def exec_specmax(ddata, opts):
p = {
'expmt_group': '',
'n_sim': 0,
'n_trial': 0,
't_interval': None,
'f_interval': None,
'f_sort': None,
# 't_interval': [0., -1],
# 'f_interval': [0., -1],
}
args_check(p, opts)
p_exp = paramrw.ExpParams(ddata.fparam)
# trial_prefix = p_exp.trial_prefix_str % (p['n_sim'], p['n_trial'])
if not p['expmt_group']:
p['expmt_group'] = ddata.expmt_groups[0]
# Get the associated dipole and spec file
fspec = ddata.return_specific_filename(p['expmt_group'], 'rawspec', p['n_sim'], p['n_trial'])
# Load the spec data
spec = specfn.Spec(fspec)
# get max data
data_max = spec.max('agg', p['t_interval'], p['f_interval'], p['f_sort'])
if data_max:
print "Max power of %4.2e at f of %4.2f Hz at %4.3f ms" % (data_max['pwr'], data_max['f_at_max'], data_max['t_at_max'])
def exec_spec_stationary_avg(ddata, dsim, maxpwr):
# Prompt user for type of analysis (per expmt or whole sim)
analysis_type = raw_input('Would you like analysis per expmt or for whole sim? (expmt or sim): ')
fspec_list = fio.file_match(ddata.dsim, '-spec.npz')
fparam_list = fio.file_match(ddata.dsim, '-param.txt')
# fspec_list = fio.file_match(ddata.dsim, '-spec.npz')
# fparam_list = fio.file_match(ddata.dsim, '-param.txt')
p_exp = paramrw.ExpParams(ddata.fparam)
key_types = p_exp.get_key_types()
# If no saved spec results exist, redo spec analysis
if not fspec_list:
print "No saved spec data found. Performing spec analysis...",
exec_spec_regenerate(ddata)
fspec_list = fio.file_match(ddata.dsim, '-spec.npz')
# spec_results = exec_spec_regenerate(ddata)
print "now doing spec freq-pwr analysis"
# perform time-averaged stationary analysis
# specpwr_results = [specfn.specpwr_stationary_avg(fspec) for fspec in fspec_list]
specpwr_results = []
for fspec in fspec_list:
spec = specfn.Spec(fspec)
specpwr_results.append(spec.stationary_avg())
# plot for whole simulation
if analysis_type == 'sim':
file_name = os.path.join(dsim, 'specpwr.eps')
pspec.pspecpwr(file_name, specpwr_results, fparam_list, key_types)
# if maxpwr plot indicated
if maxpwr:
f_name = os.path.join(dsim, 'maxpwr.png')
specfn.pmaxpwr(f_name, specpwr_results, fparam_list)
# plot per expmt
if analysis_type == 'expmt':
for expmt_group in ddata.expmt_groups:
# create name for figure. Figure saved to expmt directory
file_name = os.path.join(dsim, expmt_group, 'specpwr.png')
# compile list of freqpwr results and param pathways for expmt
partial_results_list = [result for result in specpwr_results if result['expmt']==expmt_group]
partial_fparam_list = [fparam for fparam in fparam_list if expmt_group in fparam]
# plot results
pspec.pspecpwr(file_name, partial_results_list, partial_fparam_list, key_types)
# if maxpwr plot indicated
if maxpwr:
f_name = os.path.join(dsim, expmt_group, 'maxpwr.png')
specfn.pmaxpwr(f_name, partial_results_list, partial_fparam_list)
def exec_specmax_dpl_tmpl(ddata, opts):
p = {
'expmt_group': '',
'n_sim': 0,
'trials': [0, -1],
't_interval': None,
'f_interval': None,
'f_sort': None,
}
args_check(p, opts)
# set expmt group
if not p['expmt_group']:
p['expmt_group'] = ddata.expmt_groups[0]
# set directory to save template in and check that it exists
dir_out = os.path.join(ddata.dsim, p['expmt_group'], 'tmpldpl')
fio.dir_create(dir_out)
# if p['trials'][1] is -1, assume all trials are wanted
# 1 is subtracted from N_trials to be consistent with manual entry of trial range
if p['trials'][1] == -1:
p_exp = paramrw.ExpParams(ddata.fparam)
p['trials'][1] = p_exp.N_trials - 1
# Get spec, dpl, and param files
# Sorry for lack of readability
spec_list = [ddata.return_specific_filename(p['expmt_group'], 'rawspec', p['n_sim'], i) for i in range(p['trials'][0], p['trials'][1]+1)]
dpl_list = [ddata.return_specific_filename(p['expmt_group'], 'rawdpl', p['n_sim'], i) for i in range(p['trials'][0], p['trials'][1]+1)]
param_list = [ddata.return_specific_filename(p['expmt_group'], 'param', p['n_sim'], i) for i in range(p['trials'][0], p['trials'][1]+1)]
# Get max spectral data
data_max_list = []
for fspec in spec_list:
spec = specfn.Spec(fspec)
data_max_list.append(spec.max('agg', p['t_interval'], p['f_interval'], p['f_sort']))
# Get time intervals of max spectral pwr
t_interval_list = [dmax['t_int'] for dmax in data_max_list if dmax is not None]
# truncate dpl_list to include only sorted trials
# kind of crazy that this works. Just sayin'...
dpl_list = [fdpl for fdpl, dmax in zip(dpl_list, data_max_list) if dmax is not None]
# create file name
if p['f_sort']:
fname_short = "sim-%03i-T%03i-T%03d-sort-%i-%i-tmpldpl.txt" %(p['n_sim'], p['trials'][0], p['trials'][1], p['f_sort'][0], p['f_sort'][1])
else:
fname_short = "sim-%03i-T%03i-T%03i-tmpldpl.txt" %(p['n_sim'], p['trials'][0], p['trials'][1])
fname = os.path.join(dir_out, fname_short)
# Create dpl template
dipolefn.create_template(fname, dpl_list, param_list, t_interval_list)
def exec_specmax_dpl_match(ddata, opts):
p = {
'expmt_group': '',
'n_sim': 0,
'trials': [0, -1],
't_interval': None,
'f_interval': None,
'f_sort': None,
}
args_check(p, opts)
# set expmt group
if not p['expmt_group']:
p['expmt_group'] = ddata.expmt_groups[0]
# set directory to save fig in and check that it exists
dir_fig = os.path.join(ddata.dsim, p['expmt_group'], 'figint')
fio.dir_create(dir_fig)
# if p['trials'][1] is -1, assume all trials are wanted
# 1 is subtracted from N_trials to be consistent with manual entry of trial range
if p['trials'][1] == -1:
p_exp = paramrw.ExpParams(ddata.fparam)
p['trials'][1] = p_exp.N_trials - 1
# Get spec, dpl, and param files
# Sorry for lack of readability
spec_list = [ddata.return_specific_filename(p['expmt_group'], 'rawspec', p['n_sim'], i) for i in range(p['trials'][0], p['trials'][1]+1)]
dpl_list = [ddata.return_specific_filename(p['expmt_group'], 'rawdpl', p['n_sim'], i) for i in range(p['trials'][0], p['trials'][1]+1)]
param_list = [ddata.return_specific_filename(p['expmt_group'], 'param', p['n_sim'], i) for i in range(p['trials'][0], p['trials'][1]+1)]
# Get max spectral data
data_max_list = []
for fspec in spec_list:
spec = specfn.Spec(fspec)
data_max_list.append(spec.max('agg', p['t_interval'], p['f_interval'], p['f_sort']))
# create fig name
if p['f_sort']:
fname_short = "sim-%03i-T%03i-T%03d-sort-%i-%i" %(p['n_sim'], p['trials'][0], p['trials'][1], p['f_sort'][0], p['f_sort'][1])
else:
fname_short = "sim-%03i-T%03i-T%03i" %(p['n_sim'], p['trials'][0], p['trials'][1])
fname = os.path.join(dir_fig, fname_short)
# plot time-series over proper intervals
dipolefn.plot_specmax_interval(fname, dpl_list, param_list, data_max_list)
def pspec_with_hist(f_spec,
f_dpl,
f_spk,
dfig,
f_param,
key_types,
xlim=None,
ylim=None):
# Generate file prefix
# print('f_spec:',f_spec)
fprefix = f_spec.split('/')[-1].split('.')[0]
# Create the fig name
fig_name = os.path.join(dfig, fprefix + '.png')
# print('fig_name:',fig_name)
# load param dict
_, p_dict = paramrw.read(f_param)
f = ac.FigSpecWithHist()
# load spec data
spec = specfn.Spec(f_spec)
# Plot TFR data and add colorbar
pc = spec.plot_TFR(f.ax['spec'], 'agg', xlim, ylim)
f.f.colorbar(pc, ax=f.ax['spec'])
# set xlim based on TFR plot
xlim_new = f.ax['spec'].get_xlim()
# grab the dipole data
dpl = dipolefn.Dipole(f_dpl)
dpl.baseline_renormalize(f_param)
dpl.convert_fAm_to_nAm()
# plot routine
dpl.plot(f.ax['dipole'], xlim_new, 'agg')
# data_dipole = np.loadtxt(open(f_dpl, 'r'))
# t_dpl = data_dipole[xmin_ind:xmax_ind+1, 0]
# dp_total = data_dipole[xmin_ind:xmax_ind+1, 1]
# f.ax['dipole'].plot(t_dpl, dp_total)
# x = (xmin, xmax)
# # grab alpha feed data. spikes_from_file() from spikefn.py
# s_dict = spikefn.spikes_from_file(f_param, f_spk)
# # check for existance of alpha feed keys in s_dict.
# s_dict = spikefn.alpha_feed_verify(s_dict, p_dict)
# # Account for possible delays
# s_dict = spikefn.add_delay_times(s_dict, p_dict)
# Get extinput data and account for delays
extinputs = spikefn.ExtInputs(f_spk, f_param)
extinputs.add_delay_times()
extinputs.get_envelope(dpl.t, feed='dist')
# set number of bins (150 bins per 1000ms)
bins = ceil(150. * (xlim_new[1] - xlim_new[0]) /
1000.) # bins should be int
# plot histograms
hist = {}
hist['feed_prox'] = extinputs.plot_hist(f.ax['feed_prox'],
'prox',
dpl.t,
bins=bins,
xlim=xlim_new,
color='red')
hist['feed_dist'] = extinputs.plot_hist(f.ax['feed_dist'],
'dist',
dpl.t,
bins=bins,
xlim=xlim_new,
color='green')
f.ax['feed_dist'].invert_yaxis()
# for now, set the xlim for the other one, force it!
f.ax['dipole'].set_xlim(xlim_new)
f.ax['spec'].set_xlim(xlim_new)
f.ax['feed_prox'].set_xlim(xlim_new)
f.ax['feed_dist'].set_xlim(xlim_new)
# set hist axis props
f.set_hist_props(hist)
# axis labels
f.ax['spec'].set_xlabel('Time (ms)')
f.ax['spec'].set_ylabel('Frequency (Hz)')
# Add legend to histogram
for key in f.ax.keys():
if 'feed' in key:
f.ax[key].legend()
# create title
title_str = ac.create_title(p_dict, key_types)
f.f.suptitle(title_str)
f.savepng(fig_name)
f.close()
def pspec_dpl(f_spec,
f_dpl,
dfig,
p_dict,
key_types,
xlim=None,
ylim=None,
f_param=None):
# Generate file prefix
fprefix = f_spec.split('/')[-1].split('.')[0]
# using png for now
# fig_name = os.path.join(dfig, fprefix+'.eps')
fig_name = os.path.join(dfig, fprefix + '.png')
# f.f is the figure handle!
f = ac.FigSpec()
# load spec data
spec = specfn.Spec(f_spec)
# Plot TFR data and add colorbar
pc = spec.plot_TFR(f.ax['spec'], 'agg', xlim, ylim)
f.f.colorbar(pc, ax=f.ax['spec'])
# grab the dipole data
# data_dipole = np.loadtxt(open(f_dpl, 'r'))
dpl = dipolefn.Dipole(f_dpl)
# If f_param supplied, renormalize dipole data
if f_param:
dpl.baseline_renormalize(f_param)
dpl.convert_fAm_to_nAm()
# plot routine
dpl.plot(f.ax['dipole'], xlim, 'agg')
# Plot Welch data
# Use try/except for backwards compatibility
try:
spec.plot_pgram(f.ax['pgram'])
except KeyError:
pgram = specfn.Welch(dpl.t, dpl.dpl['agg'], p_dict['dt'])
pgram.plot_to_ax(f.ax['pgram'], spec.spec['agg']['f'][-1])
# plot and create an xlim
xlim_new = f.ax['spec'].get_xlim()
xticks = f.ax['spec'].get_xticks()
xticks[0] = xlim_new[0]
# for now, set the xlim for the other one, force it!
f.ax['dipole'].set_xlim(xlim_new)
f.ax['dipole'].set_xticks(xticks)
f.ax['spec'].set_xticks(xticks)
# axis labels
f.ax['spec'].set_xlabel('Time (ms)')
f.ax['spec'].set_ylabel('Frequency (Hz)')
# create title
title_str = ac.create_title(p_dict, key_types)
f.f.suptitle(title_str)
# use our fig classes to save and close
f.savepng(fig_name)
# f.saveeps(dfig, fprefix)
f.close()
def aggregate_with_hist(f, ax, f_spec, f_dpl, f_spk, f_param):
# load param dict
_, p_dict = paramrw.read(f_param)
# load spec data from file
spec = specfn.Spec(f_spec)
# data_spec = np.load(f_spec)
# timevec = data_spec['time']
# freqvec = data_spec['freq']
# TFR = data_spec['TFR']
xmin = timevec[0]
xmax = p_dict['tstop']
x = (xmin, xmax)
pc = spec.plot_TFR(ax['spec'], layer='agg', xlim=x)
# pc = ax['spec'].imshow(TFR, extent=[timevec[0], timevec[-1], freqvec[-1], freqvec[0]], aspect='auto', origin='upper')
f.f.colorbar(pc,
ax=ax['spec'],
norm=plt.colors.Normalize(vmin=0, vmax=90000),
cmap=plt.get_cmap('jet'))
# grab the dipole data
dpl = dipolefn.Dipole(f_dpl)
dpl.plot(ax['dipole'], x, layer='agg')
# data_dipole = np.loadtxt(open(f_dpl, 'r'))
# t_dpl = data_dipole[xmin/p_dict['dt']:, 0]
# dp_total = data_dipole[xmin/p_dict['dt']:, 1]
# ax['dipole'].plot(t_dpl, dp_total)
# grab alpha feed data. spikes_from_file() from spikefn.py
s_dict = spikefn.spikes_from_file(f_param, f_spk)
# check for existance of alpha feed keys in s_dict.
s_dict = spikefn.alpha_feed_verify(s_dict, p_dict)
# Account for possible delays
s_dict = spikefn.add_delay_times(s_dict, p_dict)
# set number of bins (150 bins/1000ms)
bins = 150. * (xmax - xmin) / 1000.
hist = {}
# Proximal feed
hist['feed_prox'] = ax['feed_prox'].hist(
s_dict['alpha_feed_prox'].spike_list,
bins,
range=[xmin, xmax],
color='red',
label='Proximal feed')
# Distal feed
hist['feed_dist'] = ax['feed_dist'].hist(
s_dict['alpha_feed_dist'].spike_list,
bins,
range=[xmin, xmax],
color='green',
label='Distal feed')
# for now, set the xlim for the other one, force it!
ax['dipole'].set_xlim(x)
ax['spec'].set_xlim(x)
ax['feed_prox'].set_xlim(x)
ax['feed_dist'].set_xlim(x)
# set hist axis props
f.set_hist_props(ax, hist)
# axis labels
ax['spec'].set_xlabel('Time (ms)')
ax['spec'].set_ylabel('Frequency (Hz)')
# Add legend to histogram
for key in ax.keys():
if 'feed' in key:
ax[key].legend()
def exec_spec_avg_stationary_avg(ddata, dsim, opts):
# Prompt user for type of analysis (per expmt or whole sim)
analysis_type = raw_input('Would you like analysis per expmt or for whole sim? (expmt or sim): ')
spec_results_avged = fio.file_match(ddata.dsim, '-specavg.npz')
fparam_list = fio.file_match(ddata.dsim, '-param.txt')
p_exp = paramrw.ExpParams(ddata.fparam)
key_types = p_exp.get_key_types()
# If no avg spec data found, generate it.
if not spec_results_avged:
exec_avgtrials(ddata, 'spec')
spec_results_avged = fio.file_match(ddata.dsim, '-specavg.npz')
# perform time-averaged stationarity analysis
# specpwr_results = [specfn.specpwr_stationary_avg(dspec) for dspec in spec_results_avged]
specpwr_results = []
for fspec in spec_results_avged:
spec = specfn.Spec(fspec)
specpwr_results.append(spec.stationary_avg())
# create fparam list to match avg'ed data
N_trials = p_exp.N_trials
nums = np.arange(0, len(fparam_list), N_trials)
fparam_list = [fparam_list[num] for num in nums]
# plot for whole simulation
if analysis_type == 'sim':
# if error bars indicated
if opts['errorbars']:
# get raw (non avg'ed) spec data
raw_spec_data = fio.file_match(ddata.dsim, '-spec.npz')
# perform freqpwr analysis on raw data
# raw_specpwr = [specfn.specpwr_stationary_avg(dspec)['p_avg'] for dspec in raw_spec_data]
raw_specpwr = []
for fspec in raw_spec_data:
spec = specfn.Spec(fspec)
raw_specpwr.append(spec.stationary_avg()['p_avg'])
# calculate standard error
error_vec = specfn.calc_stderror(raw_specpwr)
else:
error_vec = []
file_name = os.path.join(dsim, 'specpwr-avg.eps')
pspec.pspecpwr(file_name, specpwr_results, fparam_list, key_types, error_vec)
# # if maxpwr plot indicated
# if maxpwr:
# f_name = os.path.join(dsim, 'maxpwr-avg.png')
# specfn.pmaxpwr(f_name, freqpwr_results_list, fparam_list)
# plot per expmt
if analysis_type == 'expmt':
for expmt_group in ddata.expmt_groups:
# if error bars indicated
if opts['errorbars']:
# get exmpt group raw spec data
raw_spec_data = ddata.file_match(expmt_group, 'rawspec')
# perform stationary analysis on raw data
raw_specpwr = [specfn.specpwr_stationary_avg(dspec)['p_avg'] for dspec in raw_spec_data]
# calculate standard error
error_vec = specfn.calc_stderror(raw_specpwr)
else:
error_vec = []
# create name for figure. Figure saved to expmt directory
file_name = os.path.join(dsim, expmt_group, 'specpwr-avg.png')
# compile list of specpwr results and param pathways for expmt
partial_results_list = [result for result in specpwr_results if result['expmt']==expmt_group]
partial_fparam_list = [fparam for fparam in fparam_list if expmt_group in fparam]
# plot results
pspec.pspecpwr(file_name, partial_results_list, partial_fparam_list, key_types, error_vec)
def exec_phaselock(ddata, opts):
p = {
't_interval': [50, 1000],
'f_max': 60.,
}
args_check(p, opts)
# Do this per expmt group
for expmt_group in ddata.expmt_groups:
# Get paths to relevant files
list_dpl = ddata.file_match(expmt_group, 'rawdpl')
list_spk = ddata.file_match(expmt_group, 'rawspk')
list_param = ddata.file_match(expmt_group, 'param')
avg_spec = ddata.file_match(expmt_group, 'avgspec')[0]
tmp_array_dpl = []
tmp_array_spk = []
for f_dpl, f_spk, f_param in zip(list_dpl, list_spk, list_param):
# load Dpl data, do stuff, and store it
print f_dpl
dpl = dipolefn.Dipole(f_dpl)
dpl.baseline_renormalize(f_param)
dpl.convert_fAm_to_nAm()
t, dp = dpl.truncate_ext(p['t_interval'][0], p['t_interval'][1])
dp = dp['agg']
tmp_array_dpl.append(dp)
# Load extinput data, do stuff, and store it
try:
extinput = spikefn.ExtInputs(f_spk, f_param)
except ValueError:
print("Error: could not load spike timings from %s" % f_spk)
return
extinput.add_delay_times()
extinput.get_envelope(dpl.t, feed='dist', bins=150)
inputs, t = extinput.truncate_ext('env', p['t_interval'])
tmp_array_spk.append(inputs)
# Convert tmp arrays (actually lists) to numpy nd arrays
array_dpl = np.array(tmp_array_dpl)
array_spk = np.array(tmp_array_spk)
# Phase-locking analysis
phase = specfn.PhaseLock(array_dpl, array_spk, list_param[0], p['f_max'])
fname_d = os.path.join(ddata.dsim, expmt_group, 'phaselock-%iHz.npz' %p['f_max'])
np.savez_compressed(fname_d, t=phase.data['t'], f=phase.data['f'], B=phase.data['B'])
# Plotting
# Should be moved elsewhere
avg_dpl = np.mean(array_dpl, axis=0)
avg_spk = np.mean(array_spk, axis=0)
f = ac.FigPhase()
extent_xy = [t[0], t[-1], phase.data['f'][-1], 0]
pc1 = f.ax['phase'].imshow(phase.data['B'], extent=extent_xy, aspect='auto', origin='upper',cmap=plt.get_cmap('jet'))
pc1.set_clim([0, 1])
cb1 = f.f.colorbar(pc1, ax=f.ax['phase'])
# cb1.set_clim([0, 1])
spec = specfn.Spec(avg_spec)
pc2 = spec.plot_TFR(f.ax['spec'], xlim=[t[0], t[-1]])
pc2.set_clim([0, 3.8e-7])
cb2 = f.f.colorbar(pc2, ax=f.ax['spec'])
# cb2.set_clim([0, 3.6e-7])
f.ax['dipole'].plot(t, avg_dpl)
f.ax['dipole'].set_xlim([t[0], t[-1]])
f.ax['dipole'].set_ylim([-0.0015, 0.0015])
f.ax['input'].plot(t, avg_spk)
f.ax['input'].set_xlim([t[0], t[-1]])
f.ax['input'].set_ylim([-1, 5])
f.ax['input'].invert_yaxis()
f.ax['phase'].set_xlabel('Time (ms)')
f.ax['phase'].set_ylabel('Frequency (Hz)')
fname = os.path.join(ddata.dsim, expmt_group, 'phaselock-%iHz.png' %p['f_max'])
print fname
f.savepng(fname)