if list_item in keys:
data[list_item] = list(data[list_item])
clusters = data['clusters']
stas = data['stas']
filter_length = data['filter_length']
stx_w = data['stx_w']
exp_name = data['exp_name']
stimname = data['stimname']
stimname += '_corrected'
frame_duration = data['frame_duration']
quals = data['quals']
clusterids = plf.clusters_to_ids(clusters)
# Determine frame size so that the total frame covers
# an area large enough i.e. 2*700um
t = np.arange(filter_length) * frame_duration * 1000
vscale = int(stas[0].shape[0] * stx_w * px_size / 1000)
for i in range(clusters.shape[0]):
sta = stas[i]
vmax = np.max(np.abs(sta))
vmin = -vmax
plt.figure(figsize=(6, 15))
ax = plt.subplot(111)
im = ax.imshow(sta,
cmap='RdBu',
vmin=vmin,
def stripesurround(exp_name, stimnrs):
exp_dir = iof.exp_dir_fixer(exp_name)
if isinstance(stimnrs, int):
stimnrs = [stimnrs]
for stimnr in stimnrs:
data = iof.load(exp_name, stimnr)
_, metadata = asc.read_spikesheet(exp_dir)
px_size = metadata['pixel_size(um)']
clusters = data['clusters']
stas = data['stas']
max_inds = data['max_inds']
filter_length = data['filter_length']
stx_w = data['stx_w']
exp_name = data['exp_name']
stimname = data['stimname']
frame_duration = data['frame_duration']
quals = data['quals']
clusterids = plf.clusters_to_ids(clusters)
fsize = int(700 / (stx_w * px_size))
t = np.arange(filter_length) * frame_duration * 1000
vscale = fsize * stx_w * px_size
#%%
cs_inds = np.empty(clusters.shape[0])
polarities = np.empty(clusters.shape[0])
savepath = os.path.join(exp_dir, 'data_analysis', stimname)
for i in range(clusters.shape[0]):
sta = stas[i]
max_i = max_inds[i]
sta, max_i = msc.cutstripe(sta, max_i, fsize * 2)
plt.figure(figsize=(12, 10))
ax = plt.subplot(121)
plf.stashow(sta, ax)
# Isolate the time point from which the fit will
# be obtained
fitv = sta[:, max_i[1]]
# Make a space vector
s = np.arange(fitv.shape[0])
if np.max(fitv) != np.max(np.abs(fitv)):
onoroff = -1
else:
onoroff = 1
polarities[i] = onoroff
# Determine the peak values for center and surround
# to give as initial parameters for curve fitting
centerpeak = -onoroff * np.max(fitv * onoroff)
surroundpeak = -onoroff * np.max(fitv * -onoroff)
# Define initial guesses for the center and surround gaussians
# First set of values are for center, second for surround.
p_initial = [centerpeak, max_i[0], 2, surroundpeak, max_i[0], 4]
bounds = ([0, -np.inf, -np.inf, 0, -np.inf, -np.inf], np.inf)
try:
popt, _ = curve_fit(centersurround_onedim,
s,
fitv,
p0=p_initial,
bounds=bounds)
except ValueError as e:
if str(e) == "`x0` is infeasible.":
print(e)
popt, _ = curve_fit(onedgauss,
s,
onoroff * fitv,
p0=p_initial[:3])
popt = np.append(popt, [0, popt[1], popt[2]])
else:
raise
fit = centersurround_onedim(s, *popt)
# Avoid dividing by zero when calculating center-surround index
if popt[3] > 0:
csi = popt[0] / popt[3]
else:
csi = 0
cs_inds[i] = csi
ax = plt.subplot(122)
plf.spineless(ax)
ax.set_yticks([])
# We need to flip the vertical axis to match
# with the STA next to it
plt.plot(onoroff * fitv, -s, label='Data')
plt.plot(onoroff * fit, -s, label='Fit')
plt.axvline(0, linestyle='dashed', alpha=.5)
plt.title(f'Center: a: {popt[0]:4.2f}, μ: {popt[1]:4.2f},' +
f' σ: {popt[2]:4.2f}\n' +
f'Surround: a: {popt[3]:4.2f}, μ: {popt[4]:4.2f},' +
f' σ: {popt[5]:4.2f}' + f'\n CS index: {csi:4.2f}')
plt.subplots_adjust(top=.82)
plt.suptitle(f'{exp_name}\n{stimname}\n{clusterids[i]}')
os.makedirs(os.path.join(savepath, 'stripesurrounds'),
exist_ok=True)
plt.savefig(
os.path.join(savepath, 'stripesurrounds',
clusterids[i] + '.svg'))
plt.close()
data.update({'cs_inds': cs_inds, 'polarities': polarities})
np.savez(os.path.join(savepath, f'{stimnr}_data.npz'), **data)
import matplotlib.pyplot as plt
import iofuncs as iof
import plotfuncs as plf
import analysis_scripts as asc
from scipy import stats
import texplot
data = np.load('/home/ycan/Documents/thesis/analysis_auxillary_files/'
'thesis_csiplotting.npz')
cells = []
include = data['include']
colors = data['colors']
colorcategories = data['colorcategories']
maxts = np.empty([2, 1])
for i, exp_name in enumerate(['20180118', '20180124', '20180207']):
clusterids = plf.clusters_to_ids(asc.read_spikesheet(exp_name)[0])
cells.extend([(exp_name, cl_id) for cl_id in clusterids])
if '20180124' in exp_name or '20180207' in exp_name:
stripeflicker = [6, 12]
elif '20180118' in exp_name:
stripeflicker = [7, 14]
a = np.empty([2, len(clusterids)])
for j, stimnr in enumerate(stripeflicker):
data = iof.load(exp_name, stimnr)
a[j, :] = np.array(data['max_inds'])[:, 1]
maxts = np.hstack((maxts, a))
maxts = maxts[:, 1:] # Remove first element used in initialization
maxts = maxts * .0167 * 1000 # Convert to milliseconds
maxts_f = maxts[:, include]
def saccadegratingsanalyzer(exp_name, stim_nr):
"""
Analyze and save responses to saccadegratings stimulus.
"""
exp_dir = iof.exp_dir_fixer(exp_name)
exp_name = os.path.split(exp_dir)[-1]
stimname = iof.getstimname(exp_dir, stim_nr)
clusters, metadata = asc.read_spikesheet(exp_dir)
clusterids = plf.clusters_to_ids(clusters)
refresh_rate = metadata['refresh_rate']
parameters = asc.read_parameters(exp_name, stim_nr)
if parameters['stimulus_type'] != 'saccadegrating':
raise ValueError('Unexpected stimulus type: '
f'{parameters["stimulus_type"]}')
fixfr = parameters.get('fixationframes', 80)
sacfr = parameters.get('saccadeframes', 10)
barwidth = parameters.get('barwidth', 40)
averageshift = parameters.get('averageshift', 2)
# The seed is hard-coded in the Stimulator
seed = -10000
ftimes = asc.readframetimes(exp_dir, stim_nr)
ftimes.resize(int(ftimes.shape[0] / 2), 2)
nfr = ftimes.size
# Re-generate the stimulus
# Amplitude of the shift and the transition type (saccade or grey is
# determined based on the output of ran1
randnrs = np.array(randpy.ran1(seed, nfr)[0])
# Separate the amplitude and transitions into two arrays
stimpos = (4 * randnrs[::2]).astype(int)
# Transition variable, determines whether grating is moving during
# the transion or only a grey screen is presented.
trans = np.array(randnrs[1::2] > 0.5)
# Record before and after positions in a single array and remove
# The first element b/c there is no before value
stimposx = np.append(0, stimpos)[:-1]
stimtr = np.stack((stimposx, stimpos), axis=1)[1:]
trans = trans[:-1]
saccadetr = stimtr[trans, :]
greytr = stimtr[~trans, :]
# Create a time vector with defined temporal bin size
tstep = 0.01 # Bin size is defined here, unit is seconds
trialduration = (fixfr + sacfr) / refresh_rate
nrsteps = int(trialduration / tstep) + 1
t = np.linspace(0, trialduration, num=nrsteps)
# Collect saccade beginning time for each trial
trials = ftimes[1:, 0]
sacftimes = trials[trans]
greyftimes = trials[~trans]
sacspikes = np.empty((clusters.shape[0], sacftimes.shape[0], t.shape[0]))
greyspikes = np.empty((clusters.shape[0], greyftimes.shape[0], t.shape[0]))
# Collect all the psth in one array. The order is
# transision type, cluster index, start pos, target pos, time
psth = np.zeros((2, clusters.shape[0], 4, 4, t.size))
for i, (chid, clid, _) in enumerate(clusters):
spiketimes = asc.read_raster(exp_dir, stim_nr, chid, clid)
for j, _ in enumerate(sacftimes):
sacspikes[i, j, :] = asc.binspikes(spiketimes, sacftimes[j] + t)
for k, _ in enumerate(greyftimes):
greyspikes[i, k, :] = asc.binspikes(spiketimes, greyftimes[k] + t)
# Sort trials according to the transition type
# nton[i][j] contains the indexes of trials where saccade was i to j
nton_sac = [[[] for _ in range(4)] for _ in range(4)]
for i, trial in enumerate(saccadetr):
nton_sac[trial[0]][trial[1]].append(i)
nton_grey = [[[] for _ in range(4)] for _ in range(4)]
for i, trial in enumerate(greytr):
nton_grey[trial[0]][trial[1]].append(i)
savedir = os.path.join(exp_dir, 'data_analysis', stimname)
os.makedirs(savedir, exist_ok=True)
for i in range(clusters.shape[0]):
fig, axes = plt.subplots(4,
4,
sharex=True,
sharey=True,
figsize=(8, 8))
for j in range(4):
for k in range(4):
# Start from bottom left corner
ax = axes[3 - j][k]
# Average all transitions of one type
psth_sac = sacspikes[i, nton_sac[j][k], :].mean(axis=0)
psth_grey = greyspikes[i, nton_grey[j][k], :].mean(axis=0)
# Convert to spikes per second
psth_sac = psth_sac / tstep
psth_grey = psth_grey / tstep
psth[0, i, j, k, :] = psth_sac
psth[1, i, j, k, :] = psth_grey
ax.axvline(sacfr / refresh_rate * 1000,
color='red',
linestyle='dashed',
linewidth=.5)
ax.plot(t * 1000, psth_sac, label='Saccadic trans.')
ax.plot(t * 1000, psth_grey, label='Grey trans.')
ax.set_yticks([])
ax.set_xticks([])
# Cosmetics
plf.spineless(ax)
if j == k:
ax.set_facecolor((1, 1, 0, 0.15))
if j == 0:
ax.set_xlabel(f'{k}')
if k == 3:
ax.legend(fontsize='xx-small', loc=0)
if k == 0:
ax.set_ylabel(f'{j}')
# Add an encompassing label for starting and target positions
ax0 = fig.add_axes([0.08, 0.08, .86, .86])
plf.spineless(ax0)
ax0.patch.set_alpha(0)
ax0.set_xticks([])
ax0.set_yticks([])
ax0.set_ylabel('Start position')
ax0.set_xlabel('Target position')
plt.suptitle(f'{exp_name}\n{stimname}\n{clusterids[i]}')
plt.savefig(os.path.join(savedir, f'{clusterids[i]}.svg'))
plt.close()
# Save results
keystosave = [
'fixfr', 'sacfr', 't', 'averageshift', 'barwidth', 'seed', 'trans',
'saccadetr', 'greytr', 'nton_sac', 'nton_grey', 'stimname',
'sacspikes', 'greyspikes', 'psth', 'nfr', 'parameters'
]
data_in_dict = {}
for key in keystosave:
data_in_dict[key] = locals()[key]
np.savez(os.path.join(savedir, str(stim_nr) + '_data'), **data_in_dict)
print(f'Analysis of {stimname} completed.')
def allfff(exp_name, stim_nrs):
"""
Plot all of the full field flicker STAs on top of each other
to see the progression of the cell responses, their firing rates.
"""
if isinstance(stim_nrs, int) or len(stim_nrs) <= 1:
print('Multiple full field flicker stimuli expected, '
'allfff analysis will be skipped.')
return
exp_dir = iof.exp_dir_fixer(exp_name)
exp_name = os.path.split(exp_dir)[-1]
# Sanity check to ensure we are commparing the same stimuli and parameters
prev_parameters = {}
for i in stim_nrs:
pars = asc.read_parameters(exp_name, i)
currentfname = pars.pop('filename')
if len(prev_parameters) == 0:
prev_parameters = pars
for k1, k2 in zip(pars.keys(), prev_parameters.keys()):
if pars[k1] != prev_parameters[k2]:
raise ValueError(
f'Parameters for {currentfname} do not match!\n'
f'{k1}:{pars[k1]}\n{k2}:{prev_parameters[k2]}')
stimnames = []
for j, stim in enumerate(stim_nrs):
data = iof.load(exp_name, stim)
stas = data['stas']
clusters = data['clusters']
filter_length = data['filter_length']
frame_duration = data['frame_duration']
if j == 0:
all_stas = np.zeros(
(clusters.shape[0], filter_length, len(stim_nrs)))
all_spikenrs = np.zeros((clusters.shape[0], len(stim_nrs)))
all_stas[:, :, j] = stas
all_spikenrs[:, j] = data['spikenrs']
stimnames.append(iof.getstimname(exp_name, stim))
t = np.linspace(0, frame_duration * filter_length, num=filter_length)
#%%
clusterids = plf.clusters_to_ids(clusters)
for i in range(clusters.shape[0]):
fig = plt.figure()
ax1 = plt.subplot(111)
ax1.plot(t, all_stas[i, :, :])
ax1.set_xlabel('Time [ms]')
ax1.legend(stimnames, fontsize='x-small')
ax2 = fig.add_axes([.65, .15, .2, .2])
for j in range(len(stim_nrs)):
ax2.plot(j, all_spikenrs[i, j], 'o')
ax2.set_ylabel('# spikes', fontsize='small')
ax2.set_xticks([])
ax2.patch.set_alpha(0)
plf.spineless(ax1, 'tr')
plf.spineless(ax2, 'tr')
plt.suptitle(f'{exp_name}\n {clusterids[i]}')
plotpath = os.path.join(exp_dir, 'data_analysis', 'all_fff')
if not os.path.isdir(plotpath):
os.makedirs(plotpath, exist_ok=True)
plt.savefig(os.path.join(plotpath, clusterids[i]) + '.svg',
format='svg',
dpi=300)
plt.close()
print('Plotted full field flicker STAs together from all stimuli.')
