Unable to open my hdf file with hdfview -- bad dataset?


#1

Hello,

I would like to convert a binary dump (of SIFT features) to a HDF5 dataset.
I believe I have the dimensions and everything correct in my config file
which I have provided below, but I could be wrong since the info on the
binary dump I'm working from is not particularly clear.

When I run the h5import command with my config file, the outfile file is
created without error.

When I open the outfile with hdfview, I see the dataset name but not really
much else and many errors are reported, which I have copied below.

The errors seem to suggest I am not creating the data set correctly. Any
idea what I'm doing wrong?

Thanks,

Ryan

config_file:
PATH grp1/sift-test
INPUT-CLASS UIN
INPUT-SIZE 8
RANK 2
DIMENSION-SIZES 128 5328755
OUTPUT-CLASS UIN
OUTPUT-SIZE 8

errors when opening:
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Adeprec.c line 214 in H5Aopen_name(): can't open
attribute
    major: Attribute
    minor: Can't open object
  #001: ../../../src/H5A.c line 865 in H5A_open_by_name(): unable to load
attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #002: ../../../src/H5Oattribute.c line 533 in H5O_attr_open_by_name():
can't locate attribute
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Edeprec.c line 182 in H5Eget_minor(): not a error
message ID
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Adeprec.c line 214 in H5Aopen_name(): can't open
attribute
    major: Attribute
    minor: Can't open object
  #001: ../../../src/H5A.c line 865 in H5A_open_by_name(): unable to load
attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #002: ../../../src/H5Oattribute.c line 533 in H5O_attr_open_by_name():
can't locate attribute
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Edeprec.c line 182 in H5Eget_minor(): not a error
message ID
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Adeprec.c line 214 in H5Aopen_name(): can't open
attribute
    major: Attribute
    minor: Can't open object
  #001: ../../../src/H5A.c line 865 in H5A_open_by_name(): unable to load
attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #002: ../../../src/H5Oattribute.c line 533 in H5O_attr_open_by_name():
can't locate attribute
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Edeprec.c line 182 in H5Eget_minor(): not a error
message ID
    major: Invalid arguments to routine
    minor: Inappropriate type


#2

Greetings Ryan,

Does h5dump also produce errors?

I don’t think a (bug-free) h5import should be able to produce a bad
hdf5 file, regardless of the config file.

It may be helpful to tell the list what version of h5import and HDFView
you are using.

–dan

Ryan Price wrote:

···

Hdf-forum@hdfgroup.orghttp://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

-- Daniel Kahn
Science Systems and Applications Inc.
301-867-2162

#3

Dan,

Turns out the hdf5 file was fine. I just didn't realize that the dataset
created was too large to open as a single spreadsheet in hdfview and that's
why I was seeing errors when I tried to view. View subsets of the data set
works fine!

Thanks,

Ryan

···

On Thu, Aug 18, 2011 at 7:38 AM, Daniel Kahn <daniel.kahn@ssaihq.com> wrote:

**
Greetings Ryan,

Does h5dump also produce errors?

I don't think a (bug-free) h5import should be able to produce a bad hdf5
file, regardless of the config file.

It may be helpful to tell the list what version of h5import and HDFView you
are using.

--dan

Ryan Price wrote:

Hello,

I would like to convert a binary dump (of SIFT features) to a HDF5
dataset. I believe I have the dimensions and everything correct in my
config file which I have provided below, but I could be wrong since the info
on the binary dump I'm working from is not particularly clear.

When I run the h5import command with my config file, the outfile file is
created without error.

When I open the outfile with hdfview, I see the dataset name but not really
much else and many errors are reported, which I have copied below.

The errors seem to suggest I am not creating the data set correctly. Any
idea what I'm doing wrong?

Thanks,

Ryan

config_file:
PATH grp1/sift-test
INPUT-CLASS UIN
INPUT-SIZE 8
RANK 2
DIMENSION-SIZES 128 5328755
OUTPUT-CLASS UIN
OUTPUT-SIZE 8

errors when opening:
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Adeprec.c line 214 in H5Aopen_name(): can't open
attribute
    major: Attribute
    minor: Can't open object
  #001: ../../../src/H5A.c line 865 in H5A_open_by_name(): unable to load
attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #002: ../../../src/H5Oattribute.c line 533 in H5O_attr_open_by_name():
can't locate attribute
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Edeprec.c line 182 in H5Eget_minor(): not a error
message ID
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Adeprec.c line 214 in H5Aopen_name(): can't open
attribute
    major: Attribute
    minor: Can't open object
  #001: ../../../src/H5A.c line 865 in H5A_open_by_name(): unable to load
attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #002: ../../../src/H5Oattribute.c line 533 in H5O_attr_open_by_name():
can't locate attribute
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Edeprec.c line 182 in H5Eget_minor(): not a error
message ID
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Adeprec.c line 214 in H5Aopen_name(): can't open
attribute
    major: Attribute
    minor: Can't open object
  #001: ../../../src/H5A.c line 865 in H5A_open_by_name(): unable to load
attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #002: ../../../src/H5Oattribute.c line 533 in H5O_attr_open_by_name():
can't locate attribute
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 2102279024:
  #000: ../../../src/H5Edeprec.c line 182 in H5Eget_minor(): not a error
message ID
    major: Invalid arguments to routine
    minor: Inappropriate type

------------------------------

_______________________________________________
Hdf-forum is for HDF software users discussion.Hdf-forum@hdfgroup.orghttp://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

--
Daniel Kahn
Science Systems and Applications Inc.301-867-2162

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org


#4

DFView is able to open HDF5 files that have different extensions.

Does the name of the file contain non-ascii characters? HDFView will not be able to open a file with unicode characters in the name (or in the path to the file).

Can you view the file with h5dump or other HDF5 tools?