servalcat 0.4.99__cp313-cp313-macosx_10_14_x86_64.whl

servalcat/xtal/sigmaa.py

@@ -0,0 +1,1644 @@
+"""
+Author: "Keitaro Yamashita, Garib N. Murshudov"
+MRC Laboratory of Molecular Biology
+    
+This software is released under the
+Mozilla Public License, version 2.0; see LICENSE.
+"""
+from __future__ import absolute_import, division, print_function, generators
+import argparse
+import gemmi
+import numpy
+import pandas
+import itertools
+import time
+import scipy.special
+import scipy.optimize
+from servalcat.utils import logger
+from servalcat import utils
+from servalcat import ext
+from servalcat.xtal.twin import find_twin_domains_from_data, estimate_twin_fractions_from_model
+
+"""
+DFc = sum_j D_j F_c,j
+The last Fc,n is bulk solvent contribution.
+"""
+
+integr = ext.IntensityIntegrator()
+
+def add_arguments(parser):
+    parser.description = 'Sigma-A parameter estimation for crystallographic data'
+    parser.add_argument('--hklin', required=True,
+                        help='Input MTZ file')
+    parser.add_argument('--spacegroup',
+                        help='Override space group')
+    parser.add_argument('--labin',
+                        help='MTZ column for F,SIGF,FREE')
+    parser.add_argument('--free', type=int,
+                        help='flag number for test set')
+    parser.add_argument('--model', required=True, nargs="+", action="append",
+                        help='Input atomic model file(s)')
+    parser.add_argument("-d", '--d_min', type=float)
+    parser.add_argument('--d_max', type=float)
+    parser.add_argument('--nbins', type=int,
+                        help="Number of bins (default: auto)")
+    parser.add_argument('-s', '--source', choices=["electron", "xray", "neutron"], required=True,
+                        help="Scattering factor choice")
+    parser.add_argument('--D_trans', choices=["exp", "splus"],
+                        help="estimate D with positivity constraint")
+    parser.add_argument('--S_trans', choices=["exp", "splus"],
+                        help="estimate variance of unexplained signal with positivity constraint")
+    parser.add_argument('--no_solvent',  action='store_true',
+                        help="Do not consider bulk solvent contribution")
+    parser.add_argument('--use_cc',  action='store_true',
+                        help="Use CC(|F1|,|F2|) to CC(F1,F2) conversion to derive D and S")
+    parser.add_argument('--use', choices=["all", "work", "test"], default="all",
+                        help="Which reflections to be used for the parameter estimate.")
+    parser.add_argument('--twin', action="store_true", help="Turn on twin refinement")
+    parser.add_argument('--mask',
+                        help="A solvent mask (by default calculated from the coordinates)")
+    parser.add_argument('--keep_charges',  action='store_true',
+                        help="Use scattering factor for charged atoms. Use it with care.")
+    parser.add_argument('-o','--output_prefix', default="sigmaa",
+                        help='output file name prefix (default: %(default)s)')
+# add_arguments()
+
+def parse_args(arg_list):
+    parser = argparse.ArgumentParser()
+    add_arguments(parser)
+    return parser.parse_args(arg_list)
+# parse_args()
+
+def nanaverage(cc, w):
+    sel = ~numpy.isnan(cc)
+    if numpy.sum(w[sel]) == 0:
+        return numpy.nan
+    return numpy.average(cc[sel], weights=w[sel]) 
+
+def calc_r_and_cc(hkldata, centric_and_selections, twin_data=None):
+    has_int = "I" in hkldata.df
+    has_free = "FREE" in hkldata.df
+    stats = hkldata.binned_df.copy()
+    stats[["n_obs", "n_all"]] = 0
+    if has_free:
+        stats[["n_work", "n_free"]] = 0
+    rlab = "R1" if has_int else "R"
+    cclab = "CCI" if has_int else "CCF"
+    if twin_data:
+        Fc = numpy.sqrt(twin_data.i_calc_twin())
+    else:
+        Fc = numpy.abs(hkldata.df.FC * hkldata.df.k_aniso)
+    if has_int:
+        obs = hkldata.df.I
+        obs_sqrt = numpy.sqrt(numpy.maximum(0, hkldata.df.I))
+        obs_sqrt[hkldata.df.I/hkldata.df.SIGI < 2] = numpy.nan # SHELX equivalent
+        calc = Fc**2
+        calc_sqrt = Fc
+    else:
+        obs = obs_sqrt = hkldata.df.FP
+        calc = calc_sqrt = Fc
+    if has_free:
+        for lab in (cclab, rlab):
+            for suf in ("work", "free"):
+                stats[lab+suf] = numpy.nan
+    else:
+        stats[cclab] = numpy.nan
+        stats[rlab] = numpy.nan
+
+    for i_bin, idxes in hkldata.binned():
+        stats.loc[i_bin, "n_obs"] = numpy.sum(numpy.isfinite(obs[idxes]))
+        stats.loc[i_bin, "n_all"] = len(idxes)
+        if has_free:
+            for j, suf in ((1, "work"), (2, "free")):
+                idxes2 = numpy.concatenate([sel[j] for sel in centric_and_selections[i_bin]])
+                stats.loc[i_bin, "n_"+suf] = numpy.sum(numpy.isfinite(obs[idxes2]))
+                stats.loc[i_bin, cclab+suf] = utils.hkl.correlation(obs[idxes2], calc[idxes2])
+                stats.loc[i_bin, rlab+suf] = utils.hkl.r_factor(obs_sqrt[idxes2], calc_sqrt[idxes2])
+        else:
+            stats.loc[i_bin, cclab] = utils.hkl.correlation(obs[idxes], calc[idxes])
+            stats.loc[i_bin, rlab] = utils.hkl.r_factor(obs_sqrt[idxes], calc_sqrt[idxes])
+
+    # Overall
+    ret = {}
+    if has_free:
+        for suf in ("work", "free"):
+            ret[cclab+suf+"avg"] = nanaverage(stats[cclab+suf], stats["n_"+suf])
+        for j, suf in ((1, "work"), (2, "free")):
+            idxes = numpy.concatenate([sel[j] for i_bin, _ in hkldata.binned() for sel in centric_and_selections[i_bin]])
+            ret[rlab+suf] = utils.hkl.r_factor(obs_sqrt[idxes], calc_sqrt[idxes])
+    else:
+        ret[cclab+"avg"] = nanaverage(stats[cclab], stats["n_obs"])
+        ret[rlab] = utils.hkl.r_factor(obs, calc)
+        
+    return stats, ret
+# calc_r_and_cc()
+
+class VarTrans:
+    def __init__(self, D_trans, S_trans):
+        # splus (softplus) appears to be better than exp
+        # exp sometimes results in too large parameter value
+        trans_funcs = {"exp": (numpy.exp, # D = f(x)
+                               numpy.exp, # dD/dx
+                               numpy.log), # x = f^-1(D)
+                       "splus": (lambda x: numpy.logaddexp(0, x),
+                                 scipy.special.expit, # lambda x: 1. / (1. + numpy.exp(-x))
+                                 lambda x: x + numpy.log(-numpy.expm1(-x))),
+                       None: (lambda x: x,
+                              lambda x: 1,
+                              lambda x: x)}
+        
+        self.D, self.D_deriv, self.D_inv = trans_funcs[D_trans]
+        self.S, self.S_deriv, self.S_inv = trans_funcs[S_trans]
+# class VarTrans
+
+class LsqScale:
+    # parameter x = [k_overall, adp_pars, k_sol, B_sol]
+    def __init__(self, k_as_exp=False, func_type="log_cosh"):
+        assert func_type in ("sq", "log_cosh")
+        self.k_trans = lambda x: numpy.exp(x) if k_as_exp else x
+        self.k_trans_der = lambda x: numpy.exp(x) if k_as_exp else 1
+        self.k_trans_inv = lambda x: numpy.log(x) if k_as_exp else x
+        self.func_type = func_type
+        self.reset()
+        
+    def reset(self):
+        self.k_sol = 0.35 # same default as gemmi/scaling.hpp # refmac seems to use 0.33 and 100? SCALE_LS_PART
+        self.b_sol = 46.
+        self.k_overall = None
+        self.b_iso = None
+        self.b_aniso = None
+        self.stats = {}
+
+    def set_data(self, hkldata, fc_list, use_int=False, sigma_cutoff=None, twin_data=None):
+        assert 0 < len(fc_list) < 3
+        self.use_int = use_int
+        if sigma_cutoff is not None:
+            if use_int:
+                self.sel = hkldata.df.I / hkldata.df.SIGI > sigma_cutoff
+                self.labcut = "(I/SIGI>{})".format(sigma_cutoff)
+            else:
+                self.sel = hkldata.df.FP / hkldata.df.SIGFP > sigma_cutoff
+                self.labcut = "(F/SIGF>{})".format(sigma_cutoff)
+        else:
+            self.sel = hkldata.df.index
+            self.labcut = ""
+        self.obs = hkldata.df["I" if use_int else "FP"].to_numpy(copy=True)
+        self.obs[~self.sel] = numpy.nan
+        self.calc = [x for x in fc_list]
+        self.s2mat = hkldata.ssq_mat()
+        self.s2 = 1. / hkldata.d_spacings().to_numpy()**2
+        self.adpdirs = utils.model.adp_constraints(hkldata.sg.operations(), hkldata.cell, tr0=False)
+        self.twin_data = twin_data
+        if use_int:
+            self.sqrt_obs = numpy.sqrt(self.obs)
+        
+    def get_solvent_scale(self, k_sol, b_sol, s2=None):
+        if s2 is None: s2 = self.s2
+        return k_sol * numpy.exp(-b_sol * s2 / 4)
+
+    def fc_and_mask_grad(self, x):
+        fc0 = self.calc[0]
+        if len(self.calc) == 2:
+            if self.twin_data:
+                r = self.twin_data.scaling_fc_and_mask_grad(self.calc[1], x[-2], x[-1])
+                return r[:,0], r[:,1], r[:,2]
+            else:
+                fmask = self.calc[1]
+                temp_sol = numpy.exp(-x[-1] * self.s2 / 4)
+                fbulk = x[-2] * temp_sol * fmask
+                fc = fc0 + fbulk
+                re_fmask_fcconj = (fmask * fc.conj()).real
+                fc_abs = numpy.abs(fc)
+                tmp = temp_sol / fc_abs * re_fmask_fcconj
+                return fc_abs, tmp, -tmp * x[-2] * self.s2 / 4
+        else:
+            if self.twin_data:
+                return numpy.sqrt(self.twin_data.i_calc_twin()), None, None
+            else:
+                return numpy.abs(fc0), None, None
+
+    def scaled_fc(self, x):
+        fc = self.fc_and_mask_grad(x)[0]
+        nadp = self.adpdirs.shape[0]
+        B = numpy.dot(x[1:nadp+1], self.adpdirs)
+        kani = numpy.exp(numpy.dot(-B, self.s2mat))
+        return self.k_trans(x[0]) * kani * fc
+
+    def target(self, x):
+        y = self.scaled_fc(x)
+        if self.use_int:
+            diff = self.sqrt_obs - y
+            #y2 = y**2
+            #diff = self.obs - y2
+        else:
+            diff = self.obs - y
+
+        if self.func_type == "sq":
+            return numpy.nansum(diff**2)
+        elif self.func_type == "log_cosh":
+            return numpy.nansum(gemmi.log_cosh(diff))
+        else:
+            raise RuntimeError("bad func_type")
+        
+    def grad(self, x):
+        g = numpy.zeros_like(x)
+        fc_abs, der_ksol, der_bsol  = self.fc_and_mask_grad(x)
+        nadp = self.adpdirs.shape[0]
+        B = numpy.dot(x[1:nadp+1], self.adpdirs)
+        kani = numpy.exp(numpy.dot(-B, self.s2mat))
+        k = self.k_trans(x[0])
+        y = k * kani * fc_abs
+        if self.use_int:
+            diff = self.sqrt_obs - y
+            diff_der = -1
+            #diff = self.obs - y**2
+            #diff_der = -2 * y
+        else:
+            diff = self.obs - y
+            diff_der = -1
+        if self.func_type == "sq":
+            dfdy = 2 * diff * diff_der
+        elif self.func_type == "log_cosh":
+            dfdy = numpy.tanh(diff) * diff_der
+        else:
+            raise RuntimeError("bad func_type")
+        
+        dfdb = numpy.nansum(-self.s2mat * k * fc_abs * kani * dfdy, axis=1)
+        g[0] = numpy.nansum(kani * fc_abs * dfdy * self.k_trans_der(x[0]))
+        g[1:nadp+1] = numpy.dot(dfdb, self.adpdirs.T)
+        if len(self.calc) == 2:
+            g[-2] = numpy.nansum(k * kani * der_ksol * dfdy)
+            g[-1] = numpy.nansum(k * kani * der_bsol * dfdy)
+
+        return g
+
+    def calc_shift(self, x):
+        # TODO: sort out code duplication, if we use this.
+        g = numpy.zeros((len(self.obs), len(x)))
+        H = numpy.zeros((len(x), len(x)))
+        fc_abs, der_ksol, der_bsol  = self.fc_and_mask_grad(x)
+        nadp = self.adpdirs.shape[0]
+        B = numpy.dot(x[1:nadp+1], self.adpdirs)
+        kani = numpy.exp(numpy.dot(-B, self.s2mat))
+        k = self.k_trans(x[0])
+        y = k * kani * fc_abs
+        if self.use_int:
+            diff = self.sqrt_obs - y
+            diff_der = -1
+            diff_der2 = 0
+        else:
+            diff = self.obs - y
+            diff_der = -1.
+            diff_der2 = 0.
+            
+        if self.func_type == "sq":
+            dfdy = 2 * diff * diff_der
+            dfdy2 = 2 * diff_der**2 + 2 * diff * diff_der2
+        elif self.func_type == "log_cosh":
+            dfdy = numpy.tanh(diff) * diff_der
+            #dfdy2 = 1 /numpy.cosh(diff)**2 * diff_der**2 + numpy.tanh(diff) * diff_der2 # problematic with large diff
+            #dfdy2 = numpy.where(diff==0, 1., numpy.abs(numpy.tanh(diff)) / gemmi.log_cosh(diff)) * diff_der**2 + numpy.tanh(diff) * diff_der2
+            dfdy2 = numpy.where(diff==0, 1., numpy.tanh(diff) / diff) * diff_der**2 + numpy.tanh(diff) * diff_der2
+        else:
+            raise RuntimeError("bad func_type")
+        
+        dfdb = -self.s2mat * k * fc_abs * kani
+        g[:,0] = kani * fc_abs * self.k_trans_der(x[0])
+        g[:,1:nadp+1] = numpy.dot(dfdb.T, self.adpdirs.T)
+        if len(self.calc) == 2:
+            g[:,-2] = k * kani * der_ksol
+            g[:,-1] = k * kani * der_bsol
+
+        # no numpy.nandot..
+        g, dfdy, dfdy2 = g[self.sel, :], dfdy[self.sel], dfdy2[self.sel]
+        H = numpy.dot(g.T, g * dfdy2[:,None])
+        g = numpy.sum(dfdy[:,None] * g, axis=0)
+        dx = -numpy.dot(g, numpy.linalg.pinv(H))
+        return dx
+
+    def initial_kb(self):
+        fc_abs = self.fc_and_mask_grad([self.k_sol, self.b_sol])[0]
+        sel = self.obs > 0 # exclude nan as well
+        f1p, f2p, s2p = self.obs[sel], fc_abs[sel], self.s2[sel]
+        if self.use_int: f2p *= f2p
+        tmp = numpy.log(f2p) - numpy.log(f1p)
+        # g = [dT/dk, dT/db]
+        g = numpy.array([2 * numpy.sum(tmp), -numpy.sum(tmp*s2p)/2])
+        H = numpy.zeros((2,2))
+        H[0,0] = 2*len(f1p)
+        H[1,1] = numpy.sum(s2p**2/8)
+        H[0,1] = H[1,0] = -numpy.sum(s2p)/2
+        x = -numpy.dot(numpy.linalg.inv(H), g)
+        if self.use_int: x /= 2
+        k = numpy.exp(x[0])
+        b = x[1]
+        logger.writeln(" initial k,b = {:.2e} {:.2e}".format(k, b))
+        logger.writeln("           R{} = {:.4f}".format(self.labcut, utils.hkl.r_factor(f1p, f2p * k * numpy.exp(-b*self.s2[sel]/4))))
+        return k, b
+    
+    def scale(self):
+        use_sol = len(self.calc) == 2
+        msg = "Scaling Fc to {} {} bulk solvent contribution".format("Io" if self.use_int else "Fo",
+                                                                     "with" if use_sol else "without")
+        logger.writeln(msg)
+        if self.k_overall is None or self.b_iso is None:
+            k, b = self.initial_kb()
+        else:
+            k, b = self.k_overall, self.b_iso
+        if self.b_aniso is None:
+            self.b_aniso = gemmi.SMat33d(b,b,b,0,0,0)
+        x0 = [self.k_trans_inv(k)]
+        bounds = [(0, None)]
+        x0.extend(numpy.dot(self.b_aniso.elements_pdb(), self.adpdirs.T))
+        bounds.extend([(None, None)]*(len(x0)-1))
+        if use_sol:
+            x0.extend([self.k_sol, self.b_sol])
+            bounds.extend([(1e-4, None), (10., 400.)])
+        if 0:
+            f0 = self.target(x0)
+            ader = self.grad(x0)
+            e = 1e-4
+            nder = []
+            for i in range(len(x0)):
+                x = numpy.copy(x0)
+                x[i] += e
+                f1 = self.target(x)
+                nder.append((f1 - f0) / e)
+            print("ADER NDER RATIO")
+            print(ader)
+            print(nder)
+            print(ader / nder)
+            quit()
+
+        t0 = time.time()
+        if 1:
+            x = x0
+            for i in range(40):
+                x_ini = x.copy()
+                f0 = self.target(x)
+                dx = self.calc_shift(x)
+                if numpy.max(numpy.abs(dx)) < 1e-6:
+                    break
+                for s in (1, 0.5, 0.25):
+                    if 0:
+                        with open("debug.dat", "w") as ofs:
+                            for s in numpy.linspace(-2, 2, 100):
+                                f1 = self.target(x+dx * s)
+                                #print(dx, f0, f1, f0 - f1)
+                                ofs.write("{:4e} {:4e}\n".format(s, f1))
+                    shift = dx * s
+                    x = x_ini + shift
+                    if x[0] < 0: x[0] = x0[0]
+                    if use_sol:
+                        if x[-1] < 10: x[-1] = 10
+                        elif x[-1] > 400: x[-1] = 400
+                        if x[-2] < 1e-4: x[-2] = 1e-4
+                    f1 = self.target(x)
+                    if f1 < f0: break
+                #logger.writeln("cycle {} {} {} {} {} {}".format(i, f0, f1, s, shift, (f0 - f1) / f0))
+                if 0 < (f0 - f1) / f0 < 1e-6:
+                    break
+            res_x = x
+            self.stats["fun"] = f1
+            self.stats["x"] = x
+        else:
+            res = scipy.optimize.minimize(fun=self.target, x0=x0, jac=self.grad, bounds=bounds)
+            #logger.writeln(str(res))
+            logger.writeln(" finished in {} iterations ({} evaluations)".format(res.nit, res.nfev))
+            res_x = res.x
+            self.stats["fun"] = res.fun
+            self.stats["x"] = res.x
+        logger.writeln(" time: {:.3f} sec".format(time.time() - t0))
+        self.k_overall = self.k_trans(res_x[0])
+        nadp = self.adpdirs.shape[0]
+        b_overall = gemmi.SMat33d(*numpy.dot(res_x[1:nadp+1], self.adpdirs))
+        self.b_iso = b_overall.trace() / 3
+        self.b_aniso = b_overall.added_kI(-self.b_iso) # subtract isotropic contribution
+
+        logger.writeln(" k_ov= {:.2e} B_iso= {:.2e} B_aniso= {}".format(self.k_overall, self.b_iso, self.b_aniso))
+        if use_sol:
+            self.k_sol = res_x[-2] 
+            self.b_sol = res_x[-1]
+            logger.writeln(" k_sol= {:.2e} B_sol= {:.2e}".format(self.k_sol, self.b_sol))
+        calc = self.scaled_fc(res_x)
+        if self.use_int: calc *= calc
+        self.stats["cc"] = utils.hkl.correlation(self.obs, calc)
+        self.stats["r"] = utils.hkl.r_factor(self.obs, calc)
+        logger.writeln(" CC{} = {:.4f}".format(self.labcut, self.stats["cc"]))
+        logger.writeln(" R{}  = {:.4f}".format(self.labcut, self.stats["r"]))
+# class LsqScale
+
+def calc_abs_DFc(Ds, Fcs):
+    DFc = sum(Ds[i] * Fcs[i] for i in range(len(Ds)))
+    return numpy.abs(DFc)
+# calc_abs_DFc()
+
+#import line_profiler
+#profile = line_profiler.LineProfiler()
+#import atexit
+#atexit.register(profile.print_stats)
+#@profile
+def mlf(df, fc_labs, Ds, S, k_ani, idxes):
+    Fcs = numpy.vstack([df[lab].to_numpy()[idxes] for lab in fc_labs]).T
+    DFc = (Ds * Fcs).sum(axis=1)
+    ll = numpy.nansum(ext.ll_amp(df.FP.to_numpy()[idxes], df.SIGFP.to_numpy()[idxes],
+                                 k_ani[idxes], S * df.epsilon.to_numpy()[idxes],
+                                 numpy.abs(DFc), df.centric.to_numpy()[idxes]+1))
+    return numpy.nansum(ll)
+# mlf()
+
+#@profile
+def deriv_mlf_wrt_D_S(df, fc_labs, Ds, S, k_ani, idxes):
+    Fcs = [df[lab].to_numpy()[idxes] for lab in fc_labs]
+    r = ext.ll_amp_der1_DS(df.FP.to_numpy()[idxes], df.SIGFP.to_numpy()[idxes], k_ani[idxes], S,
+                           numpy.vstack(Fcs).T, Ds,
+                           df.centric.to_numpy()[idxes]+1, df.epsilon.to_numpy()[idxes])
+    g = numpy.zeros(len(fc_labs)+1)
+    g[:len(fc_labs)] = numpy.nansum(r[:,:len(fc_labs)], axis=0) # D
+    g[-1] = numpy.nansum(r[:,-1]) # S
+    return g
+# deriv_mlf_wrt_D_S()
+
+#@profile
+def mlf_shift_S(df, fc_labs, Ds, S, k_ani, idxes):
+    Fcs = [df[lab].to_numpy()[idxes] for lab in fc_labs]
+    r = ext.ll_amp_der1_DS(df.FP.to_numpy()[idxes], df.SIGFP.to_numpy()[idxes], k_ani[idxes], S,
+                           numpy.vstack(Fcs).T, Ds,
+                           df.centric.to_numpy()[idxes]+1, df.epsilon.to_numpy()[idxes])
+    g = numpy.nansum(r[:,-1])
+    H = numpy.nansum(r[:,-1]**2) # approximating expectation value of second derivative
+    return -g / H
+# mlf_shift_S()
+
+def mli(df, fc_labs, Ds, S, k_ani, idxes):
+    Fcs = numpy.vstack([df[lab].to_numpy()[idxes] for lab in fc_labs]).T
+    DFc = (Ds * Fcs).sum(axis=1)
+    ll = integr.ll_int(df.I.to_numpy()[idxes], df.SIGI.to_numpy()[idxes],
+                       k_ani[idxes], S * df.epsilon.to_numpy()[idxes],
+                       numpy.abs(DFc), df.centric.to_numpy()[idxes]+1)
+    return numpy.nansum(ll)
+# mli()
+
+def deriv_mli_wrt_D_S(df, fc_labs, Ds, S, k_ani, idxes):
+    Fcs = numpy.vstack([df[lab].to_numpy()[idxes] for lab in fc_labs]).T
+    r = integr.ll_int_der1_DS(df.I.to_numpy()[idxes], df.SIGI.to_numpy()[idxes], k_ani[idxes], S,
+                              Fcs, Ds,
+                              df.centric.to_numpy()[idxes]+1, df.epsilon.to_numpy()[idxes])
+    g = numpy.zeros(len(fc_labs)+1)
+    g[:len(fc_labs)] = numpy.nansum(r[:,:len(fc_labs)], axis=0) # D
+    g[-1] = numpy.nansum(r[:,-1]) # S
+    return g
+# deriv_mli_wrt_D_S()
+
+def mli_shift_D(df, fc_labs, Ds, S, k_ani, idxes):
+    Fcs = numpy.vstack([df[lab].to_numpy()[idxes] for lab in fc_labs]).T
+    r = integr.ll_int_der1_DS(df.I.to_numpy()[idxes], df.SIGI.to_numpy()[idxes], k_ani[idxes], S,
+                              Fcs, Ds,
+                              df.centric.to_numpy()[idxes]+1, df.epsilon.to_numpy()[idxes])[:,:len(fc_labs)]
+    g = numpy.nansum(r, axis=0)# * trans.D_deriv(x[:len(fc_labs)]) # D
+    #tmp = numpy.hstack([r[:,:len(fc_labs)] #* trans.D_deriv(x[:len(fc_labs)]),
+    #                    r[:,-1,None] * trans.S_deriv(x[-1])])
+    H = numpy.nansum(numpy.matmul(r[:,:,None], r[:,None]), axis=0)
+    return -numpy.dot(g, numpy.linalg.pinv(H))
+# mli_shift_D()
+
+def mli_shift_S(df, fc_labs, Ds, S, k_ani, idxes):
+    Fcs = numpy.vstack([df[lab].to_numpy()[idxes] for lab in fc_labs]).T
+    r = integr.ll_int_der1_DS(df.I.to_numpy()[idxes], df.SIGI.to_numpy()[idxes], k_ani[idxes], S,
+                              Fcs, Ds,
+                              df.centric.to_numpy()[idxes]+1, df.epsilon.to_numpy()[idxes])
+    g = numpy.nansum(r[:,-1])
+    H = numpy.nansum(r[:,-1]**2) # approximating expectation value of second derivative
+    return -g / H
+# mli_shift_S()
+
+def mltwin_est_ftrue(twin_data, df, k_ani, idxes):
+    kani2_inv = 1 / k_ani**2
+    i_sigi = numpy.empty((2, len(df.index)))
+    i_sigi[:] = numpy.nan
+    i_sigi[0, idxes] = (df.I.to_numpy() * kani2_inv)[idxes]
+    i_sigi[1, idxes] = (df.SIGI.to_numpy() * kani2_inv)[idxes]
+    twin_data.est_f_true(i_sigi[0,:], i_sigi[1,:])
+# mltwin_est_ftrue()
+
+def mltwin(df, twin_data, Ds, S, k_ani, idxes, i_bin):
+    twin_data.ml_sigma[i_bin] = S
+    twin_data.ml_scale[i_bin, :] = Ds
+    mltwin_est_ftrue(twin_data, df, k_ani, idxes)
+    return twin_data.ll()
+# mltwin()
+    
+def deriv_mltwin_wrt_D_S(df, twin_data, Ds, S, k_ani, idxes, i_bin):
+    twin_data.ml_sigma[i_bin] = S
+    twin_data.ml_scale[i_bin, :] = Ds
+    mltwin_est_ftrue(twin_data, df, k_ani, idxes)
+    r = twin_data.ll_der_D_S()
+    g = numpy.zeros(r.shape[1])
+    g[:-1] = numpy.nansum(r[:,:-1], axis=0) # D
+    g[-1] = numpy.nansum(r[:,-1]) # S
+    return g
+# deriv_mlf_wrt_D_S()
+
+def mltwin_shift_S(df, twin_data, Ds, S, k_ani, idxes, i_bin):
+    twin_data.ml_sigma[i_bin] = S
+    twin_data.ml_scale[i_bin, :] = Ds
+    mltwin_est_ftrue(twin_data, df, k_ani, idxes)
+    r = twin_data.ll_der_D_S()
+    g = numpy.nansum(r[:,-1])
+    H = numpy.nansum(r[:,-1]**2) # approximating expectation value of second derivative
+    return -g / H
+# mlf_shift_S()
+
+def determine_mlf_params_from_cc(hkldata, fc_labs, D_labs, centric_and_selections, use="all", smoothing="gauss"):
+    # theorhetical values
+    cc_a = lambda cc: (numpy.pi/4*(1-cc**2)**2 * scipy.special.hyp2f1(3/2, 3/2, 1, cc**2) - numpy.pi/4) / (1-numpy.pi/4)
+    cc_c = lambda cc: 2/(numpy.pi-2) * (cc**2*numpy.sqrt(1-cc**2) + cc * numpy.arctan(cc/numpy.sqrt(1-cc**2)) + (1-cc**2)**(3/2)-1)
+    table_fsc = numpy.arange(0, 1, 1e-3)
+    table_cc = [cc_a(table_fsc), cc_c(table_fsc)]
+
+    for lab in D_labs: hkldata.binned_df[lab] = 1.
+    hkldata.binned_df["S"] = 1.
+    
+    stats = hkldata.binned_df[["d_max", "d_min"]].copy()
+    for i, labi in enumerate(fc_labs):
+        stats["CC(FP,{})".format(labi)] = numpy.nan
+    for i, labi in enumerate(fc_labs):
+        for j in range(i+1, len(fc_labs)):
+            labj = fc_labs[j]
+            stats["CC({},{})".format(labi, labj)] = numpy.nan
+
+    # sqrt of eps * c; c = 1 for acentrics and 2 for centrics
+    inv_sqrt_c_eps = 1. / numpy.sqrt(hkldata.df.epsilon.to_numpy() * (hkldata.df.centric.to_numpy() + 1))
+    for i_bin, _ in hkldata.binned():
+        # assume they are all acentrics.. only correct by c
+        if use == "all":
+            cidxes = numpy.concatenate([sel[i] for sel in centric_and_selections[i_bin] for i in (1,2)])
+        else:
+            i = 1 if use == "work" else 2
+            cidxes = numpy.concatenate([sel[i] for sel in centric_and_selections[i_bin]])
+        valid_sel = numpy.isfinite(hkldata.df.FP.to_numpy()[cidxes])
+        cidxes = cidxes[valid_sel]
+        factor = inv_sqrt_c_eps[cidxes]
+        k_ani = hkldata.df.k_aniso.to_numpy()[cidxes]
+        Fo = hkldata.df.FP.to_numpy()[cidxes] * factor / k_ani
+        mean_Fo2 = numpy.mean(Fo**2)
+        SigFo = hkldata.df.SIGFP.to_numpy()[cidxes] / k_ani
+        Fcs = [hkldata.df[lab].to_numpy()[cidxes] * factor for lab in fc_labs]
+        mean_Fk2 = numpy.array([numpy.mean(numpy.abs(fk)**2) for fk in Fcs])
+        
+        # estimate D
+        cc_fo_fj = [numpy.corrcoef(numpy.abs(fj), Fo)[1,0] for fj in Fcs]
+        for i in range(len(fc_labs)): stats.loc[i_bin, "CC(FP,{})".format(fc_labs[i])] = cc_fo_fj[i]
+        mat = [[numpy.sqrt(numpy.mean(numpy.abs(fk)**2)/mean_Fo2) * numpy.real(numpy.corrcoef(fk, fj)[1,0])
+                for fk in Fcs]
+               for fj in Fcs]
+        A = [[numpy.sqrt(numpy.mean(numpy.abs(fk)**2) * numpy.mean(numpy.abs(fj)**2))/mean_Fo2 * numpy.real(numpy.corrcoef(fk, fj)[1,0])
+                for fk in Fcs]
+               for fj in Fcs]
+        A = numpy.array([[numpy.real(numpy.corrcoef(fk, fj)[1,0]) for fk in Fcs] for fj in Fcs])
+        v = numpy.interp(cc_fo_fj, table_cc[0], table_fsc)
+
+        for i in range(len(fc_labs)):
+            labi = fc_labs[i]
+            for j in range(i+1, len(fc_labs)):
+                labj = fc_labs[j]
+                stats.loc[i_bin, "CC({},{})".format(labi, labj)] = numpy.real(numpy.corrcoef(Fcs[i], Fcs[j])[1,0])
+
+        # test all signs, fixing first Fc positive.
+        cc_max = -2
+        for v_test in itertools.product(*((x, -x) for x in v[1:])):
+            v_test = numpy.array((v[0],)+v_test)
+            Dj_test = numpy.dot(numpy.linalg.pinv(A), v_test) * numpy.sqrt(mean_Fo2 / mean_Fk2)
+            DFc_test = calc_abs_DFc(Dj_test, Fcs)
+            cc_test = numpy.corrcoef(Fo, numpy.abs(DFc_test))[1,0]
+            if cc_test > cc_max:
+                cc_max = cc_test
+                v_max = v_test
+                DFc = DFc_test
+                Dj = Dj_test
+
+        for lab, D in zip(D_labs, Dj):
+            hkldata.binned_df.loc[i_bin, lab] = D
+
+        # estimate S
+        mean_DFc2 = numpy.mean(DFc**2)
+        est_fsc_fo_fc = numpy.interp(numpy.corrcoef(Fo, DFc)[1,0], table_cc[0], table_fsc)
+        S = mean_Fo2 - 2 * numpy.sqrt(mean_Fo2 * mean_DFc2) * est_fsc_fo_fc + mean_DFc2 - numpy.mean(SigFo**2)
+        hkldata.binned_df.loc[i_bin, "S"] = S
+
+    logger.writeln("\nCC:")
+    logger.writeln(stats.to_string())
+    logger.writeln("\nEstimates:")
+    logger.writeln(hkldata.binned_df.to_string())
+    smooth_params(hkldata, D_labs, smoothing)
+# determine_mlf_params_from_cc()
+
+def initialize_ml_params(hkldata, use_int, D_labs, b_aniso, centric_and_selections, use, twin_data=None):
+    # Initial values
+    for lab in D_labs: hkldata.binned_df[lab] = 1.
+    hkldata.binned_df["S"] = 10000.
+    k_ani = hkldata.debye_waller_factors(b_cart=b_aniso)
+    lab_obs = "I" if use_int else "FP"
+    for i_bin, _ in hkldata.binned():
+        if use == "all":
+            idxes = numpy.concatenate([sel[i] for sel in centric_and_selections[i_bin] for i in (1,2)])
+        else:
+            i = 1 if use == "work" else 2
+            idxes = numpy.concatenate([sel[i] for sel in centric_and_selections[i_bin]])
+        valid_sel = numpy.isfinite(hkldata.df.loc[idxes, lab_obs]) # as there is no nan-safe numpy.corrcoef
+        if numpy.sum(valid_sel) < 2:
+            continue
+        idxes = idxes[valid_sel]
+        if use_int:
+            Io = hkldata.df.I.to_numpy()[idxes]
+        else:
+            Io = hkldata.df.FP.to_numpy()[idxes]**2
+        Io /= k_ani[idxes]**2
+        if twin_data:
+            Ic = twin_data.i_calc_twin()[idxes]
+        else:
+            Ic = numpy.abs(hkldata.df.FC.to_numpy()[idxes])**2
+        mean_Io = numpy.mean(Io)
+        mean_Ic = numpy.mean(Ic)
+        cc = numpy.corrcoef(Io, Ic)[1,0]
+        if cc > 0 and mean_Io > 0:
+            D = numpy.sqrt(mean_Io / mean_Ic * cc)
+        else:
+            D = 0 # will be taken care later
+        hkldata.binned_df.loc[i_bin, D_labs[0]] = D
+        if mean_Io > 0:
+            S = mean_Io - 2 * numpy.sqrt(mean_Io * mean_Ic * numpy.maximum(0, cc)) + mean_Ic
+        else:
+            S = numpy.std(Io) # similar initial to french_wilson
+        hkldata.binned_df.loc[i_bin, "S"] = S
+
+    for D_lab in D_labs:
+        if hkldata.binned_df[D_lab].min() <= 0:
+            min_D = hkldata.binned_df[D_lab][hkldata.binned_df[D_lab] > 0].min() * 0.1
+            logger.writeln("WARNING: negative {} is detected from initial estimates. Replacing it using minimum positive value {:.2e}".format(D_lab, min_D))
+            hkldata.binned_df[D_lab].where(hkldata.binned_df[D_lab] > 0, min_D, inplace=True) # arbitrary
+
+    if twin_data:
+        twin_data.ml_scale[:] = hkldata.binned_df.loc[:, D_labs]
+        twin_data.ml_sigma[:] = hkldata.binned_df.loc[:, "S"]
+            
+    logger.writeln("Initial estimates:")
+    logger.writeln(hkldata.binned_df.to_string())
+# initialize_ml_params()
+
+def determine_ml_params(hkldata, use_int, fc_labs, D_labs, b_aniso, centric_and_selections,
+                        D_trans=None, S_trans=None, use="all", n_cycle=1, smoothing="gauss",
+                        twin_data=None):
+    assert use in ("all", "work", "test")
+    assert smoothing in (None, "gauss")
+    logger.writeln("Estimating sigma-A parameters using {}..".format(("intensities" if use_int else "amplitudes") + " (twin)" if twin_data else ""))
+    trans = VarTrans(D_trans, S_trans)
+    lab_obs = "I" if use_int else "FP"
+    def get_idxes(i_bin):
+        if use == "all":
+            return numpy.concatenate([sel[i] for sel in centric_and_selections[i_bin] for i in (1,2)])
+        else:
+            i = 1 if use == "work" else 2
+            return numpy.concatenate([sel[i] for sel in centric_and_selections[i_bin]])
+
+    if not set(D_labs + ["S"]).issubset(hkldata.binned_df):
+        initialize_ml_params(hkldata, use_int, D_labs, b_aniso, centric_and_selections, use, twin_data=twin_data)
+        for dlab, fclab in zip(D_labs, fc_labs):
+            hkldata.binned_df["Mn(|{}*{}|)".format(dlab, fclab)] = numpy.nan
+
+    refpar = "all"
+    for i_cyc in range(n_cycle):
+        t0 = time.time()
+        nfev_total = 0
+        k_ani = hkldata.debye_waller_factors(b_cart=b_aniso)
+        for i_bin, _ in hkldata.binned():
+            idxes = get_idxes(i_bin)
+            valid_sel = numpy.isfinite(hkldata.df.loc[idxes, lab_obs]) # as there is no nan-safe numpy.corrcoef
+            if numpy.sum(valid_sel) < 5:
+                logger.writeln("WARNING: bin {} has no sufficient reflections".format(i_bin))
+                continue
+
+            def target(x):
+                if refpar == "all":
+                    Ds = trans.D(x[:len(fc_labs)])
+                    S = trans.S(x[-1])
+                elif refpar == "D":
+                    Ds = trans.D(x[:len(fc_labs)])
+                    S = hkldata.binned_df.loc[i_bin, "S"]
+                else:
+                    Ds = [hkldata.binned_df.loc[i_bin, lab] for lab in D_labs]
+                    S = trans.S(x[-1])
+
+                if twin_data:
+                    return mltwin(hkldata.df, twin_data, Ds, S, k_ani, idxes, i_bin)
+                else:
+                    f = mli if use_int else mlf
+                    return f(hkldata.df, fc_labs, Ds, S, k_ani, idxes)
+
+            def grad(x):
+                if refpar == "all":
+                    Ds = trans.D(x[:len(fc_labs)])
+                    S = trans.S(x[-1])
+                    n_par = len(fc_labs)+1
+                elif refpar == "D":
+                    Ds = trans.D(x[:len(fc_labs)])
+                    S = hkldata.binned_df.loc[i_bin, "S"]
+                    n_par = len(fc_labs)
+                else:
+                    Ds = [hkldata.binned_df.loc[i_bin, lab] for lab in D_labs]
+                    S = trans.S(x[-1])
+                    n_par = 1
+                if twin_data:
+                    r = deriv_mltwin_wrt_D_S(hkldata.df, twin_data, Ds, S, k_ani, idxes, i_bin)
+                else:
+                    calc_deriv = deriv_mli_wrt_D_S if use_int else deriv_mlf_wrt_D_S
+                    r = calc_deriv(hkldata.df, fc_labs, Ds, S, k_ani, idxes)
+                g = numpy.zeros(n_par)
+                if refpar in ("all", "D"):
+                    g[:len(fc_labs)] = r[:len(fc_labs)]
+                    g[:len(fc_labs)] *= trans.D_deriv(x[:len(fc_labs)])
+                if refpar in ("all", "S"):
+                    g[-1] = r[-1]
+                    g[-1] *= trans.S_deriv(x[-1])
+                return g
+
+            if 0:
+                refpar = "S"
+                x0 = trans.S_inv(hkldata.binned_df.loc[i_bin, "S"])
+                with open("s_line_{}.dat".format(i_bin), "w") as ofs:
+                    for sval in numpy.linspace(1, x0*2, 100):
+                        ofs.write("{:.4e} {:.10e} {:.10e}\n".format(sval,
+                                                                    target([sval]),
+                                                                    grad([sval])[0]))
+                continue
+            #print("Bin", i_bin)
+            if 1: # refine D and S iteratively
+                vals_last = None
+                for ids in range(10):
+                    refpar = "D"
+                    x0 = numpy.array([trans.D_inv(hkldata.binned_df.loc[i_bin, lab]) for lab in D_labs])
+                    #print("MLTWIN=", target(x0))
+                    #quit()
+                    if 0:
+                        h = 1e-3
+                        f00 = target(x0)
+                        g00 = grad(x0)
+                        for ii in range(len(x0)):
+                            xx = x0.copy()
+                            xx[ii] += h
+                            f01 = target(xx)
+                            nder = (f01 - f00) / h
+                            logger.writeln(f"DEBUG_der_D bin_{i_bin} {ii} ad={g00[ii]} nd={nder} r={g00[ii]/nder}")
+                    vals_now = []
+                    if 0:
+                        f0 = target(x0)
+                        nfev_total += 1
+                        shift = mli_shift_D(hkldata.df, fc_labs, trans.D(x0), hkldata.binned_df.loc[i_bin, "S"], k_ani, idxes)
+                        shift /= trans.D_deriv(x0)
+                        #if abs(shift) < 1e-3: break
+                        for itry in range(10):
+                            x1 = x0 + shift
+                            if (D_trans and any(x1 < -3)) or (not D_trans and any(x1 < 5e-2)):
+                                #print(i_bin, cyc_s, trans.S(x0), trans.S(x1), shift, "BAD")
+                                shift /= 2
+                                continue
+                            f1 = target(x1)
+                            nfev_total += 1
+                            if f1 > f0:
+                                shift /= 2
+                                continue
+                            else: # good
+                                for i, lab in enumerate(D_labs):
+                                    hkldata.binned_df.loc[i_bin, lab] = trans.D(x1[i])
+                                    vals_now.append(hkldata.binned_df.loc[i_bin, lab])
+                                break
+                        else:
+                            break
+                    else:
+                        #print(mli_shift_D(hkldata.df, fc_labs, trans.D(x0), hkldata.binned_df.S[i_bin], k_ani, idxes))
+                        res = scipy.optimize.minimize(fun=target, x0=x0, jac=grad,
+                                                      bounds=((-5 if D_trans else 1e-5, None),)*len(x0))
+                        nfev_total += res.nfev
+                        #print(i_bin, "mini cycle", ids, refpar)
+                        #print(res)
+                        for i, lab in enumerate(D_labs):
+                            hkldata.binned_df.loc[i_bin, lab] = trans.D(res.x[i])
+                            vals_now.append(hkldata.binned_df.loc[i_bin, lab])
+                        if twin_data:
+                            twin_data.ml_scale[i_bin, :] = trans.D(res.x)
+                    refpar = "S"
+                    if 1:
+                        for cyc_s in range(1):
+                            x0 = trans.S_inv(hkldata.binned_df.loc[i_bin, "S"])
+                            if 0:
+                                h = 1e-1
+                                f00 = target([x0])
+                                g00 = grad([x0])
+                                xx = x0 + h
+                                f01 = target([xx])
+                                nder = (f01 - f00) / h
+                                logger.writeln(f"DEBUG_der_S bin_{i_bin} ad={g00} nd={nder} r={g00/nder}")
+
+                            f0 = target([x0])
+                            Ds = [hkldata.binned_df.loc[i_bin, lab] for lab in D_labs]
+                            nfev_total += 1
+                            if twin_data:
+                                shift = mltwin_shift_S(hkldata.df, twin_data, Ds, trans.S(x0), k_ani, idxes, i_bin)
+                            else:
+                                calc_shift_S = mli_shift_S if use_int else mlf_shift_S
+                                shift = calc_shift_S(hkldata.df, fc_labs, Ds, trans.S(x0), k_ani, idxes)
+                            shift /= trans.S_deriv(x0)
+                            if abs(shift) < 1e-3: break
+                            for itry in range(10):
+                                x1 = x0 + shift
+                                if (S_trans and x1 < -3) or (not S_trans and x1 < 5e-2):
+                                    #print(i_bin, cyc_s, trans.S(x0), trans.S(x1), shift, "BAD")
+                                    shift /= 2
+                                    continue
+                                f1 = target([x1])
+                                nfev_total += 1
+                                if f1 > f0:
+                                    shift /= 2
+                                    continue
+                                else: # good
+                                    #print(i_bin, cyc_s, trans.S(x0), trans.S(x1), shift)
+                                    hkldata.binned_df.loc[i_bin, "S"] = trans.S(x1)
+                                    break
+                            else:
+                                #print("all bad")
+                                break
+                        if twin_data:
+                            twin_data.ml_sigma[i_bin] = hkldata.binned_df.loc[i_bin, "S"]
+                    else:
+                        # somehow this does not work well.
+                        x0 = [trans.S_inv(hkldata.binned_df.loc[i_bin, "S"])]
+                        res = scipy.optimize.minimize(fun=target, x0=x0, jac=grad,
+                                                      bounds=((-3 if S_trans else 5e-2, None),))
+                        nfev_total += res.nfev
+                        #print(i_bin, "mini cycle", ids, refpar)
+                        #print(res)
+                        hkldata.binned_df.loc[i_bin, "S"] = trans.S(res.x[-1])
+                        if twin_data:
+                            twin_data.ml_sigma[i_bin] = trans.S(res.x[-1])
+                    vals_now.append(hkldata.binned_df.loc[i_bin, "S"])
+                    vals_now = numpy.array(vals_now)
+                    if vals_last is not None and numpy.all(numpy.abs((vals_last - vals_now) / vals_now) < 1e-2):
+                        #logger.writeln("converged in mini cycle {}".format(ids+1))
+                        break
+                    vals_last = vals_now
+            else:
+                x0 = [trans.D_inv(hkldata.binned_df.loc[i_bin, lab]) for lab in D_labs] + [trans.S_inv(hkldata.binned_df.loc[i_bin, "S"])]
+                res = scipy.optimize.minimize(fun=target, x0=x0, jac=grad,
+                                              bounds=((-5 if D_trans else 1e-5, None), )*len(D_labs) + ((-3 if S_trans else 5e-2, None),))
+                nfev_total += res.nfev
+                #print(i_bin)
+                #print(res)
+                for i, lab in enumerate(D_labs):
+                    hkldata.binned_df.loc[i_bin, lab] = trans.D(res.x[i])
+                hkldata.binned_df.loc[i_bin, "S"] = trans.S(res.x[-1])
+                if twin_data:
+                    twin_data.ml_scale[i_bin, :] = trans.D(res.x[:-1])
+                    twin_data.ml_sigma[i_bin] = trans.S(res.x[-1])
+
+        if twin_data:
+            dfc = numpy.abs(twin_data.f_calc) * twin_data.ml_scale_array()
+            for i_bin, idxes in hkldata.binned():
+                dfc_bin = dfc[numpy.asarray(twin_data.bin)==i_bin,:]
+                mean_dfc = numpy.nanmean(dfc_bin, axis=0)
+                for i, (dlab, fclab) in enumerate(zip(D_labs, fc_labs)):
+                    hkldata.binned_df.loc[i_bin, "Mn(|{}*{}|)".format(dlab, fclab)] = mean_dfc[i]
+        else:
+            for i_bin, idxes in hkldata.binned():
+                for dlab, fclab in zip(D_labs, fc_labs):
+                    mean_dfc = numpy.nanmean(numpy.abs(hkldata.binned_df[dlab][i_bin] * hkldata.df[fclab][idxes]))
+                    hkldata.binned_df.loc[i_bin, "Mn(|{}*{}|)".format(dlab, fclab)] = mean_dfc
+                
+        logger.writeln("Refined estimates:")
+        logger.writeln(hkldata.binned_df.to_string())
+        #numpy.testing.assert_allclose(hkldata.binned_df.S, twin_data.ml_sigma)
+        #numpy.testing.assert_allclose(hkldata.binned_df[D_labs], twin_data.ml_scale)
+        logger.writeln("time: {:.1f} sec ({} evaluations)".format(time.time() - t0, nfev_total))
+
+        if not use_int or twin_data:
+            break # did not implement MLF B_aniso optimization
+        
+        # Refine b_aniso
+        adpdirs = utils.model.adp_constraints(hkldata.sg.operations(), hkldata.cell, tr0=True)
+        SMattolist = lambda B: [B.u11, B.u22, B.u33, B.u12, B.u13, B.u23]
+
+        def target_ani(x):
+            b = gemmi.SMat33d(*numpy.dot(x, adpdirs))
+            k_ani = hkldata.debye_waller_factors(b_cart=b)
+            ret = 0.
+            for i_bin, idxes in hkldata.binned():
+                Ds = [hkldata.binned_df.loc[i_bin, lab] for lab in D_labs]
+                ret += mli(hkldata.df, fc_labs, Ds, hkldata.binned_df.loc[i_bin, "S"], k_ani, idxes)
+            return ret
+        def grad_ani(x):
+            b = gemmi.SMat33d(*numpy.dot(x, adpdirs))
+            k_ani = hkldata.debye_waller_factors(b_cart=b)
+            S2mat = hkldata.ssq_mat() # ssqmat
+            g = numpy.zeros(6)
+            for i_bin, idxes in hkldata.binned():
+                r = integr.ll_int_der1_ani(hkldata.df.I.to_numpy()[idxes], hkldata.df.SIGI.to_numpy()[idxes],
+                                           k_ani[idxes], hkldata.binned_df.loc[i_bin, "S"],
+                                           hkldata.df[fc_labs].to_numpy()[idxes], hkldata.binned_df.loc[i_bin, D_labs],
+                                           hkldata.df.centric.to_numpy()[idxes]+1, hkldata.df.epsilon.to_numpy()[idxes])
+                S2 = S2mat[:,idxes]
+                g += -numpy.nansum(S2 * r[:,0], axis=1) # k_ani is already multiplied in r
+            return numpy.dot(g, adpdirs.T)
+        def shift_ani(x):
+            b = gemmi.SMat33d(*numpy.dot(x, adpdirs))
+            k_ani = hkldata.debye_waller_factors(b_cart=b)
+            S2mat = hkldata.ssq_mat() # ssqmat
+            g = numpy.zeros(6)
+            H = numpy.zeros((6, 6))
+            for i_bin, idxes in hkldata.binned():
+                r = integr.ll_int_der1_ani(hkldata.df.I.to_numpy()[idxes], hkldata.df.SIGI.to_numpy()[idxes],
+                                           k_ani[idxes], hkldata.binned_df.loc[i_bin, "S"],
+                                           hkldata.df[fc_labs].to_numpy()[idxes], list(hkldata.binned_df.loc[i_bin, D_labs]),
+                                           hkldata.df.centric.to_numpy()[idxes]+1, hkldata.df.epsilon.to_numpy()[idxes])
+                S2 = S2mat[:,idxes]
+                g += -numpy.nansum(S2 * r[:,0], axis=1) # k_ani is already multiplied in r
+                H += numpy.nansum(numpy.matmul(S2[None,:].T, S2.T[:,None]) * (r[:,0]**2)[:,None,None], axis=0)
+
+            g, H = numpy.dot(g, adpdirs.T), numpy.dot(adpdirs, numpy.dot(H, adpdirs.T))
+            return -numpy.dot(g, numpy.linalg.pinv(H))
+
+        logger.writeln("Refining B_aniso. Current = {}".format(b_aniso))
+        if 0:
+            x0 = numpy.dot(SMattolist(b_aniso), numpy.linalg.pinv(adpdirs))
+            res = scipy.optimize.minimize(fun=target_ani, x0=x0, jac=grad_ani)
+            print(res)
+            b_aniso = gemmi.SMat33d(*numpy.dot(res.x, adpdirs))
+            f1 = res.fun
+        else:
+            B_converged = False
+            for j in range(10):
+                x = numpy.dot(SMattolist(b_aniso), numpy.linalg.pinv(adpdirs))
+                f0 = target_ani(x)
+                shift = shift_ani(x)
+                for i in range(3):
+                    ss = shift / 2**i
+                    f1 = target_ani(x + ss)
+                    #logger.writeln("{:2d} f0 = {:.3e} shift = {} df = {:.3e}".format(j, f0, ss, f1 - f0))
+                    if f1 < f0:
+                        b_aniso = gemmi.SMat33d(*numpy.dot(x+ss, adpdirs))
+                        if numpy.max(numpy.abs(ss)) < 1e-4: B_converged = True
+                        break
+                else:
+                    B_converged = True
+                if B_converged: break
+
+        logger.writeln("Refined B_aniso = {}".format(b_aniso))
+        logger.writeln("cycle {} f= {}".format(i_cyc, f1))
+
+    smooth_params(hkldata, D_labs, smoothing)
+    return b_aniso
+# determine_ml_params()
+
+def smooth_params(hkldata, D_labs, smoothing): # XXX twin_data
+    if smoothing is None or len(hkldata.binned()) < 2:
+        for i, lab in enumerate(D_labs + ["S"]):
+            hkldata.df[lab] = hkldata.binned_data_as_array(lab)
+
+    elif smoothing == "gauss":
+        bin_centers = (0.5 / hkldata.binned_df[["d_min", "d_max"]]**2).sum(axis=1).to_numpy()
+        vals = ext.smooth_gauss(bin_centers,
+                                hkldata.binned_df[D_labs + ["S"]].to_numpy(),
+                                1./hkldata.df.d.to_numpy()**2,
+                                100, # min(n_ref?)
+                                (bin_centers[1] - bin_centers[0]))
+        for i, lab in enumerate(D_labs + ["S"]):
+            hkldata.df[lab] = vals[:, i]
+        # Update smoothened average; this affects next refinement.
+        # TODO: update Mn(|Dj*FCj|) as well.
+        #for i_bin, idxes in hkldata.binned():
+        #    for lab in D_labs + ["S"]:
+        #        hkldata.binned_df.loc[i_bin, lab] = numpy.mean(hkldata.df[lab].to_numpy()[idxes])
+    else:
+        raise RuntimeError("unknown smoothing method: {}".format(smoothing))
+# smooth_params()
+
+def expected_F_from_int(Io, sigIo, k_ani, DFc, eps, c, S):
+    k_num = numpy.repeat(0.5 if c == 0 else 0., Io.size) # 0.5 if acentric
+    k_den = k_num - 0.5
+    if numpy.isscalar(c): c = numpy.repeat(c, Io.size)
+    to = Io / sigIo - sigIo / (c+1) / k_ani**2 / S / eps
+    tf = k_ani * numpy.abs(DFc) / numpy.sqrt(sigIo)
+    sig1 = k_ani**2 * S * eps / sigIo
+    f = ext.integ_J_ratio(k_num, k_den, True, to, tf, sig1, c+1, integr.exp2_threshold, integr.h, integr.N, integr.ewmax)
+    f *= numpy.sqrt(sigIo) / k_ani
+    m_proxy = ext.integ_J_ratio(k_num, k_num, True, to, tf, sig1, c+1, integr.exp2_threshold, integr.h, integr.N, integr.ewmax)
+    return f, m_proxy
+# expected_F_from_int()
+
+def calculate_maps_int(hkldata, b_aniso, fc_labs, D_labs, centric_and_selections, use="all"):
+    nmodels = len(fc_labs)
+    hkldata.df["FWT"] = 0j * numpy.nan
+    hkldata.df["DELFWT"] = 0j * numpy.nan
+    hkldata.df["FOM"] = numpy.nan # FOM proxy, |<F>| / <|F|>
+    has_ano = "I(+)" in hkldata.df and "I(-)" in hkldata.df
+    if has_ano:
+        hkldata.df["FAN"] = 0j * numpy.nan
+        ano_data = hkldata.df[["I(+)", "SIGI(+)", "I(-)", "SIGI(-)"]].to_numpy()
+    Io = hkldata.df.I.to_numpy()
+    sigIo = hkldata.df.SIGI.to_numpy()
+    k_ani = hkldata.debye_waller_factors(b_cart=b_aniso)
+    eps = hkldata.df.epsilon.to_numpy()
+    Ds = numpy.vstack([hkldata.df[lab].to_numpy() for lab in D_labs]).T
+    Fcs = numpy.vstack([hkldata.df[lab].to_numpy() for lab in fc_labs]).T
+    DFc = (Ds * Fcs).sum(axis=1)
+    hkldata.df["DFC"] = DFc
+    for i_bin, idxes in hkldata.binned():
+        for c, work, test in centric_and_selections[i_bin]:
+            cidxes = numpy.concatenate([work, test])
+            S = hkldata.df["S"].to_numpy()[cidxes]
+            f, m_proxy = expected_F_from_int(Io[cidxes], sigIo[cidxes], k_ani[cidxes], DFc[cidxes], eps[cidxes], c, S)
+            exp_ip = numpy.exp(numpy.angle(DFc[cidxes])*1j)
+            if c == 0:
+                hkldata.df.loc[cidxes, "FWT"] = 2 * f * exp_ip - DFc[cidxes]
+            else:
+                hkldata.df.loc[cidxes, "FWT"] = f * exp_ip
+            hkldata.df.loc[cidxes, "DELFWT"] = f * exp_ip - DFc[cidxes]
+            hkldata.df.loc[cidxes, "FOM"] = m_proxy
+            if has_ano:
+                f_p, _ = expected_F_from_int(ano_data[cidxes,0], ano_data[cidxes,1],
+                                             k_ani[cidxes], DFc[cidxes], eps[cidxes], c, S)
+                f_m, _ = expected_F_from_int(ano_data[cidxes,2], ano_data[cidxes,3],
+                                             k_ani[cidxes], DFc[cidxes], eps[cidxes], c, S)
+                hkldata.df.loc[cidxes, "FAN"] = (f_p - f_m) * exp_ip / 2j
+            # remove reflections that should be hidden
+            if use != "all":
+                # usually use == "work"
+                tohide = test if use == "work" else work
+                hkldata.df.loc[tohide, "FWT"] = 0j * numpy.nan
+                hkldata.df.loc[tohide, "DELFWT"] = 0j * numpy.nan
+            fill_sel = numpy.isnan(hkldata.df["FWT"][cidxes].to_numpy())
+            hkldata.df.loc[cidxes[fill_sel], "FWT"] = DFc[cidxes][fill_sel]
+# calculate_maps_int()
+
+def calculate_maps_twin(hkldata, b_aniso, fc_labs, D_labs, twin_data, centric_and_selections, use="all"):
+    k_ani2_inv = 1 / hkldata.debye_waller_factors(b_cart=b_aniso)**2
+    Io = hkldata.df.I.to_numpy(copy=True) * k_ani2_inv
+    sigIo = hkldata.df.SIGI.to_numpy(copy=True) * k_ani2_inv
+    # Mask Io
+    for i_bin, idxes in hkldata.binned():
+        for c, work, test in centric_and_selections[i_bin]:
+            if use != "all":
+                tohide = test if use == "work" else work
+                Io[tohide] = numpy.nan
+    
+    twin_data.est_f_true(Io, sigIo)
+    Ds = twin_data.ml_scale_array()
+    DFc = (twin_data.f_calc * Ds).sum(axis=1)
+    exp_ip = numpy.exp(numpy.angle(DFc)*1j)
+    Ft = numpy.asarray(twin_data.f_true_max)
+    m = twin_data.calc_fom()
+    Fexp = twin_data.expected_F(Io, sigIo)
+    if 1:
+        fwt = numpy.where(numpy.asarray(twin_data.centric) == 0,
+                          2 * m * Ft * exp_ip - DFc,
+                          m * Ft * exp_ip)
+        delfwt = m * Ft * exp_ip - DFc
+    else: # based on "more accurate" evaluation of <m|F|>
+        fwt = numpy.where(numpy.asarray(twin_data.centric) == 0,
+                          2 * Fexp * exp_ip - DFc,
+                          m * Fexp * exp_ip)
+        delfwt = Fexp * exp_ip - DFc
+
+    sel = numpy.isnan(fwt)
+    fwt[sel] = DFc[sel]
+    
+    hkldata2 = utils.hkl.HklData(hkldata.cell, hkldata.sg,
+                                 utils.hkl.df_from_twin_data(twin_data, fc_labs))
+    hkldata2.df["FWT"] = fwt
+    hkldata2.df["DELFWT"] = delfwt
+    hkldata2.df["FOM"] = m
+    hkldata2.df["F_est"] = Ft
+    hkldata2.df["F_exp"] = Fexp
+    hkldata2.df["FC"] = twin_data.f_calc.sum(axis=1)
+    hkldata2.df["DFC"] = DFc
+    hkldata2.df[D_labs] = Ds
+    hkldata2.df["S"] = twin_data.ml_sigma_array()
+    return hkldata2
+# calculate_maps_twin()
+
+def merge_models(sts): # simply merge models. no fix in chain ids etc.
+    st2 = sts[0].clone()
+    del st2[:]
+    model = gemmi.Model(1)
+    for st in sts:
+        for m in st:
+            for c in m:
+                model.add_chain(c)
+    st2.add_model(model)
+    return st2
+# merge_models()
+
+def decide_mtz_labels(mtz, find_free=True, require=None):
+    # F is preferred for now by default
+    obs_types = ("F", "J", "G", "K")
+    if require:
+        assert set(require).issubset(obs_types)
+    else:
+        require = obs_types
+    dlabs = utils.hkl.mtz_find_data_columns(mtz)
+    logger.writeln("Finding possible options from MTZ:")
+    for typ in dlabs:
+        for labs in dlabs[typ]:
+            logger.writeln(" --labin '{}'".format(",".join(labs)))
+    for typ in require:
+        if dlabs[typ]:
+            labin = dlabs[typ][0]
+            break
+    else:
+        raise RuntimeError("Data not found from mtz")
+    if find_free:
+        flabs = utils.hkl.mtz_find_free_columns(mtz)
+        if flabs:
+            labin += [flabs[0]]
+    logger.writeln("MTZ columns automatically selected: {}".format(labin))
+    return labin
+# decide_mtz_labels()
+
+def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=None,
+                  n_per_bin=None, use="all", max_bins=None, cif_index=0, keep_charges=False,
+                  allow_unusual_occupancies=False, space_group=None):
+    if labin: assert 1 < len(labin) < 6
+    assert use in ("all", "work", "test")
+    assert n_bins or n_per_bin #if n_bins not set, n_per_bin should be given
+
+    if len(xyzins) > 0 and type(xyzins[0]) is gemmi.Structure:
+        sts = xyzins
+    else:
+        sts = []
+    
+    if type(hklin) is gemmi.Mtz or utils.fileio.is_mmhkl_file(hklin):
+        if type(hklin) is gemmi.Mtz:
+            mtz = hklin
+        else:
+            mtz = utils.fileio.read_mmhkl(hklin, cif_index=cif_index)
+        if not sts:
+            sts = [utils.fileio.read_structure(f) for f in xyzins]
+    else:
+        assert len(xyzins) == 1
+        assert not sts
+        st, mtz = utils.fileio.read_small_molecule_files([hklin, xyzins[0]])
+        sts = [st]
+
+    for st in sts:
+        utils.model.check_occupancies(st, raise_error=not allow_unusual_occupancies)
+        
+    if not labin:
+        labin = decide_mtz_labels(mtz)
+    col_types = {x.label:x.type for x in mtz.columns}
+    if labin[0] not in col_types:
+        raise RuntimeError("MTZ column not found: {}".format(labin[0]))
+    labs_and_types = {"F": ("amplitude", ["FP","SIGFP"], ["F", "Q"]),
+                      "J": ("intensity", ["I","SIGI"], ["J", "Q"]),
+                      "G": ("anomalous amplitude", ["F(+)","SIGF(+)", "F(-)", "SIGF(-)"], ["G", "L", "G", "L"]),
+                      "K": ("anomalous intensity", ["I(+)","SIGI(+)", "I(-)", "SIGI(-)"], ["K", "M", "K", "M"])}
+    if col_types[labin[0]] not in labs_and_types:
+        raise RuntimeError("MTZ column {} is neither amplitude nor intensity".format(labin[0]))
+    name, newlabels, require_types = labs_and_types[col_types[labin[0]]]
+    logger.writeln("Observation type: {}".format(name))
+    if len(newlabels) < len(labin): newlabels.append("FREE")
+    hkldata = utils.hkl.hkldata_from_mtz(mtz, labin, newlabels=newlabels, require_types=require_types)
+    if newlabels[0] == "F(+)":
+        hkldata.merge_anomalous(newlabels[:4], ["FP", "SIGFP"])
+        newlabels = ["FP", "SIGFP"] + newlabels[4:]
+    elif newlabels[0] == "I(+)":
+        hkldata.merge_anomalous(newlabels[:4], ["I", "SIGI"])
+        newlabels = ["I", "SIGI"] + newlabels[4:]
+
+    if hkldata.df.empty:
+        raise RuntimeError("No data in hkl data")
+    
+    if space_group is None:
+        sg_use = None
+    else:
+        sg_use = gemmi.SpaceGroup(space_group)
+        logger.writeln(f"Space group overridden by user. Using {sg_use.xhm()}")
+    
+    if sts:
+        assert source in ["electron", "xray", "neutron"]
+        for st in sts:
+            if st[0].count_atom_sites() == 0:
+                raise RuntimeError("No atom in the model")
+        if not hkldata.cell.approx(sts[0].cell, 1e-3):
+            logger.writeln("Warning: unit cell mismatch between model and reflection data")
+            logger.writeln("         using unit cell from mtz")
+
+        for st in sts: st.cell = hkldata.cell # mtz cell is used in any case
+
+        sg_st = sts[0].find_spacegroup() # may be None
+        if sg_use is None:
+            sg_use = hkldata.sg
+            if hkldata.sg != sg_st:
+                if st.cell.is_crystal() and sg_st and sg_st.laue_str() != hkldata.sg.laue_str():
+                    raise RuntimeError("Crystal symmetry mismatch between model and data")
+                logger.writeln("Warning: space group mismatch between model and mtz")
+                if sg_st and sg_st.laue_str() == hkldata.sg.laue_str():
+                    logger.writeln("         using space group from model")
+                    sg_use = sg_st
+                else:
+                    logger.writeln("         using space group from mtz")
+                logger.writeln("")
+            
+        for st in sts:
+            st.spacegroup_hm = sg_use.xhm()
+            st.setup_cell_images()
+
+        if not keep_charges:
+            utils.model.remove_charge(sts)
+        utils.model.check_atomsf(sts, source)
+
+    if sg_use is not None:
+        hkldata.sg = sg_use
+    if newlabels[0] == "FP":
+        hkldata.remove_nonpositive(newlabels[0])
+    hkldata.remove_nonpositive(newlabels[1])
+    hkldata.switch_to_asu()
+    hkldata.remove_systematic_absences()
+    #hkldata.df = hkldata.df.astype({name: 'float64' for name in ["I","SIGI","FP","SIGFP"] if name in hkldata.df})
+    d_min_data = hkldata.d_min_max(newlabels)[0]
+    if d_min is None and hkldata.d_min_max()[0] != d_min_data:
+        d_min = d_min_data
+        logger.writeln(f"Changing resolution to {d_min:.3f} A")
+    if (d_min, d_max).count(None) != 2:
+        hkldata = hkldata.copy(d_min=d_min, d_max=d_max)
+    if hkldata.df.empty:
+        raise RuntimeError("No data left in hkl data")
+        
+    hkldata.complete()
+    hkldata.sort_by_resolution()
+    hkldata.calc_epsilon()
+    hkldata.calc_centric()
+
+    if "FREE" in hkldata.df and free is None:
+        free = hkldata.guess_free_number(newlabels[0])
+
+    if n_bins is None:
+        sel = hkldata.df[newlabels[0]].notna()
+        if use == "work":
+            sel &= hkldata.df.FREE != free
+        elif use == "test":
+            sel &= hkldata.df.FREE == free
+        s_array = 1/hkldata.d_spacings()[sel]
+        if len(s_array) == 0:
+            raise RuntimeError("no reflections in {} set".format(use))
+        n_bins = utils.hkl.decide_n_bins(n_per_bin, s_array, max_bins=max_bins)
+        logger.writeln("n_per_bin={} requested for {}. n_bins set to {}".format(n_per_bin, use, n_bins))
+
+    hkldata.setup_binning(n_bins=n_bins)
+    logger.writeln("Data completeness: {:.2f}%".format(hkldata.completeness()*100.))
+
+    fc_labs = ["FC{}".format(i)  for i, _ in enumerate(sts)]
+
+    # Create a centric selection table for faster look up
+    centric_and_selections = {}
+    stats = hkldata.binned_df.copy()
+    stats["n_all"] = 0
+    stats["n_obs"] = 0
+    stats[newlabels[0]] = numpy.nan
+    snr = "I/sigma" if newlabels[0] == "I" else "F/sigma"
+    stats[snr] = numpy.nan
+    if newlabels[0] == "I":
+        stats["Mn(I)/Std(I)"] = numpy.nan
+    if "FREE" in hkldata.df:
+        stats["n_work"] = 0
+        stats["n_test"] = 0
+        
+    for i_bin, idxes in hkldata.binned():
+        centric_and_selections[i_bin] = []
+        n_obs = 0
+        n_work, n_test = 0, 0
+        for c, g2 in hkldata.df.loc[idxes].groupby("centric", sort=False):
+            valid_sel = numpy.isfinite(g2[newlabels[0]])
+            if "FREE" in g2:
+                test_sel = (g2.FREE == free).fillna(False)
+                test = g2.index[test_sel]
+                work = g2.index[~test_sel]
+                n_work += (valid_sel & ~test_sel).sum()
+                n_test += (valid_sel & test_sel).sum()
+            else:
+                work = g2.index
+                test = type(work)([], dtype=work.dtype)
+            centric_and_selections[i_bin].append((c, work, test))
+            n_obs += numpy.sum(valid_sel)
+            
+        stats.loc[i_bin, "n_obs"] = n_obs
+        stats.loc[i_bin, "n_all"] = len(idxes)
+        obs = hkldata.df[newlabels[0]].to_numpy()[idxes]
+        sigma = hkldata.df[newlabels[1]].to_numpy()[idxes]
+        if n_obs > 0:
+            stats.loc[i_bin, snr] = numpy.nanmean(obs / sigma)
+            mean_obs = numpy.nanmean(obs)
+            stats.loc[i_bin, newlabels[0]] = mean_obs
+            if newlabels[0] == "I":
+                stats.loc[i_bin, "Mn(I)/Std(I)"] = mean_obs / numpy.nanstd(obs)
+        if "FREE" in hkldata.df:
+            stats.loc[i_bin, "n_work"] = n_work
+            stats.loc[i_bin, "n_test"] = n_test
+            
+    stats["completeness"] = stats["n_obs"] / stats["n_all"] * 100
+    logger.writeln(stats.to_string())
+    return hkldata, sts, fc_labs, centric_and_selections, free
+# process_input()
+
+def update_fc(st_list, fc_labs, d_min, monlib, source, mott_bethe, hkldata=None, twin_data=None):
+    #assert (hkldata, twin_data).count(None) == 1
+    # hkldata not updated when twin_data is given
+    for i, st in enumerate(st_list):
+        if st.ncs:
+            st = st.clone()
+            st.expand_ncs(gemmi.HowToNameCopiedChain.Dup, merge_dist=0)
+        if twin_data:
+            hkl = twin_data.asu
+        else:
+            hkl = hkldata.miller_array()
+        fc = utils.model.calc_fc_fft(st, d_min - 1e-6,
+                                     monlib=monlib,
+                                     source=source,
+                                     mott_bethe=mott_bethe,
+                                     miller_array=hkl)
+        if twin_data:
+            twin_data.f_calc[:,i] = fc
+        else:
+            hkldata.df[fc_labs[i]] = fc
+    if not twin_data:
+        hkldata.df["FC"] = hkldata.df[fc_labs].sum(axis=1)
+# update_fc()
+
+def calc_Fmask(st, d_min, miller_array):
+    logger.writeln("Calculating solvent contribution..")
+    grid = gemmi.FloatGrid()
+    grid.setup_from(st, spacing=min(0.6, (d_min-1e-6) / 2 - 1e-9))
+    masker = gemmi.SolventMasker(gemmi.AtomicRadiiSet.Refmac)
+    masker.put_mask_on_float_grid(grid, st[0])
+    fmask_gr = gemmi.transform_map_to_f_phi(grid)
+    Fmask = fmask_gr.get_value_by_hkl(miller_array)
+    return Fmask
+# calc_Fmask()
+
+def bulk_solvent_and_lsq_scales(hkldata, sts, fc_labs, use_solvent=True, use_int=False, mask=None, func_type="log_cosh", twin_data=None):
+    # fc_labs must have solvent part at the end
+    miller_array = twin_data.asu if twin_data else hkldata.miller_array()
+    d_min = twin_data.d_min(sts[0].cell) if twin_data else hkldata.d_min_max()[0]
+    if use_solvent:
+        if mask is None:
+            Fmask = calc_Fmask(merge_models(sts), d_min, miller_array)
+        else:
+            fmask_gr = gemmi.transform_map_to_f_phi(mask)
+            Fmask = fmask_gr.get_value_by_hkl(miller_array)
+        if twin_data:
+            fc_sum = twin_data.f_calc[:,:-1].sum(axis=1)
+        else:
+            fc_sum = hkldata.df[fc_labs[:-1]].sum(axis=1).to_numpy()
+        fc_list = [fc_sum, Fmask]
+    else:
+        if twin_data:
+            fc_list = [twin_data.f_calc.sum(axis=1)]
+        else:
+            fc_list = [hkldata.df[fc_labs].sum(axis=1).to_numpy()]
+
+    scaling = LsqScale(func_type=func_type)
+    scaling.set_data(hkldata, fc_list, use_int, sigma_cutoff=0, twin_data=twin_data)
+    scaling.scale()
+    b_iso = scaling.b_iso
+    k_aniso = hkldata.debye_waller_factors(b_cart=scaling.b_aniso)
+    hkldata.df["k_aniso"] = k_aniso # we need it later when calculating stats
+    
+    if use_solvent:
+        if twin_data:
+            s2 = numpy.asarray(twin_data.s2_array)
+        else:
+            s2 = 1. / hkldata.d_spacings().to_numpy()**2
+        Fbulk = Fmask * scaling.get_solvent_scale(scaling.k_sol, scaling.b_sol, s2)
+        if twin_data:
+            twin_data.f_calc[:,-1] = Fbulk
+        else:
+            hkldata.df[fc_labs[-1]] = Fbulk
+
+    # Apply scales
+    if use_int:
+        # in intensity case, we try to refine b_aniso with ML. perhaps we should do it in amplitude case also
+        o_labs = ["I", "SIGI", "I(+)","SIGI(+)", "I(-)", "SIGI(-)"]
+        hkldata.df[hkldata.df.columns.intersection(o_labs)] /= scaling.k_overall**2
+    else:
+        o_labs = ["FP", "SIGFP", "F(+)","SIGF(+)", "F(-)", "SIGF(-)"]
+        hkldata.df[hkldata.df.columns.intersection(o_labs)] /= scaling.k_overall
+    if twin_data:
+        twin_data.f_calc[:] *= twin_data.debye_waller_factors(b_iso=b_iso)[:,None]
+    else:
+        k_iso = hkldata.debye_waller_factors(b_iso=b_iso)
+        for lab in fc_labs: hkldata.df[lab] *= k_iso
+        # total Fc
+        hkldata.df["FC"] = hkldata.df[fc_labs].sum(axis=1)
+    return scaling
+# bulk_solvent_and_lsq_scales()
+
+def calculate_maps(hkldata, b_aniso, centric_and_selections, fc_labs, D_labs, log_out, use="all"):
+    nmodels = len(fc_labs)
+    hkldata.df["FWT"] = 0j * numpy.nan
+    hkldata.df["DELFWT"] = 0j * numpy.nan
+    hkldata.df["FOM"] = numpy.nan
+    hkldata.df["X"] = numpy.nan # for FOM
+    has_ano = "F(+)" in hkldata.df and "F(-)" in hkldata.df
+    if has_ano:
+        hkldata.df["FAN"] = 0j * numpy.nan
+    stats_data = []
+    k_ani = hkldata.debye_waller_factors(b_cart=b_aniso)
+    Ds = numpy.vstack([hkldata.df[lab].to_numpy() for lab in D_labs]).T
+    Fcs = numpy.vstack([hkldata.df[lab].to_numpy() for lab in fc_labs]).T
+    DFc = (Ds * Fcs).sum(axis=1)
+    hkldata.df["DFC"] = DFc
+    for i_bin, idxes in hkldata.binned():
+        bin_d_min = hkldata.binned_df.d_min[i_bin]
+        bin_d_max = hkldata.binned_df.d_max[i_bin]
+        # 0: acentric 1: centric
+        mean_fom = [numpy.nan, numpy.nan]
+        nrefs = [0, 0]
+        for c, work, test in centric_and_selections[i_bin]:
+            cidxes = numpy.concatenate([work, test])
+            S = hkldata.df["S"].to_numpy()[cidxes]
+            expip = numpy.exp(numpy.angle(DFc[cidxes])*1j)
+            Fo = hkldata.df.FP.to_numpy()[cidxes] / k_ani[cidxes]
+            SigFo = hkldata.df.SIGFP.to_numpy()[cidxes] / k_ani[cidxes]
+            epsilon = hkldata.df.epsilon.to_numpy()[cidxes]
+            nrefs[c] = numpy.sum(numpy.isfinite(Fo))
+            DFc_abs = numpy.abs(DFc[cidxes])
+            if c == 0:
+                Sigma = 2 * SigFo**2 + epsilon * S
+                X = 2 * Fo * DFc_abs / Sigma
+                m = gemmi.bessel_i1_over_i0(X)
+                hkldata.df.loc[cidxes, "FWT"] = (2 * m * Fo - DFc_abs) * expip
+            else:
+                Sigma = SigFo**2 + epsilon * S
+                X = Fo * DFc_abs / Sigma
+                m = numpy.tanh(X)
+                hkldata.df.loc[cidxes, "FWT"] = (m * Fo) * expip
+
+            hkldata.df.loc[cidxes, "DELFWT"] = (m * Fo - DFc_abs) * expip
+            hkldata.df.loc[cidxes, "FOM"] = m
+            hkldata.df.loc[cidxes, "X"] = X
+            if has_ano:
+                Fo_dano = (hkldata.df["F(+)"].to_numpy()[cidxes] - hkldata.df["F(-)"].to_numpy()[cidxes]) / k_ani[cidxes]
+                hkldata.df.loc[cidxes, "FAN"] = m * Fo_dano * expip / 2j
+            if nrefs[c] > 0: mean_fom[c] = numpy.nanmean(m)
+
+            # remove reflections that should be hidden
+            if use != "all":
+                # usually use == "work"
+                tohide = test if use == "work" else work
+                hkldata.df.loc[tohide, "FWT"] = 0j * numpy.nan
+                hkldata.df.loc[tohide, "DELFWT"] = 0j * numpy.nan
+            fill_sel = numpy.isnan(hkldata.df["FWT"][cidxes].to_numpy())
+            hkldata.df.loc[cidxes[fill_sel], "FWT"] = DFc[cidxes][fill_sel]
+
+        Fc = hkldata.df.FC.to_numpy()[idxes] * k_ani[idxes]
+        Fo = hkldata.df.FP.to_numpy()[idxes]
+        mean_DFc2 = numpy.nanmean(numpy.abs((Ds[idxes,:] * Fcs[idxes,:]).sum(axis=1) * k_ani[idxes])**2)
+        mean_log_DFcs = numpy.log(numpy.nanmean(numpy.abs(Ds[idxes,:] * Fcs[idxes,:] * k_ani[idxes,None]), axis=0)).tolist()
+        mean_Ds = numpy.nanmean(Ds[idxes,:], axis=0).tolist()
+        if sum(nrefs) > 0:
+            r = numpy.nansum(numpy.abs(numpy.abs(Fc)-Fo)) / numpy.nansum(Fo)
+            cc = utils.hkl.correlation(Fo, numpy.abs(Fc))
+            mean_Fo2 = numpy.nanmean(numpy.abs(Fo)**2)
+        else:
+            r, cc, mean_Fo2 = numpy.nan, numpy.nan, numpy.nan
+        stats_data.append([i_bin, nrefs[0], nrefs[1], bin_d_max, bin_d_min,
+                           numpy.log(mean_Fo2),
+                           numpy.log(numpy.nanmean(numpy.abs(Fc)**2)),
+                           numpy.log(mean_DFc2),
+                           numpy.log(numpy.mean(hkldata.df["S"].to_numpy()[idxes])),
+                           mean_fom[0], mean_fom[1], r, cc] + mean_Ds + mean_log_DFcs)
+
+    DFc_labs = ["log(Mn(|{}{}|))".format(dl,fl) for dl,fl in zip(D_labs, fc_labs)]
+    cols = ["bin", "n_a", "n_c", "d_max", "d_min",
+            "log(Mn(|Fo|^2))", "log(Mn(|Fc|^2))", "log(Mn(|DFc|^2))",
+            "log(Sigma)", "FOM_a", "FOM_c", "R", "CC(|Fo|,|Fc|)"] + D_labs + DFc_labs
+    stats = pandas.DataFrame(stats_data, columns=cols)
+    title_labs = [["log(Mn(|F|^2)) and variances", ["log(Mn(|Fo|^2))", "log(Mn(|Fc|^2))", "log(Mn(|DFc|^2))", "log(Sigma)"]],
+                  ["FOM", ["FOM_a", "FOM_c"]],
+                  ["D", D_labs],
+                  ["DFc", DFc_labs],
+                  ["R-factor", ["R"]],
+                  ["CC", ["CC(|Fo|,|Fc|)"]],
+                  ["number of reflections", ["n_a", "n_c"]]]
+    with open(log_out, "w") as ofs:
+        ofs.write(utils.make_loggraph_str(stats, main_title="Statistics",
+                                          title_labs=title_labs,
+                                          s2=1/stats["d_min"]**2))
+    logger.writeln("output log: {}".format(log_out))
+# calculate_maps()
+
+def main(args):
+    n_per_bin = {"all": 500, "work": 500, "test": 50}[args.use]
+    try:
+        hkldata, sts, fc_labs, centric_and_selections,free = process_input(hklin=args.hklin,
+                                                                           labin=args.labin.split(",") if args.labin else None,
+                                                                           n_bins=args.nbins,
+                                                                           free=args.free,
+                                                                           xyzins=sum(args.model, []),
+                                                                           source=args.source,
+                                                                           d_max=args.d_max,
+                                                                           d_min=args.d_min,
+                                                                           n_per_bin=n_per_bin,
+                                                                           use=args.use,
+                                                                           max_bins=30,
+                                                                           keep_charges=args.keep_charges,
+                                                                           space_group=args.spacegroup)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+
+    if args.twin:
+        twin_data = find_twin_domains_from_data(hkldata)
+    else:
+        twin_data = None
+    if twin_data:
+        twin_data.setup_f_calc(len(sts) + (0 if args.no_solvent else 1))
+
+    update_fc(sts, fc_labs, d_min=hkldata.d_min_max()[0], monlib=None,
+              source=args.source, mott_bethe=(args.source=="electron"),
+              hkldata=hkldata, twin_data=twin_data)
+    is_int = "I" in hkldata.df
+
+    if args.mask:
+        mask = utils.fileio.read_ccp4_map(args.mask)[0]
+    else:
+        mask = None
+    
+    # Overall scaling & bulk solvent
+    # FP/SIGFP will be scaled. Total FC will be added.
+    if not args.no_solvent:
+        fc_labs.append("Fbulk")
+    lsq = bulk_solvent_and_lsq_scales(hkldata, sts, fc_labs, use_solvent=not args.no_solvent,
+                                      use_int=is_int, mask=mask, twin_data=twin_data)
+    b_aniso = lsq.b_aniso
+    # stats
+    stats, overall = calc_r_and_cc(hkldata, centric_and_selections, twin_data)
+    for lab in "R", "CC":
+        logger.writeln(" ".join("{} = {:.4f}".format(x, overall[x]) for x in overall if x.startswith(lab)))
+    if is_int:
+        logger.writeln("R1 is calculated for reflections with I/sigma>2.")
+
+    if twin_data:
+        estimate_twin_fractions_from_model(twin_data, hkldata)
+        #del hkldata.df["FC"]
+        #del hkldata.df["Fbulk"]
+        # Need to redo scaling?
+        lsq = bulk_solvent_and_lsq_scales(hkldata, sts, fc_labs, use_solvent=not args.no_solvent,
+                                          use_int=is_int, mask=mask, twin_data=twin_data)
+        b_aniso = lsq.b_aniso
+        stats, overall = calc_r_and_cc(hkldata, centric_and_selections, twin_data)
+        for lab in "R", "CC":
+            logger.writeln(" ".join("{} = {:.4f}".format(x, overall[x]) for x in overall if x.startswith(lab)))
+
+    # Estimate ML parameters
+    D_labs = ["D{}".format(i) for i in range(len(fc_labs))]
+
+    if args.use_cc:
+        assert not is_int
+        assert not args.twin
+        logger.writeln("Estimating sigma-A parameters from CC..")
+        determine_mlf_params_from_cc(hkldata, fc_labs, D_labs, centric_and_selections, args.use)
+    else:
+        b_aniso = determine_ml_params(hkldata, is_int, fc_labs, D_labs, b_aniso, centric_and_selections, args.D_trans, args.S_trans, args.use,
+                                      twin_data=twin_data)
+    use = {"all": "all", "work": "work", "test": "work"}[args.use]
+    if twin_data:
+        # replace hkldata
+        hkldata = calculate_maps_twin(hkldata, b_aniso, fc_labs, D_labs, twin_data, centric_and_selections, use)
+    elif is_int:
+        calculate_maps_int(hkldata, b_aniso, fc_labs, D_labs, centric_and_selections, use)
+    else:
+        log_out = "{}.log".format(args.output_prefix)
+        calculate_maps(hkldata, b_aniso, centric_and_selections, fc_labs, D_labs, log_out, use)
+
+    # Write mtz file
+    if twin_data:
+        labs = ["F_est", "F_exp"]
+    elif is_int:
+        labs = ["I", "SIGI"]
+    else:
+        labs = ["FP", "SIGFP"]
+    labs.extend(["FOM", "FWT", "DELFWT", "FC", "DFC"])
+    if "FAN" in hkldata.df:
+        labs.append("FAN")
+    if not args.no_solvent:
+        labs.append("Fbulk")
+    if "FREE" in hkldata.df:
+        labs.append("FREE")
+    if "F_true_est" in hkldata.df:
+        labs.append("F_true_est")
+    labs += D_labs + ["S"]
+    mtz_out = args.output_prefix+".mtz"
+    hkldata.write_mtz(mtz_out, labs=labs, types={"FOM": "W", "FP":"F", "SIGFP":"Q", "F_est": "F", "F_exp": "F"})
+    return hkldata
+# main()
+if __name__ == "__main__":
+    import sys
+    args = parse_args(sys.argv[1:])
+    main(args)