def plinear_regression(ffig_dpl, fdpl):
dpl = Dipole(fdpl)
layer = 'L5'
t0 = 750.
# dipole for the given layer, truncated
# order matters here
x_dpl = dpl.dpl[layer][(dpl.t > t0)]
t = dpl.t[dpl.t > t0]
# take the transpose (T) of a vector of the times and ones for each element
A = np.vstack([t, np.ones(len(t))]).T
# find the slope and the y-int of the line fit with least squares method (min. of Euclidean 2-norm)
m, c = np.linalg.lstsq(A, x_dpl)[0]
print(m, c)
# plot me
f = ac.FigStd()
f.ax0.plot(t, x_dpl)
f.ax0.hold(True)
f.ax0.plot(t, m*t + c, 'r')
# save over the original
f.savepng(ffig_dpl)
f.close()
def pmaxpwr(file_name, results_list, fparam_list):
f = ac.FigStd()
f.ax0.hold(True)
# instantiate lists for storing x and y data
x_data = []
y_data = []
# plot points
for result, fparam in zip(results_list, fparam_list):
p = paramrw.read(fparam)[1]
x_data.append(p['f_input_prox'])
y_data.extend(result['freq_at_max'])
f.ax0.plot(x_data[-1], y_data[-1], 'kx')
# add trendline
fit = np.polyfit(x_data, y_data, 1)
fit_fn = np.poly1d(fit)
f.ax0.plot(x_data, fit_fn(x_data), 'k-')
# Axis stuff
f.ax0.set_xlabel('Proximal/Distal Input Freq (Hz)')
f.ax0.set_ylabel('Freq at which max avg power occurs (Hz)')
f.save(file_name)
def pspecpwr(file_name, results_list, fparam_list, key_types, error_vec=[]):
# instantiate fig
f = ac.FigStd()
f.set_fontsize(18)
# pspecpwr_ax is a plot kernel for specpwr plotting
legend_list = pspecpwr_ax(f.ax0, results_list, fparam_list, key_types)
# Add error bars if necessary
if len(error_vec):
# errors are only used with avg'ed data. There will be only one entry in results_list
pyerrorbars_ax(f.ax0, results_list[0]['freq'],
results_list[0]['p_avg'], error_vec)
# insert legend
f.ax0.legend(legend_list, loc='upper right', prop={'size': 8})
# axes labels
f.ax0.set_xlabel('Freq (Hz)')
f.ax0.set_ylabel('Avgerage Power (nAm^2)')
# add title
# f.set_title(fparam_list[0], key_types)
f.savepng(file_name)
# f.save(file_name)
# f.saveeps(file_name)
f.close()
def pdipole_exp(ddata, ylim=[]):
""" over ALL trials in ALL conditions in EACH experiment
"""
# sim_prefix
fprefix = ddata.sim_prefix
# create the figure name
fname_exp = '%s_dpl' % (fprefix)
fname_exp_fig = os.path.join(ddata.dsim, fname_exp + '.png')
# create one figure comparing across all
N_expmt_groups = len(ddata.expmt_groups)
f_exp = ac.FigDipoleExp(ddata.expmt_groups)
# empty list for the aggregate dipole data
dpl_exp = []
# go through each expmt
for expmt_group in ddata.expmt_groups:
# create the filename
dexp = ddata.dexpmt_dict[expmt_group]
fname_short = '%s-%s-dpl' % (fprefix, expmt_group)
fname_data = os.path.join(dexp, fname_short + '.txt')
fname_fig = os.path.join(ddata.dfig[expmt_group]['figdpl'], fname_short + '.png')
# grab the list of raw data dipoles and assoc params in this expmt
dpl_list = ddata.file_match(expmt_group, 'rawdpl')
param_list = ddata.file_match(expmt_group, 'param')
for f_dpl, f_param in zip(dpl_list, param_list):
dpl = Dipole(f_dpl)
dpl.baseline_renormalize(f_param)
# x_tmp = np.loadtxt(open(file, 'r'))
# initialize and use x_dpl
if f_dpl is dpl_list[0]:
# assume time vec stays the same throughout
t_vec = dpl.t
x_dpl = dpl.dpl['agg']
else:
# guaranteed to exist after dpl_list[0]
x_dpl += dpl.dpl['agg']
# poor man's mean
x_dpl /= len(dpl_list)
# save this in a list to do comparison figure
# order is same as ddata.expmt_groups
dpl_exp.append(x_dpl)
# write this data to the file
with open(fname_data, 'w') as f:
for t, x in zip(t_vec, x_dpl):
f.write("%03.3f\t%5.4f\n" % (t, x))
# create the plot I guess?
f = ac.FigStd()
f.ax0.plot(t_vec, x_dpl)
if len(ylim):
f.ax0.set_ylim(ylim)
f.savepng(fname_fig)
f.close()
# plot the aggregate data using methods defined in FigDipoleExp()
f_exp.plot(t_vec, dpl_exp)
# attempt at setting titles
for ax, expmt_group in zip(f_exp.ax, ddata.expmt_groups):
ax.set_title(expmt_group)
f_exp.savepng(fname_exp_fig)
f_exp.close()
def pdipole_evoked(dfig, f_dpl, f_spk, f_param, ylim=[]):
""" for each individual simulation/trial
"""
gid_dict, p_dict = paramrw.read(f_param)
# get the spike dict from the files
s_dict = spikefn.spikes_from_file(f_param, f_spk)
s = s_dict.keys()
s.sort()
# create an empty dict 'spk_unique'
spk_unique = dict.fromkeys([key for key in s_dict.keys() if key.startswith(('evprox', 'evdist'))])
for key in spk_unique:
spk_unique[key] = s_dict[key].unique_all(0)
# draw vertical lines for each item in this
# x_dipole is dipole data
# x_dipole = np.loadtxt(open(f_dpl, 'r'))
dpl = Dipole(f_dpl)
# split to find file prefix
file_prefix = f_dpl.split('/')[-1].split('.')[0]
# # set xmin value
# xmin = xlim[0] / p_dict['dt']
# # set xmax value
# if xlim[1] == 'tstop':
# xmax = p_dict['tstop'] / p_dict['dt']
# else:
# xmax = xlim[1] / p_dict['dt']
# these are the vectors for now, but this is going to change
t_vec = dpl.t
dp_total = dpl.dpl['agg']
f = ac.FigStd()
# hold on
f.ax0.hold(True)
f.ax0.plot(t_vec, dp_total)
lines_spk = dict.fromkeys(spk_unique)
print(spk_unique)
# plot the lines
for key in spk_unique:
print(key, spk_unique[key])
x_val = spk_unique[key][0]
lines_spk[key] = plt.axvline(x=x_val, linewidth=0.5, color='r')
# title_txt = [key + ': {:.2e}' % p_dict[key] for key in key_types['dynamic_keys']]
title_txt = 'test'
f.ax0.set_title(title_txt)
if ylim:
f.ax0.set_ylim(ylim)
fig_name = os.path.join(dfig, file_prefix+'.png')
plt.savefig(fig_name, dpi=300)
f.close()
def pdipole(f_dpl, dfig, plot_dict, f_param=None, key_types={}):
""" single dipole file combination (incl. param file)
this should be done with an axis input too
two separate functions, a pdipole kernel function and a specific function for this simple plot
"""
# dpl is an obj of Dipole() class
dpl = Dipole(f_dpl)
if f_param:
dpl.baseline_renormalize(f_param)
dpl.convert_fAm_to_nAm()
# split to find file prefix
file_prefix = f_dpl.split('/')[-1].split('.')[0]
# parse xlim from plot_dict
if plot_dict['xlim'] is None:
xmin = dpl.t[0]
xmax = dpl.t[-1]
else:
xmin, xmax = plot_dict['xlim']
if xmin < 0.:
xmin = 0.
if xmax < 0.:
xmax = self.f[-1]
# # get xmin and xmax from the plot_dict
# if plot_dict['xmin'] is None:
# xmin = 0.
# else:
# xmin = plot_dict['xmin']
# if plot_dict['xmax'] is None:
# xmax = p_dict['tstop']
# else:
# xmax = plot_dict['xmax']
# truncate them using logical indexing
t_range = dpl.t[(dpl.t >= xmin) & (dpl.t <= xmax)]
dpl_range = dpl.dpl['agg'][(dpl.t >= xmin) & (dpl.t <= xmax)]
f = ac.FigStd()
f.ax0.plot(t_range, dpl_range)
# sorry about the parity between vars here and above with xmin/xmax
if plot_dict['ylim'] is None:
# if plot_dict['ymin'] is None or plot_dict['ymax'] is None:
pass
else:
f.ax0.set_ylim(plot_dict['ylim'][0], plot_dict['ylim'][1])
# f.ax0.set_ylim(plot_dict['ymin'], plot_dict['ymax'])
# Title creation
if f_param and key_types:
# grabbing the p_dict from the f_param
_, p_dict = paramrw.read(f_param)
# useful for title strings
title_str = ac.create_title(p_dict, key_types)
f.f.suptitle(title_str)
# create new fig name
fig_name = os.path.join(dfig, file_prefix+'.png')
# savefig
plt.savefig(fig_name, dpi=300)
f.close()