#calculate pole figure y's
sph = np.array(np.divmod(np.ravel(pf_grid), pf_grid.shape[1])).T
sph = sph * pf.res
sph[:, 0] = np.where(sph[:, 0] == 0, 0.004363323,
sph[:, 0]) #1/4deg tilt off center to avoid issues
#convert to xyz
xyz_pf = np.zeros((sph.shape[0], 3))
xyz_pf[:, 0] = np.sin(sph[:, 0]) * np.cos(sph[:, 1])
xyz_pf[:, 1] = np.sin(sph[:, 0]) * np.sin(sph[:, 1])
xyz_pf[:, 2] = np.cos(sph[:, 0])
od = bunge(cellSize, crystalSym, sampleSym)
""" refl weights """
a = 4.046 #Angstrom
latt = Lattice.cubic(a)
structure = Structure(latt, ["Al", "Al", "Al", "Al"],
[[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5]])
rad = 'CuKa'
refl_wgt = calc_XRDreflWeights(structure, hkls, rad='CuKa')
refl_wgt = {0: 1.0, 1: 1.0, 2: 1.0}
omega = np.radians(np.arange(0, 365, 5))
""" symmetry after """
hkls = normalize(np.array(hkls))
#def200path = '/home/nate/wimv/ARL/Microbeam Collimator/Defocus_220_Si.xrdml'
#def220path = '/home/nate/wimv/ARL/Microbeam Collimator/Defocus_311_Si.xrdml'
#
#defs = [def111path,def200path,def220path]
#defocus = poleFigure(defs, hkls, crystalSym, 'xrdml',subtype='defocus')
#
#pf111path = '/home/nate/wimv/ARL/Microbeam Collimator/Ti18_asrec/beta_110_Ti18_asrec.xrdml'
#pf200path = '/home/nate/wimv/ARL/Microbeam Collimator/Ti18_asrec/beta_200_Ti18_asrec.xrdml'
#pf220path = '/home/nate/wimv/ARL/Microbeam Collimator/Ti18_asrec/beta_211_Ti18_asrec.xrdml'
pfs = [pf111path,pf200path,pf220path]
pf = poleFigure(pfs, hkls, crystalSym, 'xrdml')
pf.correct(bkgd=bkgd,defocus=defocus)
pf.normalize()
od = bunge(cellSize, crystalSym, sampleSym)
pf_grid, alp, bet = pf.grid(full=True,ret_ab=True)
recalc_pf, calc_od, pf_od, od_pf = wimv(pf, od, ret_pointer=True)
# %%
### FIBER CALC ###
import rowan
from tqdm import tqdm
from pyTex.orientation import ro2ax, ax2om, om2eu
#calculate pole figure y's
@author: nate
"""
## testing fiber
import numpy as np
from scipy.spatial.transform import Rotation as R
from pyTex.orientation import symmetrise as symOri
from pyTex.orientation import om2eu, eu2om
from pyTex.utils import genSymOps
from pyTex import bunge
cs = 'm-3m'
ss = 'mmm'
od = bunge(np.deg2rad(5), cs, ss)
hkl = np.array([2, 1, 3])
hkl = np.divide(hkl, np.linalg.norm(hkl))
test = R.from_euler('ZXZ', [40.5, 42.7, 85.0], degrees=True)
testSym = symOri(test.as_matrix(), cs, ss)
#try transpose
testSym = testSym.transpose((0, 2, 1))
# convert to euler
testSym_eu = om2eu(testSym)
# pick fundamental zone
fz = (testSym_eu[:, 0] <= 2 * np.pi) & (testSym_eu[:, 1] <= np.pi / 2) & (