<div dir="ltr"><div><div><div>Hi Martin,<br><br></div>We're working on some infrastructure to document API changes. I'd like to wait to merge your changes for switching the tensor order output for vtkCellDerivatives until that's done. That way it will be easier to notify everyone of this change (even though it's not technically changing the API, just how the output should be interpreted). We're hoping it will be ready in a week. Is that ok to wait for merging your changes into VTK master?<br><br></div>Thanks,<br></div>Andy<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 22, 2016 at 2:42 PM, Andy Bauer <span dir="ltr"><<a href="mailto:andy.bauer@kitware.com" target="_blank">andy.bauer@kitware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Martin,<br><br></div>In case you didn't receive the email notice, your changes have been merged into master. Thanks for your contribution to VTK! This looks like it was your first contribution. I hope it wasn't too onerous to get done but the community works hard to make sure that the code is high quality and well tested.<br><br></div>Best regards,<br></div>Andy<br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 22, 2016 at 10:22 AM, Andy Bauer <span dir="ltr"><<a href="mailto:andy.bauer@kitware.com" target="_blank">andy.bauer@kitware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">It looks like vtkCellDerivates is the only class that uses vtkTensor. When we switch vtkCellDerivatives to C ordering I think we'll just remove vtkTensor. Less code with the same functionality and probably better efficiency -- tough to beat that :)<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 22, 2016 at 9:03 AM, Martin Genet <span dir="ltr"><<a href="mailto:martin.genet@polytechnique.edu" target="_blank">martin.genet@polytechnique.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Sounds good.<br>
<br>
However, here the culprit seems to be vtkTensor, which stores the
data in column. vtkCellDerivatives simply fills a vtkTensor (filling
is storage independent, since one provides the actual components),
and then returns the underlying vector.<br>
<br>
One option would be to make vtkCellDerivatives independent of
vtkTensor.<br>
<br>
But I think it would be better to correct the storage in vtkTensor.
Actually, it seems that vtkTensor is used only in
vtkCellDerivatives, so it would not change the rest of the library.<br>
<br>
Let me know what you would prefer.<span><font color="#888888"><br>
<br>
Martin</font></span><div><div><br>
<br>
<div>On 20/01/2016 19:19, Andy Bauer wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>I've looked at this a bit more along with others and
unfortunately there's some inconsistency in VTK for tensor
ordering. If you look at the vtkCell::Derivatives()
documentation (<a href="http://www.vtk.org/doc/nightly/html/classvtkCell.html#aff3d8332e9d7d556a9d2e9f91173d068" target="_blank">http://www.vtk.org/doc/nightly/html/classvtkCell.html#aff3d8332e9d7d556a9d2e9f91173d068</a>),
it's using a C/row-major ordering. There's some places in
that have done row-major and others that have done column
major. For the most part it hasn't been an issue since
many/most of the uses of tensor have been symmetric but it
should be fixed regardless.<br>
<br>
</div>
I've entered a mantis issue for this at <a href="http://www.paraview.org/Bug/view.php?id=15949" target="_blank"></a><a href="http://www.paraview.org/Bug/view.php?id=15949" target="_blank">http://www.paraview.org/Bug/view.php?id=15949</a>.<br>
<br>
</div>
Would you be willing to go in and make the change to
vtkCellDerivatives? I'm hoping to go through your changes to
that class sometime today.<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 20, 2016 at 7:52 AM, Andy
Bauer <span dir="ltr"><<a href="mailto:andy.bauer@kitware.com" target="_blank">andy.bauer@kitware.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hmm, in fact it does. I was looking at
vtkGradientFilter instead of vtkCellDerivatives for the
ordering of the output of the gradient of a vector. I
think the output order is supposed to be
fortran/column-major ordering like vtkCellDerivatives
instead of C/row-major ordering like vtkGradientFilter.
Well, you can see the confusion that crops up and maybe
that's why vtkTensors was done that way. In any case, let
me verify for sure which way is correct and get back to
you on this.<br>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 20, 2016 at 5:24
AM, Martin Genet <span dir="ltr"><<a href="mailto:martin.genet@polytechnique.edu" target="_blank"></a><a href="mailto:martin.genet@polytechnique.edu" target="_blank">martin.genet@polytechnique.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Thanks
Andy.<br>
<br>
Well, I might be wrong but I'm under the
impression that vtkCellDerivatives returns
[du/dx, dv/dx, dw/dx, du/dy, dv/dy, ...]. Am I
wrong?<span><font color="#888888"><br>
<br>
Martin</font></span>
<div>
<div><br>
<br>
<div>On 20/01/2016 03:07, Andy Bauer wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Hi Martin,<br>
<br>
</div>
I haven't looked closely enough at
vtkTensors (I don't know if I even
knew about it before today) but
indeed the ordering output in
vtkCellDerivatives for a velocity
vector {u,v,w} needs to be [du/dx,
du/dy, du/dz, dv/dx, dv/dy, ...]
like you have it. I'm not sure when
vtkTensors is ordered the way it is.<br>
<br>
</div>
Cheers,<br>
</div>
Andy<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jan 19,
2016 at 5:02 PM, Martin Genet <span dir="ltr"><<a href="mailto:martin.genet@polytechnique.edu" target="_blank"></a><a href="mailto:martin.genet@polytechnique.edu" target="_blank">martin.genet@polytechnique.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Thanks Andy.<br>
<br>
I need to clarify something: the
Derivatives function of vtkCell
objects returns a derivs vector
containing the components of the
gradient of some vector field
defined at the cell nodes; the
components are ordered in row (as
usually in C, i.e., (0,0), (0,1),
(0,2), (1,0), (1,1), (1,2), (2,0),
(2,1), (2,2)). Now in the
CellDerivatives filter the derivs
vector is used to fill a
vtkTensors, and then the filter
returns the internal vector
storing the data of the
vtkTensors. However, the
components of the vtkTensors are
ordered in column (as usually in
fortran, i.e., (0,0), (1,0),
(2,0), (0,1), (1,1), (2,1), (0,2),
(1,2), (2,2)). Is it on purpose
that the vtkTensors store their
data in column and not in row?
Isn't it a little dangerous to mix
both storage in the code? Thanks
for the clarification!<span><font color="#888888"><br>
<br>
Martin</font></span>
<div>
<div><br>
<br>
<div>On 18/01/2016 13:32, Andy
Bauer wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Hi Martin,<br>
<br>
</div>
Thanks for following
up on this. I found
the merge request now
and will look at this.
In general, developers
should request others
to do a code review on
this. This can be done
via something like
"@acbauer please
review this" or
sending an email on
this VTK list with a
link to the merge
request.<br>
<br>
</div>
Best,<br>
</div>
Andy<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
Mon, Jan 18, 2016 at
6:23 AM, Martin Genet <span dir="ltr"><<a href="mailto:martin.genet@polytechnique.edu" target="_blank"></a><a href="mailto:martin.genet@polytechnique.edu" target="_blank">martin.genet@polytechnique.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Andy,<br>
<br>
I followed the
directions, and
submitted a patch
(19 days ago), but
haven't heard
anything back.<br>
<br>
In GitLab the merge
requests counter is
at 0, but when I try
to create a new
merge request from
my commit, it tells
the merge request
already exists. Is
it being reviewed
somewhere? Thanks!<span><font color="#888888"><br>
<br>
Martin</font></span>
<div>
<div><br>
<br>
<div>On
29/12/2015
13:22, Andy
Bauer wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Hi
Martin,<br>
<br>
</div>
This patch
makes sense.
It would need
a test if you
want to get
your changes
into VTK. The
directions for
contributing
to VTK are at
<a href="https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/develop.md" target="_blank"></a><a href="https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/develop.md" target="_blank">https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/develop.md</a>.<br>
<br>
</div>
Cheers,<br>
</div>
Andy<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
Mon, Dec 28,
2015 at 5:50
PM, Martin
Genet <span dir="ltr"><<a href="mailto:martin.genet@polytechnique.edu" target="_blank"></a><a href="mailto:martin.genet@polytechnique.edu" target="_blank">martin.genet@polytechnique.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Thanks Andy.<br>
<br>
What about
simply adding
another mode,
e.g.
SetTensorModeToComputeGreenLagrangeStrain,
to the
vtkCellDerivatives
filter? Would
the attached
patch make
sense?<br>
<br>
Martin<br>
<br>
<div>On
28/12/2015
14:12, Andy
Bauer wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Hi
Martin,<br>
<br>
</div>
Changing the
name of the
SetTensorModeToComputeStrain
method to
something else
would break
backward
compatibility
which is
generally
avoided in
VTK. Other
options for
this include
deriving a
class to
compute
non-linear
strain from
vtkCellDerivatives
if it shares
enough of the
algorithm with
the linearized
version or
maybe just
creating a new
filter.<br>
<br>
</div>
Cheers,<br>
</div>
Andy<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
Sat, Dec 26,
2015 at 4:36
PM, Martin
Genet <span dir="ltr"><<a href="mailto:martin.genet@polytechnique.edu" target="_blank"></a><a href="mailto:martin.genet@polytechnique.edu" target="_blank">martin.genet@polytechnique.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear
VTK users:<br>
<br>
I realize that
the
vtkCellDerivatives
filter, when
SetTensorModeToComputeStrain
is activated,
returns the
symmetric part
of the
gradient of
the input
vector field,
which is the
linearized
strain tensor,
i.e., not a
proper measure
of deformation
when large
displacements
are involved.
Would that
make sense to
have two
different
modes,
SetTensorModeToComputeLinearizedStrain
or
SetTensorModeToComputeSymmetricGradient,
and
SetTensorModeToComputeStrain
or
SetTensorModeToComputeGreenLagrangeStrain?
Thanks!<br>
<br>
Martin<br>
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