[MOAB-dev] Questions about Tags and Topology

Mon Feb 13 15:05:06 CST 2012

Hi Iulian,

At this point, we do have a need to use PyTAPS due to the fact that the rest of our development is in python.  So we're trying to see how far down the road we can get using PyTAPS and so far things are looking promising!  The simplicity is a definite bonus!! :)

Thanks for the second round of responses (comments inline)

Best,
Chris

From: Iulian Grindeanu <iulian at mcs.anl.gov<mailto:iulian at mcs.anl.gov>>
Date: Mon, 13 Feb 2012 13:22:49 -0500
To: Christopher Mueller <cmueller at asascience.com<mailto:cmueller at asascience.com>>
Cc: Guy De Wardener <gdewardener at asascience.com<mailto:gdewardener at asascience.com>>, David Stuebe <DStuebe at asascience.com<mailto:DStuebe at asascience.com>>, don brittain <don.brittain at instanteffects.com<mailto:don.brittain at instanteffects.com>>, "moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>" <moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>>
Subject: Re: [MOAB-dev] Questions about Tags and Topology

Hello,
Please see below. For some of those, Jim or Tim would know the right answer.
Do you need to use PyTaps, or do you prefer it because it is simpler?
________________________________
Hi Iulian,

Thank you for the rapid response and great information.  I have a couple of follow-up questions (inline).

From: Iulian Grindeanu <iulian at mcs.anl.gov<mailto:iulian at mcs.anl.gov>>
Date: Sat, 11 Feb 2012 01:02:03 -0500
To: Christopher Mueller <cmueller at asascience.com<mailto:cmueller at asascience.com>>
Cc: Guy De Wardener <gdewardener at asascience.com<mailto:gdewardener at asascience.com>>, David Stuebe <DStuebe at asascience.com<mailto:DStuebe at asascience.com>>, don brittain <don.brittain at instanteffects.com<mailto:don.brittain at instanteffects.com>>, "moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>" <moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>>
Subject: Re: [MOAB-dev] Questions about Tags and Topology

Hello,
I will try to answer to some of those questions;

________________________________
Hi Tim,

I've had a good deal of success this week and have been able to represent a couple of our simpler datasets in what seems to be a reasonable manner.  I have also come up with a few questions.

Tags:

 *   DataTypes – from what I can see, tags do not support a few of the numpy datatypes, namely: float32, int16, and int64.  Is this a constraint of the PyTAPS wrapper or the underlying iMesh/MOAB infrastructure?

itaps has a limited data type set; see MOAB/itaps/iBase.h
pytaps is closely related to itaps;

some types can be "manufactured" out of byte type, but it is the user responsibility to interpret / convert correctly (so interpret an int16 as a 2-byte value, etc). I am not sure if something like that is possible in python/pytaps. It is for sure possible in c/c++

 *
 *   Tags-of-tags – Is this possible?  I've tried a couple of ways but can't seem to get it to go.

tags can be set/get on anything that is an "EntityHandle" in moab. So anything that is an entity handle (node, element, mesh set) can set and get tag values, using a tag handle.
I am not sure I understand the question. Would you need to set a tag value on a tag handle? That is not possible.

Unfortunately, it is the latter case that I was hoping for – the ability to set a tag value on a tag handle.  For example:
tag1=mesh.createTag("tag1",1,bytes)
tag2=mesh.createTag("tag2,1,bytes)
tag2[tag1]=value

Yes, we cannot do that. Sorry :(

OK – we can find another pathway (perhaps even using the "opaque" data type suggested in Jim's reply from a moment ago?)

 *

Topology:

 *   Is it possible to apply topology over entity sets?  One way I've found for dealing with time is to have a "temporal" EntitySet that has child EntitySets for each timestep.  This seems to work well, but I can't find a way of relating the various timesteps aside from the inherent indexing of the "temporal" EntitySet.  I hoped that it would be possible to do something like make a line_segment that related the timestep EntitySets, but that didn't seem to work.

maybe you can set a tag with the time value for each of the child EntitySets. I am not sure I understand what do you mean by "line_segment".
Also, if set1 is a child of set2, it does not mean that the set2 is a parent of set1 (and viceversa)  see the difference between
add_parent_child and add_child_meshset, for example

Another thing that can help:
 you add child1 to set1, then add child2 to set1
When you ask for children of set1, you will always get them in order child1, child2. So maybe you can use that for a natural ordering of your children ( EntitySets ).

This is the method I'm currently using and it works well as long as the relationship is a linear one (unfortunately, this may not always be the case for us).
Do you know if it is possible to "insert" a child into an existing list of children?  For example:
set1_children=[c1,c2,c3,c4]
set.add(c2a,index=2)
set1_children=[c1,c2,c2a,c3,c4]

We do not have a method exposed to insert at an index (even in MOAB)
The lists of parents or children is stored inside as an array (except if 1 or 2 parents/children, but that is not that important)

Inserting at an index could be accomplished right now with the interface only be removing c3, c4, then add c2a, c3, c4. I know it is not optimal; if performance is a concern, we would need to add a method to the interface to insert at an index;  even with that change, the performance gain will not be that important (we would still need to reallocate the array inside, but only once)

Alright – as you said, not the best in terms of performance, but definitely a functional work-around.

Another question: Is the mesh changing in time? That is one reason you may want EntitySets changing in time. Or maybe some solution uses different mesh elements at a given time

This is certainly a possibility, so having an entityset/time is valuable to us.

 *
 *   Edges from quadrilaterals:  After building a set of quadrilateral entities from an array of vertices, I was surprised that there were not edge entities generated as well.  Is there a method for doing this?  I realize I could generate the edges from the vertex array (perhaps after some reworking), but it seems to me that it might also be possible to get them from the quadrilaterals themselves.

this is the easiest question:)
you have to use the flag create_if_missing=true in a call like:
ErrorCode get_adjacencies(const EntityHandle *from_entities,
                                      const int num_entities,
                                      const int to_dimension,
                                      const bool create_if_missing,
                                      std::vector<EntityHandle>& adj_entities,
                                      const int operation_type = Interface::INTERSECT) = 0;

from_entities are your quads, to_dimension is 1 (edges), and you will get the edges in adj_entities vector.

This is great news!  I tried applying the argument "create_if_missing" as a kwarg in a handful of the iMesh functions exposed in PyTAPS (mesh.createEntArr, mesh.getEntArr, mesh.getEntAdj), but I kept getting a TypeError stating that "'create_if_missing' is an invalid keyword argument for this function".  Do you know if this functionality is available from PyTAPS?

So, do you use PyTaps here? there is no "create_if_missing" argument in imesh functions. This works directly with MOAB only.

With iMesh, you may be able to use "AdjTable" methods. Again, I am not sure about pytaps.

With AdjTable, you would need to set the AdjTable [5] to 1; then, when loading a mesh, the edge entities will be created if missing
(so use iMesh_setAdjTable , and pass an AdjTable that has 1 at index 5, corresponding to adjacency cost edge/edge of 1)
So with iMesh, after setting adjTable, a subsequent iMesh_load will generate the edges too, if they are missing.

It seems that adjTable is exposed in pytaps, but I can't change it :(
Maybe Jim knows a way to set it in pytaps too.

Thanks for the suggestion, I'll poke around with the AdjTable a bit and see if I can find a way to generate the edges.

Iulian

Another question: Is the mesh changing in time? That is one reason you may want EntitySets changing in time. Or maybe some solution uses different mesh elements at a given time

This is certainly a possibility, so having an entityset/time is valuable to us.

 *
 *   Edges from quadrilaterals:  After building a set of quadrilateral entities from an array of vertices, I was surprised that there were not edge entities generated as well.  Is there a method for doing this?  I realize I could generate the edges from the vertex array (perhaps after some reworking), but it seems to me that it might also be possible to get them from the quadrilaterals themselves.

this is the easiest question:)
you have to use the flag create_if_missing=true in a call like:
ErrorCode get_adjacencies(const EntityHandle *from_entities,
                                      const int num_entities,
                                      const int to_dimension,
                                      const bool create_if_missing,
                                      std::vector<EntityHandle>& adj_entities,
                                      const int operation_type = Interface::INTERSECT) = 0;

from_entities are your quads, to_dimension is 1 (edges), and you will get the edges in adj_entities vector.

This is great news!  I tried applying the argument "create_if_missing" as a kwarg in a handful of the iMesh functions exposed in PyTAPS (mesh.createEntArr, mesh.getEntArr, mesh.getEntAdj), but I kept getting a TypeError stating that "'create_if_missing' is an invalid keyword argument for this function".  Do you know if this functionality is available from PyTAPS?

Thanks in advance,
Chris
Hope this helps,
Iulian

Thanks,
Chris

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