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computeSyntheticHelixTransverseSheetAngles.py
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computeSyntheticHelixTransverseSheetAngles.py
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#coding=utf8
########################################################################
### ###
### Created by Martin Genet, 2012-2016 ###
### ###
### University of California at San Francisco (UCSF), USA ###
### Swiss Federal Institute of Technology (ETH), Zurich, Switzerland ###
### École Polytechnique, Palaiseau, France ###
### ###
########################################################################
import random
import numpy
import myVTKPythonLibrary as myVTK
########################################################################
def computeSyntheticHelixTransverseSheetAngles(
farray_rr,
farray_cc,
farray_ll,
angles="+/-60",
sigma=0.,
farray_angle_helix=None,
farray_angle_trans=None,
farray_angle_sheet=None,
verbose=0):
myVTK.myPrint(verbose, "*** computeSyntheticHelixTransverseSheetAngles ***")
if (angles == "+/-60"):
angles = [[[[+60], [+60]], [[-60], [-60]]],
[[[ 0], [ 0]], [[ 0], [ 0]]],
[[[ 0], [ 0]], [[ 0], [ 0]]]]
n_l = [[0. for k_r in xrange(2)] for k_angle in xrange(3)]
d_l = [[0. for k_r in xrange(2)] for k_angle in xrange(3)]
n_c = [[0. for k_r in xrange(2)] for k_angle in xrange(3)]
d_c = [[0. for k_r in xrange(2)] for k_angle in xrange(3)]
for k_angle in xrange(3):
#print "k_angle = "+str(k_angle)
for k_r in xrange(2):
#print "k_r = "+str(k_r)
n_l[k_angle][k_r] = len(angles[k_angle][k_r])
assert (n_l[k_angle][k_r] > 1), "Must have more than 1 longitudinal dof. Aborting."
#print "n_l = "+str(n_l)
d_l[k_angle][k_r] = 1./(n_l[k_angle][k_r]-1)
#print "d_l = "+str(d_l)
n_c[k_angle][k_r] = len(angles[k_angle][k_r][0])
assert (n_c[k_angle][k_r] > 0), "Must have more than 0 circumferential dof. Aborting."
#print "n_c = "+str(n_c)
d_c[k_angle][k_r] = 1./n_c[k_angle][k_r]
#print "d_c = "+str(d_c)
n_tuples = farray_rr.GetNumberOfTuples()
if (farray_angle_helix is None):
farray_angle_helix = myVTK.createFloatArray(
"angle_helix",
1,
n_tuples)
if (farray_angle_trans is None):
farray_angle_trans = myVTK.createFloatArray(
"angle_trans",
1,
n_tuples)
if (farray_angle_sheet is None):
farray_angle_sheet = myVTK.createFloatArray(
"angle_sheet",
1,
n_tuples)
farray_angles = [farray_angle_helix,\
farray_angle_trans,\
farray_angle_sheet]
for k_tuple in xrange(n_tuples):
#print "k_tuple = "+str(k_tuple)
angles_in_degrees = numpy.empty(3)
for k_angle in xrange(3):
#print "k_angle = "+str(k_angle)
rr = farray_rr.GetTuple1(k_tuple)
cc = farray_cc.GetTuple1(k_tuple)
i_c_end = int(cc/d_c[k_angle][0]/1.000001)
i_c_epi = int(cc/d_c[k_angle][1]/1.000001)
#print "i_c_end = "+str(i_c_end)
#print "i_c_epi = "+str(i_c_epi)
zeta_end = (cc - i_c_end*d_c[k_angle][0])/d_c[k_angle][0]
zeta_epi = (cc - i_c_epi*d_c[k_angle][1])/d_c[k_angle][1]
#print "zeta_end = "+str(zeta_end)
#print "zeta_epi = "+str(zeta_epi)
ll = farray_ll.GetTuple1(k_tuple)
i_l_end = int(ll/d_l[k_angle][0]/1.000001)
i_l_epi = int(ll/d_l[k_angle][1]/1.000001)
#print "i_l_end = "+str(i_l_end)
#print "i_l_epi = "+str(i_l_epi)
eta_end = (ll - i_l_end*d_l[k_angle][0])/d_l[k_angle][0]
eta_epi = (ll - i_l_epi*d_l[k_angle][1])/d_l[k_angle][1]
#print "eta_end = "+str(eta_end)
#print "eta_epi = "+str(eta_epi)
t_ii_end = angles[k_angle][0][i_l_end ][ i_c_end %n_c[k_angle][0]]
t_ji_end = angles[k_angle][0][i_l_end ][(i_c_end+1)%n_c[k_angle][0]]
t_ij_end = angles[k_angle][0][i_l_end+1][ i_c_end %n_c[k_angle][0]]
t_jj_end = angles[k_angle][0][i_l_end+1][(i_c_end+1)%n_c[k_angle][0]]
t_ii_epi = angles[k_angle][1][i_l_epi ][ i_c_epi %n_c[k_angle][1]]
t_ji_epi = angles[k_angle][1][i_l_epi ][(i_c_epi+1)%n_c[k_angle][1]]
t_ij_epi = angles[k_angle][1][i_l_epi+1][ i_c_epi %n_c[k_angle][1]]
t_jj_epi = angles[k_angle][1][i_l_epi+1][(i_c_epi+1)%n_c[k_angle][1]]
#print "t_ii_end = "+str(t_ii_end)
#print "t_ji_end = "+str(t_ji_end)
#print "t_ij_end = "+str(t_ij_end)
#print "t_jj_end = "+str(t_jj_end)
#print "t_ii_epi = "+str(t_ii_epi)
#print "t_ji_epi = "+str(t_ji_epi)
#print "t_ij_epi = "+str(t_ij_epi)
#print "t_jj_epi = "+str(t_jj_epi)
angle_end = t_ii_end * (1 - zeta_end - eta_end + zeta_end*eta_end) \
+ t_ji_end * ( zeta_end - zeta_end*eta_end) \
+ t_ij_end * ( eta_end - zeta_end*eta_end) \
+ t_jj_end * ( zeta_end*eta_end)
angle_epi = t_ii_epi * (1 - zeta_epi - eta_epi + zeta_epi*eta_epi) \
+ t_ji_epi * ( zeta_epi - zeta_epi*eta_epi) \
+ t_ij_epi * ( eta_epi - zeta_epi*eta_epi) \
+ t_jj_epi * ( zeta_epi*eta_epi)
angles_in_degrees[k_angle] = (1.-rr) * angle_end \
+ rr * angle_epi
if (sigma > 0.):
angles_in_degrees[k_angle] += random.normalvariate(0., sigma)
angles_in_degrees[k_angle] = (angles_in_degrees[k_angle]+90)%180-90
farray_angles[k_angle].SetTuple1(
k_tuple,
angles_in_degrees[k_angle])
return (farray_angle_helix,
farray_angle_trans,
farray_angle_sheet)
########################################################################
def addSyntheticHelixTransverseSheetAngles(
ugrid,
angles="+/-60",
type_of_support="cell",
sigma=0.,
verbose=0):
myVTK.myPrint(verbose, "*** addSyntheticHelixTransverseSheetAngles ***")
if (type_of_support == "cell"):
ugrid_data = ugrid.GetCellData()
elif (type_of_support == "point"):
ugrid_data = ugrid.GetPointData()
farray_rr = ugrid_data.GetArray("rr")
farray_cc = ugrid_data.GetArray("cc")
farray_ll = ugrid_data.GetArray("ll")
farray_angle_helix = ugrid_data.GetArray("angle_helix")
farray_angle_trans = ugrid_data.GetArray("angle_trans")
farray_angle_sheet = ugrid_data.GetArray("angle_sheet")
(farray_angle_helix,
farray_angle_trans,
farray_angle_sheet) = computeSyntheticHelixTransverseSheetAngles(
farray_rr=farray_rr,
farray_cc=farray_cc,
farray_ll=farray_ll,
angles=angles,
sigma=sigma,
farray_angle_helix=farray_angle_helix,
farray_angle_trans=farray_angle_trans,
farray_angle_sheet=farray_angle_sheet,
verbose=verbose-1)
ugrid_data.AddArray(farray_angle_helix)
ugrid_data.AddArray(farray_angle_trans)
ugrid_data.AddArray(farray_angle_sheet)
return (farray_angle_helix,
farray_angle_trans,
farray_angle_sheet)