def change_exp(self, evt):
dat = self.data
alt_i = dat.get("alt I")
exp = dat["data"].get("Exp. data")
if exp is None or alt_i is None:
return
rv = v_input(dat["window"], _("Believe factor"),
(_("The visible part only"), False),
(_("Believe factor:"), dat["eic_bf"]))
if rv is None:
return
ov, bf = rv
dat["eic_bf"] = bf
if ov:
if dat["plot"].get_cur_key() != PN_AIC:
return
beg, end = dat["plot"].axes1.get_xbound()
ib, ie = sqc.get_from_to(exp.x_data, beg, end)
chy = exp.y_data[ib:ie]
sqc.change_curve(chy, alt_i[ib:ie], bf)
exp.y_data[ib:ie] = chy
else:
sqc.change_curve(exp.y_data, alt_i, bf)
from v_plot import plot_exp_data
plot_exp_data(dat["plot"], exp, dat["menu"])
dat.pop("alt I")
dat["menu"].action_catch("exp I changed")
def rft_calc(self, evt):
"changes experimental intensity"
dat = self.data
rdf = dat.get("RDFd")
if rdf is None:
return
strt = _("Start:"), dat["rft_start"]
end = _("End:"), rdf.get("tail_s", dat["rft_end"])
rang = _("Steps:"), dat["rft_steps"], 100, 100000
refur = v_input(dat["window"], _("RFT params"), strt, end, rang)
if refur is None:
return
q = rdf["q"]
strt, end, rang = refur
dat["rft_start"], dat["rft_end"], dat["rft_steps"] = strt, end, rang
rarr = np.linspace(strt, end, rang)
gr = sqc.calc_gr_arr(rarr, **rdf)
q2 = np.linspace(q[0], q[-1], len(q) * 10)
sq2 = sqc.calc_rft_arr(q2, rarr, gr, **rdf)
dat["data"]["RFT sq"] = sqc.calc_rft_arr(q, rarr, gr, **rdf)
pld = dat["plot"].set_data(
PN_RFT, [(q, rdf["sq"], 1, None, "o"), (q2, sq2, 1)],
r"$q,\,\AA^{-1}$", "s(q)", "A^{-1}")
pld.discards.update(("liq samp", "sq found", "sq changed"))
pld.journal.set_parent(dat["plot"].get_data(PN_RDF).journal)
pld.journal.log("Reverse Fourier Transform")
dat["menu"].action_catch("RFT made")
dat["plot"].plot_dataset(PN_RFT)
def sq_tail(self, evt):
dat = self.data
if "SSF" not in dat["data"]:
return
q, sq, sqd = dat["data"]["SSF"][:3]
if "SQ point" in dat:
tail = len(q) - dat["SQ point"]
else:
tail = sqd.get("tail", {"points": 4})["points"]
if tail < 4:
tail = 4
a, b, c, d = sqd.get("tail", {"coefs": [1., 2., 1., .1]})["coefs"]
if d < .1:
d = .1
tail = _("Points:"), tail, 4, len(q)
a = "a:", float(a)
b = "b:", float(b)
c = "c:", float(c)
d = "d:", float(d)
rv = v_input(dat["window"], _("Tail init params"), tail, a, b, c, d)
if rv is None:
return
tail, a, b, c, d = rv
lmn = sqd["Elements"]
prevc = a, b, c, d
coefs = sqc.sq_tail(q[-tail:], sq[-tail:], lmn, prevc)
sqd["tail"] = {"coefs": coefs, "points": tail}
plot_sq(dat, q, sq, sqd)
dat["menu"].action_catch("SF tail found")
def rft_calc(self, evt):
"changes experimental intensity"
dat = self.data
rdf = dat.get("RDFd")
if rdf is None:
return
strt = _("Start:"), dat["rft_start"]
end = _("End:"), rdf.get("tail_s", dat["rft_end"])
rang = _("Steps:"), dat["rft_steps"], 100, 100000
refur = v_input(dat["window"], _("RFT params"), strt, end, rang)
if refur is None:
return
q = rdf["q"]
strt, end, rang = refur
dat["rft_start"], dat["rft_end"], dat["rft_steps"] = strt, end, rang
rarr = np.linspace(strt, end, rang)
gr = sqc.calc_gr_arr(rarr, **rdf)
q2 = np.linspace(q[0], q[-1], len(q) * 10)
sq2 = sqc.calc_rft_arr(q2, rarr, gr, **rdf)
dat["data"]["RFT sq"] = sqc.calc_rft_arr(q, rarr, gr, **rdf)
pld = dat["plot"].set_data(PN_RFT, [(q, rdf["sq"], 1, None, "o"),
(q2, sq2, 1)], r"$q,\,\AA^{-1}$",
"s(q)", "A^{-1}")
pld.discards.update(("liq samp", "sq found", "sq changed"))
pld.journal.set_parent(dat["plot"].get_data(PN_RDF).journal)
pld.journal.log("Reverse Fourier Transform")
dat["menu"].action_catch("RFT made")
dat["plot"].plot_dataset(PN_RFT)
def change_exp(self, evt):
dat = self.data
alt_i = dat.get("alt I")
exp = dat["data"].get("Exp. data")
if exp is None or alt_i is None:
return
rv = v_input(dat["window"], _("Believe factor"),
(_("The visible part only"), False),
(_("Believe factor:"), dat["eic_bf"]))
if rv is None:
return
ov, bf = rv
dat["eic_bf"] = bf
if ov:
if dat["plot"].get_cur_key() != PN_AIC:
return
beg, end = dat["plot"].axes1.get_xbound()
ib, ie = sqc.get_from_to(exp.x_data, beg, end)
chy = exp.y_data[ib:ie]
sqc.change_curve(chy, alt_i[ib:ie], bf)
exp.y_data[ib:ie] = chy
else:
sqc.change_curve(exp.y_data, alt_i, bf)
from v_plot import plot_exp_data
plot_exp_data(dat["plot"], exp, dat["menu"])
dat.pop("alt I")
dat["menu"].action_catch("exp I changed")
def sq_head(self, evt):
dat = self.data
if "SSF" not in dat["data"]:
return
q, sq, sqd = dat["data"]["SSF"][:3]
if "SQ point" not in dat:
head = int(sq.argmax() + 1)
else:
head = dat["SQ point"] + 1
diam = 2.
dens = float(dat["data"]["Exp. data"].rho0)
rv = v_input(dat["window"], _("Head init. params"),
(_("Points:"), head, 3, len(q)), (_("Diam:"), diam),
(_("Dens:"), dens))
if rv is None:
return
head, diam, dens = rv
diam, dens = sqc.calc_hs_head(diam, dens, q[:head], sq[:head])
sqd["head"] = {
"diam": diam,
"dens": dens,
"points": head,
"S(0)": sqc.calc_hs_s0(diam, dens)
}
plot_sq(dat, q, sq, sqd)
dat["menu"].action_catch("SF head found")
def sq_tail(self, evt):
dat = self.data
if "SSF" not in dat["data"]:
return
q, sq, sqd = dat["data"]["SSF"][:3]
if "SQ point" in dat:
tail = len(q) - dat["SQ point"]
else:
tail = sqd.get("tail", {"points": 4})["points"]
if tail < 4:
tail = 4
a, b, c, d = sqd.get("tail", {"coefs": [1., 2., 1., .1]})["coefs"]
if d < .1:
d = .1
tail = _("Points:"), tail, 4, len(q)
a = "a:", float(a)
b = "b:", float(b)
c = "c:", float(c)
d = "d:", float(d)
rv = v_input(dat["window"], _("Tail init params"), tail, a, b, c, d)
if rv is None:
return
tail, a, b, c, d = rv
lmn = sqd["Elements"]
prevc = a, b, c, d
coefs = sqc.sq_tail(q[-tail:], sq[-tail:], lmn, prevc)
sqd["tail"] = {"coefs": coefs, "points": tail}
plot_sq(dat, q, sq, sqd)
dat["menu"].action_catch("SF tail found")
def calc_s0(self, evt):
if not self.Validate():
return
internal = self.internal
diam = internal.get("diam", 2.)
rv = v_input(self, _("Diameter"), (_("Diam:"), diam))
if rv is None:
return
diam = rv[0]
dens = self.get_rho0()
s0 = sqc.calc_hs_s0(diam, dens, *internal['data']["SSF"][:2])
self.s_0.SetValue(loc.format(u"%g", s0))
def calc_s0(self, evt):
if not self.Validate():
return
internal = self.internal
diam = internal.get("diam", 2.)
rv = v_input(self, _("Diameter"), (_("Diam:"), diam))
if rv is None:
return
diam = rv[0]
dens = self.get_rho0()
s0 = sqc.calc_hs_s0(diam, dens, *internal['data']["SSF"][:2])
self.s_0.SetValue(loc.format(u"%g", s0))
def shift_data(self, evt):
dat = self.data
tfn = _("Intensity curve")
plot = dat['plot']
if plot.get_cur_key() != tfn:
plot.plot_dataset(tfn)
return
x_sh = _("Shift X by:"), 0.
y_sh = _("Shift Y by:"), 0.
rv = v_input(dat["window"], _("Shift data"), x_sh, y_sh)
if rv is None:
return
x_sh, y_sh = rv
edat = dat['data'].get("Exp. data")
if edat is None:
return
if x_sh != 0.:
edat.x_data += x_sh
if y_sh != 0.:
edat.y_data += y_sh
plot_exp_data(plot, edat, dat['menu'])
def shift_data(self, evt):
dat = self.data
tfn = _("Intensity curve")
plot = dat['plot']
if plot.get_cur_key() != tfn:
plot.plot_dataset(tfn)
return
x_sh = _("Shift X by:"), 0.
y_sh = _("Shift Y by:"), 0.
rv = v_input(dat["window"], _("Shift data"), x_sh, y_sh)
if rv is None:
return
x_sh, y_sh = rv
edat = dat['data'].get("Exp. data")
if edat is None:
return
if x_sh != 0.:
edat.x_data += x_sh
if y_sh != 0.:
edat.y_data += y_sh
plot_exp_data(plot, edat, dat['menu'])
def sq_head(self, evt):
dat = self.data
if "SSF" not in dat["data"]:
return
q, sq, sqd = dat["data"]["SSF"][:3]
if "SQ point" not in dat:
head = int(sq.argmax() + 1)
else:
head = dat["SQ point"] + 1
diam = 2.
dens = float(dat["data"]["Exp. data"].rho0)
rv = v_input(dat["window"], _("Head init. params"),
(_("Points:"), head, 3, len(q)),
(_("Diam:"), diam), (_("Dens:"), dens))
if rv is None:
return
head, diam, dens = rv
diam, dens = sqc.calc_hs_head(diam, dens, q[:head], sq[:head])
sqd["head"] = {"diam": diam, "dens": dens, "points": head,
"S(0)": sqc.calc_hs_s0(diam, dens)}
plot_sq(dat, q, sq, sqd)
dat["menu"].action_catch("SF head found")
def tail_gr(self, evt):
dat = self.data
plot = dat["plot"]
rdf = dat.get("RDFd")
if rdf is None:
return
beg, end = plot.axes1.get_xbound()
pts = _("Points:"), dat["gr_tail_pts"], 10, 10000
beg = _("Start:"), float(beg)
end = _("End:"), float(end)
a = "a:", 1.
b = "b:", 2.
c = "c:", .1
d = "d:", .1
rv = v_input(dat["window"], _("RDF tail"), pts, beg, end, a, b, c, d)
if rv is None:
return
pts, beg, end, a, b, c, d = rv
dat["gr_tail_pts"] = pts
rarr = np.linspace(beg, end, pts)
grarr = sqc.calc_gr_arr(rarr, **rdf)
coefs = sqc.gr_tail(rarr, grarr, (a, b, c, d))
x, y = sqc.tail_xy(coefs, beg, end, pts)
y += 1
rdf["tail"] = coefs
rdf["tail_s"] = beg
pdt = plot.set_data(PN_RDFT, [(rarr, grarr, 1), (x, y, 1)],
r"$r,\,\AA$", "g(r)", "A")
pdt.discards.update(("liq samp", "sq found", "sq changed", "gr found"))
pdt.journal.log("find RDF's tail")
info = ["\n\n",
"''g(r) = 1 + a * cos(b * r - c) * exp(-d * r) / r''",
"\n\n----\n\n{|\n! %s\n! %s\n"] +\
["|-\n| %s\n| %%s\n" % (i,) for i in "a b c d".split()] + ["|}"]
info = u"".join(info) % ((_("parameter"), _("value")) +
tuple([loc.format("%g", i) for i in coefs]))
pdt.set_info(info)
plot.plot_dataset(PN_RDFT)
def tail_gr(self, evt):
dat = self.data
plot = dat["plot"]
rdf = dat.get("RDFd")
if rdf is None:
return
beg, end = plot.axes1.get_xbound()
pts = _("Points:"), dat["gr_tail_pts"], 10, 10000
beg = _("Start:"), float(beg)
end = _("End:"), float(end)
a = "a:", 1.
b = "b:", 2.
c = "c:", .1
d = "d:", .1
rv = v_input(dat["window"], _("RDF tail"), pts, beg, end, a, b, c, d)
if rv is None:
return
pts, beg, end, a, b, c, d = rv
dat["gr_tail_pts"] = pts
rarr = np.linspace(beg, end, pts)
grarr = sqc.calc_gr_arr(rarr, **rdf)
coefs = sqc.gr_tail(rarr, grarr, (a, b, c, d))
x, y = sqc.tail_xy(coefs, beg, end, pts)
y += 1
rdf["tail"] = coefs
rdf["tail_s"] = beg
pdt = plot.set_data(PN_RDFT, [(rarr, grarr, 1), (x, y, 1)],
r"$r,\,\AA$", "g(r)", "A")
pdt.discards.update(("liq samp", "sq found", "sq changed", "gr found"))
pdt.journal.log("find RDF's tail")
info = ["\n\n",
"''g(r) = 1 + a * cos(b * r - c) * exp(-d * r) / r''",
"\n\n----\n\n{|\n! %s\n! %s\n"] +\
["|-\n| %s\n| %%s\n" % (i,) for i in "a b c d".split()] + ["|}"]
info = u"".join(info) % ((_("parameter"), _("value")) +
tuple([loc.format("%g", i) for i in coefs]))
pdt.set_info(info)
plot.plot_dataset(PN_RDFT)
def calculate_reflexes(idata):
"Search reflexes shapes"
parent = idata["window"]
exd = idata["data"]["Exp. data"]
x, y, bg, sig2 = idata["data"]["Background"][:4]
if exd.lambda2:
l21 = exd.lambda2 / exd.lambda1
else:
l21 = None
dreflexes = {}
dreflexes["lambda"] = exd.lambda1
I2 = exd.I2
sigmin = _(u"Min. \u03c3:"), idata["refl_sigmin"]
consig = _(u"Const. \u03c3"), idata["refl_consig"]
mbells = _("Max. bells:"), idata["refl_mbells"]
bell_t = _("Shape function:"), _BELL_NAMES, idata["refl_bt"]
pts_mi = _("Ignore points:"), idata["refl_ptm"], 4
bf = _("Believe factor:"), idata["refl_bf"]
if idata["data"]["User refl"]:
alg = 1
else:
alg = 0
algorithm = _("Algorithm:"), [_("alg 1"), _("alg 2")], alg
rv = v_input(parent, _("Shapes of reflexes"), sigmin, consig, mbells,
bell_t, bf, pts_mi, algorithm)
if rv is None:
return
sigmin, consig, mbells, bell_t, bf, pts_mi, algorithm = rv
idata["refl_sigmin"] = sigmin
idata["refl_consig"] = consig
idata["refl_mbells"] = mbells
idata["refl_bt"] = bell_t
idata["refl_ptm"] = pts_mi
idata["refl_bf"] = bf
sects = refl_sects(x, y, bg, sig2, bf)
sects = [i for i in sects if len(i) > pts_mi]
lsec = len(sects)
titl = _("Calculate shapes")
msg = _("Calculating shapes of the reflexes...")
if lsec:
dlgp = DlgProgressCallb(parent, titl, msg, lsec, can_abort=True)
done = 0
totreflexes = []
totsigmas = []
plts = []
plts.append((x, y - bg, 1, 'black', '.'))
if algorithm == 1:
apposs = [(i[0], i[3]) for i in idata["data"]["User refl"].get()]
for sect in sects:
rfd = ReflexDedect(sect, l21, I2)
if algorithm == 0:
reflexes, stdev = rfd.find_bells(sigmin, not consig,
mbells, _BELL_TYPES[bell_t])
else:
mi = sect[0][0]
ma = sect[-1][0]
pposs = [i for i in apposs if mi <= i[0] <= ma]
posfxs = [i for i in range(len(pposs)) if pposs[i][1]]
pposs = [i[0] for i in pposs]
reflexes, stdev = rfd.find_bells_pp(_BELL_TYPES[bell_t],
pposs, posfxs)
totreflexes += reflexes
totsigmas += [stdev] * len(reflexes)
plts.append((rfd.x_ar, rfd.y_ar - rfd.calc_shape(), 1,
'magenta', '-'))
rfd.x_ar = np.linspace(rfd.x_ar[0], rfd.x_ar[-1], len(rfd.x_ar) * 10)
plts.append((rfd.x_ar, rfd.calc_shape(), 1, 'green', '-'))
rfd.lambda21 = None
for peak in reflexes:
pv = np.array(peak)[:3]
plts.append((rfd.x_ar, rfd.calc_shape(pv), 1, 'b', '-'))
done += 1
if not dlgp(done):
break
dreflexes["shape"] = _BELL_TYPES[bell_t]
dreflexes["items"] = [i + (j,) for i, j in zip(totreflexes, totsigmas)]
return dreflexes, plts