Note

Go to the end to download the full example code.

Run AMICA on EEG Data

In this tutorial we will:

  1. Run AMICA on EEG data

  2. Compare our results to Fortran AMICA.

  3. Export our AMICA instance to an mne.preprocessing.ICA object.

import amica
from amica import AMICA
import matplotlib.pyplot as plt
import mne

import numpy as np

Download sample data

data_path = amica.datasets.data_path()

Load Fortran AMICA initial weights and results

This is not necessary to run AMICA in Python, but we are going to compare amica-python results to those obtained from the original Fortran implementation.

initial_weights, initial_scales, initial_locations = amica.utils.load_initial_weights(
    data_path / "eeglab_sample_data" / "amicaout_test", n_components=32, n_mixtures=3
    )

Load EEG data

amica_outdir = data_path / "eeglab_sample_data" / "amicaout_test"
fortran_results = amica.utils.load_fortran_results(
    amica_outdir, n_components=32, n_mixtures=3
    )

raw = mne.io.read_raw_eeglab(
    data_path / "eeglab_sample_data"/ "eeglab_data.set", preload=True
    )
data = raw.get_data().T  # Shape (n_samples, n_channels)
data *= 1e6  # Convert from Volts to microVolts

Reading /home/circleci/amica_test_data/eeglab_sample_data/eeglab_data.fdt
Reading 0 ... 30503  =      0.000 ...   238.305 secs...

Run AMICA-Python

transformer = AMICA(
        max_iter=200,
        w_init=initial_weights,
        sbeta_init=initial_scales,
        mu_init=initial_locations,
        verbose=2
)
transformer.fit(data)

INFO     getting the mean ...
INFO      Getting the covariance matrix ...
INFO     doing eigenvalue decomposition for 32 features ...
INFO     minimum eigenvalues: [4.87990051 6.92011971 7.65621479]
INFO     maximum eigenvalues: [9711.14308385 3039.68504351 1244.41294471]
INFO     num eigvals kept: 32
INFO     Sphering the data...
INFO     numeigs = 32, nw = 32
INFO     1: block size = 30504
INFO     Solving. (please be patient, this may take a while)...
INFO     Iteration 1, lrate = 0.05000, LL = -3.5136812, nd = 0.0578126, D =
         0.00446 took 0.39 seconds
INFO     Iteration 2, lrate = 0.05000, LL = -3.4687938, nd = 0.0254382, D =
         0.00391 took 0.40 seconds
INFO     Iteration 3, lrate = 0.05000, LL = -3.4616091, nd = 0.0243398, D =
         0.00376 took 0.35 seconds
INFO     Iteration 4, lrate = 0.05000, LL = -3.4589193, nd = 0.0270364, D =
         0.00554 took 0.31 seconds
INFO     Iteration 5, lrate = 0.05000, LL = -3.4569812, nd = 0.0277558, D =
         0.00994 took 0.39 seconds
INFO     Iteration 6, lrate = 0.05000, LL = -3.4553322, nd = 0.0273357, D =
         0.01680 took 0.36 seconds
INFO     Iteration 7, lrate = 0.05000, LL = -3.4538623, nd = 0.0264404, D =
         0.02561 took 0.44 seconds
INFO     Iteration 8, lrate = 0.05000, LL = -3.4525343, nd = 0.0253345, D =
         0.03580 took 0.46 seconds
INFO     Iteration 9, lrate = 0.05000, LL = -3.4513420, nd = 0.0240416, D =
         0.04681 took 0.46 seconds
INFO     Iteration 10, lrate = 0.05000, LL = -3.4502899, nd = 0.0225474, D =
         0.05812 took 0.49 seconds
INFO     Iteration 11, lrate = 0.05000, LL = -3.4493808, nd = 0.0208839, D =
         0.06920 took 0.49 seconds
INFO     Iteration 12, lrate = 0.05000, LL = -3.4486104, nd = 0.0191346, D =
         0.07957 took 0.41 seconds
INFO     Iteration 13, lrate = 0.05000, LL = -3.4479753, nd = 0.0173030, D =
         0.08886 took 0.30 seconds
INFO     Iteration 14, lrate = 0.05000, LL = -3.4474542, nd = 0.0157035, D =
         0.09674 took 0.40 seconds
INFO     Iteration 15, lrate = 0.05000, LL = -3.4470249, nd = 0.0143385, D =
         0.10318 took 0.40 seconds
INFO     Iteration 16, lrate = 0.05000, LL = -3.4466649, nd = 0.0132064, D =
         0.10822 took 0.31 seconds
INFO     Iteration 17, lrate = 0.05000, LL = -3.4463600, nd = 0.0123116, D =
         0.11195 took 0.35 seconds
INFO     Iteration 18, lrate = 0.05000, LL = -3.4460919, nd = 0.0116319, D =
         0.11453 took 0.35 seconds
INFO     Iteration 19, lrate = 0.05000, LL = -3.4458499, nd = 0.0111276, D =
         0.11612 took 0.40 seconds
INFO     Iteration 20, lrate = 0.05000, LL = -3.4456295, nd = 0.0107475, D =
         0.11690 took 0.40 seconds
INFO     Iteration 21, lrate = 0.05000, LL = -3.4454234, nd = 0.0104643, D =
         0.11704 took 0.40 seconds
INFO     Iteration 22, lrate = 0.05000, LL = -3.4452293, nd = 0.0102432, D =
         0.11667 took 0.41 seconds
INFO     Iteration 23, lrate = 0.05000, LL = -3.4450445, nd = 0.0100656, D =
         0.11591 took 0.36 seconds
INFO     Iteration 24, lrate = 0.05000, LL = -3.4448657, nd = 0.0099188, D =
         0.11485 took 0.30 seconds
INFO     Iteration 25, lrate = 0.05000, LL = -3.4446937, nd = 0.0097926, D =
         0.11356 took 0.45 seconds
INFO     Iteration 26, lrate = 0.05000, LL = -3.4445265, nd = 0.0096849, D =
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INFO     Iteration 27, lrate = 0.05000, LL = -3.4443632, nd = 0.0095877, D =
         0.11055 took 0.36 seconds
INFO     Iteration 28, lrate = 0.05000, LL = -3.4442048, nd = 0.0094986, D =
         0.10891 took 0.39 seconds
INFO     Iteration 29, lrate = 0.05000, LL = -3.4440489, nd = 0.0094179, D =
         0.10722 took 0.30 seconds
INFO     Iteration 30, lrate = 0.05000, LL = -3.4438959, nd = 0.0093394, D =
         0.10550 took 0.40 seconds
INFO     Iteration 31, lrate = 0.05000, LL = -3.4437453, nd = 0.0092646, D =
         0.10377 took 0.40 seconds
INFO     Iteration 32, lrate = 0.05000, LL = -3.4435975, nd = 0.0091968, D =
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INFO     Iteration 33, lrate = 0.05000, LL = -3.4434514, nd = 0.0091354, D =
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INFO     Iteration 34, lrate = 0.05000, LL = -3.4433079, nd = 0.0090763, D =
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INFO     Iteration 35, lrate = 0.05000, LL = -3.4431670, nd = 0.0090245, D =
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INFO     Iteration 36, lrate = 0.05000, LL = -3.4430282, nd = 0.0089752, D =
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INFO     Iteration 37, lrate = 0.05000, LL = -3.4428901, nd = 0.0089295, D =
         0.09360 took 0.35 seconds
INFO     Iteration 38, lrate = 0.05000, LL = -3.4427538, nd = 0.0088829, D =
         0.09199 took 0.40 seconds
INFO     Iteration 39, lrate = 0.05000, LL = -3.4426194, nd = 0.0088388, D =
         0.09042 took 0.45 seconds
INFO     Iteration 40, lrate = 0.05000, LL = -3.4424860, nd = 0.0087975, D =
         0.08887 took 0.40 seconds
INFO     Iteration 41, lrate = 0.05000, LL = -3.4423547, nd = 0.0087559, D =
         0.08736 took 0.36 seconds
INFO     Iteration 42, lrate = 0.05000, LL = -3.4422239, nd = 0.0087198, D =
         0.08588 took 0.40 seconds
INFO     Iteration 43, lrate = 0.05000, LL = -3.4420943, nd = 0.0086848, D =
         0.08444 took 0.36 seconds
INFO     Iteration 44, lrate = 0.05000, LL = -3.4419655, nd = 0.0086506, D =
         0.08303 took 0.35 seconds
INFO     Iteration 45, lrate = 0.05000, LL = -3.4418378, nd = 0.0086188, D =
         0.08165 took 0.40 seconds
INFO     Iteration 46, lrate = 0.05000, LL = -3.4417113, nd = 0.0085873, D =
         0.08031 took 0.35 seconds
INFO     Iteration 47, lrate = 0.05000, LL = -3.4415855, nd = 0.0085544, D =
         0.07900 took 0.40 seconds
INFO     Iteration 48, lrate = 0.05000, LL = -3.4414606, nd = 0.0085211, D =
         0.07772 took 0.39 seconds
INFO     Iteration 49, lrate = 0.05000, LL = -3.4413366, nd = 0.0084888, D =
         0.07648 took 0.31 seconds
INFO     Iteration 50, lrate = 0.05000, LL = -3.4412137, nd = 0.0073552, D =
         0.07526 took 0.50 seconds
INFO     Starting Newton ... setting numdecs to 0
INFO     Iteration 51, lrate = 0.10000, LL = -3.4410148, nd = 0.0073394, D =
         0.07393 took 0.49 seconds
INFO     Iteration 52, lrate = 0.20000, LL = -3.4406292, nd = 0.0072835, D =
         0.07137 took 0.46 seconds
INFO     Iteration 53, lrate = 0.30000, LL = -3.4400637, nd = 0.0072115, D =
         0.06776 took 0.54 seconds
INFO     Iteration 54, lrate = 0.40000, LL = -3.4393283, nd = 0.0071184, D =
         0.06333 took 0.41 seconds
INFO     Iteration 55, lrate = 0.50000, LL = -3.4384312, nd = 0.0070108, D =
         0.05839 took 0.39 seconds
INFO     Iteration 56, lrate = 0.60000, LL = -3.4373842, nd = 0.0068979, D =
         0.05327 took 0.51 seconds
INFO     Iteration 57, lrate = 0.70000, LL = -3.4361985, nd = 0.0067652, D =
         0.04822 took 0.49 seconds
INFO     Iteration 58, lrate = 0.80000, LL = -3.4348911, nd = 0.0065756, D =
         0.04348 took 0.50 seconds
INFO     Iteration 59, lrate = 0.90000, LL = -3.4334900, nd = 0.0063576, D =
         0.03913 took 0.39 seconds
INFO     Iteration 60, lrate = 1.00000, LL = -3.4320193, nd = 0.0061072, D =
         0.03525 took 0.50 seconds
INFO     Iteration 61, lrate = 1.00000, LL = -3.4306365, nd = 0.0058443, D =
         0.03208 took 0.50 seconds
INFO     Iteration 62, lrate = 1.00000, LL = -3.4293493, nd = 0.0055605, D =
         0.02950 took 0.45 seconds
INFO     Iteration 63, lrate = 1.00000, LL = -3.4281693, nd = 0.0052842, D =
         0.02745 took 0.42 seconds
INFO     Iteration 64, lrate = 1.00000, LL = -3.4270925, nd = 0.0050450, D =
         0.02597 took 0.46 seconds
INFO     Iteration 65, lrate = 1.00000, LL = -3.4261108, nd = 0.0048195, D =
         0.02502 took 0.59 seconds
INFO     Iteration 66, lrate = 1.00000, LL = -3.4252153, nd = 0.0046346, D =
         0.02454 took 0.50 seconds
INFO     Iteration 67, lrate = 1.00000, LL = -3.4243916, nd = 0.0044608, D =
         0.02437 took 0.50 seconds
INFO     Iteration 68, lrate = 1.00000, LL = -3.4236341, nd = 0.0042997, D =
         0.02439 took 0.50 seconds
INFO     Iteration 69, lrate = 1.00000, LL = -3.4229293, nd = 0.0041611, D =
         0.02453 took 0.59 seconds
INFO     Iteration 70, lrate = 1.00000, LL = -3.4222690, nd = 0.0040368, D =
         0.02470 took 0.60 seconds
INFO     Iteration 71, lrate = 1.00000, LL = -3.4216481, nd = 0.0039236, D =
         0.02492 took 0.50 seconds
INFO     Iteration 72, lrate = 1.00000, LL = -3.4210605, nd = 0.0038293, D =
         0.02514 took 0.51 seconds
INFO     Iteration 73, lrate = 1.00000, LL = -3.4205003, nd = 0.0037451, D =
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INFO     Iteration 74, lrate = 1.00000, LL = -3.4199601, nd = 0.0036840, D =
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INFO     Iteration 75, lrate = 1.00000, LL = -3.4194357, nd = 0.0036248, D =
         0.02601 took 0.50 seconds
INFO     Iteration 76, lrate = 1.00000, LL = -3.4189283, nd = 0.0035608, D =
         0.02632 took 0.55 seconds
INFO     Iteration 77, lrate = 1.00000, LL = -3.4184328, nd = 0.0035077, D =
         0.02665 took 0.51 seconds
INFO     Iteration 78, lrate = 1.00000, LL = -3.4179502, nd = 0.0034498, D =
         0.02700 took 0.54 seconds
INFO     Iteration 79, lrate = 1.00000, LL = -3.4174823, nd = 0.0033849, D =
         0.02735 took 0.46 seconds
INFO     Iteration 80, lrate = 1.00000, LL = -3.4170301, nd = 0.0033202, D =
         0.02772 took 0.54 seconds
INFO     Iteration 81, lrate = 1.00000, LL = -3.4165961, nd = 0.0032324, D =
         0.02812 took 0.50 seconds
INFO     Iteration 82, lrate = 1.00000, LL = -3.4161830, nd = 0.0031522, D =
         0.02853 took 0.59 seconds
INFO     Iteration 83, lrate = 1.00000, LL = -3.4157921, nd = 0.0030533, D =
         0.02897 took 0.51 seconds
INFO     Iteration 84, lrate = 1.00000, LL = -3.4154224, nd = 0.0029692, D =
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INFO     Iteration 85, lrate = 1.00000, LL = -3.4150725, nd = 0.0028897, D =
         0.02989 took 0.41 seconds
INFO     Iteration 86, lrate = 1.00000, LL = -3.4147412, nd = 0.0028215, D =
         0.03038 took 0.59 seconds
INFO     Iteration 87, lrate = 1.00000, LL = -3.4144243, nd = 0.0027518, D =
         0.03085 took 0.50 seconds
INFO     Iteration 88, lrate = 1.00000, LL = -3.4141217, nd = 0.0026904, D =
         0.03132 took 0.55 seconds
INFO     Iteration 89, lrate = 1.00000, LL = -3.4138322, nd = 0.0026328, D =
         0.03178 took 0.50 seconds
INFO     Iteration 90, lrate = 1.00000, LL = -3.4135558, nd = 0.0025808, D =
         0.03224 took 0.51 seconds
INFO     Iteration 91, lrate = 1.00000, LL = -3.4132903, nd = 0.0025351, D =
         0.03268 took 0.60 seconds
INFO     Iteration 92, lrate = 1.00000, LL = -3.4130349, nd = 0.0024919, D =
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INFO     Iteration 93, lrate = 1.00000, LL = -3.4127878, nd = 0.0024396, D =
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INFO     Iteration 94, lrate = 1.00000, LL = -3.4125515, nd = 0.0023929, D =
         0.03395 took 0.61 seconds
INFO     Iteration 95, lrate = 1.00000, LL = -3.4123236, nd = 0.0023507, D =
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INFO     Iteration 96, lrate = 1.00000, LL = -3.4121046, nd = 0.0023118, D =
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INFO     Iteration 97, lrate = 1.00000, LL = -3.4118917, nd = 0.0022843, D =
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INFO     Iteration 98, lrate = 1.00000, LL = -3.4116854, nd = 0.0022630, D =
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INFO     Iteration 99, lrate = 1.00000, LL = -3.4114822, nd = 0.0022459, D =
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INFO     Iteration 100, lrate = 1.00000, LL = -3.4112831, nd = 0.0022394, D =
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INFO     Iteration 101, lrate = 1.00000, LL = -3.4112498, nd = 0.0022958, D =
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INFO     Iteration 102, lrate = 1.00000, LL = -3.4112233, nd = 0.0023264, D =
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INFO     Iteration 103, lrate = 1.00000, LL = -3.4111987, nd = 0.0023474, D =
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INFO     Iteration 104, lrate = 1.00000, LL = -3.4111754, nd = 0.0023640, D =
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INFO     Iteration 105, lrate = 1.00000, LL = -3.4111530, nd = 0.0023774, D =
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INFO     Iteration 106, lrate = 1.00000, LL = -3.4111324, nd = 0.0023891, D =
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INFO     Iteration 108, lrate = 1.00000, LL = -3.4107273, nd = 0.0022918, D =
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INFO     Iteration 109, lrate = 1.00000, LL = -3.4105318, nd = 0.0022727, D =
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INFO     Iteration 110, lrate = 1.00000, LL = -3.4103369, nd = 0.0022641, D =
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INFO     Iteration 111, lrate = 1.00000, LL = -3.4101420, nd = 0.0022599, D =
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INFO     Iteration 112, lrate = 1.00000, LL = -3.4099467, nd = 0.0022437, D =
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INFO     Iteration 113, lrate = 1.00000, LL = -3.4097545, nd = 0.0022286, D =
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INFO     Iteration 114, lrate = 1.00000, LL = -3.4095622, nd = 0.0022082, D =
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INFO     Iteration 115, lrate = 1.00000, LL = -3.4093724, nd = 0.0021893, D =
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INFO     Iteration 116, lrate = 1.00000, LL = -3.4091839, nd = 0.0021746, D =
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INFO     Iteration 117, lrate = 1.00000, LL = -3.4089963, nd = 0.0021577, D =
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INFO     Iteration 118, lrate = 1.00000, LL = -3.4088109, nd = 0.0021374, D =
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INFO     Iteration 119, lrate = 1.00000, LL = -3.4086289, nd = 0.0021174, D =
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INFO     Iteration 120, lrate = 1.00000, LL = -3.4084500, nd = 0.0020963, D =
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INFO     Iteration 121, lrate = 1.00000, LL = -3.4082740, nd = 0.0020709, D =
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INFO     Iteration 122, lrate = 1.00000, LL = -3.4081012, nd = 0.0020386, D =
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INFO     Iteration 123, lrate = 1.00000, LL = -3.4079335, nd = 0.0020010, D =
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INFO     Iteration 124, lrate = 1.00000, LL = -3.4077697, nd = 0.0019664, D =
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INFO     Iteration 125, lrate = 1.00000, LL = -3.4076116, nd = 0.0019212, D =
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INFO     Iteration 126, lrate = 1.00000, LL = -3.4074604, nd = 0.0018721, D =
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INFO     Iteration 127, lrate = 1.00000, LL = -3.4073149, nd = 0.0018282, D =
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INFO     Iteration 128, lrate = 1.00000, LL = -3.4071761, nd = 0.0017893, D =
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INFO     Iteration 129, lrate = 1.00000, LL = -3.4070432, nd = 0.0017520, D =
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INFO     Iteration 130, lrate = 1.00000, LL = -3.4069132, nd = 0.0017223, D =
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INFO     Iteration 131, lrate = 1.00000, LL = -3.4067873, nd = 0.0016955, D =
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INFO     Iteration 140, lrate = 1.00000, LL = -3.4055960, nd = 0.0017083, D =
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INFO     Iteration 141, lrate = 1.00000, LL = -3.4054582, nd = 0.0016882, D =
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         0.04636 took 0.50 seconds
INFO     Iteration 163, lrate = 1.00000, LL = -3.4034098, nd = 0.0010182, D =
         0.04649 took 0.51 seconds
INFO     Iteration 164, lrate = 1.00000, LL = -3.4033514, nd = 0.0009982, D =
         0.04664 took 0.51 seconds
INFO     Iteration 165, lrate = 1.00000, LL = -3.4032967, nd = 0.0009739, D =
         0.04678 took 0.55 seconds
INFO     Iteration 166, lrate = 1.00000, LL = -3.4032475, nd = 0.0009558, D =
         0.04693 took 0.50 seconds
INFO     Iteration 167, lrate = 1.00000, LL = -3.4032000, nd = 0.0009387, D =
         0.04706 took 0.50 seconds
INFO     Iteration 168, lrate = 1.00000, LL = -3.4031536, nd = 0.0009255, D =
         0.04720 took 0.50 seconds
INFO     Iteration 169, lrate = 1.00000, LL = -3.4031080, nd = 0.0009100, D =
         0.04733 took 0.50 seconds
INFO     Iteration 170, lrate = 1.00000, LL = -3.4030636, nd = 0.0008974, D =
         0.04745 took 0.41 seconds
INFO     Iteration 171, lrate = 1.00000, LL = -3.4030199, nd = 0.0008862, D =
         0.04757 took 0.59 seconds
INFO     Iteration 172, lrate = 1.00000, LL = -3.4029767, nd = 0.0008749, D =
         0.04769 took 0.58 seconds
INFO     Iteration 173, lrate = 1.00000, LL = -3.4029340, nd = 0.0008627, D =
         0.04781 took 0.70 seconds
INFO     Iteration 174, lrate = 1.00000, LL = -3.4028920, nd = 0.0008521, D =
         0.04793 took 0.51 seconds
INFO     Iteration 175, lrate = 1.00000, LL = -3.4028504, nd = 0.0008435, D =
         0.04805 took 0.60 seconds
INFO     Iteration 176, lrate = 1.00000, LL = -3.4028090, nd = 0.0008381, D =
         0.04817 took 0.68 seconds
INFO     Iteration 177, lrate = 1.00000, LL = -3.4027686, nd = 0.0008318, D =
         0.04829 took 0.61 seconds
INFO     Iteration 178, lrate = 1.00000, LL = -3.4027279, nd = 0.0008218, D =
         0.04841 took 0.61 seconds
INFO     Iteration 179, lrate = 1.00000, LL = -3.4026881, nd = 0.0008168, D =
         0.04854 took 0.54 seconds
INFO     Iteration 180, lrate = 1.00000, LL = -3.4026476, nd = 0.0008093, D =
         0.04865 took 0.60 seconds
INFO     Iteration 181, lrate = 1.00000, LL = -3.4026071, nd = 0.0008022, D =
         0.04877 took 0.50 seconds
INFO     Iteration 182, lrate = 1.00000, LL = -3.4025668, nd = 0.0007969, D =
         0.04889 took 0.60 seconds
INFO     Iteration 183, lrate = 1.00000, LL = -3.4025265, nd = 0.0007888, D =
         0.04900 took 0.71 seconds
INFO     Iteration 184, lrate = 1.00000, LL = -3.4024863, nd = 0.0007816, D =
         0.04912 took 0.90 seconds
INFO     Iteration 185, lrate = 1.00000, LL = -3.4024490, nd = 0.0007768, D =
         0.04925 took 0.89 seconds
INFO     Iteration 186, lrate = 1.00000, LL = -3.4024112, nd = 0.0007712, D =
         0.04937 took 0.76 seconds
INFO     Iteration 187, lrate = 1.00000, LL = -3.4023730, nd = 0.0007647, D =
         0.04949 took 0.71 seconds
INFO     Iteration 188, lrate = 1.00000, LL = -3.4023342, nd = 0.0007579, D =
         0.04961 took 0.80 seconds
INFO     Iteration 189, lrate = 1.00000, LL = -3.4022947, nd = 0.0007573, D =
         0.04972 took 0.70 seconds
INFO     Iteration 190, lrate = 1.00000, LL = -3.4022533, nd = 0.0007581, D =
         0.04984 took 0.81 seconds
INFO     Iteration 191, lrate = 1.00000, LL = -3.4022101, nd = 0.0007578, D =
         0.04996 took 0.59 seconds
INFO     Iteration 192, lrate = 1.00000, LL = -3.4021649, nd = 0.0007592, D =
         0.05008 took 0.78 seconds
INFO     Iteration 193, lrate = 1.00000, LL = -3.4021169, nd = 0.0007580, D =
         0.05020 took 0.51 seconds
INFO     Iteration 194, lrate = 1.00000, LL = -3.4020689, nd = 0.0007561, D =
         0.05033 took 0.60 seconds
INFO     Iteration 195, lrate = 1.00000, LL = -3.4020312, nd = 0.0007540, D =
         0.05047 took 0.89 seconds
INFO     Iteration 196, lrate = 1.00000, LL = -3.4019944, nd = 0.0007498, D =
         0.05061 took 0.70 seconds
INFO     Iteration 197, lrate = 1.00000, LL = -3.4019574, nd = 0.0007469, D =
         0.05075 took 0.71 seconds
INFO     Iteration 198, lrate = 1.00000, LL = -3.4019203, nd = 0.0007458, D =
         0.05089 took 0.69 seconds
INFO     Iteration 199, lrate = 1.00000, LL = -3.4018827, nd = 0.0007426, D =
         0.05103 took 0.75 seconds
INFO     Iteration 200, lrate = 1.00000, LL = -3.4018446, nd = 0.0007414, D =
         0.05116 took 0.66 seconds
/home/circleci/project/amica-python/src/amica/core.py:890: ConvergenceWarning: Maximum number of iterations reached before convergence. Consider increasing max_iter or relaxing tol.
  warn(
INFO     Finished in 103.70 seconds

AMICA(max_iter=200,
      mu_init=array([[0.50965947, 0.04527889, 0.35247896],
       [0.8762351 , 0.26628711, 0.99480272],
       [0.40212523, 0.27389552, 0.20770561],
       [0.65411987, 0.34182142, 0.09300251],
       [0.80444938, 0.44339815, 0.8126825 ],
       [0.97930402, 0.74877807, 0.04348142],
       [0.78631199, 0.60419269, 0.85805117],
       [0.02165665, 0.84801097, 0.85489792],
       [0.27966586, 0.56910808, 0.53418476],
       [0....
       [0.76343641, 0.05840647, 0.34338642, ..., 0.97308572, 0.76182668,
        0.83096944],
       [0.58233765, 0.04081942, 0.43449808, ..., 0.33150471, 0.73984712,
        0.66007229],
       ...,
       [0.63443108, 0.33966091, 0.97756094, ..., 0.92677176, 0.24606719,
        0.54599154],
       [0.85448053, 0.88756462, 0.86326901, ..., 0.93752582, 0.87834654,
        0.02637342],
       [0.93852255, 0.64263167, 0.14632447, ..., 0.74057343, 0.5679117 ,
        0.47788761]], shape=(32, 32)))
In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook.
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Compare results

def plot_topomaps(A, output="python"):
    fig, ax = plt.subplots(
        nrows=8,
        ncols=4,
        figsize=(8, 12),
        constrained_layout=True
        )
    for i, this_ax in zip(range(32), ax.flat):
        mne.viz.plot_topomap(
            A[:, i],
            pos=raw.info,
            axes=this_ax,
            show=False,
        )
        this_ax.set_title(f"Component {i}")
    fig.suptitle(f"AMICA Component Topomaps ({output})", fontsize=16)
    return fig, ax

fig1, ax1 = plot_topomaps(transformer.mixing_, output="python")
AMICA Component Topomaps (python), Component 0, Component 1, Component 2, Component 3, Component 4, Component 5, Component 6, Component 7, Component 8, Component 9, Component 10, Component 11, Component 12, Component 13, Component 14, Component 15, Component 16, Component 17, Component 18, Component 19, Component 20, Component 21, Component 22, Component 23, Component 24, Component 25, Component 26, Component 27, Component 28, Component 29, Component 30, Component 31

The Fortran mixing matrix is in sphered space. We need to unwhiten it first.

A_fortran = np.linalg.pinv(fortran_results['S']) @ fortran_results['A']
fig2, ax2 = plot_topomaps(A_fortran, output="fortran")
AMICA Component Topomaps (fortran), Component 0, Component 1, Component 2, Component 3, Component 4, Component 5, Component 6, Component 7, Component 8, Component 9, Component 10, Component 11, Component 12, Component 13, Component 14, Component 15, Component 16, Component 17, Component 18, Component 19, Component 20, Component 21, Component 22, Component 23, Component 24, Component 25, Component 26, Component 27, Component 28, Component 29, Component 30, Component 31

Export to MNE

ica = transformer.to_mne(info=raw.info)
ica.plot_components(nrows=8, ncols=4)
ICA components, ICA000, ICA001, ICA002, ICA003, ICA004, ICA005, ICA006, ICA007, ICA008, ICA009, ICA010, ICA011, ICA012, ICA013, ICA014, ICA015, ICA016, ICA017, ICA018, ICA019, ICA020, ICA021, ICA022, ICA023, ICA024, ICA025, ICA026, ICA027, ICA028, ICA029, ICA030, ICA031
<MNEFigure size 780x1909 with 32 Axes>

Total running time of the script: (1 minutes 54.949 seconds)

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