So, HDF5 will handle all the 'conversion' from whatever type is used to store
the data in the file to whatever type you are using to store the data in
memory. So, for mem_type arg to h5dread_f, all you need to do is inform HDF5
what the datatype is of the buffer (data_out) you are reading into. You have
defined data_out as INTEGER in your programming language. So, I suspect the
right thing to do is. . .
CALL h5dread_f(dset_id,H5T_NATIVE_INTEGER, data_out, data_dims, error)
That tells HDF5 that data_out is the caller's *native* integer type and it will
convert from whatever is in the file H5T_STD_I64BE (a 64 bit big endianne
integer) to that type automatically when it reads it.
Mark
From: Hdf-forum
<[email protected]<mailto:[email protected]>>
on behalf of Richa Mathur
<[email protected]<mailto:[email protected]>>
Reply-To: HDF Users Discussion List
<[email protected]<mailto:[email protected]>>
Date: Tuesday, August 4, 2015 6:43 PM
To: HDF Users Discussion List
<[email protected]<mailto:[email protected]>>
Subject: Re: [Hdf-forum] h5dopen returns error
Hi Marc,
Thanks again. That link is helpful. I was able to read in the data directly
using the path in the h5read_f. I use
INTEGER, dimension(12,96):: data_out
data_dims(1) = 12, data_dims(2) =96
CALL h5dread_f(dset_id,H5T_STD_I64BE , data_out, data_dims, error) as
the h5dump indicates DATA_TYPE as H5T_STF_I64BE.
But it does not read properly ( gives core dump). I compile on a x86_64 m/c
gfortran.
GROUP "All_Data" {
GROUP "AMS-SDR_All" {
DATASET "BeamTime" {
DATATYPE H5T_STD_I64BE
Gompie
On Tue, Aug 4, 2015 at 4:24 PM, Miller, Mark C.
<[email protected]<mailto:[email protected]>> wrote:
Hmm. At this point, I think it may be more productive for everyone if you would
review the manual, https://www.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html, a bit
more to be sure you are attempting to use the HDF5 interface correctly.
In particular, your 2nd call to h5gopen_f is still specfying 'file_id' for
first arg when it should be specifing 'grp_id1'. AMS-SDR_All is a group that
'lives in' the "All_Data" group (grp_id1), not the root group (file_id).
Next, I am pretty certain you can just directly h5dopen_f
"All_Data/AMS-SDR_All/BeamTime" and avoid all the business with the groups.
Mark
From: Hdf-forum
<[email protected]<mailto:[email protected]>>
on behalf of Richa Mathur
<[email protected]<mailto:[email protected]>>
Reply-To: HDF Users Discussion List
<[email protected]<mailto:[email protected]>>
Date: Tuesday, August 4, 2015 1:06 PM
To: HDF Users Discussion List
<[email protected]<mailto:[email protected]>>
Subject: Re: [Hdf-forum] h5dopen returns error
Thanks Mark, Christian , the problem was case sensitivety and the first level
All_Data did not return any error.
Now since the path to BeamTime is All_Data/AMS-SDR_All/BeamTime I gave
CALL h5gopen_f(file_id,"All_Data" , grp_id1, grp_hdferr)
print *,"Open Group ID ID ERROR",grp_id1, grp_hdferr
CALL h5gopen_f(file_id,"AMS-SDR_All" , grp_id2, grp_hdferr) [should I give
the grp_id1 instead of file_id ?]
print *,"Open Group AMS-SDR ID ERROR",grp_id2, grp_hdferr ( here the hdferr is
-1)
CALL h5dopen_f(grp_id1,"BeamTime", dset_id, error)
Please help
On Tue, Aug 4, 2015 at 3:53 PM, Christian Oyarzun
<[email protected]<mailto:[email protected]>> wrote:
It is case sensitive. it should be:
CALL h5gopen_f(file_id,"All_Data" , grp_id1, grp_hdferr)
not:
CALL h5gopen_f(file_id,"All_data" , grp_id1, grp_hdferr)
—Christian
On Aug 4, 2015, at 3:45 PM, Richa Mathur
<[email protected]<mailto:[email protected]>> wrote:
Thanks Mark and Corey.
after CALL h5fopen_f(filename, H5F_ACC_RDONLY_F, file_id, error)
I gave CALL h5gopen_f(file_id,"All_data" , grp_id1, grp_hdferr) as the first
call to open the group and got grp_hdrerr as -1.
I guess there is an error opening the group All_data.
the h5dump -n output is
HDF5
"SAMS_npp_d20150728_t2359556_e0000273_b19431_c20150729063134831043_nasa_ops.h5"
{
FILE_CONTENTS {
group /
group /All_Data
group /All_Data/AMS-SDR_All
dataset /All_Data/AMS-SDR_All/BeamTime
dataset /All_Data/AMS-SDR_All/BrightnessTemperature
dataset /All_Data/AMS-SDR_All/BrightnessTemperatureFactors
Any help....
On Tue, Aug 4, 2015 at 3:11 PM, Miller, Mark C.
<[email protected]<mailto:[email protected]>> wrote:
yeah, agree. "BeamTime" is in group "All_Data". To get to BeamTime, you have to
H5Gopen the group and use the hid_t you get from that group in place of
'file_id' arg in h5dopen. Don't forget to close the group (and dataset) after
you're done.
Mark
From: Hdf-forum
<[email protected]<mailto:[email protected]>>
on behalf of Richa Mathur
<[email protected]<mailto:[email protected]>>
Reply-To: HDF Users Discussion List
<[email protected]<mailto:[email protected]>>
Date: Tuesday, August 4, 2015 12:03 PM
To: HDF Users Discussion List
<[email protected]<mailto:[email protected]>>
Subject: Re: [Hdf-forum] h5dopen returns error
Thanks Mark !!!
Filename is complete. The file_id that is returned from hdfopen_f (filename,
H5F_ACC_RDONLY_F, file_id, error) is 16777217 and error code is 0.
How do I find if 'BeamTime' is in root group or sub group ?
The H5Dump is as below I guess the BeamTime is inside a GROUP "All_Data",
GROUP "All_Data" {
GROUP "AMS-SDR_All" {
DATASET "BeamTime" {
DATATYPE H5T_STD_I64BE
DATASPACE SIMPLE { ( 12, 96 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
DATA {
(0,0): 1816819231684734, 1816819231702752, 1816819231720770,
(0,3): 1816819231738788, 1816819231756806, 1816819231774824
Gompie
On Tue, Aug 4, 2015 at 2:52 PM, Miller, Mark C.
<[email protected]<mailto:[email protected]>> wrote:
Are you sure you are getting a valid file_id back from the h5fopen_f call? Are
you by chance missing an extension on the filename such as 'satfilename.h5' and
is the dataset 'BeamTime' in the 'root group' of the file or perhaps some
sub-group?
Mark
From: Hdf-forum
<[email protected]<mailto:[email protected]>>
on behalf of Richa Mathur
<[email protected]<mailto:[email protected]>>
Reply-To: HDF Users Discussion List
<[email protected]<mailto:[email protected]>>
Date: Tuesday, August 4, 2015 10:42 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [Hdf-forum] h5dopen returns error
Hi
I am trying to read a hdf5 file in fortran95 ( gfortran). Peice of code is
INTEGER(HID_T) :: file_id ! File identifier
INTEGER(HID_T) :: dset_id ! Dataset identifier
INTEGER :: error ! Error flag
INTEGER :: i, j
INTEGER, DIMENSION(96,12) :: dset_data, data_out ! Data buffers
INTEGER(HSIZE_T), DIMENSION(2) :: data_dims
filename='satfilename'
CALL h5fopen_f(filename, H5F_ACC_RDONLY_F, file_id, error)
CALL h5dopen_f(file_id,"BeamTime", dset_id, error)
print *,"Data Set(ATMS) ID ERROR",dset_id, error .
The h5dopen_f returns error as -1.
Later on when I use
CALL h5dread_f(dset_id, H5T_STD_I64BE, data_out, data_dims, error)
error -1 is returned from this function as well and I get incorrect values of
my variable in data_out.
Can you help
Gompie
The h5dump of my hdf5 file has
GROUP "All_Data" {
GROUP "AMS-SDR_All" {
DATASET "BeamTime" {
DATATYPE H5T_STD_I64BE
DATASPACE SIMPLE { ( 12, 96 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
DATA {
(0,0): 1816819231684734, 1816819231702752, 1816819231720770,
(0,3): 1816819231738788, 1816819231756806, 1816819231774824
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Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
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Twitter: https://twitter.com/hdf5
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