def show_cell(file,
n=[0, 0, 1],
bopt=1,
x0=[0, 0, 0],
rep=[1, 1, 1],
**kwargs):
crys = Crystal.from_cif(file)
tail = ''.join(np.array(n, dtype=str))
n = get_vec(n, crys, bopt)
#unit cells,lattice vectors,atom coordinates
cell_mesh = crys.mesh(range(rep[0] + 1), range(rep[1] + 1),
range(rep[2] + 1))
surfs = get_unit_cell(cell_mesh, n)
uvw = rcc.orient_crystal(np.array(crys.lattice_vectors), n_u=n, T=True)
pattern, lat_params = APAP_xyz(name, n, rep, dopt='s', tail=tail)
E, X, Y, Z = pattern[:, :4].T
scat = [X, Y, Z, [cs[int(e)] for e in E]]
scat2 = []
# pattern2,lat_params = APAP_xyz(name,n,rep,dopt='')
# E2,X2,Y2,Z2 = pattern2[:,:4].T
# scat2 = [X2,Y2,Z2, [cs[int(e)] for e in E2]];#print(E2)
#display options
c1, c2, c3 = (X.min() + X.max()) / 2, (Y.min() + Y.max()) / 2, (
Z.min() + Z.max()) / 2
w = 0.75 * max(X.max() - X.min(), Y.max() - Y.min(), Z.max() - Z.min())
xylims = [
c1 - w / 2, c1 + w / 2, c2 - w / 2, c2 + w / 2, c3 - w / 2, c3 + w / 2
]
fig, ax = dsp.stddisp(scat=scat, ms=100, surfs=surfs, rc='3d', std=0)
rcc.show_trihedron(ax,
uvw=uvw,
x0=[0, 0, 0],
cs=['r', 'g', 'b'],
labs=['$a$', '$b$', '$c$'],
lw=2,
rc=0.1,
h=0.2)
rcc.show_trihedron(ax,
x0=x0,
labs=['$x$', '$y$', '$z$'],
lw=2,
rc=0.1,
h=0.2)
dsp.stddisp(ax=ax,
ms=50,
scat=scat2,
xylims=xylims,
axPos=[0, 0, 1, 1],
pOpt='eXp',
**kwargs)
hdl = handler_3d(fig, persp=False)
def show_Fhkl(self, s=None, opts='m', h3D=0, **kwargs):
'''Displays structure factor over grid
- opts : see get_fz
- s : slice or str('k=0' => Fhkl(k=0)) or int('l==<int>')
'''
fz, fz_str = get_fz(opts)
s, s_str = self._get_slice(s)
tle = 'Structure factor($\AA$), showing %s in %s' % (fz_str, s_str)
h, k, l = self.hklF
Fhkl = self.Fhkl #.copy()
if isinstance(s, tuple):
Fhkl = Fhkl[s]
nx, ny = np.array((np.array(Fhkl.shape) - 1) / 2, dtype=int)
i, j = np.meshgrid(np.arange(-nx, nx + 1), np.arange(-ny, ny + 1))
fig, ax = dsp.stddisp(scat=[i, j, fz(Fhkl)], title=tle, **kwargs)
else:
fig, ax = dsp.stddisp(scat=[h, k, l, fz(self.Fhkl)],
title=tle,
rc='3d',
**kwargs)
if h3D: h3d.handler_3d(fig, persp=False)
def show_cell(file,
n=[0, 0, 1],
bopt=1,
x0=None,
rep=[1, 1, 1],
h3D=1,
xylims=None,
axPos=[],
**kwargs):
'''Show unit cell and coords from cif file '''
crys = Crystal.from_cif(file)
n = get_vec(n, crys, bopt)
#unit cells,lattice vectors,atom coordinates
cell_mesh = crys.mesh(range(rep[0] + 1), range(rep[1] + 1),
range(rep[2] + 1))
surfs = get_unit_cell(cell_mesh, n)
uvw = rcc.orient_crystal(np.array(crys.lattice_vectors), n_u=n, T=True)
pattern = import_cif(file, n=n, rep=rep)
E, X, Y, Z = pattern[:, :4].T
scat = [X, Y, Z, [cs[int(e)] for e in E]]
#display options
if x0 == None: x0 = -1
if isinstance(x0, float) or isinstance(x0, int): x0 = np.array([x0] * 3)
if not xylims:
c1, c2, c3 = (X.min() + X.max()) / 2, (Y.min() + Y.max()) / 2, (
Z.min() + Z.max()) / 2
w = 0.75 * max(X.max() - X.min(), Y.max() - Y.min(), Z.max() - Z.min())
xylims = [
c1 - w / 2, c1 + w / 2, c2 - w / 2, c2 + w / 2, c3 - w / 2,
c3 + w / 2
]
# print(xylims)
if not axPos: axPos = [0, 0, 1, 0.95]
fig, ax = dsp.stddisp(scat=scat, ms=100, surfs=surfs, rc='3d', std=0)
show_trihedron(ax,
uvw=uvw,
x0=[0, 0, 0],
cs=['r', 'g', 'b'],
labs=['$a$', '$b$', '$c$'],
lw=2,
rc=0.1,
h=0.2)
show_trihedron(ax, x0=x0, labs=['$x$', '$y$', '$z$'], lw=2, rc=0.1, h=0.2)
dsp.stddisp(ax=ax, xylims=xylims, axPos=axPos, pOpt='Xpt', **kwargs)
if h3D: hdl = h3d.handler_3d(fig, persp=False)
def show_ewald_sphere(self,frame=None,Smax=0.01,Nmax=10,h3d=0,
nts=100,nps=200,**kwargs):
K = self.get_beam(frame)
Kx,Ky,Kz = K
(h,k,l),(qx,qy,qz) = self.get_lattice(Nmax)
x,y,z = self.get_ewald(frame,nts,nps)
df = self.get_excitation_errors(frame,Smax=Smax,Nmax=Nmax)
print('small excitation error beams',uvw)
if frame:print('frame %d:' %frame)
print(df[['h','k','l']])
scat = ([qx,qy,qz,5,'b','o'],[0,0,0,'r','s'])
scat+= ([df.qx,df.qy,df.qz,50,'g','s'],)
surf = [x,y,z,{'alpha':0.4,'color':'r'}]
plts = [[0,Kx],[0,Ky],[0,Kz],'r']
# scat+=([x0,y0,z0])
fig,ax = dsp.stddisp(plts,scat=scat,surfs=[surf],lw=3,
labs=['x','y','z'],rc='3d',**kwargs)
if h3d:h3d = h3D.handler_3d(fig,persp=False)
def compare_xyz_pxpy(self,frame=32,opts='oa',view=[90,90],**kwargs):
rpl0 = self.rpl.loc[self.rpl.F==frame]
pxc,pyc = self.cen.iloc[frame-1][['px','py']].values.T
alpha = rpl0.alpha.iloc[0]
px,py = rpl0[['px','py']].values.T
px = self.aper*(px-pxc)
py = -self.aper*(py-pyc)
xyz0 = np.vstack([px,py,np.zeros(px.shape)])
R = np.identity(3)
if 'o' in opts:
omega_r = np.deg2rad(self.omega)
ct,st = np.cos(omega_r),np.sin(omega_r)
Romega = np.array([[ct,st,0],[-st,ct,0],[0,0,1]]) #get_crystal_rotation(u=[0,0,-1],alpha=self.omega)
R = Romega
if 'a' in opts:
alpha_r = np.deg2rad(alpha)
ct,st = np.cos(alpha_r),np.sin(alpha_r)
Ra = np.array([[1,0,0],[0,ct,st],[0,-st,ct]])
R = Ra.dot(R)
x0,y0,z0 = R.dot(xyz0)
xyz = rpl0[['x','y','z']].values.T
x,y,z = xyz
Im = np.array(rpl0.Im.values/10,dtype=int)
if isinstance(view,str):
if view=='x':labs,scat = ['y','z'],([y,z,Im,'b','o'],[y0,z0,Im,'r','o'])
elif view=='y':labs,scat = ['x','z'],([x,z,Im,'b','o'],[x0,z0,Im,'r','o'])
elif view=='z':labs,scat = ['x','y'],([x,y,Im,'b','o'],[x0,y0,Im,'r','o'])
dsp.stddisp(xylims=1.5,scat=scat,labs=labs,legElt={'pxpy':'bo','xyz':'ro'},**kwargs)
else:
scat = ([x,y,z,Im,'b','o'],[x0,y0,z0,Im,'r','o'])
fig,ax = dsp.stddisp(rc='3d',view=view,xylims=1.5,scat=scat,labs=['x','y','z'],**kwargs)
h3d = h3D.handler_3d(fig,persp=True)
def show_hkl(self,**kwargs):
h,k,l,I = self.HKL[['h','k','l','I']].values.T
fig2,ax = dsp.stddisp(rc='3d',scat=[h,k,l,I,'b'],labs=['h','k','l'],**kwargs)
h3d2 = h3D.handler_3d(fig2,persp=False)
def show_xyz(self,**kwargs):
x,y,z = self.XYZ
fig2,ax = dsp.stddisp(rc='3d',scat=[x,y,z,2,'b'],labs=['x','y','z'],**kwargs)
h3d2 = h3D.handler_3d(fig2,persp=False)