def dict_to_colfile(c):
titles = list(c.keys())
nrows = len(c[titles[0]])
for t in titles:
assert len(c[t]) == nrows, t
colf = columnfile.newcolumnfile(titles=titles)
colf.nrows = nrows
colf.set_bigarray([c[t] for t in titles])
return colf
def tocolumnfile(self):
"""
Return a columnfile
"""
cof = columnfile.newcolumnfile(self.alltitles)
dlist = [self.data[t] for t in self.alltitles]
cof.bigarray = numpy.array(dlist, numpy.float)
cof.nrows = len(self.data[self.alltitles[0]])
cof.ncols = len(self.alltitles)
cof.set_attributes()
return cof
allpeaks[key] = mytransformer.colfile.bigarray[:,i]
nold = nold + 1
else:
nnew = nnew + 1
allpeaks[key] = mytransformer.colfile.bigarray[:,i]
print("total peaks",len(list(allpeaks.keys())), "ignored", nignore, "new",nnew, "replacements",nold)
assert nignore + nold + nnew == mytransformer.colfile.nrows
keys = list(allpeaks.keys())
keys.sort()
c = newcolumnfile( titles )
assert len(titles) == len(allpeaks[keys[0]])
bigarray = [allpeaks[k] for k in keys]
c.bigarray = numpy.array(bigarray).T
print(c.bigarray.shape)
c.nrows = len(keys)
c.set_attributes()
c.setcolumn(numpy.array(list(range(len(keys)))),"spot3d_id")
c.writefile( outf )
mytransformer = transformer.transformer()
mytransformer.loadfileparameters( pars )
U12.append(U[0, 1])
U13.append(U[0, 2])
U21.append(U[1, 0])
U22.append(U[1, 1])
U23.append(U[1, 2])
U31.append(U[2, 0])
U32.append(U[2, 1])
U33.append(U[2, 2])
eps11.append(eps[0])
eps12.append(eps[1])
eps13.append(eps[2])
eps22.append(eps[3])
eps23.append(eps[4])
eps33.append(eps[5])
gff = ic.newcolumnfile(titles)
gff.ncols = len(titles)
gff.nrows = len(grainno)
gff.bigarray = n.zeros((gff.ncols, gff.nrows))
gff.set_attributes()
gff.addcolumn(grainno, "grainno")
gff.addcolumn(x, "x")
gff.addcolumn(y, "y")
gff.addcolumn(z, "z")
gff.addcolumn(rodx, "rodx")
gff.addcolumn(rody, "rody")
gff.addcolumn(rodz, "rodz")
gff.addcolumn(U11, "U11")
gff.addcolumn(U12, "U12")
gff.addcolumn(U13, "U13")
gff.addcolumn(U21, "U21")
def ubi_to_gff(ubi,par):
from ImageD11 import grain as ig
from ImageD11 import parameters as ip
from string import split
from xfab import tools
from six.moves import range
list_of_grains = ig.read_grain_file(ubi)
p = ip.parameters()
p.loadparameters(par)
uc = [p.parameters['cell__a'],p.parameters['cell__b'],p.parameters['cell__c'],p.parameters['cell_alpha'],p.parameters['cell_beta'],p.parameters['cell_gamma']]
#print(uc)
grainno = []
x = []
y = []
z = []
rodx = []
rody = []
rodz = []
unitcell_a = []
unitcell_b = []
unitcell_c = []
unitcell_alpha = []
unitcell_beta = []
unitcell_gamma = []
U11 = []
U12 = []
U13 = []
U21 = []
U22 = []
U23 = []
U31 = []
U32 = []
U33 = []
eps11 = []
eps22 = []
eps33 = []
eps23 = []
eps13 = []
eps12 = []
titles = ["grainno","x","y","z","rodx","rody","rodz","U11","U12","U13","U21","U22","U23","U31","U32","U33","unitcell_a","unitcell_b","unitcell_c","unitcell_alpha","unitcell_beta","unitcell_gamma","eps11","eps22","eps33","eps23","eps13","eps12"]
for i in range(len(list_of_grains)):
if hasattr(list_of_grains,'name') == False:
grainno.append(i)
elif hasattr(list_of_grains,'name') == True:
grainno.append(eval(split(list_of_grains[i].name,':')[0]))
x.append(list_of_grains[i].translation[0]/1000.)
y.append(list_of_grains[i].translation[1]/1000.)
z.append(list_of_grains[i].translation[2]/1000.)
ubi = list_of_grains[i].ubi
(U,eps) = tools.ubi_to_u_and_eps(ubi,uc)
uc_a, uc_b, uc_c, uc_alpha, uc_beta, uc_gamma = tools.ubi_to_cell(ubi)
unitcell_a.append(uc_a)
unitcell_b.append(uc_b)
unitcell_c.append(uc_c)
unitcell_alpha.append(uc_alpha)
unitcell_beta.append(uc_beta)
unitcell_gamma.append(uc_gamma)
rod = tools.u_to_rod(U)
rodx.append(rod[0])
rody.append(rod[1])
rodz.append(rod[2])
U11.append(U[0,0])
U12.append(U[0,1])
U13.append(U[0,2])
U21.append(U[1,0])
U22.append(U[1,1])
U23.append(U[1,2])
U31.append(U[2,0])
U32.append(U[2,1])
U33.append(U[2,2])
eps11.append(eps[0])
eps12.append(eps[1])
eps13.append(eps[2])
eps22.append(eps[3])
eps23.append(eps[4])
eps33.append(eps[5])
gff = cl.newcolumnfile(titles)
gff.ncols = len(titles)
gff.nrows = len(grainno)
gff.bigarray = np.zeros((gff.ncols,gff.nrows))
gff.set_attributes()
gff.addcolumn(grainno,"grainno")
gff.addcolumn(x,"x")
gff.addcolumn(y,"y")
gff.addcolumn(z,"z")
gff.addcolumn(rodx,"rodx")
gff.addcolumn(rody,"rody")
gff.addcolumn(rodz,"rodz")
gff.addcolumn(U11,"U11")
gff.addcolumn(U12,"U12")
gff.addcolumn(U13,"U13")
gff.addcolumn(U21,"U21")
gff.addcolumn(U22,"U22")
gff.addcolumn(U23,"U23")
gff.addcolumn(U31,"U31")
gff.addcolumn(U32,"U32")
gff.addcolumn(U33,"U33")
gff.addcolumn(unitcell_a,"unitcell_a")
gff.addcolumn(unitcell_b,"unitcell_b")
gff.addcolumn(unitcell_c,"unitcell_c")
gff.addcolumn(unitcell_alpha,"unitcell_alpha")
gff.addcolumn(unitcell_beta,"unitcell_beta")
gff.addcolumn(unitcell_gamma,"unitcell_gamma")
gff.addcolumn(eps11,"eps11")
gff.addcolumn(eps22,"eps22")
gff.addcolumn(eps33,"eps33")
gff.addcolumn(eps23,"eps23")
gff.addcolumn(eps13,"eps13")
gff.addcolumn(eps12,"eps12")
return gff, uc