| Reopen HDF5 file to add more data? [message #90187] |
Mon, 09 February 2015 08:25  |
dg86
Messages: 118
Registered: September 2012
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Senior Member |
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Dear Folks,
It appears not to be possible to add more data to an HDF5 file once
the file has been closed, at least not in the IDL implementation.
Is that correct?
Here's a minimal example of what I'm trying to do. This triggers
the error that inspires my question.
Is there a way to reopen an file for writing, or do I have to read in the
old archive and recopy everything to a new archive?
Many thanks,
David
;--- cut here for minimal example ---
filename = 'testfile.h5'
group = 'group'
name = 'testdata'
;;; Create and close an HDF5 archive with one group and no data
fid = h5f_create(filename)
gid = h5g_create(fid, group)
h5g_close, gid
h5f_close, fid
;;; Reopen the HDF5 archive to add some data to the group
fid = h5f_open(filename)
gid = h5g_open(fid, group)
;;; attempt to write some data
a = bindgen(640, 480)
tid = h5t_idl_create(a)
sid = h5s_create_simple(a.dim)
did = h5d_create(gid, name, tid, sid) ;;; <-- this fails
h5d_write, did, a
;;; close the file
h5d_close, did
h5s_close, sid
h5t_close, tid
h5g_close, gid
h5f_close, fid
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| Re: Reopen HDF5 file to add more data? [message #90195 is a reply to message #90187] |
Tue, 10 February 2015 00:17  |
markb77
Messages: 217
Registered: July 2006
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Senior Member |
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On Monday, February 9, 2015 at 5:25:56 PM UTC+1, David Grier wrote:
> Dear Folks,
>
> It appears not to be possible to add more data to an HDF5 file once
> the file has been closed, at least not in the IDL implementation.
> Is that correct?
>
> Here's a minimal example of what I'm trying to do. This triggers
> the error that inspires my question.
>
> Is there a way to reopen an file for writing, or do I have to read in the
> old archive and recopy everything to a new archive?
>
> Many thanks,
>
> David
>
> ;--- cut here for minimal example ---
> filename = 'testfile.h5'
> group = 'group'
> name = 'testdata'
>
> ;;; Create and close an HDF5 archive with one group and no data
> fid = h5f_create(filename)
> gid = h5g_create(fid, group)
> h5g_close, gid
> h5f_close, fid
>
> ;;; Reopen the HDF5 archive to add some data to the group
> fid = h5f_open(filename)
> gid = h5g_open(fid, group)
>
> ;;; attempt to write some data
> a = bindgen(640, 480)
> tid = h5t_idl_create(a)
> sid = h5s_create_simple(a.dim)
> did = h5d_create(gid, name, tid, sid) ;;; <-- this fails
> h5d_write, did, a
>
> ;;; close the file
> h5d_close, did
> h5s_close, sid
> h5t_close, tid
> h5g_close, gid
> h5f_close, fid
hi David,
You need to use H5D_EXTEND to increase the size of your dataset before you can append additional data.
best
Mark
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| Re: Reopen HDF5 file to add more data? [message #90198 is a reply to message #90195] |
Tue, 10 February 2015 09:25 |
dg86
Messages: 118
Registered: September 2012
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Senior Member |
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On Tuesday, February 10, 2015 at 3:17:39 AM UTC-5, superchromix wrote:
> On Monday, February 9, 2015 at 5:25:56 PM UTC+1, David Grier wrote:
>> Dear Folks,
>>
>> It appears not to be possible to add more data to an HDF5 file once
>> the file has been closed, at least not in the IDL implementation.
>> Is that correct?
>>
>> Here's a minimal example of what I'm trying to do. This triggers
>> the error that inspires my question.
>>
>> Is there a way to reopen an file for writing, or do I have to read in the
>> old archive and recopy everything to a new archive?
>>
>> Many thanks,
>>
>> David
>>
>> ;--- cut here for minimal example ---
>> filename = 'testfile.h5'
>> group = 'group'
>> name = 'testdata'
>>
>> ;;; Create and close an HDF5 archive with one group and no data
>> fid = h5f_create(filename)
>> gid = h5g_create(fid, group)
>> h5g_close, gid
>> h5f_close, fid
>>
>> ;;; Reopen the HDF5 archive to add some data to the group
>> fid = h5f_open(filename)
>> gid = h5g_open(fid, group)
>>
>> ;;; attempt to write some data
>> a = bindgen(640, 480)
>> tid = h5t_idl_create(a)
>> sid = h5s_create_simple(a.dim)
>> did = h5d_create(gid, name, tid, sid) ;;; <-- this fails
>> h5d_write, did, a
>>
>> ;;; close the file
>> h5d_close, did
>> h5s_close, sid
>> h5t_close, tid
>> h5g_close, gid
>> h5f_close, fid
>
>
> hi David,
>
> You need to use H5D_EXTEND to increase the size of your dataset before you can append additional data.
>
> best
> Mark
It turns out the answer is even simpler than that.
H5F_OPEN opens a file read-only by default. The /WRITE switch opens it
read-write. Everything is working now!
TTFN,
David
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