch_length

incr_mode

int incr_mode

lower_hr_threshold

double lower_hr_threshold

increment

double increment

apply_max_increment

boolean apply_max_increment

max_increment

long max_increment

flash_incr_mode

int flash_incr_mode

flash_multiple

double flash_multiple

flash_threshold

double flash_threshold

decr_mode

int decr_mode

upper_hr_threshold

double upper_hr_threshold

decrement

double decrement

apply_max_decrement

boolean apply_max_decrement

max_decrement

long max_decrement

epochs_before_eviction

int epochs_before_eviction

apply_empty_reserve

boolean apply_empty_reserve

empty_reserve

double empty_reserve

dirty_bytes_threshold

int dirty_bytes_threshold

metadata_write_strategy

int metadata_write_strategy

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

serialVersionUID: -3746463015312132912L

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

serialVersionUID: -4754320605310155033L

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

serialVersionUID: 7883826382952577189L

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

serialVersionUID: 4691681163544054518L

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.HDFDeprecated extends HDFLibrary implements Serializable

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.HDFLibrary extends java.lang.Object implements Serializable

serialVersionUID: -1695429510319126910L

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: 2072473407027648309L

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.


isScalar

boolean isScalar
flag to indicate if the dataset is a single scalar point

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

serialVersionUID: -4880399929644095662L

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

serialVersionUID: -3360885430038261178L

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

serialVersionUID: -581324710549963177L

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

serialVersionUID: -4700692313888420796L

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: 3913174542591568052L

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: -1723666708199882519L

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

serialVersionUID: 8925371455928203981L

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: -1342029403385521874L

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

serialVersionUID: 8985533001471224030L

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: 1029672744963360976L

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: 3785240955078867900L

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: 2557157923292438696L

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: -5978700886955419959L

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: -5968625125574032736L

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: -750546422258749792L

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: 6247335559471526045L

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: -951164512330444150L

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: -8137277460521594367L

Serialized Fields

obj_info

H5O_info_t obj_info

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

serialVersionUID: 2887517608230611642L

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


isArrayOfCompound

boolean isArrayOfCompound

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