def fib2meshalyzer(filename):
"""
Given a filename for a CARP mesh (.pts, .elem and .lon) this functions
generates the .vec and .vpts files necessary to visualize vector data
in meshalyzer.
"""
ptsFile = "%s.pts" % filename
lonFile = "%s.lon" % filename
vecFile = "%s.vec" % filename
elemFile = "%s.elem" % filename
vptsFile = "%s.vpts" % filename
np_xyz = read_array_pts(ptsFile)
elemList = read_array_elem(elemFile)
# copy filename.lon to filename.vec
shutil.copy(lonFile, vecFile)
# create .vpts file
f = open(vptsFile, "w")
f.write("%d\n" % len(elemList))
for e in elemList:
numNode = getNumNode[e[0]]
nodeList = [e[j + 1] for j in xrange(numNode)]
centroid = get_element_center(nodeList, np_xyz)
f.write("%f %f %f\n" % (centroid[0], centroid[1], centroid[2]))
f.close()
print ".vec and .vpts files were generated!"
def fit_lambda(igb_file, pts_file, resolution=100):
"""
Function to fit the space constant lambda
Input: igb_file - with Vm at each time slice
pts_file - file describing the mesh
resolution - of the mesh
"""
[vm, hd] = read_igb_slice(igb_file)
Vm = vm.squeeze()
xyz = read_array_pts(pts_file)
ytmp = xyz[:,1]
ztmp = xyz[:,2]
size = len(xyz[:,1])
# list with the nodes' indexes of the line
aux = -resolution/2
lindx = [i for i in xrange(size) if ytmp[i] == aux and ztmp[i] == aux]
value1 = Vm[100,:]
x = zeros((len(lindx))) # space
data = zeros((len(lindx))) # vm at t=100ms
###
### improve the loop and assignments below
###
for i in lindx:
x[i] = xyz[i,0]
data[i] = value1[i]
def dbexpl(x,p):
"""
Example of curve fitting for
a*exp(-x/p1)
"""
return( p[0]*exp(-(x+25000)/p[1]) + data[-1] )
def residuals(p,data,x):
err = data - dbexpl(x,p)
return err
### vm curve fitting ###
p0 = [10,1000] # initial guesses
guessfit = dbexpl(x,p0) # data evaluated with p0
pbest = leastsq(residuals,p0,args=(data,x),full_output=1) # minimize the sum of squares of a set of equations
bestparams = pbest[0] # solution (estimated parameters)
cov_x = pbest[1] # estimate of the covariance matrix of the solution
print 'Best fit parameters: ' , bestparams
#print cov_x
datafit = dbexpl(x,bestparams)
plot(x,data,'b',x,datafit,'r')
legend(['Vm(x,t=100ms)','fitting'], 'upper right')
xlabel('Time')
title('Space constant ''$\lambda$'' fitting')
grid(True)
show()
def condVelocity(ptsFile, actFile, output=True):
"""
Function to calculate the conduction velocity in a cable slab
Input: ptsFile - description of the nodes
actFile - file with activation time of the nodes
Example:
0 1 2 3 4 5 6 7 8
A B
Bernardo Martins Rocha, 2008
"""
xyz = read_array_pts(ptsFile)
#act = read_array(actFile) # deprecated under new SciPy/Numpy
act = loadtxt(actFile)
actTeste = act
distA = max(xyz[:,0]/4)
distB = 3*max(xyz[:,0]/4)
# node A
tmp = abs(xyz[:,0] - distA)
tmpID = where(tmp == tmp.min()) # where return tuple
aux = tmpID[0][0] + 1
nodeA = xyz[aux]
actTI = where(act[:,0] == aux) # activation time index
if size(actTI) == 0:
if output: print " NodeA was not activated. CV is unknown!"
return nan
else:
actTI = actTI[0][0] # from tuple to scalar
actTA = act[actTI , 1] # activation time for node A
# node B
tmp = abs(xyz[:,0] - distB)
tmpID = where(tmp == tmp.min()) # where return tuple
aux = tmpID[0][0] + 1
nodeB = xyz[aux]
actTI = where(act[:,0] == aux) # activation time index
if size(actTI) == 0:
if output: print " NodeB was not activated. CV is unknown!"
return nan
else:
actTI = actTI[0][0] # from tuple to scalar
actTB = act[actTI , 1] # activation time for node B
distAB = sqrt(sum(pow(nodeB - nodeA,2)))
condve = distAB / (actTB - actTA)
if output: print " CV = %.3f m/s" % (condve/1000)
return (condve/1000)
def tag_elem_file (elem_file, node_file, region_list):
"""
Function to tag rectangular areas in structured meshes in CARP
Bernardo M. Rocha, 2009
"""
new_efile = open('element.elem', 'w')
elem = read_array_elem (elem_file)
pts = read_array_pts (node_file)
for r in region_list:
for e in elem:
elem_type = e[0]
if elem_type == 'Qd':
node_range = xrange(1,4+1)
node_tag = e[5]
for n in node_range:
g = int( e[n] )
node = Point ( pts[g][0], pts[g][1], pts[g][2] )
# check if node is inside region
if ( (node.x >= r.bottom.x) and
(node.x <= r.bottom.x + r.width) and
(node.y >= r.top.y - r.height) and
(node.y <= r.top.y)):
node_tag = r.tag
# end if
# end for n
e[5] = node_tag
# end if Qd
# end for e
# end for r
# write to file
new_efile.write('%d\n' % len(elem))
for e in elem:
new_efile.write('Qd %d %d %d %d %d \n' %
(int(e[1]), int(e[2]),int(e[3]),int(e[4]),int(e[5])))
new_efile.close()
new_efile.close()
