Dear Konstantinos
This worked
Maybe not the most elegant solution
file = open("Gfield.txt","r")
gdata = np.loadtxt(file,dtype=float)
#print(gdata)
x = gdata[:,0:3]
#print(x)
tree = KDTree(x)
#print(tree)
print(mfpb.basic_dof_nodes(0))
Pt=mfpb.basic_dof_nodes(1)
print(Pt)
Pt=mfpb.basic_dof_nodes(2)
print(Pt)
a = np.empty([meshb.nbpts(),3])
for i in range(meshb.nbpts()):
Pt=mfpb.basic_dof_nodes(i)
a[i][0]=Pt[0]
a[i][1]=Pt[1]
a[i][2]=Pt[2]
#
#a = mfpb.basic_dof_nodes()
#y = a.transpose()
print(a[1][0])
dd,ii = tree.query(a)
for i in range(10):
print(ii[i])
print('Read G as field on nodes');
md.add_fem_data("gf", mfpb)
md.set_variable("gf", gdata[ii,3])
mfoutb = gf.MeshFem(meshb)
mfoutb.set_classical_discontinuous_fem(2)
mfoutb.export_to_vtu("gf.vtu",
mfpb, md.variable("gf"), "ShearMod")
From: Lesage,Anne Cecile J <ajles...@mdanderson.org>
Sent: Monday, December 13, 2021 5:53 PM
To: Lesage,Anne Cecile J <ajles...@mdanderson.org>; Konstantinos Poulios
<logar...@googlemail.com>
Cc: getfem-users@nongnu.org
Subject: RE: [EXT] Re: defining a field on the mesh dofs
It seems that mfpb.basic_dof_nodes() does not have the right structure to be
compared to tree
From: Getfem-users
<getfem-users-bounces+ajlesage=mdanderson....@nongnu.org<mailto:getfem-users-bounces+ajlesage=mdanderson....@nongnu.org>>
On Behalf Of Lesage,Anne Cecile J
Sent: Monday, December 13, 2021 11:57 AM
To: Konstantinos Poulios
<logar...@googlemail.com<mailto:logar...@googlemail.com>>
Cc: getfem-users@nongnu.org<mailto:getfem-users@nongnu.org>
Subject: RE: [EXT] Re: defining a field on the mesh dofs
WARNING: This email originated from outside of MD Anderson. Please validate the
sender's email address before clicking on links or attachments as they may not
be safe.
Dear Konstantinos
I adapted your solution to the interpolation of a shear modulus field on the
mesh.
from scipy.spatial import KDTree
file = open("Gfield.txt","r")
gdata = np.loadtxt(file,dtype=float)
tree = KDTree(gdata[:,0:3])
dd,ii = tree.query(mfpb.basic_dof_nodes())
md.add_fem_data("gf", mfpb)
md.set_variable("gf", gdata[ii,3])
However I get the following error
Traceback (most recent call last):
File "testresect5poroelasticbrainheadv1.py", line 208, in <module>
dd,ii = tree.query(mfpb.basic_dof_nodes())
File
"/home/ajlesage/.local/lib/python3.8/site-packages/scipy/spatial/kdtree.py",
line 472, in query
d, i = super().query(x, k, eps, p, distance_upper_bound, workers)
File "ckdtree.pyx", line 779, in scipy.spatial.ckdtree.cKDTree.query
File "ckdtree.pyx", line 1604, in scipy.spatial.ckdtree.num_points
ValueError: x must consist of vectors of length 4 but has shape (3, 18154)
What do you think is the issue there?
My data is a four column ascii file x, y, z, value
From: Konstantinos Poulios
<logar...@googlemail.com<mailto:logar...@googlemail.com>>
Sent: Thursday, December 2, 2021 2:09 AM
To: Lesage,Anne Cecile J
<ajles...@mdanderson.org<mailto:ajles...@mdanderson.org>>
Cc: getfem-users@nongnu.org<mailto:getfem-users@nongnu.org>
Subject: [EXT] Re: defining a field on the mesh dofs
WARNING: This email originated from outside of MD Anderson. Please validate the
sender's email address before clicking on links or attachments as they may not
be safe.
Dear Anne-Ceclie
I guess what pfield.txt contains is a list of values ordered in the same order
as the mesh nodes. In general there is no guarantee that the mesh nodes will be
in the same order in GetFEM but if your original numbering of nodes is
contiguous, chances are good that GetFEM will keep the same numbering. Then the
next point is that dof numbering and mesh node numbering do not need to be the
same. In fact you can even have a larger or smaller number of dofs than the
number of mesh nodes.
A more general solution for you would be to save in the pfield.txt file 4
values, x,y,z coordinates and field value. Then you can always read the value
of the closest point for each dof with something like:
import numpy as np
from scipy.spatial import KDTree
file = open("pfield.txt", "r") # assuming it contains 4 columns: x,y,z,value
pdata = np.loadtxt(file,dtype=float)
tree = KDTree(pdata[:,0:3])
dd,ii = tree.query(mfp.basic_dof_nodes())
md.add_fem_data("pc", mfp)
md.set_variable("pc", pdata[ii,3])
Best regards
Kostas
On Wed, Dec 1, 2021 at 10:42 PM Lesage,Anne Cecile J
<ajles...@mdanderson.org<mailto:ajles...@mdanderson.org>> wrote:
Dear all
I would like to define a non-constant pressure field on the mesh dofs
I would like to read the value from an ascii file
I am thinking of using the following python scripting
import numpy as np
file = open('pfield.txt', 'r') # 'r' = read
pfield = np.loadtxt(file,dtype=fload)
md.add_fem_data(“pc”,mfp)
md.set_variable("pc", pfield)
Will it be correct to use pc in building a week form?
Thank you
Regards
Anne-Cecile
The information contained in this e-mail message may be privileged,
confidential, and/or protected from disclosure. This e-mail message may contain
protected health information (PHI); dissemination of PHI should comply with
applicable federal and state laws. If you are not the intended recipient, or an
authorized representative of the intended recipient, any further review,
disclosure, use, dissemination, distribution, or copying of this message or any
attachment (or the information contained therein) is strictly prohibited. If
you think that you have received this e-mail message in error, please notify
the sender by return e-mail and delete all references to it and its contents
from your systems.
The information contained in this e-mail message may be privileged,
confidential, and/or protected from disclosure. This e-mail message may contain
protected health information (PHI); dissemination of PHI should comply with
applicable federal and state laws. If you are not the intended recipient, or an
authorized representative of the intended recipient, any further review,
disclosure, use, dissemination, distribution, or copying of this message or any
attachment (or the information contained therein) is strictly prohibited. If
you think that you have received this e-mail message in error, please notify
the sender by return e-mail and delete all references to it and its contents
from your systems.
The information contained in this e-mail message may be privileged,
confidential, and/or protected from disclosure. This e-mail message may contain
protected health information (PHI); dissemination of PHI should comply with
applicable federal and state laws. If you are not the intended recipient, or an
authorized representative of the intended recipient, any further review,
disclosure, use, dissemination, distribution, or copying of this message or any
attachment (or the information contained therein) is strictly prohibited. If
you think that you have received this e-mail message in error, please notify
the sender by return e-mail and delete all references to it and its contents
from your systems.
