File Format Examples:
This section has several small programs and describes the format of a file
created with each of them.
Example program one - Create an empty file:
#include "hdf5.h"
#include
int main()
{
hid_t fid; /* File ID */
herr_t ret; /* Generic return value */
/* Create the file */
fid=H5Fcreate("example1.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
assert(fid>=0);
/* Close the file */
ret=H5Fclose(fid);
assert(ret>=0);
return(0);
}
Super Block
| byte |
byte |
byte |
byte |
| \211 |
'H' |
'D' |
'F' |
| \r |
\n |
\032 |
\n |
| 0 |
0 |
0 |
0 |
| 0 |
8 |
8 |
0 |
| 4 |
16 |
| 0x00000003 |
| 0 |
0xffffffffffffffff
|
| ? |
0xffffffffffffffff
|
| 0 |
928
|
| H5G_CACHED_STAB (1) |
| 0 |
|
|
|
%h5debug example1.h5
Reading signature at address 0 (rel)
File Super Block...
File name: example1.h5
File access flags 0x00000000
File open reference count: 1
Address of super block: 0 (abs)
Size of user block: 0 bytes
Super block version number: 0
Free list version number: 0
Root group symbol table entry version number: 0
Shared header version number: 0
Size of file offsets (haddr_t type): 8 bytes
Size of file lengths (hsize_t type): 8 bytes
Symbol table leaf node 1/2 rank: 4
Symbol table internal node 1/2 rank: 16
File consistency flags: 0x00000003
Base address: 0 (abs)
Free list address: UNDEF (rel)
Address of driver information block: UNDEF (rel)
Root group symbol table entry:
Name offset into private heap: 0
Object header address: 928
Dirty: Yes
Cache info type: Symbol Table
Cached information:
B-tree address: 384
Heap address: 96
Root Group Object Header
| byte |
byte |
byte |
byte |
| 1 |
0 |
2 |
| 1 |
| 32 |
| 0x0011 |
16 |
| 0x01 |
0 |
|
|
| 0 |
0 |
| 0x00 |
0 |
%h5debug example1.h5 928
New address: 928
Reading signature at address 928 (rel)
Object Header...
Dirty: 0
Version: 1
Header size (in bytes): 16
Number of links: 1
Number of messages (allocated): 2 (32)
Number of chunks (allocated): 1 (8)
Chunk 0...
Dirty: 0
Address: 944
Size in bytes: 32
Message 0...
Message ID (sequence number): 0x0011 stab(0)
Shared message: No
Constant: Yes
Raw size in obj header: 16 bytes
Chunk number: 0
Message Information:
B-tree address: 384
Name heap address: 96
Message 1...
Message ID (sequence number): 0x0000 null(0)
Shared message: No
Constant: No
Raw size in obj header: 0 bytes
Chunk number: 0
Message Information:
Root Group Local Heap
| byte |
byte |
byte |
byte |
| 'H' |
'E' |
'A' |
'P' |
| 0 |
| 256 |
| 8 |
| 128 |
%h5debug example1.h5 96
New address: 96
Reading signature at address 96 (rel)
Local Heap...
Dirty: 0
Header size (in bytes): 32
Address of heap data: 128
Data bytes allocated on disk: 256
Data bytes allocated in core: 256
Free Blocks (offset, size):
Block #0: 8, 248
Percent of heap used: 3.12%
Data follows (`__' indicates free region)...
0: 00 00 00 00 00 00 00 00 __ __ __ __ __ __ __ __ ........
16: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
32: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
48: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
64: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
80: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
96: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
112: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
128: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
144: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
160: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
176: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
192: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
208: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
224: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
240: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
Root Group B-tree
| byte |
byte |
byte |
byte |
| 'T' |
'R' |
'E' |
'E' |
| 0 |
0 |
0 |
0xffffffffffffffff
|
0xffffffffffffffff
|
%h5debug example1.h5 384 96
New address: 384
Reading signature at address 384 (rel)
Tree type ID: H5B_SNODE_ID
Size of node: 544
Size of raw (disk) key: 8
Dirty flag: False
Number of initial dirty children: 0
Level: 0
Address of left sibling: UNDEF
Address of right sibling: UNDEF
Number of children (max): 0 (32)
Example program two - Create a file with a single dataset in it:
#include "hdf5.h"
#include
int main()
{
hid_t fid; /* File ID */
hid_t sid; /* Dataspace ID */
hid_t did; /* Dataset ID */
herr_t ret; /* Generic return value */
/* Create the file */
fid=H5Fcreate("example2.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
assert(fid>=0);
/* Create a scalar dataspace for the dataset */
sid=H5Screate(H5S_SCALAR);
assert(sid>=0);
/* Create a trivial dataset */
did=H5Dcreate(fid, "Dataset", H5T_NATIVE_INT, sid, H5P_DEFAULT);
assert(did>=0);
/* Close the dataset */
ret=H5Dclose(did);
assert(ret>=0);
/* Close the dataspace */
ret=H5Sclose(sid);
assert(ret>=0);
/* Close the file */
ret=H5Fclose(fid);
assert(ret>=0);
return(0);
}
Super Block
| byte |
byte |
byte |
byte |
| \211 |
'H' |
'D' |
'F' |
| \r |
\n |
\032 |
\n |
| 0 |
0 |
0 |
0 |
| 0 |
8 |
8 |
0 |
| 4 |
16 |
| 0x00000003 |
| 0 |
0xffffffffffffffff
|
| ? |
0xffffffffffffffff
|
| 0 |
928
|
| H5G_CACHED_STAB (1) |
| 0 |
|
|
|
%h5debug example2.h5
Reading signature at address 0 (rel)
File Super Block...
File name: example2.h5
File access flags 0x00000000
File open reference count: 1
Address of super block: 0 (abs)
Size of user block: 0 bytes
Super block version number: 0
Free list version number: 0
Root group symbol table entry version number: 0
Shared header version number: 0
Size of file offsets (haddr_t type): 8 bytes
Size of file lengths (hsize_t type): 8 bytes
Symbol table leaf node 1/2 rank: 4
Symbol table internal node 1/2 rank: 16
File consistency flags: 0x00000003
Base address: 0 (abs)
Free list address: UNDEF (rel)
Address of driver information block: UNDEF (rel)
Root group symbol table entry:
Name offset into private heap: 0
Object header address: 928
Dirty: Yes
Cache info type: Symbol Table
Cached entry information:
B-tree address: 384
Heap address: 96
Root Group Object Header
| byte |
byte |
byte |
byte |
| 1 |
0 |
2 |
| 1 |
| 32 |
| 0x0011 |
16 |
| 0x01 |
0 |
|
|
| 0 |
0 |
| 0x00 |
0 |
%h5debug example2.h5 928
New address: 928
Reading signature at address 928 (rel)
Object Header...
Dirty: 0
Version: 1
Header size (in bytes): 16
Number of links: 1
Number of messages (allocated): 2 (32)
Number of chunks (allocated): 1 (8)
Chunk 0...
Dirty: 0
Address: 944
Size in bytes: 32
Message 0...
Message ID: 0x0011 stab(0)
Shared message: No
Constant: Yes
Raw size in obj header: 16 bytes
Chunk number: 0
Message Information:
B-tree address: 384
Name heap address: 96
Message 1...
Message ID: 0x0000 null(0)
Shared message: No
Constant: No
Raw size in obj header: 0 bytes
Chunk number: 0
Message Information:
Root Group Local Heap
| byte |
byte |
byte |
byte |
| 'H' |
'E' |
'A' |
'P' |
| 0 |
| 256 |
| 16 |
| 128 |
%h5debug example2.h5 96
New address: 96
Reading signature at address 96 (rel)
Local Heap...
Dirty: 0
Header size (in bytes): 32
Address of heap data: 128
Data bytes allocated on disk: 256
Data bytes allocated in core: 256
Free Blocks (offset, size):
Block #0: 16, 240
Percent of heap used: 6.25%
Data follows (`__' indicates free region)...
0: 00 00 00 00 00 00 00 00 44 61 74 61 73 65 74 00 ........Dataset.
16: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
32: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
48: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
64: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
80: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
96: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
112: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
128: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
144: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
160: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
176: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
192: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
208: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
224: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
240: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
Root Group B-tree
| byte |
byte |
byte |
byte |
| 'T' |
'R' |
'E' |
'E' |
| 0 |
0 |
1 |
0xffffffffffffffff
|
0xffffffffffffffff
|
0
|
1248
|
8
|
%h5debug example2.h5 384 96
New address: 384
Reading signature at address 384 (rel)
Tree type ID: H5B_SNODE_ID
Size of node: 544
Size of raw (disk) key: 8
Dirty flag: False
Number of initial dirty children: 0
Level: 0
Address of left sibling: UNDEF
Address of right sibling: UNDEF
Number of children (max): 1 (32)
Child 0...
Address: 1248
Left Key:
Heap offset: 0
Name :
Right Key:
Heap offset: 8
Name : Dataset
Root Group B-tree Symbol Table Node
| byte |
byte |
byte |
byte |
| 'S' |
'N' |
'O' |
'D' |
| 1 |
0 |
1 |
|
|
%h5debug example2.h5 1248 96
New address: 1248
Reading signature at address 1248 (rel)
Symbol Table Node...
Dirty: No
Size of Node (in bytes): 328
Number of Symbols: 1 of 8
Symbol 0:
Name: `Dataset'
Name offset into private heap: 8
Object header address: 976
Dirty: No
Cache info type: Nothing Cached
'/Dataset' Object Header
| byte |
byte |
byte |
byte |
| Version: 1 |
Reserved: 0 |
Number of Header Messages: 6 |
| Object Reference Count: 1 |
| Total Object Header Size: 256 |
Fill Value Header Message
|
|
|
|
| Message Type: 0x0005 |
Message Data Size: 8 |
| Flags: 0x01 |
Reserved: 0 |
| Version: 1 |
Space Allocation Time: 2 (Late) |
Fill Value Writing Time: 0 (At allocation) |
Fill Value Defined: 0 (Undefined) |
| Fill Value Datatype Size: 0 (Use dataset's datatype for fill-value datatype) |
|
Datatype Header Message
|
|
|
|
| Message Type: 0x0003 |
Message Data Size: 16 |
| Flags: 0x01 |
Reserved: 0 |
| Version: 0x1 |
Class: 0x0 (Fixed-Point) |
|
Fixed-Point Bit-Field: 0x08 (Little-endian, No padding, Signed) |
| Size: 4 |
| Bit Offset: 0 |
Bit Precision: 32 |
| Message Alignment Filler: - |
|
Dataspace Header Message
|
|
|
|
| Message Type: 0x0001 |
Message Data Size: 8 |
| Flags: 0x00 |
Reserved: 0 |
| Version: 1 |
Rank: 0 (Scalar) |
Flags: 0x00 (No maximum dimensions, no permutation information) |
Reserved: 0 |
| Reserved: 0 |
|
Layout Header Message
|
|
|
|
| Message Type: 0x0008 |
Message Data Size: 24 |
| Flags: 0x00 |
Reserved: 0 |
| Version: 1 |
Rank: 1 (Dataspace rank+1) |
Class: 1 (Contiguous) |
Reserved: 0 |
| Reserved: 0 |
Address: 0xffffffffffffffff (Undefined)
|
| Dimension 0 Size: 4 (Datatype size) |
| Message Alignment Filler: - |
|
Modification Date & Time Header Message
|
|
|
|
| Message Type: 0x0012 |
Message Data Size: 8 |
| Flags: 0x00 |
Reserved: 0 |
| Version: 1 |
Reserved: 0 |
| Seconds Since Epoch: 1052401700 (2003-05-08 08:48:20 CDT) |
|
Null Header Message
|
|
|
|
| Message Type: 0x0000 |
Message Data Size: 144 |
| Flags: 0x00 |
Reserved: 0 |
|
%h5debug example2.h5 976
New address: 976
Reading signature at address 976 (rel)
Object Header...
Dirty: 0
Version: 1
Header size (in bytes): 16
Number of links: 1
Number of messages (allocated): 6 (32)
Number of chunks (allocated): 1 (8)
Chunk 0...
Dirty: 0
Address: 992
Size in bytes: 256
Message 0...
Message ID (sequence number): 0x0005 `fill_new' (0)
Shared: No
Constant: Yes
Raw size in obj header: 8 bytes
Chunk number: 0
Message Information:
Version: 1
Space Allocation Time: Late
Fill Time: On Allocation
Fill Value Defined: Undefined
Size: 0
Data type:
Message 1...
Message ID (sequence number): 0x0003 data_type(0)
Shared message: No
Constant: Yes
Raw size in obj header: 16 bytes
Chunk number: 0
Message Information:
Type class: integer
Size: 4 bytes
Byte order: little endian
Precision: 32 bits
Offset: 0 bits
Low pad type: zero
High pad type: zero
Sign scheme: 2's comp
Message 2...
Message ID (sequence number): 0x0001 simple_dspace(0)
Shared message: No
Constant: No
Raw size in obj header: 8 bytes
Chunk number: 0
Message Information:
Rank: 0
Message 3...
Message ID (sequence number): 0x0008 layout(0)
Shared message: No
Constant: No
Raw size in obj header: 24 bytes
Chunk number: 0
Message Information:
Data address: UNDEF
Number of dimensions: 1
Size: {4}
Message 4...
Message ID (sequence number): 0x0012 mtime_new(0)
Shared message: No
Constant: No
Raw size in obj header: 8 bytes
Chunk number: 0
Message Information:
Time: 2003-03-05 14:52:00 CST
Message 5...
Message ID (sequence number): 0x0000 null(0)
Shared message: No
Constant: No
Raw size in obj header: 144 bytes
Chunk number: 0
Message Information: