def _correlation(res):
res = filter.exclude(res, {'odor_valence': 'US'})
# for i, dff in enumerate(res['data']):
# s = res['DAQ_O_ON_F'][i]
# e = res['DAQ_W_ON_F'][i]
# amplitude = np.mean(dff[:,:, s:e], axis=2)
# corrcoefs = np.corrcoef(amplitude.T)
# mask = ~np.eye(corrcoefs.shape[0], dtype=bool)
# corrcoef = np.mean(corrcoefs[mask])
# res['consistency_corrcoef'].append(corrcoef)
for i, dff in enumerate(res['data']):
cell_mask = res['msig'][i]
s = res['DAQ_O_ON_F'][i]
e = res['DAQ_W_ON_F'][i]
dff = dff[:, :, s:e]
corrcoef = []
for dff_per_cell in dff:
corrcoefs = np.corrcoef(dff_per_cell)
diagmask = ~np.eye(corrcoefs.shape[0], dtype=bool)
nanmask = ~np.isnan(corrcoefs)
mask = np.logical_and(diagmask, nanmask)
corrcoef_per_cell = np.mean(corrcoefs[mask])
corrcoef.append(corrcoef_per_cell)
corrcoef = np.array(corrcoef)
mask = ~np.isnan(corrcoef, dtype=bool)
corrcoef_ = np.mean(corrcoef[mask])
res['consistency_corrcoef'].append(corrcoef_)
res['consistency_corrcoef'] = np.array(res['consistency_corrcoef'])
return res
def custom_get_res(start_time, end_time):
list_of_res = []
for i, condition in enumerate(conditions):
if any(s in condition.name for s in ['YFP', 'HALO', 'JAWS']):
data_path = os.path.join(Config.LOCAL_DATA_PATH,
Config.LOCAL_DATA_BEHAVIOR_FOLDER,
condition.name)
else:
data_path = os.path.join(Config.LOCAL_DATA_PATH,
Config.LOCAL_DATA_TIMEPOINT_FOLDER,
condition.name)
res = custom_analyze_behavior(data_path,
condition,
start_time=start_time,
end_time=end_time)
if condition.name == 'OFC_LONGTERM':
res = filter.exclude(res, {'mouse': 3})
if 'YFP' in condition.name:
res['condition'] = np.array(['YFP'] * len(res['mouse']))
elif 'JAWS' in condition.name:
res['condition'] = np.array(['JAWS'] * len(res['mouse']))
elif 'HALO' in condition.name:
res['condition'] = np.array(['HALO'] * len(res['mouse']))
else:
res['condition'] = np.array([condition.name] * len(res['mouse']))
list_of_res.append(res)
all_res = defaultdict(list)
for res, condition in zip(list_of_res, conditions):
reduce.chain_defaultdicts(all_res, res)
return all_res
def scalpel(res2, keys, mouse, sessions, valence='CS+'):
temp = filter.filter(res2, {'mouse': mouse, 'odor_valence': valence})
print(temp['mouse'].size)
assert temp['mouse'].size == 1
ix = np.isin(temp['session'][0], sessions)
ix = np.invert(ix)
for k in keys:
temp[k][0] = temp[k][0][ix]
_, inverse = np.unique(temp['session'][0], return_inverse=True)
temp['session'][0] = inverse
res2 = filter.exclude(res2, {'mouse': mouse, 'odor_valence': valence})
reduce.chain_defaultdicts(res2, temp)
return res2
def get_roc(res):
def _dprime(a, b):
u1, u2 = np.mean(a), np.mean(b)
s1, s2 = np.std(a), np.std(b)
return (u1 - u2) / np.sqrt(.5 * (np.square(s1) + np.square(s2)))
def _roc(a, b):
import sklearn.metrics
data = np.concatenate((a, b))
labels = np.concatenate(
(np.ones_like(a), np.zeros_like(b))).astype('bool')
roc = sklearn.metrics.roc_auc_score(labels, data)
return roc
def _rolling_window(a, window):
shape = a.shape[:-1] + (a.shape[-1] - window + 1, window)
strides = a.strides + (a.strides[-1], )
return np.lib.stride_tricks.as_strided(a, shape=shape, strides=strides)
key = 'lick'
print_key = 'roc'
x_key = 'roc_trial'
window = 10
res[print_key] = np.copy(res[key])
res[x_key] = np.copy(res['trial'])
res = filter.exclude(res, {'odor_valence': 'US'})
res_ = reduce.new_filter_reduce(res,
filter_keys=['mouse', 'odor_valence'],
reduce_key=key)
combinations, list_of_ixs = filter.retrieve_unique_entries(res_, ['mouse'])
for i, ixs in enumerate(list_of_ixs):
assert len(ixs) == 2
assert res_['odor_valence'][ixs[0]] == 'CS+'
assert res_['odor_valence'][ixs[1]] == 'CS-'
a = _rolling_window(res_[key][ixs[0]], window)
b = _rolling_window(res_[key][ixs[1]], window)
dprimes = np.array([_roc(x, y) for x, y in zip(a, b)])
res_[print_key][ixs[0]] = dprimes
res_[print_key][ixs[1]] = dprimes
res_[x_key][ixs[0]] = np.arange(len(dprimes))
res_[x_key][ixs[1]] = np.arange(len(dprimes))
return res_
def plot_summary_odor_pretraining(res,
start_days,
end_days,
arg_naive,
figure_path,
save,
excitatory=True):
ax_args_copy = ax_args.copy()
res = copy.copy(res)
list_of_days = list(zip(start_days, end_days))
mice = np.unique(res['mouse'])
start_end_day_res = filter.filter_days_per_mouse(
res, days_per_mouse=list_of_days)
get_responsive_cells(start_end_day_res)
if arg_naive:
day_start = filter.filter(start_end_day_res,
{'odor_standard': 'PT Naive'})
day_start['odor_standard'] = np.array(['PT CS+'] *
len(day_start['odor_standard']))
day_end = filter.filter_days_per_mouse(start_end_day_res,
days_per_mouse=end_days)
day_end = filter.filter(day_end, {'odor_standard': 'PT CS+'})
reduce.chain_defaultdicts(day_start, day_end)
start_end_day_res = day_start
else:
start_end_day_res = filter.exclude(start_end_day_res,
{'odor_standard': 'PT Naive'})
add_naive_learned(start_end_day_res, start_days, end_days, 'a', 'b')
filter.assign_composite(start_end_day_res,
loop_keys=['odor_standard', 'training_day'])
odor_list = ['PT CS+']
colors = ['Orange']
ax_args_copy = ax_args_copy.copy()
ax_args_copy.update({
'xlim': [-1, 10],
'ylim': [0, .4],
'yticks': [0, .1, .2, .3, .4]
})
for i, odor in enumerate(odor_list):
save_arg = False
reuse_arg = True
if i == 0:
reuse_arg = False
if save and i == len(odor_list) - 1:
save_arg = True
plot.plot_results(start_end_day_res,
select_dict={'odor_standard': odor},
x_key='odor_standard_training_day',
y_key='Fraction Responsive',
loop_keys='mouse',
colors=[colors[i]] * len(mice),
path=figure_path,
plot_args=line_args,
ax_args=ax_args_copy,
save=save_arg,
reuse=reuse_arg,
fig_size=(2.5, 1.5),
legend=False,
name_str='_E' if excitatory else '_I')
before_csm = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'a',
'odor_standard': 'PT CS+'
})
after_csm = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'b',
'odor_standard': 'PT CS+'
})
from scipy.stats import ranksums, wilcoxon, kruskal
print('Before PT CS+: {}'.format(np.mean(
before_csm['Fraction Responsive'])))
print('After PT CS+: {}'.format(np.mean(after_csm['Fraction Responsive'])))
from scipy.stats import sem
print('After PT CS+ STD: {}'.format(sem(after_csm['Fraction Responsive'])))
print('Wilcoxin:{}'.format(
wilcoxon(before_csm['Fraction Responsive'],
after_csm['Fraction Responsive'])))
def plot_summary_odor_and_water(res,
odor_start_days,
water_start_days,
end_days,
use_colors=True,
excitatory=True,
arg='odor_valence',
figure_path=None):
include_water = True
ax_args_copy = ax_args.copy()
res = copy.copy(res)
get_responsive_cells(res)
mice = np.unique(res['mouse'])
list_of_days = list(zip(odor_start_days, end_days))
start_end_day_res = filter.filter_days_per_mouse(
res, days_per_mouse=list_of_days)
start_end_day_res = filter.exclude(start_end_day_res,
{'odor_valence': 'US'})
add_naive_learned(start_end_day_res, odor_start_days, end_days, 'a', 'b')
if include_water:
list_of_days = list(zip(water_start_days, end_days))
start_end_day_res_water = filter.filter_days_per_mouse(
res, days_per_mouse=list_of_days)
start_end_day_res_water = filter.filter(start_end_day_res_water,
{'odor_valence': 'US'})
add_naive_learned(start_end_day_res_water, water_start_days, end_days,
'a', 'b')
reduce.chain_defaultdicts(start_end_day_res, start_end_day_res_water)
ax_args_copy = ax_args_copy.copy()
if arg == 'odor_valence':
start_end_day_res = reduce.new_filter_reduce(
start_end_day_res,
filter_keys=['training_day', 'mouse', 'odor_valence'],
reduce_key='Fraction Responsive')
odor_list = ['CS+', 'CS-']
ax_args_copy.update({
'xlim': [-1, 6],
'ylim': [0, .6],
'yticks': [0, .1, .2, .3, .4, .5]
})
colors = ['Green', 'Red']
elif arg == 'naive':
arg = 'odor_valence'
start_end_day_res = reduce.new_filter_reduce(
start_end_day_res,
filter_keys=['training_day', 'mouse', 'odor_valence'],
reduce_key='Fraction Responsive')
odor_list = ['CS+']
ax_args_copy.update({
'xlim': [-1, 4],
'ylim': [0, .6],
'yticks': [0, .1, .2, .3, .4, .5]
})
colors = ['GoldenRod']
else:
odor_list = ['CS+1', 'CS+2', 'CS-1', 'CS-2']
colors = ['Green', 'Green', 'Red', 'Red']
ax_args_copy.update({
'xlim': [-1, 10],
'ylim': [0, .6],
'yticks': [0, .1, .2, .3, .4, .5]
})
filter.assign_composite(start_end_day_res, loop_keys=[arg, 'training_day'])
if not use_colors:
colors = ['Black'] * 4
name_str = '_E' if excitatory else '_I'
for i, odor in enumerate(odor_list):
reuse_arg = True
if i == 0:
reuse_arg = False
plot.plot_results(start_end_day_res,
select_dict={arg: odor},
x_key=arg + '_training_day',
y_key='Fraction Responsive',
loop_keys='mouse',
colors=[colors[i]] * len(mice),
path=figure_path,
plot_args=line_args,
ax_args=ax_args_copy,
save=False,
reuse=reuse_arg,
fig_size=(2.5, 1.5),
legend=False,
name_str=','.join([str(x) for x in odor_start_days]))
plot.plot_results(start_end_day_res,
select_dict={'odor_standard': 'US'},
x_key='training_day',
y_key='Fraction Responsive',
loop_keys='mouse',
colors=['Turquoise'] * len(mice),
path=figure_path,
plot_args=line_args,
ax_args=ax_args_copy,
fig_size=(1.6, 1.5),
legend=False,
reuse=True,
save=True,
name_str=name_str)
before_odor = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'a',
'odor_valence': ['CS+', 'CS-']
})
after_odor = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'b',
'odor_valence': ['CS+', 'CS-']
})
before_csp = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'a',
'odor_valence': 'CS+'
})
after_csp = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'b',
'odor_valence': 'CS+'
})
before_csm = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'a',
'odor_valence': 'CS-'
})
after_csm = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'b',
'odor_valence': 'CS-'
})
before_water = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'a',
'odor_valence': 'US'
})
after_water = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'b',
'odor_valence': 'US'
})
try:
from scipy.stats import ranksums, wilcoxon, kruskal
print('Before Odor: {}'.format(
np.mean(before_odor['Fraction Responsive'])))
print('After Odor: {}'.format(
np.mean(after_odor['Fraction Responsive'])))
print('Wilcoxin:{}'.format(
wilcoxon(before_odor['Fraction Responsive'],
after_odor['Fraction Responsive'])))
print('Before CS+: {}'.format(
np.mean(before_csp['Fraction Responsive'])))
print('After CS+: {}'.format(np.mean(
after_csp['Fraction Responsive'])))
print('Wilcoxin:{}'.format(
wilcoxon(before_csp['Fraction Responsive'],
after_csp['Fraction Responsive'])))
print('Before CS-: {}'.format(
np.mean(before_csm['Fraction Responsive'])))
print('After CS-: {}'.format(np.mean(
after_csm['Fraction Responsive'])))
print('Wilcoxin:{}'.format(
wilcoxon(before_csm['Fraction Responsive'],
after_csm['Fraction Responsive'])))
print('Before US: {}'.format(
np.mean(before_water['Fraction Responsive'])))
print('After US: {}'.format(np.mean(
after_water['Fraction Responsive'])))
print('Wilcoxin:{}'.format(
wilcoxon(before_water['Fraction Responsive'],
after_water['Fraction Responsive'])))
except:
print('stats didnt work')
res = statistics.analyze.analyze_data(save_path,
condition_config,
m_threshold=0.04)
# naive_config = statistics.analyze.OFC_LONGTERM_Config()
# data_path_ = os.path.join(Config.LOCAL_DATA_PATH, Config.LOCAL_DATA_TIMEPOINT_FOLDER, naive_config.condition.name)
# save_path_ = os.path.join(Config.LOCAL_EXPERIMENT_PATH, 'COUNTING', naive_config.condition.name)
# res_naive = statistics.analyze.analyze_data(save_path_, condition_config, m_threshold=0.04)
# res_naive = filter.exclude(res_naive, {'mouse': 3})
# res_naive['mouse'] += 5
# temp_res_naive = behavior.behavior_analysis.analyze_behavior(data_path_, naive_config.condition)
# temp_res_naive = filter.filter(temp_res_naive, {'odor_valence': ['CS+']})
# temp_res_naive = filter.exclude(temp_res_naive, {'mouse': 3})
# temp_res_naive['mouse'] += 5
res = filter.exclude(res, {'day': 0})
# reduce.chain_defaultdicts(res, res_naive)
# reduce.chain_defaultdicts(temp_res, temp_res_naive)
# learned_days_combined = [3, 3, 2, 3, 3, 3, 2, 2]
# last_days_combined = [5, 5, 3, 4, 4, 8, 7, 5]
cory.main(res, temp_res, figure_path, excitatory=True, valence='CS+')
# cory.main(res, temp_res, figure_path, excitatory=False,valence='CS+')
# cory.main(res, temp_res, figure_path, excitatory=True,valence='CS-')
# cory.main(res, temp_res, figure_path, excitatory=False,valence='CS-')
# waveform.behavior_vs_neural_onset(res, temp_res, learned_day_per_mouse, last_day_per_mouse, figure_path,
# behavior_arg='onset')
# waveform.behavior_vs_neural_onset(res, temp_res, learned_days_combined, last_days_combined, figure_path, behavior_arg='com')
# waveform.behavior_vs_neural_onset(res, temp_res, learned_days_combined, last_days_combined, figure_path, behavior_arg='onset')
# waveform.behavior_vs_neural_onset(res, temp_res, learned_days_combined, last_days_combined, figure_path, behavior_arg='magnitude')
color_dict = {'Pretraining_CS+': 'C1', 'Discrimination_CS+':'green', 'Discrimination_CS-':'red'}
res = defaultdict(list)
for experiment in experiments:
for directory in directories:
halo_files = sorted(glob.glob(os.path.join(experiment.path, directory, constants.halo + '*')))
yfp_files = sorted(glob.glob(os.path.join(experiment.path, directory, constants.yfp + '*')))
res1 = analysis.parse(halo_files, experiment=experiment, condition=constants.halo, phase = directory,
add_raw=False)
res1['experiment'] = np.array([experiment.name] * len(res1['odor_valence']))
res2 = analysis.parse(yfp_files, experiment=experiment, condition=constants.yfp, phase = directory,
add_raw=False)
res2['experiment'] = np.array([experiment.name] * len(res2['odor_valence']))
if experiment.name == 'MPFC_DT':
res1 = filter.exclude(res1, {'mouse':['H01']})
res2 = filter.exclude(res2, {'mouse':['H01']})
if experiment.name == 'MPFC_PT':
res1 = filter.exclude(res1, {'mouse': ['Y01']})
res2 = filter.exclude(res2, {'mouse': ['Y01']})
# if experiment.name == 'OFC_DT': # the unusual mouse
# res1 = filter.exclude(res1, {'mouse': ['H03']})
# res2 = filter.exclude(res2, {'mouse': ['H03']})
keys = analysis.Indices().__dict__.keys()
if experiment.name == 'OFC_PT' and directory == constants.pretraining_directory:
mice = ['Y11','Y12','Y13']
session_list = [[2,3,4,5,6], [5,7,9,11],[4,5,6]]
for mouse, sessions in zip(mice, session_list):
res2 = scalpel(res2, keys, mouse, sessions)
def plot_power(res,
start_days,
end_days,
figure_path,
excitatory=True,
odor_valence=('CS+'),
naive=False,
colors_before={
'CS+': 'Green',
'CS-': 'Red'
},
colors_after={
'CS+': 'Green',
'CS-': 'Red'
},
ylim=[0, .1],
align=True,
pad=True):
res = copy.copy(res)
_power(res, excitatory)
if pad:
right_on = np.median(res['DAQ_O_ON_F'])
for i, odor_on in enumerate(res['DAQ_O_ON_F']):
if np.abs(odor_on - right_on) > 2:
diff = (right_on - odor_on).astype(int)
if diff > 0:
p = res['Power'][i]
newp = np.zeros_like(p)
newp[:diff] = p[0]
newp[diff:] = p[:-diff]
res['Power'][i] = newp
print('early odor time. mouse: {}, day: {}'.format(
res['mouse'][i], res['day'][i]))
else:
p = res['Power'][i]
newp = np.zeros_like(p)
newp[:diff] = p[-diff:]
newp[diff:] = p[-1]
res['Power'][i] = newp
print('late odor time. mouse: {}, day: {}'.format(
res['mouse'][i], res['day'][i]))
if align:
nF = [len(x) for x in res['Power']]
max_frame = np.max(nF)
for i, p in enumerate(res['Power']):
if len(p) < max_frame:
newp = np.zeros(max_frame)
newp[:len(p)] = p
newp[len(p):] = p[-1]
res['Power'][i] = newp
res['Time'][i] = np.arange(0, max_frame)
print('pad frames. mouse: {}, day: {}'.format(
res['mouse'][i], res['day'][i]))
list_of_days = list(zip(start_days, end_days))
start_end_day_res = filter.filter_days_per_mouse(
res, days_per_mouse=list_of_days)
add_naive_learned(start_end_day_res, start_days, end_days)
if naive:
start_end_day_res = filter.exclude(start_end_day_res, {
'odor_standard': 'PT CS+',
'training_day': 'Naive'
})
ix = start_end_day_res['odor_valence'] == 'PT Naive'
start_end_day_res['odor_valence'][ix] = 'PT CS+'
start_end_day_sum_res = reduce.new_filter_reduce(
start_end_day_res,
filter_keys=['training_day', 'odor_valence'],
reduce_key='Power')
ax_args_copy = trace_ax_args.copy()
if excitatory:
yticks = np.arange(0, .2, .05)
else:
yticks = -1 * np.arange(0, .2, .025)
ax_args_copy.update({
'xticks': [res['DAQ_O_ON_F'][-1], res['DAQ_W_ON_F'][-1]],
'xticklabels': ['ON', 'US'],
'ylim':
ylim,
'yticks':
yticks
})
colors_b = [colors_before[x] for x in odor_valence]
colors = [colors_after[x] for x in odor_valence]
strr = ','.join([str(x) for x in start_days]) + '_' + ','.join(
[str(x) for x in end_days])
if excitatory:
strr += '_E'
else:
strr += '_I'
plot.plot_results(start_end_day_sum_res,
select_dict={
'odor_valence': odor_valence,
'training_day': 'Naive'
},
x_key='Time',
y_key='Power',
loop_keys='odor_valence',
error_key='Power_sem',
path=figure_path,
plot_function=plt.fill_between,
plot_args=fill_args,
ax_args=ax_args_copy,
colors=colors_b,
fig_size=(2, 1.5),
rect=(.3, .2, .6, .6),
save=False)
plot.plot_results(start_end_day_sum_res,
select_dict={
'odor_valence': odor_valence,
'training_day': 'Naive'
},
x_key='Time',
y_key='Power',
loop_keys='odor_valence',
path=figure_path,
plot_args=trace_args,
ax_args=ax_args_copy,
colors=colors_b,
fig_size=(2, 1.5),
reuse=True,
save=False)
plot.plot_results(start_end_day_sum_res,
select_dict={
'odor_valence': odor_valence,
'training_day': 'Learned'
},
x_key='Time',
y_key='Power',
loop_keys='odor_valence',
error_key='Power_sem',
path=figure_path,
plot_function=plt.fill_between,
plot_args=fill_args,
ax_args=ax_args_copy,
colors=colors,
fig_size=(2, 1.5),
reuse=True,
save=False)
plot.plot_results(start_end_day_sum_res,
select_dict={
'odor_valence': odor_valence,
'training_day': 'Learned'
},
x_key='Time',
y_key='Power',
loop_keys='odor_valence',
path=figure_path,
plot_args=trace_args,
ax_args=ax_args_copy,
colors=colors,
fig_size=(2, 1.5),
reuse=True,
name_str=strr)
for i, x in enumerate(start_end_day_res['Power']):
on, off = [
start_end_day_res['DAQ_O_ON_F'][i],
start_end_day_res['DAQ_W_ON_F'][i]
]
y = np.max(x[on:off]) - np.min(x)
start_end_day_res['stat'].append(y)
start_end_day_res['stat'] = np.array(start_end_day_res['stat'])
for valence in odor_valence:
before_odor = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'Naive',
'odor_valence': valence
})
after_odor = filter.filter(start_end_day_res,
filter_dict={
'training_day': 'Learned',
'odor_valence': valence
})
try:
from scipy.stats import ranksums, wilcoxon, kruskal
print(before_odor['odor_valence'])
# print('Before: {}'.format(before_odor['stat']))
print('Before: {}'.format(np.mean(before_odor['stat'])))
# print('After: {}'.format(after_odor['stat']))
print('After: {}'.format(np.mean(after_odor['stat'])))
print('Wilcoxin:{}'.format(
wilcoxon(before_odor['stat'], after_odor['stat'])))
except:
print('stats didnt work')
return before_odor['stat'], after_odor['stat']
def _correlation(res, loop_keys, shuffle, odor_end=True, direction=0):
res = filter.exclude(res, {'odor_valence': 'US'})
for i, dff in enumerate(res['dff']):
s = res['DAQ_O_ON_F'][i]
e = res['DAQ_W_ON_F'][i]
if odor_end:
amplitude = np.max(dff[:, s:e], axis=1)
else:
amplitude = np.max(dff[:, s:], axis=1)
res['corr_amp'].append(amplitude)
res['corr_amp'] = np.array(res['corr_amp'])
combinations, list_of_ixs = filter.retrieve_unique_entries(
res, loop_keys=loop_keys)
loop_keys_ = loop_keys + ['odor_valence', 'odor_standard']
corrcoefs = defaultdict(list)
for ixs in list_of_ixs:
data = res['corr_amp'][ixs]
for i, data_1 in enumerate(data):
for j, data_2 in enumerate(data):
if shuffle:
n_iter = 10
corrcoef = 0
for k in range(n_iter):
corrcoef += np.corrcoef(
(np.random.permutation(data_1),
np.random.permutation(data_2)))[0, 1]
corrcoef /= (n_iter * 1.0)
else:
if i != j:
datas = res['data'][ixs[i]]
s = res['DAQ_O_ON_F'][ixs[i]]
e = res['DAQ_W_ON_F'][ixs[i]]
ds = []
for cell_data in datas:
config = psth.psth_helper.PSTHConfig()
d = psth.psth_helper.subtract_baseline(
cell_data, config.baseline_start,
s - config.baseline_end)
ds.append(d)
datas_i = np.array(ds)
datas = res['data'][ixs[j]]
s = res['DAQ_O_ON_F'][ixs[j]]
e = res['DAQ_W_ON_F'][ixs[j]]
ds = []
for cell_data in datas:
config = psth.psth_helper.PSTHConfig()
d = psth.psth_helper.subtract_baseline(
cell_data, config.baseline_start,
s - config.baseline_end)
ds.append(d)
datas_j = np.array(ds)
corrcoefs_ = []
for rep in np.arange(100):
s_ix_a = np.random.choice(datas_i.shape[1],
datas_i.shape[1] // 2,
replace=False)
s_ix_b = np.random.choice(datas_j.shape[1],
datas_j.shape[1] // 2,
replace=False)
dffa = np.mean(datas_i[:, s_ix_a, :], axis=1)
dffb = np.mean(datas_j[:, s_ix_b, :], axis=1)
if odor_end:
dffa = dffa[:, s:e]
dffb = dffb[:, s:e]
else:
dffa = dffa[:, s:]
dffb = dffb[:, s:]
if direction == 1:
dffa[dffa < 0] = 0
dffb[dffb < 0] = 0
amplitudea = np.max(dffa, axis=1)
amplitudeb = np.max(dffb, axis=1)
elif direction == -1:
dffa[dffa > 0] = 0
dffb[dffb > 0] = 0
amplitudea = np.min(dffa, axis=1)
amplitudeb = np.min(dffb, axis=1)
elif direction == 0:
amplitudea = np.max(dffa, axis=1)
amplitudeb = np.max(dffb, axis=1)
else:
raise ValueError('no direction given')
# if odor_end:
# amplitudea = np.max(dffa[:, s:e], axis=1)
# amplitudeb = np.max(dffb[:, s:e], axis=1)
# else:
# amplitudea = np.max(dffa[:, s:], axis=1)
# amplitudeb = np.max(dffb[:, s:], axis=1)
corrcoefs_.append(
np.corrcoef(amplitudea, amplitudeb)[0, 1])
corrcoef = np.mean(corrcoefs_)
# corrcoef = np.corrcoef((data_1, data_2))[0, 1]
else:
# corrcoef = np.corrcoef((data_1, data_2))[0, 1]
datas = res['data'][ixs[i]]
s = res['DAQ_O_ON_F'][ixs[i]]
e = res['DAQ_W_ON_F'][ixs[i]]
ds = []
for cell_data in datas:
config = psth.psth_helper.PSTHConfig()
d = psth.psth_helper.subtract_baseline(
cell_data, config.baseline_start,
s - config.baseline_end)
ds.append(d)
datas = np.array(ds)
corrcoefs_ = []
for rep in np.arange(100):
s_ix_a = np.random.choice(datas.shape[1],
datas.shape[1] // 2,
replace=False)
s_ix_b = [
x for x in np.arange(datas.shape[1])
if x not in s_ix_a
]
dffa = np.mean(datas[:, s_ix_a, :], axis=1)
dffb = np.mean(datas[:, s_ix_b, :], axis=1)
# if odor_end:
# amplitudea = np.max(dffa[:, s:e], axis=1)
# amplitudeb = np.max(dffb[:, s:e], axis=1)
# else:
# amplitudea = np.max(dffa[:, s:], axis=1)
# amplitudeb = np.max(dffb[:, s:], axis=1)
if direction == 1:
dffa[dffa < 0] = 0
dffb[dffb < 0] = 0
amplitudea = np.max(dffa, axis=1)
amplitudeb = np.max(dffb, axis=1)
elif direction == -1:
dffa[dffa > 0] = 0
dffb[dffb > 0] = 0
amplitudea = np.min(dffa, axis=1)
amplitudeb = np.min(dffb, axis=1)
elif direction == 0:
amplitudea = np.max(dffa, axis=1)
amplitudeb = np.max(dffb, axis=1)
else:
raise ValueError('no direction given')
corrcoefs_.append(
np.corrcoef(amplitudea, amplitudeb)[0, 1])
corrcoef = np.mean(corrcoefs_)
corrcoefs['corrcoef'].append(corrcoef)
corrcoefs['Odor_A'].append(i)
corrcoefs['Odor_B'].append(j)
for loop_key in loop_keys_:
corrcoefs[loop_key].append(res[loop_key][ixs[0]])
for key, value in corrcoefs.items():
corrcoefs[key] = np.array(value)
return corrcoefs
xticks = np.arange(0, im.shape[1]) + .5
yticks = np.arange(0, im.shape[0]) + .5
ax.set_xticks(xticks)
ax.set_yticks(yticks[::-1])
ax.set_xticklabels((xticks + .5).astype(int), fontsize=7)
ax.set_yticklabels((yticks + .5).astype(int), fontsize=7)
ax = fig.add_axes(rect_cb)
cb = plt.colorbar(cax=ax, ticks=np.arange(vmin, vmax + 0.01, 0.1))
cb.outline.set_linewidth(0.5)
cb.set_label('Correlation', fontsize=7, labelpad=2)
plt.tick_params(axis='both', which='major', labelsize=7)
plt.axis('tight')
plot._easy_save(os.path.join(save_path, 'matrix', mouse), 'across_correlation_matrix')
res = filter.exclude(res, {'mouse':'M241_ofc'})
list = ['PIR','OFC','OFC_LONGTERM','OFC_COMPOSITE','MPFC_COMPOSITE']
scatter_args = {'marker':'.', 's':8, 'alpha': .5}
error_args = {'fmt': '', 'capsize': 2, 'elinewidth': 1, 'markersize': 2, 'alpha': .5}
reduce_keys = ['within_day_crisp_average', 'across_day_mean_corrs_average']
xkey = 'experiment'
for reduce_key in reduce_keys:
res_reduce = reduce.new_filter_reduce(res, filter_keys=['experiment'], reduce_key= reduce_key)
for i, element in enumerate(list):
reuse = True if i > 0 else False
save = False if i != len(list)-1 else True
plot.plot_results(res, x_key=xkey, y_key= reduce_key,
select_dict={xkey:element},
plot_function=plt.scatter,
plot_args=scatter_args,
list_of_res = []
names = []
behavior_strings = ['YFP', 'HALO', 'JAWS']
for i, condition in enumerate(conditions):
if any(s in condition.name for s in behavior_strings):
data_path = os.path.join(Config.LOCAL_DATA_PATH,
Config.LOCAL_DATA_BEHAVIOR_FOLDER,
condition.name)
else:
data_path = os.path.join(Config.LOCAL_DATA_PATH,
Config.LOCAL_DATA_TIMEPOINT_FOLDER,
condition.name)
res = analyze_behavior(data_path, condition)
if condition.name == 'OFC_LONGTERM':
res = filter.exclude(res, {'mouse': 3})
if 'YFP' in condition.name:
res['condition'] = np.array(['YFP'] * len(res['mouse']))
elif 'JAWS' in condition.name:
res['condition'] = np.array(['JAWS'] * len(res['mouse']))
elif 'HALO' in condition.name:
res['condition'] = np.array(['HALO'] * len(res['mouse']))
else:
res['condition'] = np.array([condition.name] * len(res['mouse']))
list_of_res.append(res)
names.append(condition.name)
directory_name = ','.join(names)
all_res = defaultdict(list)
for res, condition in zip(list_of_res, conditions):
# try:
# ix_e = all_res[x_key] == 'YFP_PT CS+'
# ix_f = all_res[x_key] == 'INH_PT CS+'
# rspt = ranksums(all_res[reduce_key][ix_e], all_res[reduce_key][ix_f])
# print(all_res[reduce_key][ix_e])
# print(all_res[reduce_key][ix_f])
# print(rspt)
# except:
# print('no pt')
if 'cdf' in experiments:
valences = np.unique(all_res['odor_valence'])
for valence in valences:
all_res_ = filter.filter(all_res, {'odor_valence': valence})
ctrl = filter.filter(all_res_, {'condition': 'YFP'})
experimental = filter.exclude(all_res_, {'condition': 'YFP'})
ctrl_licks = ctrl['lick']
experimental_licks = experimental['lick']
# #shorten
ctrl_min = np.min([len(x) for x in ctrl_licks])
channel_min = np.min([len(x) for x in experimental_licks])
both_min = np.min([ctrl_min, channel_min])
_shorten = lambda array, length: [x[:length] for x in array]
ctrl_licks = _shorten(ctrl_licks, both_min)
experimental_licks = _shorten(experimental_licks, both_min)
#concatenate
ctrl_licks_cat = np.concatenate(ctrl_licks)
experimental_licks_cat = np.concatenate(experimental_licks_cat)
