Source: http://hdfeos.org/workshops/ws03/presentations/elena.ppt

1. HDF5 Abstract Data Model
Classes, Objects and their relationships
http://hdf.ncsa.uiuc.edu/HDF5/ADM_EOS_Sep99/index.htm
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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
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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!
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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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5. Example of an HDF5 File
/
File
RGroup
B
A
C
F
Datatype
Group
Dataset
H
D
G
Group
E
Dataset
K
Dataset path : /B /C/D/G
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6. Example of an HDF5 File (cont.)
/
File
RGroup
B
A
C
F
Datatype
Group
Dataset
H
D
G
Group
E
Dataset
K
Dataset path : /B /C/D/G
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7. Example of an HDF5 File (cont.)
File
/
RGroup
B
C
F
Datatype
Group
Dataset
D
Group
K
Dataset path : /B
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8. 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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9. UML Notation
Book:
UML Distilled
Applying the Standard Object Modeling Language
by Martin Fowler
Booch Jacobson Rumbaugh Object Technology Series
Addison-Wesley
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10. UML Notation
Class
Class Name
Class Name
____________
Attribute
____________
Operation
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11. 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
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1..N
0...*
Class B
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12. UML Notation
Generalization(Inheritance)
“is a” relationship
B is an A
Class A
Class B
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13. UML Notation
Aggregation
“a part of” relationship
Objects B and C are part of object A
Class A
Class B
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Class C
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14. UML Notation
Composition
“a part of” relationship
Objects B and C “live and die” with A
Class A
Class B
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Class C
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15. HDF5 Classes
–
–
–
–
–
File Class
Group Class
Dataset Class
Dataspace Class
Datatype Class
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– Named_Object Class
• Group
• Dataset
• Named Dataspace
• Named Datatype
– User_Defined_Attribute Class
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16. HDF5 Classes
– Link Class
• Root Link
• Non-Root Link
– Soft Link
– Hard Link
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– Property List Class
• File Property List
– Creation Property List
– Access Property List
• Dataset Property List
– Transfer Property List
– Storage property List
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17. File Class File , Group Class and Root Link Class
Association Diagram
File Class
1
1
Group Class
0…*
1
1
1
File Property List Class
Root Link 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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18. File and Group Classes
File Class
_______________________
_______________________
_
open/close
create
is_hdf5
get_create_prp
get_access_prp
mount/unmount
reopen
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Group Class
_____________________
_____________________
open/close
iterate
get_object_info
get_link_value
get/set_comment
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19. Group Class and Associated Classes
Group
Group Class
1
C
0…*
Non-Root Link
Class
1…*
A
D
B
0…1
Named Object Class
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... HDF5 object
HDF5 object
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20. Link Class
Link Class
Root Link Class
Non-Root Link Class
Hard Link
Soft Link
0...*
1...*
0...1
1
Named Object
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Named Object
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21. Non-Root Link Class
Non-Root Link Class
____________________________
name
______________________
link/unlink
create
move (rename)
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22. Named_Object Class
Group Class
Dataset Class
Named Datatype Class
Named Dataspace Class
Named_Object Class
0...1
1
1
0…*
1...*
0…*
Soft Link Class
Hard Link Class
User Defined Attribute
Not implemented yet
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23. Dataset Class and associated Classes
User Defined Attribute
0...*
0...*
Datatype
1
0…*
Soft Link
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1
Dataset
1
1
0...*
1...*
Hard Link
0...*
1
Dataspace
1
Storage Property List
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24. Dataset Class
Dataset Class
________________________
user defined attribute
________________________
create
open/close
write/read
extend
get_space/type/property
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25. Attribute Class and associated Classes
Named Object Class
1
0...*
Attribute Class
0...*
0...*
1
1
Datatype Class
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Dataspace Class
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26. Attribute Class
Attribute Class
_________________________
name
_____________________
create
open/close
write/read
get_space/type/property
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27. Property List Class and Subclasses
Property List
File Property List
Creation PList
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Access PList
Dataset Property List
Transfer PList
Storage PList
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28. Dataspace Class
Hard Link
0…*
1
Dataspace Class
Transient Dataspace Class
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29. Dataspace Class
Dataspace Extent
General operations
Extent operations
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Dataspace Class
_______________________________
rank
current_size
maximum_size
_______________________________
create/create_simple
open/close/lock
is_simple
copy
extent_class
extent_copy
set_extent_simple
set_extent_none
get_simple_extent_npoints/ndims/dims
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30. Transient Dataspace Class
Dataspace Selection
Set and modify selections
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Dataspace Class
______________
selection
______________
select_elements
select_none
select_hyperslab
select_valid
offset_simple
………………...
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31. Datatype Class and Subclasses
Datatype Class
Compound
Atomic
Array
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Enumeration
Variable Length
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32. Datatype Class
Datatype Class
______________
______________
copy
equal
close
convert
get_class
get_size
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33. Atomic Datatype Class and Subclasses
Atomic Datatype Class
Predefined Atomic
Userdefined Atomic
H5Tcopy
1
0…*
Link Class
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34. Predefined Atomic Datatype Class
Predefined Atomic Datatype Class
String
Time
Opaque
Integer
Reference
Object Reference
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Float
Bitfield
Region Reference
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35. 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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36. Compound Datatype Class
Compound Datatype Class
1…*
Datatype Class
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typedef struct {
int a;
float b;
my_type c[10];
} compound_t
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37. Enumeration Datatype Class
Datatype Class
RED
GREEN
BLUE
1
0
1
2
Enumeration Datatype
1…*
( string, value of type Datatype )
Only Integer datatype for now
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38. Variable Length Datatype Class
Datatype Class
1
Variable Length Datatype Class
A
1
2
3
C
RED
GREEN
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BLUE
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4
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39. Reading Dataset into Memory from File
File
2D array of integers
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Memory
3D array of floats
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40. Reading Dataset into Memory from File
File
Dataset
Memory
2D array with selected rectangle
Copy of File Dataspace
_______________________
Selection
I/O hint
Dataset Xfer Prp List
Dataspace
Data (
H5Dread
Buffer
Datatype
Memory Dataspace
___________________
Memory Datatype
Selection
floats
3D array with selected union of cubes
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)