def summary_fig(contrasts, CURVES, Ntot):
fig, AX = ge.figure(axes=(4, 1), figsize=(1., 1.))
AX[0].axis('off')
if len(CURVES) > 1:
ge.plot(contrasts,
np.mean(np.array(CURVES), axis=0),
sy=np.std(np.array(CURVES), axis=0),
ax=AX[1])
else:
AX[1].axis('off')
ge.set_plot(AX[1], xlabel='contrast', ylabel='$\delta$ dF/F')
AX[2].axis('off')
ge.annotate(AX[2],
'n=%i/%i resp. cells' % (len(CURVES), Ntot), (0.5, .0),
ha='center',
va='top')
frac_resp = len(CURVES) / Ntot
data = np.array([100 * frac_resp, 100 * (1 - frac_resp)])
ge.pie(data,
COLORS=[plt.cm.tab10(2), plt.cm.tab10(3)],
pie_labels=[' %.1f%%' % (100 * d / data.sum()) for d in data],
ext_labels=['', ''],
ax=AX[3])
return fig
def plot_row_column_of_quantity(self):
single_cond = self.build_single_conditions()
COL_CONDS = self.build_column_conditions()
ROW_CONDS = self.build_row_conditions()
COLOR_CONDS = self.build_color_conditions()
if (len(COLOR_CONDS) > 1) and (self.color.text() != ''):
COLORS = [
getattr(ge, self.color.text())((c % 10) / 10.)
for c in np.arange(len(COLOR_CONDS))
]
elif (len(COLOR_CONDS) > 1):
COLORS = [
ge.tab10((c % 10) / 10.) for c in np.arange(len(COLOR_CONDS))
]
elif self.color.text() != '':
COLORS = [getattr(ge, self.color.text())]
else:
COLORS = ['k']
if self.fig_presets.currentText() == 'raw-traces-preset':
fig, AX = ge.figure(axes=(len(COL_CONDS), len(ROW_CONDS)),
reshape_axes=False,
top=0.4,
bottom=0.4,
left=0.7,
right=0.7,
wspace=0.5,
hspace=0.5)
else:
fig, AX = ge.figure(axes=(len(COL_CONDS), len(ROW_CONDS)),
reshape_axes=False)
self.ylim = [np.inf, -np.inf]
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
for icolor, color_cond in enumerate(COLOR_CONDS):
cond = np.array(
single_cond & col_cond & row_cond
& color_cond)[:self.EPISODES['resp'].shape[0]]
if self.EPISODES['resp'][cond, :].shape[0] > 0:
my = self.EPISODES['resp'][cond, :].mean(axis=0)
if self.withSTDbox.isChecked():
sy = self.EPISODES['resp'][cond, :].std(axis=0)
ge.plot(self.EPISODES['t'],
my,
sy=sy,
ax=AX[irow][icol],
color=COLORS[icolor],
lw=1)
self.ylim = [
min([self.ylim[0],
np.min(my - sy)]),
max([self.ylim[1],
np.max(my + sy)])
]
else:
AX[irow][icol].plot(self.EPISODES['t'],
my,
color=COLORS[icolor],
lw=1)
self.ylim = [
min([self.ylim[0], np.min(my)]),
max([self.ylim[1], np.max(my)])
]
if self.screen.isChecked() and not (self.parent.visual_stim
is not None):
print('initializing stim [...]')
self.parent.load_VisualStim()
if self.screen.isChecked():
inset = ge.inset(AX[irow][icol], [.8, .9, .3, .25])
self.parent.visual_stim.show_frame(\
self.EPISODES['index_from_start'][cond][0],
ax=inset, parent=self.parent, enhance=True, label=None)
if self.withStatTest.isChecked():
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
for icolor, color_cond in enumerate(COLOR_CONDS):
cond = np.array(
single_cond & col_cond & row_cond
& color_cond)[:self.EPISODES['resp'].shape[0]]
test = stat_test_for_evoked_responses(
self.EPISODES,
cond,
interval_pre=[self.t0pre, self.t1pre],
interval_post=[self.t0post, self.t1post],
test='wilcoxon')
AX[irow][icol].plot([self.t0pre, self.t1pre],
self.ylim[0] * np.ones(2),
'k-',
lw=2)
AX[irow][icol].plot([self.t0post, self.t1post],
self.ylim[0] * np.ones(2),
'k-',
lw=2)
ps, size = pval_to_star(test)
AX[irow][icol].annotate(
ps,
((self.t1pre + self.t0post) / 2., self.ylim[0]),
va='top',
ha='center',
size=size,
xycoords='data')
if (self.ymin.text() != '') and (self.ymax.text() != ''):
self.ylim = [float(self.ymin.text()), float(self.ymax.text())]
if (self.xmin.text() != '') and (self.xmax.text() != ''):
self.xlim = [float(self.xmin.text()), float(self.xmax.text())]
else:
self.xlim = [self.EPISODES['t'][0], self.EPISODES['t'][-1]]
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
ge.set_plot(AX[irow][icol],
spines=(['left', 'bottom']
if self.axis.isChecked() else []),
ylim=self.ylim,
xlim=self.xlim,
xlabel=(self.xbarlabel.text()
if self.axis.isChecked() else ''),
ylabel=(self.ybarlabel.text()
if self.axis.isChecked() else ''))
if self.stim.isChecked():
AX[irow][icol].fill_between(
[0, np.mean(self.EPISODES['time_duration'])],
self.ylim[0] * np.ones(2),
self.ylim[1] * np.ones(2),
color='grey',
alpha=.2,
lw=0)
if not self.axis.isChecked():
ge.draw_bar_scales(AX[0][0],
Xbar=(0. if self.xbar.text() == '' else float(
self.xbar.text())),
Xbar_label=self.xbarlabel.text(),
Ybar=(0. if self.ybar.text() == '' else float(
self.ybar.text())),
Ybar_label=self.ybarlabel.text(),
Xbar_fraction=0.1,
Xbar_label_format='%.1f',
Ybar_fraction=0.2,
Ybar_label_format='%.1f',
loc='top-left')
if self.label.text() != '':
ge.annotate(fig, ' '+self.label.text()+\
(1+int(self.nlabel.text()))*'\n', (0,0), color=COLORS[0],
ha='left', va='bottom')
if self.annot.isChecked():
S = ''
if hasattr(self, 'roiPick'):
S += 'roi #%s' % self.roiPick.text()
for i, key in enumerate(self.varied_parameters.keys()):
if 'single-value' in getattr(self,
'%s_plot' % key).currentText():
S += ', %s=%.2f' % (key, getattr(
self, '%s_values' % key).currentText())
ge.annotate(fig, S, (0, 0), color='k', ha='left', va='bottom')
return fig, AX
def plot_row_column_of_quantity(self):
self.Pcond = self.data.get_protocol_cond(self.pbox.currentIndex() - 1)
single_cond = self.build_single_conditions()
COL_CONDS = self.build_column_conditions()
ROW_CONDS = self.build_row_conditions()
COLOR_CONDS = self.build_color_conditions()
if (len(COLOR_CONDS) > 1) and (self.color.text() != ''):
COLORS = [
getattr(ge, self.color.text())((c % 10) / 10.)
for c in np.arange(len(COLOR_CONDS))
]
elif (len(COLOR_CONDS) > 1):
COLORS = [
ge.tab10((c % 10) / 10.) for c in np.arange(len(COLOR_CONDS))
]
elif self.color.text() != '':
COLORS = [getattr(ge, self.color.text())]
else:
COLORS = ['k']
fig, AX = ge.figure(
axes=(len(COL_CONDS), len(ROW_CONDS)),
**dv_tools.FIGURE_PRESETS[self.fig_presets.currentText()])
self.ylim = [np.inf, -np.inf]
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
for icolor, color_cond in enumerate(COLOR_CONDS):
cond = np.array(single_cond & col_cond & row_cond
& color_cond)[:self.EPISODES.resp.shape[0]]
if self.EPISODES.resp[cond, :].shape[0] > 0:
my = self.EPISODES.resp[cond, :].mean(axis=0)
if self.withSTDbox.isChecked():
sy = self.EPISODES.resp[cond, :].std(axis=0)
ge.plot(self.EPISODES.t,
my,
sy=sy,
ax=AX[irow][icol],
color=COLORS[icolor],
lw=1)
self.ylim = [
min([self.ylim[0],
np.min(my - sy)]),
max([self.ylim[1],
np.max(my + sy)])
]
else:
AX[irow][icol].plot(self.EPISODES.t,
my,
color=COLORS[icolor],
lw=1)
self.ylim = [
min([self.ylim[0], np.min(my)]),
max([self.ylim[1], np.max(my)])
]
if self.annot.isChecked():
# column label
if (len(COL_CONDS) > 1) and (irow == 0) and (icolor
== 0):
s = ''
for i, key in enumerate(
self.varied_parameters.keys()):
if 'column' in getattr(
self,
'%s_plot' % key).currentText():
s += format_key_value(
key,
getattr(self.EPISODES,
key)[cond][0]
) + 4 * ' ' # should have a unique value
ge.annotate(AX[irow][icol],
s, (1, 1),
ha='right',
va='bottom')
# row label
if (len(ROW_CONDS) > 1) and (icol == 0) and (icolor
== 0):
s = ''
for i, key in enumerate(
self.varied_parameters.keys()):
if 'row' in getattr(self, '%s_plot' %
key).currentText():
s += format_key_value(
key,
getattr(self.EPISODES,
key)[cond][0]
) + 4 * ' ' # should have a unique value
ge.annotate(AX[irow][icol],
s, (0, 0),
ha='right',
va='bottom',
rotation=90)
# n per cond
ge.annotate(AX[irow][icol],
' n=%i' % np.sum(cond) + '\n' * icolor,
(.99, 0),
color=COLORS[icolor],
size='xx-small',
ha='left',
va='bottom')
if self.screen.isChecked() and not (self.data.visual_stim
is not None):
print('initializing stim [...]')
self.data.init_visual_stim()
if self.screen.isChecked():
inset = ge.inset(AX[irow][icol], [.8, .9, .3, .25])
self.data.visual_stim.show_frame(\
self.EPISODES.index_from_start[cond][0],
ax=inset, enhance=True, label=None)
if self.withStatTest.isChecked():
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
for icolor, color_cond in enumerate(COLOR_CONDS):
cond = np.array(
single_cond & col_cond & row_cond
& color_cond)[:self.EPISODES.resp.shape[0]]
results = self.EPISODES.stat_test_for_evoked_responses(
episode_cond=cond,
interval_pre=[self.t0pre, self.t1pre],
interval_post=[self.t0post, self.t1post],
test='wilcoxon')
ps, size = results.pval_annot()
AX[irow][icol].annotate(
ps,
((self.t1pre + self.t0post) / 2., self.ylim[0]),
va='top',
ha='center',
size=size,
xycoords='data')
AX[irow][icol].plot([self.t0pre, self.t1pre],
self.ylim[0] * np.ones(2),
'k-',
lw=2)
AX[irow][icol].plot([self.t0post, self.t1post],
self.ylim[0] * np.ones(2),
'k-',
lw=2)
# color label
if self.annot.isChecked() and (len(COLOR_CONDS) > 1):
for icolor, color_cond in enumerate(COLOR_CONDS):
cond = np.array(single_cond
& color_cond)[:self.EPISODES.resp.shape[0]]
for i, key in enumerate(self.varied_parameters.keys()):
if 'color' in getattr(self, '%s_plot' % key).currentText():
s = format_key_value(
key,
getattr(self.EPISODES, key)[cond][0])
ge.annotate(fig,
s,
(1. - icolor / (len(COLOR_CONDS) + 2), 0),
color=COLORS[icolor],
ha='right',
va='bottom')
if (self.ymin.text() != '') and (self.ymax.text() != ''):
self.ylim = [float(self.ymin.text()), float(self.ymax.text())]
if (self.xmin.text() != '') and (self.xmax.text() != ''):
self.xlim = [float(self.xmin.text()), float(self.xmax.text())]
else:
self.xlim = [self.EPISODES.t[0], self.EPISODES.t[-1]]
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
ge.set_plot(AX[irow][icol],
spines=(['left', 'bottom']
if self.axis.isChecked() else []),
ylim=self.ylim,
xlim=self.xlim,
xlabel=(self.xbarlabel.text()
if self.axis.isChecked() else ''),
ylabel=(self.ybarlabel.text()
if self.axis.isChecked() else ''))
if self.stim.isChecked():
AX[irow][icol].fill_between(
[0, np.mean(self.EPISODES.time_duration)],
self.ylim[0] * np.ones(2),
self.ylim[1] * np.ones(2),
color='grey',
alpha=.2,
lw=0)
if not self.axis.isChecked():
ge.draw_bar_scales(AX[0][0],
Xbar=(0. if self.xbar.text() == '' else float(
self.xbar.text())),
Xbar_label=self.xbarlabel.text(),
Ybar=(0. if self.ybar.text() == '' else float(
self.ybar.text())),
Ybar_label=self.ybarlabel.text() + ' ',
Xbar_fraction=0.1,
Xbar_label_format='%.1f',
Ybar_fraction=0.2,
Ybar_label_format='%.1f',
loc='top-left')
if self.label.text() != '':
ge.annotate(fig, ' '+self.label.text()+\
(1+int(self.nlabel.text()))*'\n', (0,0), color=COLORS[0],
ha='left', va='bottom')
if self.annot.isChecked():
S = ''
if hasattr(self, 'roiPick'):
S += 'roi #%s, ' % self.roiPick.text()
for i, key in enumerate(self.varied_parameters.keys()):
if 'single-value' in getattr(self,
'%s_plot' % key).currentText():
S += '%s=%s, ' % (key, getattr(
self, '%s_values' % key).currentText())
ge.annotate(fig, S, (0, 0), color='k', ha='left', va='bottom')
if self.annot.isChecked():
ge.annotate(
fig,
"%s, %s, %s, %s" %
(self.data.metadata['subject_ID'],
self.data.protocols[self.pbox.currentIndex() - 1][:20],
self.data.metadata['filename'].split('\\')[-2],
self.data.metadata['filename'].split('\\')[-1]), (0, 1),
color='k',
ha='left',
va='top',
size='x-small')
return fig, AX
def ROI_analysis(FullData,
roiIndex=0,
iprotocol=0,
verbose=False,
response_significance_threshold=0.05,
radius_threshold_for_center=20.,
with_responsive_angles=False,
stat_test_props=dict(interval_pre=[-1.5, 0],
interval_post=[0.5, 2.],
test='ttest',
positive=True),
Npanels=4):
"""
direction selectivity ROI analysis
"""
EPISODES = EpisodeResponse(
FullData,
protocol_id=iprotocol,
quantity='CaImaging',
subquantity='dF/F',
prestim_duration=-stat_test_props['interval_pre'][0],
roiIndex=roiIndex)
fig, AX = FullData.plot_trial_average(
EPISODES=EPISODES,
protocol_id=iprotocol,
quantity='CaImaging',
subquantity='dF/F',
roiIndex=roiIndex,
column_key='contrast',
row_key='angle',
ybar=1.,
ybarlabel='1dF/F',
xbar=1.,
xbarlabel='1s',
fig_preset='raw-traces-preset+right-space',
with_annotation=True,
with_std=True,
with_stat_test=True,
stat_test_props=stat_test_props,
verbose=verbose)
AXI, ylims, CURVES = [], [10, -10], []
max_response_curve, imax_response_curve = np.zeros(
len(EPISODES.varied_parameters['contrast']) + 1), -1
for ia, angle in enumerate(EPISODES.varied_parameters['angle']):
resp, contrasts, significants = [0], [0], [False]
for ic, contrast in enumerate(EPISODES.varied_parameters['contrast']):
# stat test "pre" vs "post"
stats = EPISODES.stat_test_for_evoked_responses(
episode_cond=EPISODES.find_episode_cond(['angle', 'contrast'],
[ia, ic]),
**stat_test_props)
resp.append(np.mean(stats.y - stats.x)) # "post"-"pre"
contrasts.append(contrast)
significants.append(
stats.significant(threshold=response_significance_threshold))
AXI.append(AX[ia][-1].inset_axes([1.8, .2, .7, .6]))
ge.plot(contrasts, resp, ax=AXI[-1], no_set=True, ms=3, m='o')
ylims = [
np.min([np.min(resp), ylims[0]]),
np.max([np.max(resp), ylims[1]])
]
if (np.sum(significants) >
0) and np.max(resp) > np.max(max_response_curve):
imax_response_curve = ia
max_response_curve = np.array(resp)
for ia, axi in enumerate(AXI):
ge.set_plot(axi,
xlabel='contrast',
ylabel='$\delta$ dF/F',
ylim=[
ylims[0] - .05 * (ylims[1] - ylims[0]),
ylims[1] + .05 * (ylims[1] - ylims[0])
])
if ia == imax_response_curve:
axi.fill_between(contrasts,
ylims[0] * np.ones(len(contrasts)),
ylims[1] * np.ones(len(contrasts)),
color='k',
alpha=0.1)
return fig, contrasts, max_response_curve
def DS_ROI_analysis(FullData,
roiIndex=0,
iprotocol=0,
verbose=False,
response_significance_threshold=0.01,
with_responsive_angles=False,
fig=None,
AX=None,
CaImaging_options=dict(quantity='CaImaging',
subquantity='dF/F'),
stat_test_props=dict(interval_pre=[-2, 0],
interval_post=[1, 3],
test='wilcoxon'),
inset_coords=(0.92, 0.4, 0.07, 0.4)):
"""
direction selectivity ROI analysis
"""
EPISODES = EpisodeResponse(FullData,
protocol_id=iprotocol,
roiIndex=roiIndex,
verbose=verbose,
**CaImaging_options)
fig, AX = FullData.plot_trial_average(
EPISODES=EPISODES,
protocol_id=iprotocol,
roiIndex=roiIndex,
column_key='angle',
ybar=1.,
ybarlabel='1dF/F',
xbar=1.,
xbarlabel='1s',
fig=fig,
AX=AX,
no_set=False,
fig_preset='raw-traces-preset+right-space',
with_annotation=True,
with_stat_test=True,
stat_test_props=stat_test_props,
verbose=verbose,
**CaImaging_options)
ax = ge.inset(fig, inset_coords)
angles, y, sy, responsive_angles = [], [], [], []
responsive = False
for i, angle in enumerate(EPISODES.varied_parameters['angle']):
means_pre = EPISODES.compute_stats_over_repeated_trials(
'angle',
i,
interval_cond=EPISODES.compute_interval_cond(
stat_test_props['interval_pre']),
quantity='mean')
means_post = EPISODES.compute_stats_over_repeated_trials(
'angle',
i,
interval_cond=EPISODES.compute_interval_cond(
stat_test_props['interval_post']),
quantity='mean')
stats = EPISODES.stat_test_for_evoked_responses(
episode_cond=EPISODES.find_episode_cond('angle', i),
**stat_test_props)
angles.append(angle)
y.append(np.mean(means_post))
sy.append(np.std(means_post))
if stats.significant(response_significance_threshold):
responsive = True
responsive_angles.append(angle)
ge.plot(angles,
np.array(y),
sy=np.array(sy),
ax=ax,
axes_args=dict(ylabel='<post dF/F> ',
xlabel='angle ($^{o}$)',
xticks=np.array(angles)[::int(len(angles) / 4)],
size='small'),
m='o',
ms=2,
lw=1)
SI = orientation_selectivity_index(angles, y)
ge.annotate(ax,
'SI=%.2f\n ' % SI, (1, 1),
ha='right',
weight='bold',
fontsize=8,
color=('k' if responsive else 'lightgray'))
ge.annotate(ax, ('responsive' if responsive else 'unresponsive'), (0., 1),
ha='left',
weight='bold',
fontsize=8,
color=(plt.cm.tab10(2) if responsive else plt.cm.tab10(3)))
if with_responsive_angles:
return fig, SI, responsive, responsive_angles
else:
return fig, SI, responsive
def OS_ROI_analysis(FullData,
roiIndex=0,
iprotocol=0,
subprotocol_id=0,
verbose=False,
response_significance_threshold=0.01,
with_responsive_angles=False,
stat_test_props=dict(interval_pre=[-2, 0],
interval_post=[1, 3],
test='wilcoxon',
positive=True)):
"""
orientation selectivity ROI analysis
"""
EPISODES = EpisodeResponse(FullData,
protocol_id=iprotocol,
quantity='CaImaging',
subquantity='dF/F',
roiIndex=roiIndex)
fig, AX = FullData.plot_trial_average(
EPISODES=EPISODES,
quantity='CaImaging',
subquantity='dF/F',
roiIndex=roiIndex,
column_key='angle',
ybar=1.,
ybarlabel='1dF/F',
xbar=1.,
xbarlabel='1s',
fig_preset='raw-traces-preset+right-space',
with_annotation=True,
with_stat_test=True,
stat_test_props=stat_test_props,
verbose=verbose)
ax = ge.inset(fig, (0.88, 0.4, 0.1, 0.4))
angles, y, sy, responsive_angles = [], [], [], []
responsive = False
for i, angle in enumerate(EPISODES.varied_parameters['angle']):
stats = EPISODES.stat_test_for_evoked_responses(
episode_cond=EPISODES.find_episode_cond('angle', i),
**stat_test_props)
angles.append(angle)
y.append(np.mean(stats.y)) # means "post"
sy.append(np.std(stats.y)) # std "post"
if stats.significant(threshold=response_significance_threshold):
responsive = True
responsive_angles.append(angle)
ge.plot(angles,
np.array(y),
sy=np.array(sy),
ax=ax,
axes_args=dict(ylabel='<post dF/F> ',
xlabel='angle ($^{o}$)',
xticks=angles,
size='small'),
m='o',
ms=2,
lw=1)
SI = orientation_selectivity_index(angles, y)
ge.annotate(fig,
'SI=%.2f ' % SI, (1, 0.97),
va='top',
ha='right',
xycoords='figure fraction',
weight='bold',
fontsize=8,
color=('k' if responsive else 'lightgray'))
ge.annotate(fig, ('responsive' if responsive else 'unresponsive'),
(0.78, 0.98),
ha='left',
va='top',
xycoords='figure fraction',
weight='bold',
fontsize=8,
color=(plt.cm.tab10(2) if responsive else plt.cm.tab10(3)))
if with_responsive_angles:
return fig, SI, responsive, responsive_angles
else:
return fig, SI, responsive
def tuning_modulation_fig(curves, full_resp=None):
# running vs still --- raw evoked response
fig, ax = ge.figure(figsize=(1.5, 1.5), right=6)
ge.plot(curves['angles'],
curves['all'],
label='all',
color='grey',
ax=ax,
no_set=True,
lw=2,
alpha=.5)
ge.plot(curves['angles'],
curves['running_mean'],
color=ge.orange,
ms=4,
m='o',
ax=ax,
lw=2,
label='running',
no_set=True)
ge.plot(curves['angles'],
curves['still_mean'],
color=ge.blue,
ms=4,
m='o',
ax=ax,
lw=2,
label='still',
no_set=True)
ge.legend(ax, ncol=3, loc=(.3, 1.))
ge.set_plot(ax,
xlabel='angle ($^{o}$) w.r.t. pref. orient.',
ylabel='evoked resp, ($\delta$ dF/F) ',
xticks=[0, 90, 180, 270])
if (full_resp is not None) and ('speed_level'
in full_resp) and ('pupil_level'
in full_resp):
inset = ge.inset(fig, [.8, .5, .16, .28])
ge.scatter(full_resp['pupil_level'][full_resp['running_cond']],
full_resp['speed_level'][full_resp['running_cond']],
ax=inset,
no_set=True,
color=ge.orange)
ge.scatter(full_resp['pupil_level'][~full_resp['running_cond']],
full_resp['speed_level'][~full_resp['running_cond']],
ax=inset,
no_set=True,
color=ge.blue)
ge.annotate(ax,
'n=%i cells\n' % full_resp['Ncells'], (0., 1.),
ha='center')
ge.set_plot(inset,
xlabel='pupil size (mm)',
ylabel='run. speed (cm/s) ',
title='episodes (n=%i) ' % full_resp['Neps'])
ge.annotate(inset,
'n=%i' %
(np.sum(full_resp['running_cond']) / full_resp['Ncells']),
(0., 1.),
va='top',
color=ge.orange)
ge.annotate(inset,
'\nn=%i' %
(np.sum(~full_resp['running_cond']) / full_resp['Ncells']),
(0., 1.),
va='top',
color=ge.blue)
if len(curves['constricted_mean']) > 0:
# constricted vs dilated --- raw evoked response
fig2, ax = ge.figure(figsize=(1.5, 1.5), right=6)
ge.plot(curves['angles'],
curves['all'],
label='all',
color='grey',
ax=ax,
no_set=True,
lw=2,
alpha=.5)
ge.plot(curves['angles'],
curves['constricted_mean'],
color=ge.green,
ms=4,
m='o',
ax=ax,
lw=2,
label='constricted',
no_set=True)
ge.plot(curves['angles'],
curves['dilated_mean'],
color=ge.purple,
ms=4,
m='o',
ax=ax,
lw=2,
label='dilated',
no_set=True)
ge.legend(ax, ncol=3, loc=(.1, 1.))
ge.set_plot(ax,
xlabel='angle ($^{o}$) w.r.t. pref. orient.',
ylabel='evoked resp, ($\delta$ dF/F) ',
xticks=[0, 90, 180, 270])
if (full_resp is not None) and ('speed_level'
in full_resp) and ('pupil_level'
in full_resp):
inset2 = ge.inset(fig2, [.8, .5, .16, .28])
ge.scatter(full_resp['pupil_level'][full_resp['dilated_cond']],
full_resp['speed_level'][full_resp['dilated_cond']],
ax=inset2,
no_set=True,
color=ge.purple)
ge.scatter(full_resp['pupil_level'][full_resp['constricted_cond']],
full_resp['speed_level'][full_resp['constricted_cond']],
ax=inset2,
no_set=True,
color=ge.green)
ge.annotate(ax,
'n=%i cells\n' % len(np.unique(full_resp['roi'])),
(0., 1.),
ha='right')
ge.set_plot(inset2,
xlabel='pupil size (mm)',
ylabel='run. speed (cm/s) ',
ylim=inset.get_ylim(),
title='episodes (n=%i) ' % full_resp['Neps'])
ge.annotate(
inset2,
'n=%i' %
(np.sum(full_resp['constricted_cond']) / full_resp['Ncells']),
(0., 1.),
va='top',
color=ge.green)
ge.annotate(
inset2,
'\nn=%i' %
(np.sum(full_resp['dilated_cond']) / full_resp['Ncells']),
(0., 1.),
va='top',
color=ge.purple)
else:
fig2 = None
return fig, fig2
def population_tuning_fig(full_resp):
Ncells = len(np.unique(full_resp['roi']))
Neps = len(full_resp['roi']) / Ncells
angles = np.unique(full_resp['angle_from_pref'])
fig, AX = ge.figure(axes=(3, 1), figsize=(1.5, 1.5))
for ax in AX:
ge.annotate(ax,
'n=%i resp. cells (%.0f%% of rois)' %
(Ncells, 100. * Ncells / full_resp['Nroi_tot']), (1, 1),
va='top',
ha='right')
ge.plot(angles,
np.mean(full_resp['per_cell_post'], axis=0),
sy=np.std(full_resp['per_cell_post'], axis=0),
color='grey',
ms=2,
m='o',
ax=AX[0],
no_set=True,
lw=1)
ge.set_plot(AX[0],
xlabel='angle ($^{o}$) w.r.t. pref. orient.',
ylabel='post level (dF/F)',
xticks=[0, 90, 180, 270])
ge.plot(angles,
np.mean(full_resp['per_cell'], axis=0),
sy=np.std(full_resp['per_cell'], axis=0),
color='grey',
ms=2,
m='o',
ax=AX[1],
no_set=True,
lw=1)
ge.set_plot(AX[1],
xlabel='angle ($^{o}$) w.r.t. pref. orient.',
ylabel='evoked resp. ($\delta$ dF/F)',
xticks=[0, 90, 180, 270])
ge.plot(angles,
np.mean(full_resp['per_cell'].T /
np.max(full_resp['per_cell'], axis=1).T,
axis=1),
sy=np.std(full_resp['per_cell'].T /
np.max(full_resp['per_cell'], axis=1).T,
axis=1),
color='grey',
ms=2,
m='o',
ax=AX[2],
no_set=True,
lw=1)
ge.set_plot(AX[2],
xlabel='angle ($^{o}$) w.r.t. pref. orient.',
ylabel='norm. resp ($\delta$ dF/F)',
yticks=[0, 0.5, 1],
xticks=[0, 90, 180, 270])
return fig
def plot_trial_average(
self,
# episodes props
protocol_id=0,
quantity='Photodiode-Signal',
subquantity='dF/F',
roiIndex=0,
dt_sampling=1, # ms
interpolation='linear',
baseline_substraction=False,
prestim_duration=None,
condition=None,
COL_CONDS=None,
column_keys=[],
column_key='',
ROW_CONDS=None,
row_keys=[],
row_key='',
COLOR_CONDS=None,
color_keys=[],
color_key='',
fig_preset='',
xbar=0.,
xbarlabel='',
ybar=0.,
ybarlabel='',
with_std=True,
with_screen_inset=False,
with_stim=True,
with_axis=False,
with_stat_test=False,
stat_test_props={},
color='k',
label='',
ylim=None,
xlim=None,
fig=None,
AX=None,
verbose=False):
# ----- building episodes ------
self.roiIndices = [roiIndex]
self.CaImaging_key = subquantity
self.EPISODES = build_episodes(
self,
protocol_id=protocol_id,
quantity=quantity,
prestim_duration=prestim_duration,
dt_sampling=dt_sampling,
baseline_substraction=baseline_substraction,
verbose=verbose) # this sets "self.Pcond"
if with_screen_inset and (self.visual_stim is None):
print('initializing stim [...]')
self.init_visual_stim()
if condition is None:
condition = np.ones(np.sum(self.Pcond), dtype=bool)
elif len(condition) == len(self.Pcond):
condition = condition[self.Pcond]
# ----- building episodes ------
if column_key != '':
COL_CONDS = self.build_conditions([
np.sort(
np.unique(
self.nwbfile.stimulus[column_key].data[self.Pcond]))
], [column_key])
elif column_keys != '':
COL_CONDS = self.build_conditions([
np.sort(np.unique(self.nwbfile.stimulus[key].data[self.Pcond]))
for key in column_keys
], column_keys)
elif (COL_CONDS is None):
COL_CONDS = [np.ones(np.sum(self.Pcond), dtype=bool)]
if row_key != '':
ROW_CONDS = self.build_conditions([
np.sort(
np.unique(self.nwbfile.stimulus[row_key].data[self.Pcond]))
], [row_key])
elif row_keys != '':
ROW_CONDS = self.build_conditions([
np.sort(np.unique(self.nwbfile.stimulus[key].data[self.Pcond]))
for key in row_keys
], row_keys)
elif (ROW_CONDS is None):
ROW_CONDS = [np.ones(np.sum(self.Pcond), dtype=bool)]
if COLOR_CONDS is None:
COLOR_CONDS = [np.ones(np.sum(self.Pcond), dtype=bool)]
# if (len(COLOR_CONDS)>1) and (self.color.text()!=''):
# COLORS = [getattr(ge, self.color.text())((c%10)/10.) for c in np.arange(len(COLOR_CONDS))]
# elif (len(COLOR_CONDS)>1):
# COLORS = [ge.tab10((c%10)/10.) for c in np.arange(len(COLOR_CONDS))]
# elif self.color.text()!='':
# COLORS = [getattr(ge, self.color.text())]
# else:
COLORS = [color]
if (fig is None) and (AX is None) and (fig_preset
== 'raw-traces-preset'):
fig, AX = ge.figure(axes=(len(COL_CONDS), len(ROW_CONDS)),
reshape_axes=False,
top=0.4,
bottom=0.4,
left=0.7,
right=0.7,
wspace=0.5,
hspace=0.5)
elif (fig is None) and (AX is None):
fig, AX = ge.figure(axes=(len(COL_CONDS), len(ROW_CONDS)),
reshape_axes=False)
self.ylim = [np.inf, -np.inf]
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
for icolor, color_cond in enumerate(COLOR_CONDS):
cond = np.array(
condition & col_cond & row_cond
& color_cond)[:self.EPISODES['resp'].shape[0]]
if self.EPISODES['resp'][cond, :].shape[0] > 0:
my = self.EPISODES['resp'][cond, :].mean(axis=0)
if with_std:
sy = self.EPISODES['resp'][cond, :].std(axis=0)
ge.plot(self.EPISODES['t'],
my,
sy=sy,
ax=AX[irow][icol],
color=COLORS[icolor],
lw=1)
self.ylim = [
min([self.ylim[0],
np.min(my - sy)]),
max([self.ylim[1],
np.max(my + sy)])
]
else:
AX[irow][icol].plot(self.EPISODES['t'],
my,
color=COLORS[icolor],
lw=1)
self.ylim = [
min([self.ylim[0], np.min(my)]),
max([self.ylim[1], np.max(my)])
]
if with_screen_inset:
inset = ge.inset(AX[irow][icol], [.8, .9, .3, .25])
self.visual_stim.show_frame(\
self.EPISODES['index_from_start'][cond][0],
ax=inset, enhance=True, label=None)
if with_stat_test:
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
for icolor, color_cond in enumerate(COLOR_CONDS):
cond = np.array(
single_cond & col_cond & row_cond
& color_cond)[:self.EPISODES['resp'].shape[0]]
test = stat_test_for_evoked_responses(
self.EPISODES, cond, **stat_test_props)
AX[irow][icol].plot(stat_test_props['interval_pre'],
self.ylim[0] * np.ones(2),
'k-',
lw=1)
AX[irow][icol].plot(stat_test_props['interval_post'],
self.ylim[0] * np.ones(2),
'k-',
lw=1)
ps, size = pval_to_star(test)
AX[irow][icol].annotate(
ps, ((stat_test_props['interval_post'][0] +
stat_test_props['interval_pre'][1]) / 2.,
self.ylim[0]),
va='top',
ha='center',
size=size,
xycoords='data')
if xlim is None:
self.xlim = [self.EPISODES['t'][0], self.EPISODES['t'][-1]]
else:
self.xlim = xlim
if ylim is not None:
self.ylim = ylim
for irow, row_cond in enumerate(ROW_CONDS):
for icol, col_cond in enumerate(COL_CONDS):
ge.set_plot(
AX[irow][icol],
spines=(['left', 'bottom'] if with_axis else []),
# xlabel=(self.xbarlabel.text() if with_axis else ''),
# ylabel=(self.ybarlabel.text() if with_axis else ''),
ylim=self.ylim,
xlim=self.xlim)
if with_stim:
AX[irow][icol].fill_between(
[0, np.mean(self.EPISODES['time_duration'])],
self.ylim[0] * np.ones(2),
self.ylim[1] * np.ones(2),
color='grey',
alpha=.2,
lw=0)
if not with_axis:
ge.draw_bar_scales(AX[0][0],
Xbar=xbar,
Xbar_label=xbarlabel,
Ybar=ybar,
Ybar_label=ybarlabel,
Xbar_fraction=0.1,
Xbar_label_format='%.1f',
Ybar_fraction=0.2,
Ybar_label_format='%.1f',
loc='top-left')
if label != '':
ge.annotate(fig,
label, (0, 0),
color=color,
ha='left',
va='bottom')
# if self.annot.isChecked():
# S=''
# if hasattr(self, 'roiPick'):
# S+='roi #%s' % self.roiPick.text()
# for i, key in enumerate(self.varied_parameters.keys()):
# if 'single-value' in getattr(self, '%s_plot' % key).currentText():
# S += ', %s=%.2f' % (key, getattr(self, '%s_values' % key).currentText())
# ge.annotate(fig, S, (0,0), color='k', ha='left', va='bottom')
return fig, AX
def modulation_summary_panel(t,
data,
title='',
pre_interval=[-1, 0],
post_interval=[1, 2],
responsive_only=False):
if responsive_only:
fig, AX = ge.figure(axes=(4, 1), wspace=2)
valid_cells = np.array(data['responsive'])
# pie plot for responsiveness
AX[0].pie([
100 * np.sum(valid_cells) / len(valid_cells), 100 *
(1 - np.sum(valid_cells) / len(valid_cells))
],
explode=(0, 0.1),
colors=[plt.cm.tab10(2), plt.cm.tab10(3)],
labels=['resp. ', ' unresp.'],
autopct='%1.1f%%',
shadow=True,
startangle=90)
iax = 1
else:
fig, AX = ge.figure(axes=(3, 1), wspace=2)
iax = 0
valid_cells = np.ones(len(data['control']), dtype=bool)
ge.annotate(fig,
'%s, n=%i ROIs' % (title, np.sum(valid_cells)), (0.05, 0.98),
va='top')
pre_cond = (t > pre_interval[0]) & (t < pre_interval[1])
post_cond = (t > post_interval[0]) & (t < post_interval[1])
evoked_levels = {}
if np.sum(valid_cells) > 1:
for ik, key, color in zip(range(3),
['redundant', 'control', 'deviant'],
[ge.blue, 'k', ge.red]):
y = np.array(data[key])[valid_cells, :]
ge.plot(t,
y.mean(axis=0),
sy=y.std(axis=0),
color=color,
ax=AX[iax],
no_set=True)
y_bsl = y - np.mean(y[:, pre_cond], axis=1).reshape(
(np.sum(valid_cells), 1))
ge.plot(t,
y_bsl.mean(axis=0),
sy=y_bsl.std(axis=0),
color=color,
ax=AX[iax + 1],
no_set=True)
# bar plot
evoked_levels[key] = np.mean(y_bsl[:, post_cond], axis=1)
AX[iax + 2].bar([ik],
np.mean(evoked_levels[key]),
yerr=np.std(evoked_levels[key]),
lw=2,
color=color)
# adaptation effect (control vs redundant conditions)
test = ttest_rel(evoked_levels['redundant'], evoked_levels['control'])
AX[iax + 2].plot([0, 1],
AX[iax + 2].get_ylim()[1] * np.ones(2),
'k-',
lw=1)
ge.annotate(AX[iax + 2],
ge.from_pval_to_star(test.pvalue),
(0.5, AX[iax + 2].get_ylim()[1]),
ha='center',
xycoords='data')
# surprise effect (control vs deviant conditions)
test = ttest_rel(evoked_levels['deviant'], evoked_levels['control'])
AX[iax + 2].plot([1, 2],
AX[iax + 2].get_ylim()[1] * np.ones(2),
'k-',
lw=1)
ge.annotate(AX[iax + 2],
ge.from_pval_to_star(test.pvalue),
(1.5, AX[iax + 2].get_ylim()[1]),
ha='center',
xycoords='data')
# pre / post intervals
ylim1 = AX[iax].get_ylim()[0]
AX[iax].plot(pre_interval, ylim1 * np.ones(2), lw=1, color='dimgrey')
AX[iax].plot(post_interval, ylim1 * np.ones(2), lw=1, color='dimgrey')
ge.set_plot(AX[iax], xlabel='time (s)', ylabel='dF/F')
ge.set_plot(AX[iax + 1], xlabel='time (s)', ylabel='$\Delta$ dF/F')
ge.title(AX[iax + 1], 'baseline corrected', size='x-small')
ge.set_plot(AX[iax + 2],
xlabel='',
ylabel='evoked $\Delta$ dF/F',
xticks=[0, 1, 2],
xticks_labels=['red.', 'ctrl', 'dev.'],
xticks_rotation=70)
return fig, AX
def analysis_pdf(datafile, Nmax=1000000):
data = MultimodalData(datafile)
stim_duration = data.metadata['Protocol-1-presentation-duration']
interval_post = [1. / 2. * stim_duration, stim_duration]
interval_pre = [interval_post[0] - interval_post[1], 0]
try:
# find the protocol with the many-standards
iprotocol_MS = np.argwhere([('many-standards' in p)
for p in data.protocols])[0][0]
# find the protocol with the oddball-1
iprotocol_O1 = np.argwhere([('oddball-1' in p)
for p in data.protocols])[0][0]
# find the protocol with the oddball-2
iprotocol_O2 = np.argwhere([('oddball-2' in p)
for p in data.protocols])[0][0]
# mismatch negativity angles
MM_angles = [
data.metadata['Protocol-%i-angle-redundant (deg)' %
(1 + iprotocol_O1)],
data.metadata['Protocol-%i-angle-deviant (deg)' %
(1 + iprotocol_O1)]
]
#
DATA = {'stim_duration': stim_duration}
DATA[str(int(MM_angles[0]))] = {
'iprotocol_control': iprotocol_MS,
'control': [],
'redundant': [],
'deviant': [],
'responsive': []
}
DATA[str(int(MM_angles[1]))] = {
'iprotocol_control': iprotocol_MS,
'control': [],
'redundant': [],
'deviant': [],
'responsive': []
}
DATA[str(
int(data.metadata[
'Protocol-%i-angle-redundant (deg)' %
(1 + iprotocol_O1)]))]['iprotocol_redundant'] = iprotocol_O1
DATA[str(
int(data.metadata[
'Protocol-%i-angle-deviant (deg)' %
(1 + iprotocol_O1)]))]['iprotocol_deviant'] = iprotocol_O1
DATA[str(
int(data.metadata[
'Protocol-%i-angle-redundant (deg)' %
(1 + iprotocol_O2)]))]['iprotocol_redundant'] = iprotocol_O2
DATA[str(
int(data.metadata[
'Protocol-%i-angle-deviant (deg)' %
(1 + iprotocol_O2)]))]['iprotocol_deviant'] = iprotocol_O2
# find the angle for the redundant and deviant conditions
print(data.metadata['Protocol-3-angle-redundant (deg)'],
data.metadata['Protocol-3-angle-deviant (deg)'])
Nresp, Nresp_selective, SIs = 0, 0, []
pdf_OS = PdfPages(
os.path.join(
summary_pdf_folder(datafile),
'%s-orientation_selectivity.pdf' %
data.protocols[iprotocol_MS]))
pdf_MSO = PdfPages(
os.path.join(
summary_pdf_folder(datafile),
'%s-mismatch_selective_only.pdf' %
data.protocols[iprotocol_MS]))
pdf_MA = PdfPages(
os.path.join(summary_pdf_folder(datafile),
'%s-mismatch_all.pdf' % data.protocols[iprotocol_MS]))
for roi in np.arange(data.iscell.sum())[:Nmax]:
print(' - MMN analysis for ROI #%i / %i' %
(roi + 1, data.iscell.sum()))
## ORIENTATION SELECTIVITY ANALYSIS
fig, SI, responsive, responsive_angles = ODS.OS_ROI_analysis(
data,
roiIndex=roi,
iprotocol=iprotocol_MS,
stat_test_props=dict(interval_pre=interval_pre,
interval_post=interval_post,
test='wilcoxon',
positive=True),
with_responsive_angles=True)
pdf_OS.savefig() # saves the current figure into a pdf page
plt.close()
if responsive:
Nresp += 1
SIs.append(SI)
EPISODES = EpisodeResponse(
data,
protocol_id=None, # means all
quantity='CaImaging',
subquantity='dF/F',
roiIndex=roi)
fig, AX = ge.figure(axes=(2, 1), wspace=3., right=10.)
responsive_for_at_least_one = False
ge.annotate(fig, 'ROI #%i' % (roi + 1), (0.02, 0.98), va='top')
for angle, ax in zip(MM_angles, AX):
DATA[str(int(angle))]['responsive'].append(
False) # False by default
ge.title(ax, '$\\theta$=%.1f$^{o}$' % angle)
for ik, key, color in zip(range(3),
['control', 'redundant', 'deviant'],
['k', ge.blue, ge.red]):
cond = data.get_stimulus_conditions([
np.array(DATA[str(int(angle))]['iprotocol_%s' % key]),
np.array([float(angle)])
], ['protocol_id', 'angle'], None)[0]
ge.plot(EPISODES.t,
EPISODES.resp[cond, :].mean(axis=0),
sy=EPISODES.resp[cond, :].std(axis=0),
color=color,
ax=ax,
no_set=True)
ge.annotate(ax,
ik * '\n' + '%s, n=%i' % (key, np.sum(cond)),
(0.98, 1.),
color=color,
va='top',
size='small')
# storing for population analysis:
DATA[str(int(angle))][key].append(
EPISODES.resp[cond, :].mean(axis=0))
if angle in responsive_angles:
responsive_for_at_least_one = True
DATA[str(int(
angle))]['responsive'][-1] = True # shift to True
ge.set_plot(ax, xlabel='time (s)', ylabel='dF/F')
pdf_MA.savefig()
if responsive_for_at_least_one:
pdf_MSO.savefig()
plt.close()
for angle in MM_angles:
fig, AX = modulation_summary_panel(EPISODES.t,
DATA[str(int(angle))],
title='$\\theta$=%.1f$^{o}$' %
angle)
pdf_MA.savefig()
plt.close()
fig, AX = modulation_summary_panel(EPISODES.t,
DATA[str(int(angle))],
title='$\\theta$=%.1f$^{o}$' %
angle,
responsive_only=True)
pdf_MSO.savefig()
plt.close()
# orientation selectivity summary
ODS.summary_fig(Nresp,
data.iscell.sum(),
SIs,
label='Orient. Select. Index')
pdf_OS.savefig() # saves the current figure into a pdf page
plt.close()
# modulation summary
for pdf in [pdf_OS, pdf_MSO, pdf_MA]:
pdf.close()
print('[ok] mismatch negativity analysis saved in: "%s" ' %
summary_pdf_folder(datafile))
except BaseException as be:
print('\n', be)
print('---------------------------------------')
print(' /!\ Pb with mismatch negativity analysis /!\ ')