Serialized Form

Package hdf.object

Class hdf.object.CompoundDS

class CompoundDS extends Dataset implements Serializable

serialVersionUID:

-4880399929644095662L

Serialized Fields

flatNameList

List<String> 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

List<Datatype> flatTypeList

A list of datatypes of all fields including nested fields.

isMemberSelected

boolean[] isMemberSelected

The array to store flags to indicate if a member of this 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.
 

memberNames

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 this compound dataset. 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.

memberTypes

Datatype[] memberTypes

The datatypes of compound members.

numberOfMembers

int numberOfMembers

The number of members of the compound dataset.

Class hdf.object.Dataset

class Dataset extends HObject implements Serializable

serialVersionUID:

-3360885430038261178L

Serialized Fields

chunkSize

long[] chunkSize

The array of dimension sizes for a chunk.

compression

StringBuilder compression

The compression information.

convertByteToString

boolean convertByteToString

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

datatype

Datatype datatype

The datatype object of the dataset.

dimNames

String[] dimNames

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

dims

long[] dims

The current dimension sizes of the dataset

filters

StringBuilder filters

The filters information.

inited

boolean inited

Flag to indicate if this dataset has been initialized

isDataLoaded

boolean isDataLoaded

Flag to indicate if data values are loaded into memory.

isImage

boolean isImage

True if this dataset is an image.

isNULL

boolean isNULL

Flag to indicate if the dataspace is NULL

isScalar

boolean isScalar

Flag to indicate if the data is a single scalar point

isText

boolean isText

True if this dataset is ASCII text.

maxDims

long[] maxDims

The max dimension sizes of the dataset

nPoints

long nPoints

The number of data points in the memory buffer.

rank

int rank

The number of dimensions of the dataset.

selectedDims

long[] selectedDims

Array that contains the number of data points selected (for read/write) in each dimension. The selected 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, if a 4 X 5 dataset is as follows:

     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
 

selectedIndex

int[] selectedIndex

Array that contains the indices of the dimensions selected for display. selectedIndex[] is provided for two purposes:

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 dimension 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 datasets with more than three dimensions, we need selectedIndex[] to store which three dimensions are chosen for display. For example, for a four dimension 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].

space_type

int space_type

The type of space for the dataset.

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.

storage

StringBuilder storage

The storage information.

storageLayout

StringBuilder storageLayout

The storage layout information.

Class hdf.object.Datatype

class Datatype extends HObject implements Serializable

serialVersionUID:

-581324710549963177L

Serialized Fields

arrayDims

long[] arrayDims

The dimensions of the ARRAY element of an ARRAY datatype.

baseType

Datatype baseType

The base datatype of this datatype (null if this datatype is atomic).

compoundMemberNames

List<String> compoundMemberNames

The list of names of members of a compound Datatype.

compoundMemberOffsets

List<Long> compoundMemberOffsets

The list of offsets of members of a compound Datatype.

compoundMemberTypes

List<Datatype> compoundMemberTypes

The list of types of members of a compound Datatype.

datatypeClass

int datatypeClass

The class of the datatype.

datatypeDescription

String datatypeDescription

The description of the datatype.

datatypeNATIVE

boolean datatypeNATIVE

The description 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.

datatypeSize

long datatypeSize

The size (in bytes) of the datatype.

enumMembers

Map<String,String> enumMembers

The (name, value) pairs of enum members.

isNamed

boolean isNamed

Determines whether this datatype is a named datatype

isVariableStr

boolean isVariableStr

Determines whether this datatype is a variable-length string type.

isVLEN

boolean isVLEN

Determines whether this datatype is a variable-length type.

Class hdf.object.FileFormat

class FileFormat extends File implements Serializable

serialVersionUID:

-4700692313888420796L

Serialized Fields

fid

long fid

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

fullFileName

String fullFileName

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

isReadOnly

boolean isReadOnly

Flag indicating if the file access is read-only.

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

The start number for max_members .

Class hdf.object.Group

class Group extends HObject implements Serializable

serialVersionUID:

3913174542591568052L

Serialized Fields

memberList

List<HObject> memberList

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

nMembersInFile

int nMembersInFile

Total number of members of this group in file.

parent

Group parent

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

Class hdf.object.HObject

class HObject extends Object implements Serializable

serialVersionUID:

-1723666708199882519L

Serialized Fields

fileFormat

FileFormat fileFormat

The file which contains the object

filename

String filename

The full path of the file that contains the object.

fullName

String fullName

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

linkTargetObjName

String linkTargetObjName

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

name

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.

oid

long[] oid

Array of long integer storing unique identifier for the object. HDF4 objects are uniquely identified by a (tag_id, ref_id) pair. i.e. oid[0] = tag, oid[1] = ref_id.
HDF5 objects are uniquely identified by a reference. i.e. oid[0...7] = H5R_ref_t.

path

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 be ended with a slash. For example, /arrays/ints/

Class hdf.object.ScalarDS

class ScalarDS extends Dataset implements Serializable

serialVersionUID:

8925371455928203981L

Serialized Fields

fillValue

Object fillValue

The fill value of the dataset.

filteredImageValues

List<Number> filteredImageValues

The list of filtered image values.

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.

interlace

int interlace

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

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.

isImageDisplay

boolean isImageDisplay

Flag to indicate if the dataset is displayed as an image.

isTrueColor

boolean isTrueColor

True if this dataset is a true color image.

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.

unsignedConverted

boolean unsignedConverted

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

Package hdf.object.fits

Class hdf.object.fits.FitsAttribute

class FitsAttribute extends ScalarDS implements Serializable

serialVersionUID:

2072473407027648309L

Serialized Fields

parentObject

HObject parentObject

The HObject to which this NC2Attribute is attached, Attribute interface

Class hdf.object.fits.FitsDataset

class FitsDataset extends ScalarDS implements Serializable

serialVersionUID:

3944770379558335171L

Serialized Fields

attributeList

List attributeList

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

nativeDataset

nom.tam.fits.BasicHDU nativeDataset

the native dataset

Class hdf.object.fits.FitsDatatype

class FitsDatatype extends Datatype implements Serializable

serialVersionUID:

6545936196104493765L

Serialized Fields

nativeType

long nativeType

the native type

Class hdf.object.fits.FitsFile

class FitsFile extends FileFormat implements Serializable

serialVersionUID:

-1965689032980605791L

Serialized Fields

fitsFile

nom.tam.fits.Fits fitsFile

the fits file

rootObject

HObject rootObject

The root object of the file hierarchy.

Class hdf.object.fits.FitsGroup

class FitsGroup extends Group implements Serializable

serialVersionUID:

4993155577664991838L

Serialized Fields

attributeList

List attributeList

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

Package hdf.object.h4

Class hdf.object.h4.H4CompoundAttribute

class H4CompoundAttribute extends CompoundDS implements Serializable

serialVersionUID:

2072473407027648309L

Serialized Fields

parentObject

HObject parentObject

The HObject to which this NC2Attribute is attached, Attribute interface

Class hdf.object.h4.H4Datatype

class H4Datatype extends Datatype implements Serializable

serialVersionUID:

-1342029403385521874L

Class hdf.object.h4.H4File

class H4File extends FileFormat implements Serializable

serialVersionUID:

8985533001471224030L

Serialized Fields

flag

int flag

the file access flag.

grid

long 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

if this is a netcdf file

objList

List objList

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

rootObject

HObject rootObject

The root object of this file.

sdid

long 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

secret flag: show CDF0.0, etc., to help debug

Class hdf.object.h4.H4GRImage

class H4GRImage extends ScalarDS implements Serializable

serialVersionUID:

1029672744963360976L

Serialized Fields

attributeList

List attributeList

The list of attributes of this data object. Members of the list are instance of H4ScalarAttribute.

datatypeID

long datatypeID

the datatype identifier

grid

long grid

The GR interface identifier obtained from GRstart(fid)

nAttributes

int nAttributes

the number of attributes

ncomp

int ncomp

The number of components in the raster image

Class hdf.object.h4.H4Group

class H4Group extends Group implements Serializable

serialVersionUID:

3785240955078867900L

Serialized Fields

attributeList

List attributeList

The list of attributes of this data object. Members of the list are instance of H4ScalarAttribute.

nAttributes

int nAttributes

the number of attributes

Class hdf.object.h4.H4ScalarAttribute

class H4ScalarAttribute extends ScalarDS implements Serializable

serialVersionUID:

2072473407027648309L

Serialized Fields

parentObject

HObject parentObject

The HObject to which this NC2Attribute is attached, Attribute interface

Class hdf.object.h4.H4SDS

class H4SDS extends ScalarDS implements Serializable

serialVersionUID:

2557157923292438696L

Serialized Fields

attributeList

List attributeList

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

datatypeID

long datatypeID

the datatype identifier

nAttributes

int nAttributes

the number of attributes

sdid

long sdid

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

Class hdf.object.h4.H4Vdata

class H4Vdata extends CompoundDS implements Serializable

serialVersionUID:

-5978700886955419959L

Serialized Fields

attributeList

List attributeList

The list of attributes of this data object. Members of the list are instance of H4CompoundAttribute.

memberTIDs

long[] memberTIDs

The data types of the members of the compound dataset.

nAttributes

int nAttributes

the number of attributes

numberOfRecords

int numberOfRecords

Number of records of this Vdata table.

Package hdf.object.h5

Class hdf.object.h5.H5CompoundAttr

class H5CompoundAttr extends CompoundDS implements Serializable

serialVersionUID:

2072473407027648309L

Serialized Fields

parentObject

HObject parentObject

The HObject to which this NC2Attribute is attached, Attribute interface

Class hdf.object.h5.H5CompoundDS

class H5CompoundDS extends CompoundDS implements Serializable

serialVersionUID:

-5968625125574032736L

Serialized Fields

isExternal

boolean isExternal

flag to indicate if the dataset is an external dataset

isVirtual

boolean isVirtual

flag to indicate if the dataset is a virtual dataset

objInfo

hdf.hdf5lib.structs.H5O_info_t objInfo

the object properties

objMetadata

H5MetaDataContainer objMetadata

The metadata object for this data object. Members of the metadata are instances of Attribute.

virtualNameList

List<String> virtualNameList

the list of virtual names

Class hdf.object.h5.H5Datatype

class H5Datatype extends Datatype implements Serializable

serialVersionUID:

-750546422258749792L

Serialized Fields

isRefObj

boolean isRefObj

the datatype is an object reference

isRegRef

boolean isRegRef

the datatype is a region reference

isStdRef

boolean isStdRef

the datatype is a standard reference

nativeClass

int nativeClass

The native class of the datatype.

nativeFPebias

long nativeFPebias

The native ebias properties of the float datatype.

nativeFPepos

long nativeFPepos

The native epos properties of the float datatype.

nativeFPesize

long nativeFPesize

The native esize properties of the float datatype.

nativeFPinpad

int nativeFPinpad

The native inpad properties of the float datatype.

nativeFPmpos

long nativeFPmpos

The native mpos properties of the float datatype.

nativeFPmsize

long nativeFPmsize

The native msize properties of the float datatype.

nativeFPnorm

int nativeFPnorm

The native norm properties of the float datatype.

nativeFPspos

long nativeFPspos

The native spos properties of the float datatype.

nativeOffset

int nativeOffset

The native Offset properties of the number datatype.

nativePadLSB

int nativePadLSB

The native PadLSB properties of the number datatype.

nativePadMSB

int nativePadMSB

The native PadMSB properties of the number datatype.

nativePrecision

long nativePrecision

The native Precision properties of the number datatype.

nativeStrCSET

int nativeStrCSET

The native CSET properties of the string datatype.

nativeStrPad

int nativeStrPad

The native padding properties of the string datatype.

objInfo

hdf.hdf5lib.structs.H5O_info_t objInfo

the object properties

objMetadata

H5MetaDataContainer objMetadata

The metadata object for this data object. Members of the metadata are instances of Attribute.

opaqueTag

String opaqueTag

The tag for an opaque datatype.

refdims

long[] refdims

The dimension sizes of the reference object

Class hdf.object.h5.H5File

class 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_SWMR_READ (with H5F_ACC_RDONLY) HDF5Constants.H5F_ACC_RDWR HDF5Constants.H5F_ACC_CREAT

indexOrder

int indexOrder

The index order. Valid values are HDF5Constants.H5_ITER_INC, HDF5Constants.H5_ITER_DEC.

indexType

int indexType

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

libver

int[] libver

The library version bounds

rootObject

HObject rootObject

The root object of the file hierarchy.

Class hdf.object.h5.H5Group

class H5Group extends Group implements Serializable

serialVersionUID:

-951164512330444150L

Serialized Fields

objInfo

hdf.hdf5lib.structs.H5O_info_t objInfo

the object properties

objMetadata

H5MetaDataContainer objMetadata

The metadata object for this data object. Members of the metadata are instances of Attribute.

Class hdf.object.h5.H5Link

class H5Link extends HObject implements Serializable

serialVersionUID:

-8137277460521594367L

Serialized Fields

objInfo

hdf.hdf5lib.structs.H5O_info_t objInfo

the object properties

Class hdf.object.h5.H5MetaDataContainer

class H5MetaDataContainer extends HObject implements Serializable

Serialized Fields

attributeList

List attributeList

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

nAttributes

int nAttributes

the number of attributes

parentObject

HObject parentObject

The HObject to which this MetaDataContainer is attached

Class hdf.object.h5.H5ReferenceType

class H5ReferenceType extends H5Datatype implements Serializable

serialVersionUID:

-3360885430038261178L

Serialized Fields

inited

boolean inited

Flag to indicate if this dataset has been initialized

isDataLoaded

boolean isDataLoaded

Flag to indicate if data values are loaded into memory.

refsize

long refsize

The current array size of the reference.

Class hdf.object.h5.H5ScalarAttr

class H5ScalarAttr extends ScalarDS implements Serializable

serialVersionUID:

2072473407027648309L

Serialized Fields

isNativeDatatype

boolean isNativeDatatype

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

parentObject

HObject parentObject

The HObject to which this NC2Attribute is attached, Attribute interface

Class hdf.object.h5.H5ScalarDS

class H5ScalarDS extends ScalarDS implements Serializable

serialVersionUID:

2887517608230611642L

Serialized Fields

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

isVirtual

boolean isVirtual

flag to indicate if the dataset is a virtual dataset

NumberOfPalettes

int NumberOfPalettes

the number of palettes

objInfo

hdf.hdf5lib.structs.H5O_info_t objInfo

the object properties

objMetadata

H5MetaDataContainer objMetadata

The metadata object for this data object. Members of the metadata are instances of Attribute.

refresh

boolean refresh

flag to indicate if the dataset buffers should be refreshed.

virtualNameList

List<String> virtualNameList

the list of virtual names

Package hdf.object.nc2

Class hdf.object.nc2.NC2Attribute

class NC2Attribute extends ScalarDS implements Serializable

serialVersionUID:

2072473407027648309L

Serialized Fields

parentObject

HObject parentObject

The HObject to which this NC2Attribute is attached, Attribute interface

Class hdf.object.nc2.NC2Dataset

class NC2Dataset extends ScalarDS implements Serializable

serialVersionUID:

-6031051694304457461L

Serialized Fields

attributeList

List attributeList

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

nativeDataset

ucar.nc2.Variable nativeDataset

the native dataset

Class hdf.object.nc2.NC2Datatype

class NC2Datatype extends Datatype implements Serializable

serialVersionUID:

5399364372073889764L

Serialized Fields

nativeType

ucar.ma2.DataType nativeType

the native datatype

Class hdf.object.nc2.NC2File

class NC2File extends FileFormat implements Serializable

serialVersionUID:

6941235662108358451L

Serialized Fields

ncFile

ucar.nc2.NetcdfFile ncFile

the netcdf file

objList

List objList

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

rootObject

HObject rootObject

The root object of this file.

Class hdf.object.nc2.NC2Group

class NC2Group extends Group implements Serializable

serialVersionUID:

-1261533010442193447L

Serialized Fields

attributeList

List attributeList

The list of attributes of this data object. Members of the list are instance of NC2Attribute.

netcdfAttributeList

List netcdfAttributeList

The list of netcdf attributes of this data object. Members of the list are * instance of ucar.nc2.*.

netcdfDimensionList

List netcdfDimensionList

The list of netcdf dimensions of this data object. Members of the list are instance of ucar.nc2.*.

netCDFGroup

ucar.nc2.Group netCDFGroup

The corresponding netcdf Group for this group.

netcdfTypedefList

List netcdfTypedefList

The list of netcdf typedefs of this data object. Members of the list are instance of ucar.nc2.*.