def finish_plot(E, fig, level, xbins, ybins, h, l, nrows, title, fname,
ADD_SOURCE):
percent_time_color = E.fcolors['other'][0]
set_legend(fig, h, l, text_color=percent_time_color)
if (xbins, ybins) == (2, 4):
fig.text(.94,
.25,
'percent time',
color=percent_time_color,
fontsize=10,
ha='left')
if nrows == 1:
typad = 0
sypad = -.05
elif nrows >= 2 or nrows < 6:
typad = 0
sypad = .05
add_titles_notes(E, fig, title=title, typad=typad)
plt.subplots_adjust(hspace=.3)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=sypad)
def set_panel_layout(E, fig, err_type, tbin_type='12bins'):
# legend annotation
if tbin_type.endswith('bins'):
fig.text(.7, 1.1, 'gray background: Dark Cycle', fontsize=8)
xlabel = 'Circadian Time'
add_xylabels(fig, xlabel=xlabel, xypad=-.15, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures vs CT, 12bins group avg$\pm$%s\n%s days: %s' % (
E.short_name, err_type, E.use_days.replace('_',
'-').title(), days_string)
add_titles_notes(E, fig, title=fig_title, typad=.1)
plt.subplots_adjust(hspace=.6, wspace=.6)
def set_panel_layout(E, fig, err_type, tbin_type):
fig.text(.6, .9, '0: %s, control, %s (grayscale)' %(E.strain_names[0], tbin_type), fontsize=8)
fig.text(.6, .85, '1: %s, knock-out, %s (colors)' %(E.strain_names[1], tbin_type), fontsize=8)
if tbin_type.endswith('bins'):
fig.text(.6, .8, 'gray background: Dark Cycle', fontsize=8)
xlabel = 'Circadian Time'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures vs CT, 12bins, group avg$\pm$%s\n%s days: %s' %(
E.short_name, err_type,
E.use_days.replace('_', '-').title(), days_string
)
add_titles_notes(E, fig, title=fig_title)
def draw_subplot(experiment,
avgs,
labels,
level,
cycle,
err_type,
fname,
plot_subtype,
plot_type,
ADD_SOURCE=True):
E = experiment
figsize, nrows, ncols, _, _ = get_subplot_specs(E,
num_subplots=len(E.groups))
fig, axes = plt.subplots(nrows, ncols, figsize=figsize)
slice_labels = ['M', 'F', 'W', 'other', 'IS']
colors = [E.fcolors[x][0] for x in slice_labels]
title, subtitles = get_figure_titles(E, labels, level, cycle, err_type,
plot_type)
for c in xrange(avgs.shape[0]):
try:
ax = axes.flatten()[c]
if plot_subtype == 'bar':
stop
elif plot_subtype == 'pie':
plot_as_a_pie(ax, avgs[c], colors, slice_labels, subtitles[c])
if c == 0:
h, l = ax.get_legend_handles_labels()
except IndexError:
ax.axis('off')
continue
set_legend(fig, h, l)
# plt.subplots_adjust(hspace=.4)
add_titles_notes(E, fig, title=title, typad=-.15, tlxpad=0, tlypad=-.15)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, labelsize=6, sypad=.25)
def plot_features_panel_LC_DC_ratio(experiment,
level='group',
bin_type='3cycles',
err_type='sem',
plot_type='features',
ADD_SOURCE=True):
E = experiment
print "%s, level: %s, bin_type: %s, err_type: %s, days: %s" % (
plot_features_panel_LC_DC_ratio.__name__, level, bin_type, err_type,
E.daysToUse)
features = E.features_by_activity
num_features = len(features)
days_to_use = E.daysToUse
dirname = E.figures_dir + '%s/vectors/panels_expdays/%s/%s_days/' % (
plot_type, bin_type, E.use_days)
if not os.path.isdir(dirname): os.makedirs(dirname)
fname = dirname + '%s_panel_expdays_LC_DC_ratio' % (plot_type
) #s, err_type)
# using mouseday value
# ratios = E.generate_feature_vectors_LC_DC_ratio_expdays(features, level, bin_type, err_type)
# using group averages value
data_ = E.generate_feature_vectors_expdays(features, level, bin_type,
err_type)
ratios_ = data_[:, :, :, 2, 0] / data_[:, :, :, 1, 0] # LC/DC, avgs
figsize = (14.4, 4.8)
nrows, ncols = 4, 7
fig, axes = plt.subplots(nrows, ncols, figsize=figsize, sharex=True)
xs = days_to_use
cnt = 0
for n in xrange(nrows):
for m in xrange(ncols):
ax = axes.flatten()[n * ncols + m]
if n == 0 and m >= 3:
ax.axis('off')
continue
feature = features[cnt]
colors = get_two_group_features_colors(E, feature)
subtitle = '%s %s' % (feature,
E.plot_settings_dict[feature]['unit'])
for g in xrange(E.num_strains):
# # using mouseday values
# tkw = {'fmt':'o-', 'ms':2, 'elinewidth':.5, 'capsize':1}
# ax.errorbar(xs, ratios[g, cnt, :, 0], yerr=ratios[g, cnt, :, 1],
# color=colors[g], mec=colors[g], **tkw)
# using group averages value
tkw = {'marker': 'o', 'ms': 2, 'zorder': 0}
ax.plot(xs,
ratios_[g, cnt, :],
color=colors[g],
mec=colors[g],
**tkw)
# use when plotting all for comparison
# colors_ = ['r', 'y']
# ax.plot(xs, ratios_[g, cnt, :], color=colors_[g], mec=colors_[g], **tkw)
if E.short_name == 'HFD2':
d_day = E.dietChangeDayNumbers[0]
ax.axvspan(xmin=d_day,
xmax=days_to_use[-1],
color='.9',
zorder=0)
xlims = ax.get_xlim()
ax.set_xlim((4, xlims[1]))
ax.set_ylim((0, ax.get_ylim()[1]))
ax_cleanup(ax)
ax.set_title(subtitle, fontsize=10)
cnt += 1
fig.text(.6,
.9,
'0: %s, control, 24H (grayscale)' % E.strain_names[0],
fontsize=8)
fig.text(.6,
.85,
'1: %s, knock-out, 24H (colors)' % E.strain_names[1],
fontsize=8)
fig.text(.6, .8, 'gray background: diet change', fontsize=8)
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures vs days, LC/DC ratio %s avg$\pm$%s\nacross %s days: %s' % (
E.short_name, level, err_type, E.use_days.replace(
'_', '-').title(), days_string)
add_titles_notes(E, fig, title=fig_title)
plt.subplots_adjust(hspace=.6, wspace=.34)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.02)
def plot_features_panel_DC_LC(experiment,
level='group',
bin_type='3cycles',
err_type='sem',
plot_type='features',
ADD_SOURCE=True):
E = experiment
print "%s, level: %s, bin_type: %s, err_type: %s, days: %s" % (
plot_features_panel_DC_LC.__name__, level, bin_type, err_type,
E.daysToUse)
features = E.features_by_activity
num_features = len(features)
days_to_use = E.daysToUse
dirname = E.figures_dir + '%s/vectors/panels_expdays/%s/%s_days/' % (
plot_type, bin_type, E.use_days)
if not os.path.isdir(dirname): os.makedirs(dirname)
fname = dirname + '%s_panel_expdays_DC_LC_group_%s' % (plot_type, err_type)
# groups, features, days, cycles, avg/err
data = E.generate_feature_vectors_expdays(features, level, bin_type,
err_type)
new_data = data[:, :, :, 1:, :]
figsize = (14.4, 4.8)
nrows, ncols = 4, 7
fig, axes = plt.subplots(nrows, ncols, figsize=figsize, sharex=True)
xs = days_to_use
cnt = 0
for n in xrange(nrows):
for m in xrange(ncols):
ax = axes.flatten()[n * ncols + m]
if n == 0 and m >= 3:
ax.axis('off')
continue
feature = features[cnt]
# get colors
if feature.startswith('AS'):
color1, color2 = [E.fcolors['AS'].values()[x] for x in [1, 3]]
elif feature.startswith('T'):
color1, color2 = [
E.fcolors[feature[1:]].values()[x] for x in [1, 3]
]
else:
color1, color2 = [
E.fcolors[feature[:1]].values()[x] for x in [1, 3]
]
colors = ['.4', '.7', color1, color2]
subtitle = '%s %s' % (feature,
E.plot_settings_dict[feature]['unit'])
for g in xrange(E.num_strains):
tkw = {'fmt': 'o-', 'ms': 2, 'elinewidth': .5, 'capsize': 1}
# DC
mec = '0' if g == 0 else colors[2 * g]
ax.errorbar(xs,
new_data[g, cnt, :, 0, 0],
yerr=new_data[g, cnt, :, 0, 1],
color=colors[2 * g],
mec=mec,
**tkw)
#LC
mc = '0' if g == 0 else colors[2 * g + 1]
ax.errorbar(xs,
new_data[g, cnt, :, 1, 0],
yerr=new_data[g, cnt, :, 1, 1],
color=colors[2 * g + 1],
mec=mec,
**tkw)
if E.short_name == 'HFD2':
d_day = E.dietChangeDayNumbers[0]
ax.axvspan(xmin=d_day,
xmax=days_to_use[-1],
color='.9',
zorder=0)
xlims = ax.get_xlim()
ax.set_xlim((4, xlims[1]))
ax.set_ylim([0, ax.get_ylim()[1]])
ax_cleanup(ax)
ax.set_title(subtitle, fontsize=10)
cnt += 1
fig.text(.6,
.9,
'0: %s, control (grayscale)\nDC:black, LC: gray' %
E.strain_names[0],
fontsize=8)
fig.text(.6,
.83,
'1: %s, knock-out (colors)\nDC: dark, LC: light ' %
E.strain_names[1],
fontsize=8)
fig.text(.6, .78, 'gray background: diet change', fontsize=8)
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures, DC vs. LC, %s avg and %s\nacross %s days: %s' % (
E.short_name, level, err_type, E.use_days.replace(
'_', '-').title(), days_string)
add_titles_notes(E, fig, title=fig_title)
plt.subplots_adjust(hspace=.6, wspace=.34)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.02)
def plot_features_panel_12bins(experiment,
level='group',
bin_type='12bins',
err_type='sem',
plot_type='features',
ADD_SOURCE=True):
E = experiment
print "%s, level: %s, bin_type: %s, err_type: %s, days: %s" % (
plot_features_panel_12bins.__name__, level, bin_type, err_type,
E.daysToUse)
features = E.features_by_activity
num_features = len(features)
days_to_use = E.daysToUse
num_bins = int(bin_type.strip('bins'))
tbins = my_utils.get_tbins_string(bin_type)
dirname = E.figures_dir + '%s/vectors/panels_expdays/%s/%s_days/' % (
plot_type, bin_type, E.use_days)
if not os.path.isdir(dirname): os.makedirs(dirname)
data = E.generate_feature_vectors_expdays(features, level, bin_type,
err_type)
ymaxs = get_ymaxs(data)
# stop
for b in xrange(num_bins):
new_data = data[:, :, :, b, :]
figsize = (14.4, 4.8)
nrows, ncols = 4, 7
fig, axes = plt.subplots(nrows, ncols, figsize=figsize, sharex=True)
xs = days_to_use
cnt = 0
for n in xrange(nrows):
for m in xrange(ncols):
ax = axes.flatten()[n * ncols + m]
if n == 0 and m >= 3:
ax.axis('off')
continue
feature = features[cnt]
colors = get_two_group_features_colors(E, feature)
subtitle = '%s %s' % (feature,
E.plot_settings_dict[feature]['unit'])
for g in xrange(E.num_strains):
tkw = {
'fmt': 'o-',
'ms': 2,
'elinewidth': .5,
'capsize': 1
}
ax.errorbar(xs,
new_data[g, cnt, :, 0],
yerr=new_data[g, cnt, :, 1],
color=colors[g],
mec=colors[g],
**tkw)
if E.short_name == 'HFD2':
d_day = E.dietChangeDayNumbers[0]
ax.axvspan(xmin=d_day,
xmax=days_to_use[-1],
color='.9',
zorder=0)
# xmin, xmax = ax.get_xlim()
# ax.set_xlim((xmin-.5, xmax+.5))
# ax.set_ylim([0, ymaxs[cnt]])
ax_cleanup(ax)
ax.set_title(subtitle, fontsize=10)
cnt += 1
xmin, xmax = ax.get_xlim()
ax.set_xlim((xmin - .5, xmax + .5))
fig.text(.6,
.9,
'0: %s, control, %s (grayscale)' %
(E.strain_names[0], tbins[b]),
fontsize=8)
fig.text(.6,
.85,
'1: %s, knock-out, %s (colors)' %
(E.strain_names[1], tbins[b]),
fontsize=8)
fig.text(.6, .8, 'gray background: diet change', fontsize=8)
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures, %s %s avg$\pm$%s, %s\nacross %s days: %s' % (
E.short_name, bin_type, level, err_type, tbins[b],
E.use_days.replace('_', '-').title(), days_string)
add_titles_notes(E, fig, title=fig_title)
plt.subplots_adjust(hspace=.6, wspace=.34)
fname = dirname + '%s_panel_expdays_%s_group_%s_bin%d' % (
plot_type, bin_type, err_type, b)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.02)
def draw_subplot(experiment,
data,
labels,
data_rescaled,
fname,
act='F',
level='mouse',
sub_type='line',
plot_type='ingestion',
ADD_SOURCE=False):
E = experiment
i_act = 0 if act == 'F' else 1
units = ['mg/s', 'g', 'min']
# var_names = [E.HCM_variables[x][i_act] for x in var_types]
varTypes = ['coeffs', 'tots', 'durs']
varNames = [E.HCM_derived['events'][plot_type][x][0] for x in varTypes]
m_labels = np.unique(labels[:, 1])
figsize, nrows, ncols, sharex, sharey = get_subplot_specs(
num_subplots=len(m_labels))
fig, axes = plt.subplots(nrows,
ncols,
figsize=figsize,
sharex=sharex,
sharey=sharey)
colors = [E.fcolors[act].values()[x] for x in [1, 0, 2]]
title, subtitles = get_figure_titles(E,
labels,
act=act,
plot_type=plot_type)
hls = []
for m, mouse in enumerate(m_labels):
try:
ax = axes.flatten()[m]
idx = labels[:, 1] == mouse
arr = data_rescaled[idx]
if sub_type == 'line':
for k, var in enumerate(varNames):
ax.plot(arr[:, k], lw=.5, color=colors[k], label=var)
# ax.axhline(y=arr.mean()[k], c='grey', alpha='.5', label='')
# stop
make_annotation(ax, arr, data, k, idx, colors, units)
elif sub_type == 'bar':
pass
# bar_width = .2
# for k, var in enumerate(varNames):
# ind = np.arange(len(arr)) + k * bar_width -.1
# tkw = {'lw':.2, 'label':var,
# 'color':colors[k], 'edgecolor':None,
# }
# ax.bar(ind, arr[:, k], bar_width, **tkw)
set_layout(E, ax)
ax.set_title(subtitles[m], fontsize=10)
if m == 0:
h, l = ax.get_legend_handles_labels()
except IndexError:
ax.axis('off')
continue
# legend
tkw = {
'ncol': 3,
'fontsize': 8,
'bbox_to_anchor': [0.85, .08],
'frameon': False
}
legend = fig.legend(h, l, **tkw)
for label in legend.get_lines():
label.set_linewidth(3) # the legend line width
# set subplot labels
xlabel = 'Experiment Day'
ylabel = '%s Coefficient' % act
add_xylabels(fig, xlabel, ylabel) #, xypad=0, yxpad=0, labelsize=10)
add_titles_notes(
E,
fig,
title=title,
# typad=typad,
# tlxpad=tlxpad,
# tlypad=typad
)
plt.subplots_adjust(bottom=.12, hspace=0.6, wspace=0.4)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE) #, sypad=-.05)
def draw_histogram_plot(E, mouse_data, arr_preFast, arr_postFast, mouseNumbers,
fname, plot_type, ADD_SOURCE):
# ZeroLight is one group only
# for m in xrange(num_mice):
# data = mouse_data[m]
# label = mouseNumbers[m]
# data_pre, data_post = arr_preFast[m], arr_postFast[m]
# stop
# i_act = 0 if act == 'F' else 1
units = ['mg/s', 'g', 'min']
# var_names = [E.HCM_variables[x][i_act] for x in var_types]
varTypes = ['coeffs', 'tots', 'durs']
varNames = [E.HCM_derived['events'][plot_type][x][0] for x in varTypes]
num_mice = len(mouseNumbers)
figsize = (12.8, 3.6)
nrows, ncols = len(varNames), num_mice
fig, axes = plt.subplots(nrows,
ncols,
figsize=figsize,
sharex=True,
sharey=False)
colors = [E.fcolors['F'].values()[x] for x in [1, 0, 2]]
# title, subtitles = get_figure_titles(E, labels, act=act, plot_type=plot_type)
hls = []
cnt = 0
for m in xrange(nrows): # FC, FT, FD
data = mouse_data[:, :, m]
pre, post = arr_preFast[:, m], arr_postFast[:, m]
for n in xrange(ncols): # mouseNumbers
ax = axes.flatten()[cnt]
# plot quantity across days for each mouse
ax.plot(data[n, :], lw=.5, color=colors[m])
if m == 0:
xmin, xmax = ax.get_xlim()
ax.axhline(xmin=xmin,
xmax=xmax,
y=data[n].mean(0),
linestyle='-',
color=colors[m],
zorder=0,
label='average FC - up to day 35 value')
ax.axhline(xmin=xmin,
xmax=xmax,
y=pre[n],
linestyle='--',
color='g',
zorder=1,
label='day%d, FC 4h-preFast value' %
E.fastDayNumbers[0])
ax.axhline(xmin=xmin,
xmax=xmax,
y=post[n],
linestyle=':',
color='r',
zorder=2,
label='day%d FC 1h-postFast value' %
E.fastDayNumbers[0])
ax.set_title('M%d' % mouseNumbers[n], fontsize=10)
if n == 0:
h, l = ax.get_legend_handles_labels()
if n == 0:
ax.set_ylabel('%s [%s]' % (varNames[m], units[m]), fontsize=10)
ax.set_ylim([.9 * data.min(), 1.1 * data.max()])
set_layout2(E, ax, m, n)
cnt += 1
# legend
tkw = {'fontsize': 8, 'bbox_to_anchor': [0.8, .15], 'frameon': False}
legend = fig.legend(h, l, **tkw)
for label in legend.get_lines():
label.set_linewidth(3) # the legend line width
# set subplot labels
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel)
add_titles_notes(
E,
fig,
title='F-Coefficient, F-Total Amounts, F-Total PhotoBeam BreakTime')
plt.subplots_adjust(bottom=.12) #, hspace=0.6, wspace=0.4)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.03)
def plot_HCM_system_time(E, ttype='maintenance', ADD_SOURCE=True):
"""plots system_on_off
"""
if ttype == 'maintenance':
HCM_time, labels = E.get_HCM_maintenance_time()
xlims = [2, 8]
xticks = range(2, 10+1, 2)
xticklabels = xticks
elif ttype == 'recording':
HCM_time, labels = E.get_HCM_recording_time()
xlims = [2, 34]
xticks = range(4, 32+1, 4)
xticklabels = [str(x) for x in range(4, 24+1, 4)] \
+ [str(x) for x in range(4, 10+1, 4)]
print "%s, %s days.." %(plot_HCM_system_time.__name__, E.use_days)
figsize, nrows, ncols, sharex, sharey = \
get_subplot_specs(E, num_subplots=len(E.groups), plot_type='subplot')
fig, axes = plt.subplots(nrows, ncols, figsize=figsize, sharex=sharex, sharey=sharey)
for strain in range(nrows * ncols):
ax = axes.flatten()[strain] if type(axes) == np.ndarray else axes
idx = labels [:, 0] == strain
data = HCM_time[idx] / 3600. - 7
c = 0
for row in data:
ax.plot([row[0], row[1]], [c, c], lw=0.5, color='0.5')
c += 1
ax.set_xlim(xlims)
ax.set_xticks(xticks)
ax.set_xticklabels(xticklabels)
if ttype == 'maintenance':
text = 'avg:\n%1.1fmin' %(np.diff(data).mean() * 60)
elif ttype == 'recording':
text = 'avg:\n%1.2fhrs' %np.diff(data).mean()
ax.axvline(x=12, linestyle='--', color='k')
ax.axvline(x=24, linestyle='--', color='k')
ax.text(.9, .9, text, fontsize=10,
ha='center', transform=ax.transAxes)
ax.set_xlabel('Circadian Time')
ax.set_ylabel('Obs. days', labelpad=10)
ax.set_title('group%d: %s' %(strain, E.strain_names[strain]), y=1.05)
ax_cleanup(ax, labelsize=10)
title = '%sExp\n%s days\nDaily %s Time' %(
E.short_name, E.use_days.replace('_', '-').title(), ttype.title())
add_titles_notes(E, fig,
title=title,
typad=.18,
tlxpad=-.1,
tlypad=.15,
HP_TEXT=False)
plt.subplots_adjust(wspace=0.4)
# save
dirname_out = E.figures_dir + 'HCM_recording_time/%s_days/' %E.use_days
if not os.path.isdir(dirname_out): os.makedirs(dirname_out)
fname = dirname_out + 'HCMsystem_%s_time_%s_days' %(ttype, E.use_days)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.1)
def plot_raster_groups(E, group_list, bin_type='12bins', SHOW_DAYS=True,
plot_type='raster', ADD_SOURCE=True):
""" does not plot ignored mice/mousedays
"""
dirname_out = E.figures_dir + '%ss/%s/group/%s_days/' %(plot_type, bin_type, E.use_days)
if not os.path.isdir(dirname_out): os.makedirs(dirname_out)
print "%s, %s days.." %(plot_raster_groups.__name__, E.use_days)
y_sep = 10
for strain in group_list:
group = E.get_group_object(groupNumber=strain)
num_mice = len(group.count_mice()[0]) # mice ok
if num_mice > 12 and num_mice <=16:
nrows, ncols = (4,4)
elif num_mice > 8 and num_mice <=12:
nrows, ncols = (3, 4)
figsize = (12.8, 6.4)
fig, axes = plt.subplots(nrows, ncols, figsize=figsize)
m = 0 # mouse counter
for mouse in group.individuals:
ax = axes.flatten()[m]
if mouse.ignored:
print mouse, 'excluded'
ax.text(.5, .6, 'M%d\nexcluded' %mouse.mouseNumber,
fontsize=12, color='.5', ha='center', va='center')
ax.axis('off')
else:
cnt = 0
for MD in mouse.mouse_days:
if MD.dayNumber in E.daysToUse:
y_offset = y_sep * (-cnt)
if MD.ignored:
print MD, 'excluded'
ax.text(18, y_offset-5, 'D%d excluded' %MD.dayNumber,
fontsize=8, color='.5', ha='center', va='center')
ax.axis('off')
else:
print MD
plot_events(MD, fig, ax, y_offset)
if SHOW_DAYS:
if m%4 == 0:
show_days(MD, ax, y_offset,
labelsize=8)
cnt += 1
# subtitle
ax.set_title('M%d' %mouse.mouseNumber, y=1.1, fontsize=10)
set_raster_layout(fig, ax, num_days=len(E.daysToUse)),
add_DC_rectangle_to_raster(ax, ypos=5, height=1.5)
m += 1
remove_axes_not_used(group, axes, nrows, ncols, m)
add_titles_notes(E, fig, title=group.get_figtitle())
plt.subplots_adjust(hspace=0.4)
print "saving.."
fname = dirname_out + '%s_group%d' %(plot_type, group.number)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=.03)
def plot_events(MD, fname, plot_type, bin_type='12bins', FLAG_IGNORED=False):
E = MD.experiment
varNames, colors, offsets, heights, labels, label_offsets = \
get_settings_and_annotations(MD)
figsize = (12., 3.6)
fig, ax = plt.subplots(figsize=figsize)
other_color = E.fcolors['other'][0]
c = 0
for tup in zip(varNames, colors, offsets, heights, labels, label_offsets):
name, color, offset, height, label, label_offset = tup
events = MD.load(name) / 3600. - 7 # why here did I use -6.5 ??
if name in ['CT_out_HB', 'CT_at_HB']:
ax.scatter(events,
offset * np.ones(events.shape[0]),
c=color,
marker='|',
s=150,
lw=0.01,
edgecolor=None)
else:
for x in events:
event_patch = patches.Rectangle(
(x[0], offset),
x[1] - x[0],
height, # xy lower left corner, width, height
lw=0.001,
fc=color,
ec=color)
ax.add_patch(event_patch)
if name in [
'AS_timeSet', 'FB_timeSet', 'WB_timeSet', 'MB_timeSet'
]:
print_duration(ax, events, offset, name, color)
ax.text(4.5,
label_offset,
label,
color=color,
ha='right',
va='center',
fontsize=8,
clip_on=False)
set_raster_layout(fig,
ax,
num_days=len(E.daysToUse),
bin_type=bin_type,
SHIFT=E.BIN_SHIFT,
tshift=E.binTimeShift)
add_DC_rectangle_to_raster(ax, ypos=-.3, height=.3)
add_titles_notes(
E,
fig,
title=MD.get_figtitle() + ', %s' % bin_type,
TL_NOTE=True,
)
if MD.ignored:
fig.text(.3,
1.02,
'MD excluded',
fontsize=18,
color='.5',
ha='right',
va='bottom',
transform=ax.transAxes)
# begin/end fast
if E.short_name == '2CFast':
if MD.dayNumber in E.fastDayNumbers + E.reFeedDayNumbers:
text = '"FAST"' if MD.dayNumber in E.fastDayNumbers else '"REFEED"'
fig.text(.15,
1.05,
text,
fontsize=18,
color=other_color,
ha='left',
va='bottom',
transform=ax.transAxes)
show_fast_times(E,
ax,
day_num=MD.dayNumber,
TEXT=True,
color=other_color)
print "saving.."
save_plot(fname, fig, ADD_SOURCE=True)
def draw_position_density_tbins2(E,
data,
mouseNumbers,
tbin_type,
err_type,
xbins,
ybins,
fig_title,
fname,
rect_HB=None,
obs_rect=None,
plot_type='position_density',
ADD_SOURCE=False):
C = Cage()
# figure
figsize = (6.4, 6.4)
nrows, ncols = data.shape[0], data.shape[1]
fig, axes = plt.subplots(nrows, ncols, figsize=figsize)
cmap = plt.get_cmap("viridis")
vmin, vmax = .0001, 1.
if (xbins, ybins) == (2, 4):
vmin = 0.01
extent = [C.CMXLower, C.CMXUpper, C.CMYLower, C.CMYUpper]
percent_time_color = E.fcolors['other'][0]
row_labels = ['M%d' % m for m in mouseNumbers]
column_labels = ['D%d' % d for d in E.daysToUse]
for r in xrange(nrows):
# display row labels
top, bottom, left, right = [
getattr(fig.subplotpars, x)
for x in ['top', 'bottom', 'left', 'right']
]
yy = top - .025 - (top - bottom) * r / nrows
fig.text(left - .1, yy, row_labels[r], va='center', fontsize=8)
for c in xrange(ncols):
# display column labels
if r < 1:
xx = left + .02 + (right - left) * c / ncols
fig.text(xx,
top + .02,
column_labels[c],
ha='center',
fontsize=8)
try:
ax = axes[r, c] if type(
axes) is np.ndarray else axes # when just one axis
Z3 = data[r, c, :, :, 0] # plt average only for the moment
if np.isnan(Z3).all():
ax.axis('off')
else:
Z3_ = Z3.copy()
Z3_[Z3 <
1e-4] = 1e-4 # round small numbers to almost zero for plotting
im = ax.imshow(Z3_,
interpolation='nearest',
cmap=cmap,
norm=LogNorm(vmin=vmin,
vmax=vmax)) #, extent=extent)
set_position_density_layout(fig, ax, im)
if (xbins, ybins) == (2, 4):
draw_homebase_star(ax,
rect_HB[r, c],
color=percent_time_color)
if r * c < 1:
hh, ll = ax.get_legend_handles_labels()
except IndexError:
ax.axis('off')
continue
set_colorbar(fig, ax, im)
set_legend(fig, hh, ll, xbins, ybins, text_color=percent_time_color)
add_titles_notes(E,
fig,
title=fig_title,
titlesize=14,
typad=.08,
TL_NOTE=False)
plt.subplots_adjust(hspace=.2, wspace=.05)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=.03)
def draw_position_density_tbins(E,
data,
labels,
tbin_type,
level,
err_type,
xbins,
ybins,
fname,
rect_HB=None,
obs_rect=None,
plot_type='position_density',
ADD_SOURCE=False):
C = Cage()
# figure
figsize, nrows, ncols = get_subplot_specs(E,
num_subplots=data.shape[0],
plot_type=plot_type,
sub_type=tbin_type)
fig, axes = plt.subplots(nrows, ncols, figsize=figsize)
cmap = plt.get_cmap("viridis")
vmin, vmax = .0001, 1.
if (xbins, ybins) == (2, 4):
vmin = 0.01
extent = [C.CMXLower, C.CMXUpper, C.CMYLower, C.CMYUpper]
percent_time_color = E.fcolors['other'][0]
title, subtitles = get_figure_titles(E,
labels=labels,
level=level,
tbin_type=tbin_type,
err_type=err_type,
plot_type=plot_type)
data_ = data.swapaxes(0, 1)
arr = my_utils.get_CT_bins(
bin_type=tbin_type) / 3600 - 7 # CT in hours. num_tbins=arr.shape[0]
row_labels = ['CT%d-%d' % (row[0], row[1]) for row in arr]
column_labels = subtitles
for r in xrange(nrows):
# row labels
top, bottom, left, right = [
getattr(fig.subplotpars, x)
for x in ['top', 'bottom', 'left', 'right']
]
yy = top - .03 - (top - bottom) * r / nrows
fig.text(left - .1, yy, row_labels[r], va='center', fontsize=8)
for c in xrange(ncols):
# column labels
if r < 1:
xx = left + .01 + (right - left) * c / ncols
fig.text(xx, top + .03, column_labels[c], fontsize=8)
bin_data = data_[r, c, :, :]
try:
ax = axes[r, c] if type(
axes) is np.ndarray else axes # when just one axis
Z3 = bin_data[:, :, 0] # plt average only for the moment
if np.isnan(Z3).all():
# ax.text(.5, .5, subtitles[r] + ' excluded',
# fontsize=12, color='.5', ha='center', va='center')
ax.axis('off')
else:
Z3_ = Z3.copy()
Z3_[Z3 <
1e-4] = 1e-4 # round small numbers to almost zero for plotting
im = ax.imshow(Z3_,
interpolation='nearest',
cmap=cmap,
norm=LogNorm(vmin=vmin,
vmax=vmax)) #, extent=extent)
# ax.set_title(subtitles[c])
set_position_density_layout(fig, ax, im)
if (xbins, ybins) == (2, 4):
draw_homebase_star(ax,
rect_HB[c],
color=percent_time_color)
if r * c < 1:
hh, ll = ax.get_legend_handles_labels()
except IndexError:
ax.axis('off')
continue
set_colorbar(fig, ax, im)
set_legend(fig, hh, ll, xbins, ybins, text_color=percent_time_color)
typad = .15 #if level == 'group' else 0
add_titles_notes(E,
fig,
title=title,
typad=typad,
titlesize=14,
TL_NOTE=False)
plt.subplots_adjust(hspace=.2, wspace=.05)
sypad = -.05 if level == 'group' else .05
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=sypad)
