Eric Larson larsoner

larsoner / hotelling.py

Created October 21, 2021 19:08

	"""Hotelling T2 example.

	Following the notation in
	https://en.wikipedia.org/wiki/Hotelling%27s_T-squared_distribution#Two-sample_statistic
	"""

	import numpy as np
	from scipy import stats
	import matplotlib.pyplot as plt

larsoner / t2_circ.py

Created August 30, 2021 22:00

	import numpy as np
	from scipy import stats
	import matplotlib.pyplot as plt

	rng = np.random.RandomState(0)
	M, n_sensors = 100, 1000
	# Make "Fourier coefficients" here
	data = rng.randn(M, n_sensors) + rng.randn(M, n_sensors) * 1j
	data += 0. # can be non-zero to test that it actually works for some signal
	mean = np.mean(data, axis=0)

larsoner / dics_simulation_basic.py

Last active April 22, 2021 20:45

	# -- coding: utf-8 --
	import faulthandler
	import os.path as op
	import numpy as np
	from scipy.signal import welch, coherence, unit_impulse
	from matplotlib import pyplot as plt

	import mne
	from mne.simulation import simulate_raw, add_noise
	from mne.datasets import sample

larsoner / lcmv_maxpower.py

Created March 31, 2021 20:43

lcmv_maxpower.py

	# 1. Replicate test
	# 2. Expand to left and right hemi
	# 3. Switch to oct-6

	import os.path as op
	import numpy as np
	from numpy.testing import assert_allclose, assert_array_less
	import mne
	from mne.beamformer import make_lcmv, apply_lcmv
	from mne.io.constants import FIFF

larsoner / make_bem.sh

Last active March 2, 2021 15:46

	#!/bin/csh -ef

	# Do recon-all and get flash5 and flash30 files to nii/*.nii:
	# mcverter --format nifti -ndo . ${THIS_DIR}/DICOM/
	# INRAGE=`find . -name "MEMPRAGE.nii"`
	# IN5=`find . -name "FLASH5.nii"`
	# IN30=`find . -name "FLASH30.nii"`
	# OUTNAME="${PWD##*/}"
	# SUBJ_DIR="$SUBJECTS_DIR/$OUTNAME"
	# mkdir -p $SUBJ_DIR

larsoner / mplline.py

Created February 25, 2021 14:01

Try to get speedups with mpl by using blitting, linecollection, single line, etc.

	import time
	import mne
	import numpy as np
	import matplotlib.pyplot as plt

	raw = mne.io.read_raw_fif(
	mne.datasets.sample.data_path() + '/MEG/sample/sample_audvis_raw.fif')
	data, times = raw[:, :]
	n_points = 1000
	norms = np.std(data, axis=-1, keepdims=True)

larsoner / mixed_level_model.py

Created February 22, 2021 14:44

	# Following https://m-clark.github.io/docs/mixedModels/anovamixed.html

	import numpy as np
	from scipy import stats
	from pandas import DataFrame
	import statsmodels.api as sm
	from statsmodels.stats import anova
	import statsmodels.formula.api as smf
	import pingouin

larsoner / vtkline_60.py

Created February 18, 2021 18:49

	import mne
	import numpy as np
	import vtk
	from vtk.util import numpy_support
	import pyvistaqt

	raw = mne.io.read_raw_fif(
	mne.datasets.sample.data_path() + '/MEG/sample/sample_audvis_raw.fif')
	data, times = raw[:, :]
	n_points = 1000

larsoner / qwtline.py

Created February 10, 2021 14:50

	import sys
	import mne
	import numpy as np
	from PyQt5.QtWidgets import QApplication
	from PyQt5.QtCore import Qt
	from qwt import QwtPlot, QwtLegend, QwtPlotCurve, QwtAbstractScaleDraw

	raw = mne.io.read_raw_fif(
	mne.datasets.sample.data_path() + '/MEG/sample/sample_audvis_raw.fif')
	data, times = raw[:, :] # preload

larsoner / gist:4c964e21045fc499cb5e380dc79137c0

Created February 3, 2021 20:19

bems_brainsuite_fsl.py