File: _lead_dots.py

package info (click to toggle)
python-mne 0.8.6%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 87,892 kB
  • ctags: 6,639
  • sloc: python: 54,697; makefile: 165; sh: 15
file content (309 lines) | stat: -rw-r--r-- 12,565 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
import os
from os import path as op

import numpy as np
from numpy.polynomial import legendre

from ..parallel import parallel_func
from ..utils import logger, _get_extra_data_path


##############################################################################
# FAST LEGENDRE (DERIVATIVE) POLYNOMIALS USING LOOKUP TABLE

def _next_legen_der(n, x, p0, p01, p0d, p0dd):
    """Compute the next Legendre polynomial and its derivatives"""
    # only good for n > 1 !
    help_ = p0
    helpd = p0d
    p0 = ((2 * n - 1) * x * help_ - (n - 1) * p01) / n
    p0d = n * help_ + x * helpd
    p0dd = (n + 1) * helpd + x * p0dd
    p01 = help_
    return p0, p0d, p0dd


def _get_legen(x, n_coeff=100):
    """Get Legendre polynomials expanded about x"""
    return legendre.legvander(x, n_coeff - 1)


def _get_legen_der(xx, n_coeff=100):
    """Get Legendre polynomial derivatives expanded about x"""
    coeffs = np.empty((len(xx), n_coeff, 3))
    for c, x in zip(coeffs, xx):
        p0s, p0ds, p0dds = c[:, 0], c[:, 1], c[:, 2]
        p0s[:2] = [1.0, x]
        p0ds[:2] = [0.0, 1.0]
        p0dds[:2] = [0.0, 0.0]
        for n in range(2, n_coeff):
            p0s[n], p0ds[n], p0dds[n] = _next_legen_der(n, x, p0s[n - 1],
                                            p0s[n - 2], p0ds[n - 1],
                                            p0dds[n - 1])
    return coeffs


def _get_legen_table(ch_type, volume_integral=False, n_coeff=100,
                     n_interp=20000, force_calc=False):
    """Return a (generated) LUT of Legendre (derivative) polynomial coeffs"""
    if n_interp % 2 != 0:
        raise RuntimeError('n_interp must be even')
    fname = op.join(_get_extra_data_path(), 'tables')
    if not op.isdir(fname):
        # Updated due to API chang (GH 1167)
        os.makedirs(fname)
    if ch_type == 'meg':
        fname = op.join(fname, 'legder_%s_%s.bin' % (n_coeff, n_interp))
        leg_fun = _get_legen_der
        extra_str = ' derivative'
        lut_shape = (n_interp + 1, n_coeff, 3)
    else:  # 'eeg'
        fname = op.join(fname, 'legval_%s_%s.bin' % (n_coeff, n_interp))
        leg_fun = _get_legen
        extra_str = ''
        lut_shape = (n_interp + 1, n_coeff)
    if not op.isfile(fname) or force_calc:
        n_out = (n_interp // 2)
        logger.info('Generating Legendre%s table...' % extra_str)
        x_interp = np.arange(-n_out, n_out + 1, dtype=np.float64) / n_out
        lut = leg_fun(x_interp, n_coeff).astype(np.float32)
        if not force_calc:
            with open(fname, 'wb') as fid:
                fid.write(lut.tostring())
    else:
        logger.info('Reading Legendre%s table...' % extra_str)
        with open(fname, 'rb', buffering=0) as fid:
            lut = np.fromfile(fid, np.float32)
    lut.shape = lut_shape

    # we need this for the integration step
    n_fact = np.arange(1, n_coeff, dtype=float)
    if ch_type == 'meg':
        n_facts = list()  # multn, then mult, then multn * (n + 1)
        if volume_integral:
            n_facts.append(n_fact / ((2.0 * n_fact + 1.0)
                                     * (2.0 * n_fact + 3.0)))
        else:
            n_facts.append(n_fact / (2.0 * n_fact + 1.0))
        n_facts.append(n_facts[0] / (n_fact + 1.0))
        n_facts.append(n_facts[0] * (n_fact + 1.0))
        # skip the first set of coefficients because they are not used
        lut = lut[:, 1:, [0, 1, 1, 2]]  # for multiplicative convenience later
        # reshape this for convenience, too
        n_facts = np.array(n_facts)[[2, 0, 1, 1], :].T
        n_facts = np.ascontiguousarray(n_facts)
        n_fact = n_facts
    else:  # 'eeg'
        n_fact = (2.0 * n_fact + 1.0) * (2.0 * n_fact + 1.0) / n_fact
        # skip the first set of coefficients because they are not used
        lut = lut[:, 1:].copy()
    return lut, n_fact


def _get_legen_lut_fast(x, lut):
    """Return Legendre coefficients for given x values in -1<=x<=1"""
    # map into table vals (works for both vals and deriv tables)
    n_interp = (lut.shape[0] - 1.0)
    # equiv to "(x + 1.0) / 2.0) * n_interp" but faster
    mm = x * (n_interp / 2.0) + 0.5 * n_interp
    # nearest-neighbor version (could be decent enough...)
    idx = np.round(mm).astype(int)
    vals = lut[idx]
    return vals


def _get_legen_lut_accurate(x, lut):
    """Return Legendre coefficients for given x values in -1<=x<=1"""
    # map into table vals (works for both vals and deriv tables)
    n_interp = (lut.shape[0] - 1.0)
    # equiv to "(x + 1.0) / 2.0) * n_interp" but faster
    mm = x * (n_interp / 2.0) + 0.5 * n_interp
    # slower, more accurate interpolation version
    mm = np.minimum(mm, n_interp - 0.0000000001)
    idx = np.floor(mm).astype(int)
    w2 = mm - idx
    w2.shape += tuple([1] * (lut.ndim - w2.ndim))  # expand to correct size
    vals = (1 - w2) * lut[idx] + w2 * lut[idx + 1]
    return vals


def _comp_sum_eeg(beta, ctheta, lut_fun, n_fact):
    """Lead field dot products using Legendre polynomial (P_n) series"""
    # Compute the sum occurring in the evaluation.
    # The result is
    #   sums[:]    (2n+1)^2/n beta^n P_n
    coeffs = lut_fun(ctheta)
    betans = np.cumprod(np.tile(beta[:, np.newaxis], (1, n_fact.shape[0])),
                        axis=1)
    s0 = np.dot(coeffs * betans, n_fact)  # == weighted sum across cols
    return s0


def _comp_sums_meg(beta, ctheta, lut_fun, n_fact, volume_integral):
    """Lead field dot products using Legendre polynomial (P_n) series"""
    # Compute the sums occurring in the evaluation.
    # Two point magnetometers on the xz plane are assumed.
    # The four sums are:
    #  * sums[:, 0]    n(n+1)/(2n+1) beta^(n+1) P_n
    #  * sums[:, 1]    n/(2n+1) beta^(n+1) P_n'
    #  * sums[:, 2]    n/((2n+1)(n+1)) beta^(n+1) P_n'
    #  * sums[:, 3]    n/((2n+1)(n+1)) beta^(n+1) P_n''
    coeffs = lut_fun(ctheta)
    beta = (np.cumprod(np.tile(beta[:, np.newaxis], (1, n_fact.shape[0])),
                       axis=1) * beta[:, np.newaxis])
    # This is equivalent, but slower:
    # sums = np.sum(beta[:, :, np.newaxis] * n_fact * coeffs, axis=1)
    # sums = np.rollaxis(sums, 2)
    sums = np.einsum('ij,jk,ijk->ki', beta, n_fact, coeffs)
    return sums


###############################################################################
# SPHERE DOTS

def _fast_sphere_dot_r0(r, rr1, rr2, lr1, lr2, cosmags1, cosmags2,
                        w1, w2, volume_integral, lut, n_fact, ch_type):
    """Lead field dot product computation for M/EEG in the sphere model"""
    ct = np.einsum('ik,jk->ij', rr1, rr2)  # outer product, sum over coords

    # expand axes
    rr1 = rr1[:, np.newaxis, :]  # (n_rr1, n_rr2, n_coord) e.g. 4x4x3
    rr2 = rr2[np.newaxis, :, :]
    lr1lr2 = lr1[:, np.newaxis] * lr2[np.newaxis, :]

    beta = (r * r) / lr1lr2
    if ch_type == 'meg':
        sums = _comp_sums_meg(beta.flatten(), ct.flatten(), lut, n_fact,
                              volume_integral)
        sums.shape = (4,) + beta.shape

        # Accumulate the result, a little bit streamlined version
        #cosmags1 = cosmags1[:, np.newaxis, :]
        #cosmags2 = cosmags2[np.newaxis, :, :]
        #n1c1 = np.sum(cosmags1 * rr1, axis=2)
        #n1c2 = np.sum(cosmags1 * rr2, axis=2)
        #n2c1 = np.sum(cosmags2 * rr1, axis=2)
        #n2c2 = np.sum(cosmags2 * rr2, axis=2)
        #n1n2 = np.sum(cosmags1 * cosmags2, axis=2)
        n1c1 = np.einsum('ik,ijk->ij', cosmags1, rr1)
        n1c2 = np.einsum('ik,ijk->ij', cosmags1, rr2)
        n2c1 = np.einsum('jk,ijk->ij', cosmags2, rr1)
        n2c2 = np.einsum('jk,ijk->ij', cosmags2, rr2)
        n1n2 = np.einsum('ik,jk->ij', cosmags1, cosmags2)
        part1 = ct * n1c1 * n2c2
        part2 = n1c1 * n2c1 + n1c2 * n2c2

        result = (n1c1 * n2c2 * sums[0] +
                  (2.0 * part1 - part2) * sums[1] +
                  (n1n2 + part1 - part2) * sums[2] +
                  (n1c2 - ct * n1c1) * (n2c1 - ct * n2c2) * sums[3])

        # Give it a finishing touch!
        const = 4e-14 * np.pi  # This is \mu_0^2/4\pi
        result *= (const / lr1lr2)
        if volume_integral:
            result *= r
    else:  # 'eeg'
        sums = _comp_sum_eeg(beta.flatten(), ct.flatten(), lut, n_fact)
        sums.shape = beta.shape

        # Give it a finishing touch!
        eeg_const = 1.0 / (4.0 * np.pi)
        result = eeg_const * sums / lr1lr2
    # new we add them all up with weights
    if w1 is None:  # operating on surface, treat independently
        #result = np.sum(w2[np.newaxis, :] * result, axis=1)
        result = np.dot(result, w2)
    else:
        #result = np.sum((w1[:, np.newaxis] * w2[np.newaxis, :]) * result)
        result = np.einsum('i,j,ij', w1, w2, result)
    return result


def _do_self_dots(intrad, volume, coils, r0, ch_type, lut, n_fact, n_jobs):
    """Perform the lead field dot product integrations"""
    if ch_type == 'eeg':
        intrad *= 0.7
    # convert to normalized distances from expansion center
    rmags = [coil['rmag'] - r0[np.newaxis, :] for coil in coils]
    rlens = [np.sqrt(np.sum(r * r, axis=1)) for r in rmags]
    rmags = [r / rl[:, np.newaxis] for r, rl in zip(rmags, rlens)]
    cosmags = [coil['cosmag'] for coil in coils]
    ws = [coil['w'] for coil in coils]
    parallel, p_fun, _ = parallel_func(_do_self_dots_subset, n_jobs)
    prods = parallel(p_fun(intrad, rmags, rlens, cosmags,
                           ws, volume, lut, n_fact, ch_type, idx)
                     for idx in np.array_split(np.arange(len(rmags)), n_jobs))
    products = np.sum(prods, axis=0)
    return products


def _do_self_dots_subset(intrad, rmags, rlens, cosmags, ws, volume, lut,
                         n_fact, ch_type, idx):
    """Helper for parallelization"""
    products = np.zeros((len(rmags), len(rmags)))
    for ci1 in idx:
        for ci2 in range(0, ci1 + 1):
            res = _fast_sphere_dot_r0(intrad, rmags[ci1], rmags[ci2],
                                      rlens[ci1], rlens[ci2],
                                      cosmags[ci1], cosmags[ci2],
                                      ws[ci1], ws[ci2], volume, lut,
                                      n_fact, ch_type)
            products[ci1, ci2] = res
            products[ci2, ci1] = res
    return products


def _do_surface_dots(intrad, volume, coils, surf, sel, r0, ch_type,
                     lut, n_fact, n_jobs):
    """Compute the map construction products"""
    virt_ref = False
    # convert to normalized distances from expansion center
    rmags = [coil['rmag'] - r0[np.newaxis, :] for coil in coils]
    rlens = [np.sqrt(np.sum(r * r, axis=1)) for r in rmags]
    rmags = [r / rl[:, np.newaxis] for r, rl in zip(rmags, rlens)]
    cosmags = [coil['cosmag'] for coil in coils]
    ws = [coil['w'] for coil in coils]
    rref = None
    refl = None
    if ch_type == 'eeg':
        intrad *= 0.7
        if virt_ref:
            rref = virt_ref[np.newaxis, :] - r0[np.newaxis, :]
            refl = np.sqrt(np.sum(rref * rref, axis=1))
            rref /= refl[:, np.newaxis]

    rsurf = surf['rr'][sel] - r0[np.newaxis, :]
    lsurf = np.sqrt(np.sum(rsurf * rsurf, axis=1))
    rsurf /= lsurf[:, np.newaxis]
    this_nn = surf['nn'][sel]

    parallel, p_fun, _ = parallel_func(_do_surface_dots_subset, n_jobs)
    prods = parallel(p_fun(intrad, rsurf, rmags, rref, refl, lsurf, rlens,
                           this_nn, cosmags, ws, volume, lut, n_fact, ch_type,
                           idx)
                     for idx in np.array_split(np.arange(len(rmags)), n_jobs))
    products = np.sum(prods, axis=0)
    return products


def _do_surface_dots_subset(intrad, rsurf, rmags, rref, refl, lsurf, rlens,
                            this_nn, cosmags, ws, volume, lut, n_fact, ch_type,
                            idx):
    """Helper for parallelization"""
    products = np.zeros((len(rsurf), len(rmags)))
    for ci in idx:
        res = _fast_sphere_dot_r0(intrad, rsurf, rmags[ci],
                                  lsurf, rlens[ci],
                                  this_nn, cosmags[ci],
                                  None, ws[ci], volume, lut,
                                  n_fact, ch_type)
        if rref is not None:
            vres = _fast_sphere_dot_r0(intrad, rref, rmags[ci],
                                       refl, rlens[ci],
                                       None, ws[ci], volume,
                                       lut, n_fact, ch_type)
            products[:, ci] = res - vres
        else:
            products[:, ci] = res
    return products