def PCSAxRhFitXX(transformed_coos, sse_ordered, exp_data, stage):
"""
:param transformed_coos:
:param sse_ordered:
:param exp_data:
:param stage:
:return:
"""
nh_dict = coorNHdict(transformed_coos, sse_ordered)
pcs_data = exp_data['pcs_data']
# print "pcs_data", pcs_data
ntags = len(pcs_data)
# Define Thomas's implementaion of hollow concentric shells
metal_def = exp_data['metal_spheres']
M = [metal_def[0], metal_def[1]]
nM = metal_def[2]
npts = metal_def[3]
rMx = fastT1FM.MakeDvector(npts) # allocate memmory
rMy = fastT1FM.MakeDvector(npts)
rMz = fastT1FM.MakeDvector(npts)
fixedPointsOnSpheres(M, nM, rMx, rMy, rMz)
# Temp storage of tensor values
temp_tensor = []
for tag in range(0, ntags):
xyz_HN, smotif_pcs = matchPCS(nh_dict, pcs_data[tag])
total_pcs, pcs_bool = usuablePCS(smotif_pcs)
if pcs_bool: # save some time for not running
# Thomas's fast Tensor calc code
frag_len = len(smotif_pcs)
nsets = len(smotif_pcs[0])
xyz = fastT1FM.MakeDMatrix(frag_len, 3)
pcs = fastT1FM.MakeDMatrix(nsets, frag_len)
for k in range(nsets):
for j in range(frag_len):
fastT1FM.SetDArray(k, j, pcs, smotif_pcs[j][k])
cm = [0.0, 0.0, 0.0]
for j in range(frag_len):
cm[0] = cm[0] + xyz_HN[j][0]
cm[1] = cm[1] + xyz_HN[j][1]
cm[2] = cm[2] + xyz_HN[j][2]
cm[0] /= float(frag_len)
cm[1] /= float(frag_len)
cm[2] /= float(frag_len)
for j in range(frag_len):
fastT1FM.SetDArray(j, 0, xyz, xyz_HN[j][0] - cm[0])
fastT1FM.SetDArray(j, 1, xyz, xyz_HN[j][1] - cm[1])
fastT1FM.SetDArray(j, 2, xyz, xyz_HN[j][2] - cm[2])
tensor = fastT1FM.MakeDMatrix(nsets, 8)
Xaxrh_range = fastT1FM.MakeDMatrix(nsets, 4)
for i in range(0, nsets):
fastT1FM.SetDArray(i, 0, Xaxrh_range, 0.05)
fastT1FM.SetDArray(i, 1, Xaxrh_range, 200.0)
fastT1FM.SetDArray(i, 2, Xaxrh_range, 0.05)
fastT1FM.SetDArray(i, 3, Xaxrh_range, 200.0)
# ****
chisqr = fastT1FM.rfastT1FM_multi(npts, rMx, rMy, rMz, nsets,
frag_len, xyz, pcs, tensor,
Xaxrh_range)
# ****
saupe_array = []
for kk in range(nsets):
temp_saupe = []
for j in range(3, 8):
temp_saupe.append(fastT1FM.GetDArray(kk, j, tensor))
saupe_array.append(temp_saupe)
x = fastT1FM.GetDArray(0, 0, tensor)
y = fastT1FM.GetDArray(0, 1, tensor)
z = fastT1FM.GetDArray(0, 2, tensor)
metal_pos = [x + cm[0], y + cm[1], z + cm[2]]
# Compute and check Axial and Rhombic parameters
AxRh = calcAxRh(saupe_array)
# chisqr = checkAxRh(AxRh, chisqr, total_pcs, stage) # modifies the values of chisqr
chisqr = checkAxRhCutoffs(AxRh, chisqr, total_pcs, exp_data,
stage) # modifies the values of chisqr
AxRh.append(metal_pos) # add metal pos
# Free memory
fastT1FM.FreeDMatrix(xyz)
fastT1FM.FreeDMatrix(pcs)
fastT1FM.FreeDMatrix(Xaxrh_range)
fastT1FM.FreeDMatrix(tensor)
else:
chisqr = 1.0e+30
if chisqr < 1.0e+30:
nchisqr = chisqr / float(total_pcs - (nsets * 5))
snchisqr = nchisqr / float(math.pow(total_pcs, 1 / 3.0))
temp_tensor.append([tag, snchisqr, AxRh])
else:
fastT1FM.FreeDArray(rMx)
fastT1FM.FreeDArray(rMy)
fastT1FM.FreeDArray(rMz)
tfalse = []
return tfalse
fastT1FM.FreeDArray(rMx)
fastT1FM.FreeDArray(rMy)
fastT1FM.FreeDArray(rMz)
return temp_tensor
tensor = fastT1FM.MakeDMatrix(nsets, 8)
ttmp = fastT1FM.MakeDvector(5)
Xtmp = fastT1FM.MakeDvector(2)
Xaxrh_range = fastT1FM.MakeDMatrix(nsets, 4)
# this is specific for benchmmark set ! unless you define a broad range !!
# Tm
fastT1FM.SetDArray(0, 0, Xaxrh_range, 0.05)
fastT1FM.SetDArray(0, 1, Xaxrh_range, 100.0)
fastT1FM.SetDArray(0, 2, Xaxrh_range, 0.05)
fastT1FM.SetDArray(0, 3, Xaxrh_range, 100.0)
# Tb
fastT1FM.SetDArray(1, 0, Xaxrh_range, 0.05)
fastT1FM.SetDArray(1, 1, Xaxrh_range, 100.0)
fastT1FM.SetDArray(1, 2, Xaxrh_range, 0.05)
fastT1FM.SetDArray(1, 3, Xaxrh_range, 100.0)
chisqr = fastT1FM.rfastT1FM_multi(npts, rMx, rMy, rMz, nsets, frag_len, xyz, pcs, tensor, Xaxrh_range)
if (chisqr < 1.0e+30):
x = fastT1FM.GetDArray(0, 0, tensor)
y = fastT1FM.GetDArray(0, 1, tensor)
z = fastT1FM.GetDArray(0, 2, tensor)
saupe_array=[]
for kk in range(nsets):
temp_saupe=[]
for j in range(3,8):
temp_saupe.append(fastT1FM.GetDArray(kk, j, tensor))
fastT1FM.SetDvector(j-3, ttmp, fastT1FM.GetDArray(kk, j, tensor))
saupe_array.append(temp_saupe)
metalpos=[x+cm[0], y+cm[1], z+cm[2]]
AxRh=calc_axrh(saupe_array)