def test_hdf5():
"""Test HDF5 IO
"""
test_file = op.join(tempdir, 'test.hdf5')
x = dict(a=dict(b=np.zeros(3)), c=np.zeros(2, np.complex128),
d=[dict(e=(1, -2., 'hello'))])
write_hdf5(test_file, 1)
assert_equal(read_hdf5(test_file), 1)
assert_raises(IOError, write_hdf5, test_file, x) # file exists
write_hdf5(test_file, x, overwrite=True)
assert_raises(IOError, read_hdf5, test_file + 'FOO') # not found
xx = read_hdf5(test_file)
print(object_diff(x, xx))
assert_true(object_diff(x, xx) == '') # no assert_equal, ugly output
def generate_stimuli(num_trials=10,
num_freqs=4,
stim_dur=0.5,
min_freq=500.0,
max_freq=4000.0,
fs=24414.0625,
rms=0.01,
output_dir='.',
save_as='hdf5',
rand_seed=0):
"""Make some sine waves and save in various formats. Optimized for saving
as MAT files, but can also save directly as WAV files, or can return a
python dictionary with sinewave data as values.
Parameters
----------
num_trials : int
Number of trials you want in your experiment. Ignored if save_as is
not 'mat'.
num_freqs : int
Number of frequencies (equally-spaced on a log2-scale) at which to
generate tones.
stim_dur : float
Duration of the tones in seconds.
min_freq : float
Frequency of the lowest tone in Hertz.
max_freq : float
Frequency of the highest tone in Hertz.
fs : float | None
Sampling frequency of resulting sinewaves. Defaults to 24414.0625 (a
standard rate for TDTs).
rms : float
RMS amplitude to which all sinwaves will be scaled.
output_dir : str
Directory to output the files into.
save_as : str
Format in which to return the sinewaves. 'dict' returns sinewave arrays
as values in a python dictionary; 'wav' saves them as WAV files at
sampling frequency 'fs'; 'mat' saves them as a MAT file along with
related variables 'fs', 'freqs', 'trial_order', and 'rms'.
rand_seed : int | None
Seed for the random number generator.
Returns
-------
wavs : dict | None
The stimulus dictionary.
"""
if rand_seed is None:
rng = np.random.RandomState()
else:
rng = np.random.RandomState(rand_seed)
# check input arguments
if save_as not in ['dict', 'wav', 'hdf5']:
raise ValueError('"save_as" must be "dict", "wav", or "hdf5"')
fs = float(fs)
t = np.arange(np.round(stim_dur * fs)) / fs
# frequencies equally spaced on a log-2 scale
freqs = min_freq * np.logspace(0,
np.log2(max_freq / float(min_freq)),
num_freqs,
endpoint=True,
base=2)
# strings for the filenames / dictionary keys
freq_names = [str(int(f)) for f in freqs]
names = ['stim_%s_%s' % (n, f) for n, f in enumerate(freq_names)]
# generate sinewaves & RMS normalize
wavs = [np.sin(2 * np.pi * f * t) for f in freqs]
wavs = [rms / np.sqrt(np.mean(w**2)) * w for w in wavs]
# collect into dictionary & save
wav_dict = {n: w for (n, w) in zip(names, wavs)}
if save_as == 'hdf5':
num_reps = num_trials // num_freqs + 1
trials = np.tile(range(num_freqs), num_reps)
trial_order = rng.permutation(trials[0:num_trials])
wav_dict.update({
'trial_order': trial_order,
'freqs': freqs,
'fs': fs,
'rms': rms
})
write_hdf5(op.join(output_dir, 'equally_spaced_sinewaves.hdf5'),
wav_dict,
overwrite=True)
elif save_as == 'wav':
for n in names:
write_wav(op.join(output_dir, n + '.wav'), wav_dict[n], int(fs))
return wav_dict
plt.figure()
for p in percent_correct[i]:
per_mean = p.mean(-1)
plt.plot(snrs, per_mean*100)
plt.xlabel('SNR (db)')
plt.ylabel('Percent Correct')
plt.title(sub)
plt.legend(('0', '90', '180', 'Static'))
percent_condition_subject = percent_correct.mean(-1)
mean_across_subjects = percent_condition_subject.mean(0)
sem = percent_condition_subject.std(axis=0)/np.sqrt(len(subjects))
write_hdf5('matrix1.hdf5', dict(data=percent_condition_subject), overwrite=True)
percent_across_snrs = percent_condition_subject.mean(2)
mean_across_subjects2 = percent_across_snrs.mean(0)
sem2 = percent_across_snrs.std(axis=0)/np.sqrt(len(subjects))
#plt.plot(snrs, mean_sub*100, 'o')
width = 8
height = 5
fname = 'Average Percent Correct Across SNR'
plt.figure(figsize=(width, height))
plt.errorbar(x=[0, 1, 2, 3], y=mean_across_subjects2*100, yerr=sem2*100, fmt='o')
plt.xticks([0, 1, 2, 3], [0, 1, 2, 3])
plt.gca().set_xticklabels(['0', '90', '180', 'Static'])
plt.xlabel('Angle (deg)')
for n in np.arange(10000):
sub_ind = np.random.choice(np.arange(23), (n_sub, ))
disagree_tvm_resamp = disagree_tvm.mean(1)[sub_ind]
t, p_tvm = scipy.stats.ttest_1samp(disagree_tvm_resamp, 0, axis=0)
disagree_inv_resamp = disagree_up_vs_inv[sub_ind]
t, p_inv = scipy.stats.ttest_1samp(disagree_inv_resamp, 0, axis=0)
pval_tvm.append(p_tvm)
pval_inv.append(p_inv)
percent_sig_tvm.append(100 * sum(np.array(pval_tvm) < 0.05) /
len(pval_tvm))
percent_sig_inv.append(100 * sum(np.array(pval_inv) < 0.05) /
len(pval_inv))
from expyfun.io import write_hdf5
write_hdf5(
'power_analysis_sim.hdf5',
dict(percent_sig_inv=percent_sig_inv, percent_sig_tvm=percent_sig_tvm))
plt.figure()
plt.plot(np.arange(2, 1000), percent_sig_tvm)
plt.plot(np.arange(2, 1000), percent_sig_inv)
plt.plot([2, 1000], [80, 80], 'k')
plt.legend(('Target vs. Masker', 'Upright vs. Inverted'))
plt.xlabel('Number of simulated subjects')
plt.ylabel('% of 1000 observations significant')
import scipy.stats
import statsmodels.stats.power as smp
import matplotlib.pyplot as plt
power_analysis = smp.TTestIndPower()
sample_size = power_analysis.solve_power(effect_size=0.064,
(ti + 1, attns[ai], spatials[si], idents[ii],
int(1e3 * gap_durs[gi]), ''.join(t), ''.join(m)))
write_wav(op.join(stim_dir, fname), stim, fs, verbose=False)
print(' Writing %s (%s/%s)' % (fname, ti + 1, n_trials))
stim_names.append(fname)
##############################################################################
# Write out result
params = dict(gap_durs=gap_durs,
spatials=spatials,
idents=idents,
attns=attns,
inter_trial_dur=inter_trial_dur,
targ_pos=targ_pos,
cond_mat=cond_mat,
cond_readme=cond_readme,
blocks=blocks,
block_trials=block_trials,
stim_names=stim_names,
stim_dir=stim_dir_end,
n_targ_let=n_targ_let,
n_cue_let=n_cue_let,
trial_durs=trial_durs,
stim_times=ts,
n_blocks=n_blocks,
letter_mat=letter_mat,
letters=letters,
gap_after=gap_after)
write_hdf5(op.join(work_dir, 'params.hdf5'), params, overwrite=True)
if w:
print(':\'(')
thresholds = np.array([np.power(10, m / 20) for m in [params[0][0], params[1][0]]])
thresholds = np.array([-1. / ok[1] * np.log((ok[2] - .5) / (.75 - .5) - 1) + p[0] for p in params])
thresholds = np.power(10, thresholds / 20)
perform_imp = (sigmoid(20 * np.log10(thresholds[0]), lower=.5, upper=ok[2], midpt=params[1][0], slope=ok[1]) - .75) * 100
# %% save the data
data = dict(responses=responses[-1],
thresholds=thresholds,
ok = ok,
params=params,
percent=percent,
perform_imp = perform_imp)
write_hdf5((path + 'percent_' + subject), data, overwrite=True)
# %% plot an example
if subject=='016':
from collections import OrderedDict
from matplotlib.transforms import blended_transform_factory
from matplotlib import rc
from matplotlib import rcParams
rcParams['font.sans-serif'] = "Arial"
linestyles = OrderedDict(
[('densely dotted', (0, (1, 1))),
('densely dashed', (0, (5, 1))),
('loosely dashdotted', (0, (3, 10, 1, 10))),
def generate_stimuli(num_trials=10, num_freqs=4, stim_dur=0.5, min_freq=500.0,
max_freq=4000.0, fs=24414.0625, rms=0.01, output_dir='.',
save_as='hdf5', rand_seed=0):
"""Make some sine waves and save in various formats. Optimized for saving
as MAT files, but can also save directly as WAV files, or can return a
python dictionary with sinewave data as values.
Parameters
----------
num_trials : int
Number of trials you want in your experiment. Ignored if save_as is
not 'mat'.
num_freqs : int
Number of frequencies (equally-spaced on a log2-scale) at which to
generate tones.
stim_dur : float
Duration of the tones in seconds.
min_freq : float
Frequency of the lowest tone in Hertz.
max_freq : float
Frequency of the highest tone in Hertz.
fs : float | None
Sampling frequency of resulting sinewaves. Defaults to 24414.0625 (a
standard rate for TDTs).
rms : float
RMS amplitude to which all sinwaves will be scaled.
output_dir : str
Directory to output the files into.
save_as : str | None
Format in which to return the sinewaves. 'dict' returns sinewave arrays
as values in a python dictionary; 'wav' saves them as WAV files at
sampling frequency 'fs'; 'mat' saves them as a MAT file along with
related variables 'fs', 'freqs', 'trial_order', and 'rms'.
None will not save any data.
rand_seed : int | None
Seed for the random number generator.
Returns
-------
wavs : dict | None
The stimulus dictionary.
"""
if rand_seed is None:
rng = np.random.RandomState()
else:
rng = np.random.RandomState(rand_seed)
# check input arguments
if save_as is not None and save_as not in ['dict', 'wav', 'hdf5']:
raise ValueError('"save_as" must be "dict", "wav", or "hdf5"')
fs = float(fs)
t = np.arange(np.round(stim_dur * fs)) / fs
# frequencies equally spaced on a log-2 scale
freqs = min_freq * np.logspace(0, np.log2(max_freq / float(min_freq)),
num_freqs, endpoint=True, base=2)
# strings for the filenames / dictionary keys
freq_names = [str(int(f)) for f in freqs]
names = ['stim_%s_%s' % (n, f) for n, f in enumerate(freq_names)]
# generate sinewaves & RMS normalize
wavs = [np.sin(2 * np.pi * f * t) for f in freqs]
wavs = [rms / np.sqrt(np.mean(w ** 2)) * w for w in wavs]
# collect into dictionary & save
wav_dict = {n: w for (n, w) in zip(names, wavs)}
if save_as == 'hdf5':
num_reps = num_trials // num_freqs + 1
trials = np.tile(range(num_freqs), num_reps)
trial_order = rng.permutation(trials[0:num_trials])
wav_dict.update({'trial_order': trial_order, 'freqs': freqs, 'fs': fs,
'rms': rms})
write_hdf5(op.join(output_dir, 'equally_spaced_sinewaves.hdf5'),
wav_dict, overwrite=True)
elif save_as == 'wav':
for n in names:
write_wav(op.join(output_dir, n + '.wav'), wav_dict[n], int(fs))
return wav_dict
c_flash_locs = np.tile(c_flash_locations, 5)
condition_stamp_controls = np.array((range(1, 49)))
c_stamp_controls = np.tile(condition_stamp, 5)
cc = np.vstack(([control_stim], [cflashes], [c_flash_locs], [control_C],
[c_stamp_controls])).T
############################################################################
# create and store the blocks (should be 15)
blocks = {}
bn = ['Block1', 'Block2', 'Block3', 'Block4', 'Block5', 'Block6', 'Block7',
'Block8', 'Block9', 'Block10', 'Block11', 'Block12', 'Block13',
'Block14', 'Block15']
blocks.fromkeys(bn)
n_blocks = total_trials / trials_per_block
for bi in range(1, 16):
d = c[0:96] # iter over this to stack into blocks
stack = cc[:12]
dd = np.append(d, stack, 0)
blocks["Block{0}".format(bi)] = rng.permutation(dd)
np.delete(c, np.s_[:96], 0)
np.delete(cc, np.s_[:12], 0)
# write out result:
print('Saving stimuli variables')
Stim_vars = dict(space_conditions=space_conditions,
nocomp_stim_name=nocomp_stim_name, taud_stim=taud_stim,
blocks=blocks, flashes=flashes)
np.savez('stim', **Stim_vars)
write_hdf5(op.join(work_dir, 'Stim_vars.hdf5'), Stim_vars, overwrite=True)
plt.gca().spines['right'].set_visible(False)
plt.xlim([0,21.25])
plt.xlabel(u'Central threshold (°)')
plt.ylabel('Performance improvement \n (% correct)')
plt.subplots_adjust(left=0.4, right=.97, top=0.95, bottom=0.2)
plt.savefig(path + 'stem_correct.pdf', dpi=600)
improvements = -np.diff(thresholds, 1, -1)
# %% some stats
ax = plt.figure(figsize=(4.2, 2.8))
dist = np.mean(np.diff(per_cor, 1, -2), -1).squeeze()
inds = np.argsort(dist)
write_hdf5('effectsize.hdf5', dist, overwrite=True)
plt.plot(np.arange(20) + 1, dist[inds], '^', c='C2', ms=7)
plt.plot(np.arange(20) + 1, perform_imp[inds], 'd', mec='C2', mfc='w', ms=7)
plt.errorbar(23.6, dist.mean(), dist.std() / np.sqrt(20), fmt='^', color='C2',
ms=10, lw=1.5, capsize=3)
plt.errorbar(24.4, perform_imp.mean(), perform_imp.std() / np.sqrt(20),
fmt='d', mec='C2', mfc='w', color='C2', ms=10, lw=1.5, capsize=3)
plt.plot([0, 28], [0,0], 'k--', zorder=-5)
plt.xlim([0, 25])
plt.xlabel('Subjects')
plt.ylabel('Improvement \n (percent correct)')