HDF5 Abstract Data Model

1
HDF5 Abstract Data Model

• Classes, Objects and their relationships
• http//hdf.ncsa.uiuc.edu/HDF5/ADM_EOS_Sep99/index.
  htm

2
Outline

• Motivation and goals
• Overview of HDF5 file structure and HDF5 objects
• UML notation
• Formal description of HDF5 file, HDF5 objects and
  operations in UML

3
Motivation and Goals

• Need a formal description of HDF5 file and
  library
• Need an HDF5 abstract data model (ADM) for high
  level C, F90, Java, Ada(?) APIs
• Attempt to look at HDF5 ADM from OO point of view
  
• HDF group does not have experience in OO design
  and languages
• Universal Modeling Language (UML) has been chosen
  to document current HDF5 ADM and HDF5 Library
• Suggestions and help from HDF5 OO users is
  WELCOME!

4
HDF5 File (conceptual view)

• Container for storing scientific data
• Primary Objects
• Groups
• Datasets
• Secondary Objects
• Datatypes
• Dataspaces
• Additional means to organize data
• Attributes
• Sharable objects
• Storage and access properties

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Example of an HDF5 File
Dataset path /B /C/D/G
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Example of an HDF5 File (cont.)
/
RGroup
B
C
F
Group
Dataset
Datatype
D
G
Group
K
Dataset path /B /C/D/G
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Example of an HDF5 File (cont.)
/
File
RGroup
B
C
F
Group
Dataset
Datatype
D
Group
K
Dataset path /B
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HDF5 File (logical view)

• Directed graph with an entry point (root group)
• nodes are HDF5 objects
• Group, Dataset, Dataspace, Datatype
• each object may have more than one path to it
• edges are inclusion directions (HDF5 links)
• graph may have
• loops
• isolated nodes
• dangling edges

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UML Notation Book
UML Distilled Applying the
Standard Object Modeling Language
by Martin Fowler
Booch Jacobson Rumbaugh Object Technology
Series
Addison-Wesley
10
UML Notation
Class
Class Name ____________ Attribute __________
__ Operation
Class Name
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UML Notation

Association Describes connection
between object instances, should be a verb.

Object A has object B associated with it.
Class A
Class B
Multiplicity of Association Object A
has zero or more objects B associated with it.
Object B belongs to at least one and up to N
objects A
Class A
Class B
1..N
0...
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UML Notation
Generalization(Inheritance)
is a relationship
B is an A
Class A
Class B
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UML Notation
Aggregation
a part of relationship Objects B
and C are part of object A
Class A
Class B
Class C
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UML Notation
Composition
a part of relationship Objects B
and C live and die with A
Class A
Class B
Class C
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HDF5 Classes

• Named_Object Class
• Group
• Dataset
• Named Dataspace
• Named Datatype
• User_Defined_Attribute Class

• File Class
• Group Class
• Dataset Class
• Dataspace Class
• Datatype Class

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HDF5 Classes

• Property List Class
• File Property List
• Creation Property List
• Access Property List
• Dataset Property List
• Transfer Property List
• Storage property List

• Link Class
• Root Link
• Non-Root Link
• Soft Link
• Hard Link

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File Class File , Group Class and Root Link
Class Association Diagram
1
1
File Class
Group Class
1
0
1
1
Root Link Class
File Property List Class
File is a composition of a Group. Root Link is
created when File is created. Root Link points
to the Group which is called Root Group. Root
Group is automatically created/opened/closed
when File is created/opened/closed.
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File and Group Classes
File Class _______________________________________
________ open/close create is_hdf5 get_create_prp
get_access_prp mount/unmount reopen
Group Class _____________________ ________________
_____ open/close iterate get_object_info get_link
_value get/set_comment
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Group Class and Associated Classes
Group
Group Class
1
C
0
Non-Root Link Class
1
D
A
B
01
...
HDF5 object
HDF5 object
Named Object Class
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Link Class
Link Class
Non-Root Link Class
Root Link Class
Hard Link
Soft Link
0...
1...
0...1
1
Named Object
Named Object
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Non-Root Link Class
Non-Root Link Class ____________________________ n
ame ______________________ link/unlink create move
(rename)
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Named_Object Class
Named Datatype Class
Group Class
Dataset Class
Named Dataspace Class
Named_Object Class
1
0...1
1
0
0
1...
User Defined Attribute
Hard Link Class
Soft Link Class
Not implemented yet
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Dataset Class and associated Classes
0...
1
0...
0...
1
1
0...
1
1
1
1...
0
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Dataset Class
Dataset Class ________________________ u
ser defined attribute ________________________ cre
ate open/close write/read extend get_space/type/pr
operty
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Attribute Class and associated Classes
Named Object Class
1
0...
Attribute Class
0...
0...
1
1
Dataspace Class
Datatype Class
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Attribute Class
Attribute Class ________________________
_ name _____________________ create open/close wri
te/read get_space/type/property
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Property List Class and Subclasses
Property List
File Property List
Dataset Property List
Transfer PList
Storage PList
Access PList
Creation PList
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Dataspace Class
Dataspace Class
Hard Link
0
1
Transient Dataspace Class
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Dataspace Class
Dataspace Class _______________________________ ra
nk current_size maximum_size _____________________
__________ create/create_simple open/close/lock is
_simple copy extent_class extent_copy set_extent_s
imple set_extent_none get_simple_extent_npoints/nd
ims/dims
Dataspace Extent
General operations
Extent operations
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Transient Dataspace Class
Dataspace Class ______________ selection _________
_____ select_elements select_none select_hyperslab
select_valid offset_simple ...
Dataspace Selection
Set and modify selections
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Datatype Class and Subclasses
Datatype Class
Compound
Enumeration
Atomic
Variable Length
Array
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Datatype Class
Datatype Class ______________ ______________ copy
equal close convert get_class get_size
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Atomic Datatype Class and Subclasses
Atomic Datatype Class
Predefined Atomic
Userdefined Atomic
H5Tcopy
1
0
Link Class
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Predefined Atomic Datatype Class
Predefined Atomic Datatype Class
String
Time
Integer
Float
Opaque
Reference
Bitfield
Object Reference
Region Reference
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Examples of Predefined Atomic Datatype
Predefined Atomic Datatype _______________________
name H5T_arch_base _______________________
H5T_IEEE_F64LE Eight-byte little-endian, IEEE
floating-point H5T_STD_U16BE Two-byte
big-endian, unsigned integer H5T_C_S1
One-byte null-terminated string of eight-bit

characters H5T_CRAY_F64 Eight-byte Cray
floating point H5T_STD_ROBJ Reference
to entire object in a file H5T_NATIVE_LONG long
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Compound Datatype Class
Compound Datatype Class
typedef struct int a float b
my_type c10 compound_t
1
Datatype Class
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Enumeration Datatype Class
Enumeration Datatype
1
Datatype Class
1
RED 0 GREEN 1 BLUE 2
( string, value of type Datatype )

Only Integer datatype for now
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Variable Length Datatype Class
Variable Length Datatype Class
1
Datatype Class
1
2
3
4
5
A
C
RED
GREEN
BLUE
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Reading Dataset into Memory from File

File
Memory
2D array of integers
3D array of floats
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Reading Dataset into Memory from File

Memory
2D array with selected rectangle
I/O hint
floats
3D array with selected union of cubes