current behavior is
if DCPL has creation order tracked for attributes then sort the attributes by creation order otherwise by name
regarding sort order (ascending or descending) it is done in whatever is requested
tested: linux
Bug fixes
Avoid passing iteration flags on the dump_group function parameters but instead inspect the groups's property list just before calling H5Literate and H5Aiterate, in this later case checking the creation order flags with H5Pget_attr_creation_order
Tested: windows, linux
Added support for displaying several iteration orders on dataset attributes, 4 new tests in test script (name ascending, name descending, creation_order ascending, creation_order descending)
New h5 file is made on the generator program
Tested: windows, linux
Make H5Aiterate() versioned and change all internal use to H5Aiterate2()
Leave some regression tests that exercise H5Aiterate1()
Fix attribute display in h5dump & h5ls to be "by name" by default
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
tested: windows, linux, solaris 5.10
usage: h5dump [OPTIONS] file
OPTIONS
-h, --help Print a usage message and exit
-n, --contents Print a list of the file contents and exit
-B, --bootblock Print the content of the boot block
-H, --header Print the header only; no data is displayed
-A, --onlyattr Print the header and value of attributes
-i, --object-ids Print the object ids
-r, --string Print 1-byte integer datasets as ASCII
-e, --escape Escape non printing characters
-V, --version Print version number and exit
-a P, --attribute=P Print the specified attribute
-d P, --dataset=P Print the specified dataset
-y, --noindex Do not print array indices with the data
-p, --properties Print dataset filters, storage layout and fill value
-f D, --filedriver=D Specify which driver to open the file with
-g P, --group=P Print the specified group and all members
-l P, --soft-link=P Print the value(s) of the specified soft link
-o F, --output=F Output raw data into file F
-b B, --binary=B Binary file output, of form B
-t P, --datatype=P Print the specified named datatype
-w N, --width=N Set the number of columns of output
-q Q, --sort_by=Q Sort groups and attributes by index Q
-z Z, --sort_order=Z Sort groups and attributes by order Z
-x, --xml Output in XML using Schema
-u, --use-dtd Output in XML using DTD
-D U, --xml-dtd=U Use the DTD or schema at U
-X S, --xml-ns=S (XML Schema) Use qualified names n the XML
":": no namespace, default: "hdf5:"
E.g., to dump a file called `-f', use h5dump -- -f
Subsetting is available by using the following options with a dataset
attribute. Subsetting is done by selecting a hyperslab from the data.
Thus, the options mirror those for performing a hyperslab selection.
The START and COUNT parameters are mandatory if you do subsetting.
The STRIDE and BLOCK parameters are optional and will default to 1 in
each dimension.
-s L, --start=L Offset of start of subsetting selection
-S L, --stride=L Hyperslab stride
-c L, --count=L Number of blocks to include in selection
-k L, --block=L Size of block in hyperslab
D - is the file driver to use in opening the file. Acceptable values
are "sec2", "family", "split", "multi", "direct", and "stream". Without
the file driver flag, the file will be opened with each driver in
turn and in the order specified above until one driver succeeds
in opening the file.
F - is a filename.
P - is the full path from the root group to the object.
N - is an integer greater than 1.
L - is a list of integers the number of which are equal to the
number of dimensions in the dataspace being queried
U - is a URI reference (as defined in [IETF RFC 2396],
updated by [IETF RFC 2732])
B - is the form of binary output: MEMORY for a memory type, FILE for the
file type, LE or BE for pre-existing little or big endian types.
Must be used with -o (output file) and it is recommended that
-d (dataset) is used
Q - is the sort index type. It can be "creation_order" or "name" (default)
Z - is the sort order type. It can be "descending" or "ascending" (default)
Examples:
1) Attribute foo of the group /bar_none in file quux.h5
h5dump -a /bar_none/foo quux.h5
2) Selecting a subset from dataset /foo in file quux.h5
h5dump -d /foo -s "0,1" -S "1,1" -c "2,3" -k "2,2" quux.h5
3) Saving dataset 'dset' in file quux.h5 to binary file 'out.bin' using a litt
le-endian type
h5dump -d /dset -b LE -o out.bin quux.h5
bug fix
the binary option expects a full path in -o
TOOLTEST tbin1.ddl -d integer -o $TESTDIR/out1.bin -b LE tbinary.h5
and it prints it in the expected output , making it absolutely not portable
Solution: made a special macro function TOOLTEST1 identical to TOOLTEST except that it does not print the Expected output header
#############################
Expected output for 'h5dump -d integer -o /home/pvn/kagiso/build_hdf5/tools/h5dump/../testfiles/out1.bin -b LE tbinary.h5'
#############################
Tested : linux
1) added 5 new tests for the group creation order
2) modified the h5dump test script to automatically generated non existing (new) output files
3) cleaning of unused DDL files
4) new modified DDL files include tcomp-3.ddl ( new form of named datatype) and the binary output files
tested : linux
first batch for displaying groups in creation order
1) Added extra parameter to dump_group of type H5_index_t , to be passed to H5Literate.
When a group is tried to be displayed, an inquiry of its creation properties is made. If H5P_CRT_ORDER_TRACKED is present on the group property list then the display is made by creation order, otherwise it is made by name
2) Added a new file to h5dumpgentest that generates a file with a hierarchy of groups with creation order on and off in alternately
Note : XML code was not modified
Tested : windows, linux
Move H5Gget_num_objs() and several minor macros, etc. to deprecated
symbols section, replacing it with H5Gget_info().
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
AIX/32 5.3 (copper)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
Regenerate the h5diff_types.h5 file, which had somehow gotten mangled
in some earlier checkin (prior to ~2-3 days ago, at least).
Clean up formatting a bit also..
Tested on:
Mac OS X/32 10.4.10 (amazon)
On Windows, Mingw interprets all parameters starting with '/' as paths, and replaces the '/' with its home directory, "C:\Windows\msys\". This was a problem in h5diff tests such as:
h5diff h5diff_101.txt $FILE1 $FILE1 /g1/d1 g1/d2 -v
I've removed the leading '/', as h5diff will interpret it the same either way.
Tested:
kagiso, linew, and smirom, via h5committest
mingw on Windows XP
Modified the current h5dump test script to use h5import/h5diff calls to validate the binary output. At this moment it can only be used with the native test, since h5import does not deal with input endianess.
tested: linux, sunos 5.10
Change H5[D|G|T]<foo>_expand() "temporary" API routines to
H5[D|G|T]<foo>2() "versioned" routines. Also added
H5[D|G|T](create|commit)_anon() routines to continue to allow "anonymous"
objects to be created in a file.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Add version # and flags to external link format (as fields in a single
byte), in order to accomodate future changes/expansions.
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Bug fixes
Reset external file list slots name_offset to a state when created (0) in H5P_dcrt_copy
so that it conforms to an assertion in H5D_update_entry_info that assumes the name_offset is 0 at this point
this fixes the problem of h5repack and external files, add a new test and files for an external file
h5diff, check for an error return in H5D_get_storage_size
tested linux 32, 64
Eliminate storing # of links in "link info" message, regenerate it
when the object is opened instead.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
Move ref. count of # of links to an object out of the object header's
prefix and make it a header message instead (since it's a "rare" occurence),
eliminating some more space for each object in the file.
Inserting this "ref. count" message exposed a flaw in the library's
mechanism for locating a message to promote to another chunk and replace
with a continuation message, which required some additional work to fix.
It's still not completely robust, but it's working for more cases now and
detects failures robustly.
Reduced the minimum size of an object header chunk to just enough to
contain a header message prefix and continuation message.
Tested on:
FreeBSD/32 6.2 (duty)
Move "creation order tracked" flag from "group info" to "link info"
object header message and make the "max. creation order value" optional in the
"link info", if the creation order for links is not tracked.
Also, get rid of unused "index names" flag - names are always indexed
currently.
Tested on:
FreeBSD/32 6.2 (duty)
Eliminate message count from new version of object header prefix -
it can be computed when the header is loaded and the table of messages is
built.
Tested on:
FreeBSD/32 6.2 (duty)
Move attribute tracking information out of object header prefix and
make it into a message that is inserted only when attributes are present on
the object.
Tested on:
FreeBSD/32 6.2 (duty)
The main purpose of this checkin was to eliminate the
space used for tracking creation time indices when there is no way they
can be used (i.e. attributes can't be shared in the file and the user hasn't
turned on attribute creation tracking), however there were some other minor
changes which crept in:
- Fix a cache locking deadlock when a shared attribute and one of its
components end up in the same fractal heap direct block.
(This is fixed the "slow" way for right now, until John has time
to add support for readers/writer locking to the cache.
- Optimize attribute copying when a copy will be kept during a v2 B-tree
search.
- When freeing a block on disk, attempt to merge it with the metadata
and "small data" aggregators.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
Revise latest form of superblock format pretty drastically, to
eliminate unused fields and move rarely used fields into superblock extension.
Finished removing last vestiges of references to (never used) i"shared"
object header message ID.
Added object header messages for non-default v1 B-tree 'K' values
and for driver info.
Updated testfiles to reflect size changes, etc.
Various minor cleanups, etc.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
Bug fix: the macro used for percentage in the unsigned types needed a cast to signed (the difference can be negative)
Unlike the 1.6 branch the unsigned long long conversion to float is supported by H5Tconvert , so the test commented for 1.6 is run (tools/testfiles/h5diff_16_2.txt)
Update the file offsets for files created with "latest version" flag of
h5mkgrp to reflect changes to superblock size.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Mask off the storage utilization for the h5ls output, so that the
h5ls output is more portable (VL datatype size is reported as the memory size
instead of the file size, making the storage utilization incorrect - entered
in bugzilla)
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Blank out the modification time, to eliminate another portability issue.
Tested on:
Linux/32 2.6 (chicago)
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
