[MOAB-dev] Questions about Tags and Topology

[Iulian Grindeanu]

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? ----- Original Message -----
| 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 >
| Date: Sat, 11 Feb 2012 01:02:03 -0500
| To: Christopher Mueller < cmueller at asascience.com >
| Cc: Guy De Wardener < gdewardener at asascience.com >, David Stuebe <
| DStuebe at asascience.com >, don brittain <
| don.brittain at instanteffects.com >, " moab-dev at mcs.anl.gov " <
| 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;
| | ----- Original Message -----
| | | 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 :( | | | •
| | | 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) | | 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. 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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