[MOAB-dev] h5m with data

Sun Nov 8 22:55:03 CST 2015

Nico, as Patrick mentioned, Tags are the abstract ways to represent,
serialize and manipulate data associated with entities in a MOAB mesh.
Tags can be associated directly with entities such as vertex or
element, or you could choose to create sets of entities and associate
data to these sets. So based on this degree of representation, we have
the terminology that a tag can be dense or sparse. This is just an
internal way to store these tags to optimize memory layout and does
slightly affect how data is serialized/read-back to/from h5m files.

Now in terms of usage, just get the tag handle, and you can either
read or write to the tag by using tag_get_data and tag_set_data
respectively.

The SetsNTags [1], VisTags [2] examples show how to read the data
stored in h5m. You can use set_tag_data to write this a priori. If
needed, we can also create a simplistic example to create/manipulate
tag data on a mesh, but I think this may be overkill. Let me know if
this would help though.

Vijay

[1] ftp://ftp.mcs.anl.gov/pub/fathom/moab-docs/SetsNTags_8cpp-example.html
[2] ftp://ftp.mcs.anl.gov/pub/fathom/moab-docs/VisTags_8cpp-example.html

On Sun, Nov 8, 2015 at 8:32 PM, Patrick Shriwise <shriwise at wisc.edu> wrote:
> Hey Nico,
>
> Ok. There doesn't appear to be a great example for applying data. Applying
> data works in a very similar way to the way you retrieve tagged data, using
> tag_set_data with a Tag which can be created for a certain type of data with
> a given name by calling tag_get_handle with the MBCREAT option at the end.
> I'd like to be clear that you can apply/retrieve data from MOAB Entities or
> MOAB EntitySets. So you can either apply data directly to entities like
> vertices or you can group them together in a set and apply data to that set
> instead. For the purpose you're indicating, it sounds like it'd be best to
> apply the data directly to the vertices.
>
> Sample code for creating a MOAB Tag:
>   Tag name_tag;
>   rval = mdbImpl->tag_get_handle(NAME_TAG_NAME, NAME_TAG_SIZE,
> MB_TYPE_OPAQUE,
>                                  name_tag, MB_TAG_SPARSE | MB_TAG_CREAT);
> Cheers,
>
> Patrick C. Shriwise
> Research Fellow
> University of Wisconsin - Madison
> Engineering Research Building - Rm. 428
> 1500 Engineering Drive
> Madison, WI 53706
> (608) 446-8173
>
> On 11/08/15 21:01, Nico Schlömer wrote:
>
> In both ways, actually. I need to build h5m files from data and I need to
> extract data from h5m meshes.
> With [1], I'm digging my way through understanding the sets group now.
>
> --Nico
>
> [1] https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB/h5m
>
> On Mon, Nov 9, 2015 at 2:53 AM Patrick Shriwise <shriwise at wisc.edu> wrote:
>>
>> Hi Nico,
>>
>> I see. I may have misunderstood your problem. It seems you're trying to
>> apply data to the mesh. Is that right?
>>
>>
>> Cheers,
>>
>> Patrick C. Shriwise
>> Research Fellow
>> University of Wisconsin - Madison
>> Engineering Research Building - Rm. 428
>> 1500 Engineering Drive
>> Madison, WI 53706
>> (608) 446-8173
>>
>> On 11/08/15 20:03, Nico Schlömer wrote:
>>
>> Thanks Patrick for your reply.
>>
>> I'm still having problems where data should be stores. In a h5m file, I
>> see tags, I see sets with tags in them, and it seems they are somehow
>> related, but I don't know where and how to put the actual data. I would help
>> to see a file with some mesh and a custom data element in it, e.g., an array
>> of values associated with the vertices.
>>
>> Cheers,
>> Nico
>>
>> On Sun, Nov 8, 2015 at 9:20 PM Patrick Shriwise <shriwise at wisc.edu> wrote:
>>>
>>> Hi Nico,
>>>
>>> The vertex data should be stored in MOAB tags. You can access these tags
>>> via their name. There is a set of conventions for the tag names in an Exodus
>>> file (here I think). However, if the tag has a custom name and isn't
>>> recognized by the Exodus reader, then the data might not be read in from the
>>> Exodus file and as a result won't be saved into the .h5m. Do you have an
>>> idea of what the tag name might be for your data?
>>>
>>> There's also a good example here of how to access the tag data on an
>>> entity. The example I linked you to accesses EntitySets rather than
>>> Entities, but they work the same way.
>>>
>>> If you think the data might be in the .h5m, you can use
>>> tag_get_tags_on_entity to get all of the tags on a vertex and then check for
>>> the tag data you're looking for. An easier way of doing this in the cmd line
>>> is by using mbsize -t <your_file>.h5m to print out the count by tag.
>>>
>>> Hope this helps!
>>>
>>> Cheers,
>>>
>>> Patrick C. Shriwise
>>> Research Fellow
>>> University of Wisconsin - Madison
>>> Engineering Research Building - Rm. 428
>>> 1500 Engineering Drive
>>> Madison, WI 53706
>>> (608) 446-8173
>>>
>>> On 11/08/15 13:43, Nico Schlömer wrote:
>>>
>>> Hi everyone,
>>>
>>> I have an Exodus file with vertex data in it (i.e., "a function" defined
>>> on the vertices). When converting this file to h5m, where does the vertex
>>> data go? And how to I retrieve the data after having it read with
>>> `load_file()`?
>>>
>>> Cheers,
>>> Nico
>>>
>>>
>>
>