def plot_strain_AS_structure(experiment, level, group, ax, AS_list, day,
num_AS, num_mins):
E = experiment
colors = [E.fcolors[x][0] for x in ['F', 'W', 'M']]
lw = 1.5 if level == 'mouse' else .5
k = 0
for fwm_arrays in AS_list:
ypos = len(AS_list) - k
col = 0
for arr in fwm_arrays:
for xs in arr:
ax.plot(xs / 60, [ypos, ypos], lw=lw, color=colors[col])
col += 1
print_progress(k, len(AS_list))
k += 1
print
set_layout(ax, level, num_mins)
ax.set_title('%s, day%d' % (E.strain_names[group.number], day),
fontsize=10)
if day == E.transition1DayNumber:
ax.text(.7,
.7,
'diet\ntransition',
fontsize=10,
transform=ax.transAxes)
def _check_bout_counts_in_bins(experiment, act, vec_type='12bins'):
num_bins = 12
print "%s, %s, %dbins" % (_check_bout_counts_in_bins.__name__, act,
num_bins)
arr = np.zeros((experiment.num_md_ok, num_bins + 3))
cnt = 0
for group in experiment.groups:
for mouse in group.individuals:
if not mouse.ignored:
for MD in mouse.mouse_days:
if MD.dayNumber in experiment.daysToUse:
if not MD.ignored:
arr[cnt, :
3] = MD.groupNumber, MD.mouseNumber, MD.dayNumber
arr[cnt, 3:] = MD._check_bout_counts_in_bins(act)
my_utils.print_progress(cnt, experiment.num_md_ok)
cnt += 1
dirname = experiment.features_dir + 'vectors/_bout_counts_check/'
import os
if not os.path.isdir(dirname): os.makedirs(dirname)
np.save(dirname + '%s_bout_counts_check' % act, arr)
return arr
def plot_mouse_AS_structure(experiment,
level,
mouse,
ax,
colors,
EARLY=False,
num_mins=15,
days=None,
cycle='24H'):
E = experiment
days_to_use = E.daysToUse if days is None else days
AS_list = mouse.generate_AS_structure(days=days_to_use, cycle=cycle)
lws = [1.5, 1.5, 1.5, .3] if level == 'mouse' else [.5, .5, .5, .1]
k = 0
for fwmo_arrays in AS_list:
ypos = len(AS_list) - k
col = 0
for arr in fwmo_arrays:
for xs in arr:
ax.plot(xs / 60, [ypos, ypos], lw=lws[col], color=colors[col])
col += 1
print_progress(k, len(AS_list))
k += 1
set_layout(ax, level, EARLY, num_mins)
subtitle = 'M%d' % (mouse.mouseNumber)
ax.set_title(subtitle, fontsize=10)
plt.subplots_adjust(hspace=.4)
def generate_breakfast_data(experiment,
act='F',
ONSET=True,
num_mins=15,
tbin_size=5,
days=None,
GET_AVGS=False,
strain_avg_type='over_mds',
GENERATE=False,
VERBOSE=False):
E = experiment
days_to_use = E.daysToUse if days is None else days
_, num_md_ok = E.count_mousedays(days=days_to_use)
print "%s, %s, ONSET: %s" % (generate_breakfast_data.__name__, act, ONSET)
num_bins = int(num_mins * 60 / tbin_size)
text = 'AS_onset' if ONSET else 'AS_offset'
md_data = np.zeros((num_md_ok, num_bins))
md_labels = np.zeros((num_md_ok, 3), dtype=int)
cnt = 0
for group in E.groups:
for mouse in group.individuals:
if not mouse.ignored:
for MD in mouse.mouse_days:
if MD.dayNumber in days_to_use:
if not MD.ignored:
md_data[cnt] = MD.generate_breakfast_data(
act, ONSET, num_mins, tbin_size, GENERATE)
md_labels[
cnt] = MD.groupNumber, MD.mouseNumber, MD.dayNumber
if not VERBOSE:
my_utils.print_progress(cnt, E.num_md_ok)
else:
print MD
cnt += 1
cstart = time.clock()
cstop = time.clock()
if GENERATE:
if not VERBOSE:
print
dirname = E.breakfast_dir + \
'%s/%s/prob_%dmin_tbin%ds/' %(
act, text, num_mins, tbin_size)
print "binary output saved to: %s" % dirname
print "..took %1.2f minutes" % ((cstop - cstart) / 60.)
if GET_AVGS:
s_data, s_labels, m_data, m_labels = \
my_utils.get_1d_mouse_strain_averages(E, md_data, md_labels, strain_avg_type)
return s_data, s_labels, m_data, m_labels, md_data, md_labels
return md_data, md_labels
def generate_feature_vectors(experiment,
feat='ASP',
vec_type='12bins',
days=None,
GET_AVGS=False,
strain_avg_type='over_mds',
GENERATE=False,
VERBOSE=False):
""" returns:
array with data for all legit mousedays
arr: (num_mousedays, num_bins)
mice and strain data
data[0]: avgs
data[1]: stdev
data[2]: stderr
labels
"""
E = experiment
cstart = time.clock()
num_bins = 12 if vec_type.endswith('bins') else 3
print "%s, %s, %s" % (generate_feature_vectors.__name__, feat, vec_type)
days_to_use = E.daysToUse if days is None else days
_, num_md_ok = E.count_mousedays(days=days_to_use)
md_data = np.zeros((num_md_ok, num_bins))
md_labels = np.zeros((num_md_ok, 3), dtype=int)
cnt = 0
for group in E.groups:
for mouse in group.individuals:
if not mouse.ignored:
for MD in mouse.mouse_days:
if MD.dayNumber in days_to_use:
if not MD.ignored:
md_data[cnt] = MD.generate_feature_vector(
feat, vec_type, GENERATE, VERBOSE)
md_labels[
cnt] = MD.groupNumber, MD.mouseNumber, MD.dayNumber
if GENERATE and not VERBOSE:
my_utils.print_progress(cnt, E.num_md_ok)
cnt += 1
cstop = time.clock()
if GENERATE:
if not VERBOSE:
print
print "binary output saved to: %s" % E.features_dir
print "..took %1.2f minutes" % ((cstop - cstart) / 60.)
if GET_AVGS:
s_data, s_labels, m_data, m_labels = \
my_utils.get_1d_mouse_strain_averages(
E, md_data, md_labels, strain_avg_type)
return s_data, s_labels, m_data, m_labels, md_data, md_labels
return md_data, md_labels
def generate_time_budgets(experiment,
cycle='24H',
AS=False,
days=None,
GET_AVGS=False,
strain_avg_type='over_mds',
GENERATE=False,
VERBOSE=False):
E = experiment
cstart = time.clock()
print "%s, %s" % (generate_time_budgets.__name__, cycle)
days_to_use = E.daysToUse if days is None else days
_, num_md_ok = E.count_mousedays(days=days_to_use)
num_slices = 5 if not AS else 4 #move, feed, drink, other_AS, inactive
md_data = np.zeros((num_md_ok, num_slices))
md_labels = np.zeros((num_md_ok, 3), dtype=int)
cnt = 0
for group in E.groups:
for mouse in group.individuals:
if not mouse.ignored:
for MD in mouse.mouse_days:
if MD.dayNumber in days_to_use:
if not MD.ignored:
md_data[cnt] = MD.generate_time_budgets(
cycle, num_slices, GENERATE)
md_labels[
cnt] = MD.groupNumber, MD.mouseNumber, MD.dayNumber
if not VERBOSE:
my_utils.print_progress(cnt, E.num_md_ok)
else:
print MD
cnt += 1
cstop = time.clock()
if GENERATE:
if not VERBOSE:
print
dirname = E.time_budgets_dir + '%s/' % cycle
print "binary output saved to: %s" % dirname
print "..took %1.2f minutes" % ((cstop - cstart) / 60.)
if GET_AVGS:
s_data, s_labels, m_data, m_labels = \
my_utils.get_1d_mouse_strain_averages(E, md_data, md_labels, strain_avg_type)
return s_data, s_labels, m_data, m_labels, md_data, md_labels
return md_data, md_labels
def generate_active_states(self, mouseNumber=None, dayNumber=None):
cstart = time.clock()
if mouseNumber is None:
cnt = 0
for group in self.groups:
for mouse in group.individuals:
for MD in mouse.mouse_days:
if MD.dayNumber in self.daysToUse:
MD.generate_active_states()
my_utils.print_progress(cnt, self.num_md_ok)
cnt += 1
else:
mouse = self.get_mouse_object(mouseNumber)
MD = mouse.mouse_days[dayNumber - 1]
MD.generate_active_states()
cstop = time.clock()
if mouseNumber is None:
print "binary output saved to: %s" % self.active_states_dir
print "..took: %1.2f minutes" % ((cstop - cstart) / 60.)
def generate_active_states(experiment, mouseNumber=None, dayNumber=5):
cstart = time.clock()
if mouseNumber is None:
cnt = 0
for group in experiment.groups:
for mouse in group.individuals:
if not mouse.ignored:
for MD in mouse.mouse_days:
if MD.dayNumber in experiment.daysToUse:
if not MD.ignored:
MD.generate_active_states()
my_utils.print_progress(
cnt, experiment.num_md_ok)
cnt += 1
else:
mouse = experiment.get_mouse_object(mouseNumber)
if not mouse.ignored:
MD = mouse.mouse_days[dayNumber - 1]
if not MD.ignored:
MD.generate_active_states()
cstop = time.clock()
if mouseNumber is None:
print "binary output saved to: %s" % experiment.active_states_dir
print "..took: %1.2f minutes" % ((cstop - cstart) / 60.)
def generate_breakfast_data(self,
cycle='24H',
level='mouseday',
act='F',
err_type='sd',
ONSET=True,
num_mins=15,
tbin_size=5,
days=None,
group_avg_type='over_mds',
GENERATE=False,
VERBOSE=False):
cstart = time.clock()
if days is None:
days_to_use = self.daysToUse
num_md = self.num_mousedays
else:
days_to_use = days
num_md, _ = self.count_mousedays(days=days_to_use)
print "Exp: %s, %s, %s, ONSET: %s, cycle: %s, GENERATE:%s" % (
self.short_name, self.generate_breakfast_data.__name__, act, ONSET,
cycle, GENERATE)
num_bins = int(num_mins * 60 / tbin_size)
text = 'AS_onset' if ONSET else 'AS_offset'
md_data = np.zeros((num_md, num_bins))
md_labels = np.zeros((num_md, 3), dtype=int)
cnt = 0
for group in self.groups:
for mouse in group.individuals:
for MD in mouse.mouse_days:
if MD.dayNumber in days_to_use:
if MD.ignored:
md_data[cnt] = np.nan
else:
md_data[cnt] = MD.generate_breakfast_data(
cycle, act, ONSET, num_mins, tbin_size,
GENERATE)
md_labels[
cnt] = MD.groupNumber, MD.mouseNumber, MD.dayNumber
if not VERBOSE:
my_utils.print_progress(cnt, self.num_md_ok)
else:
print MD
cnt += 1
cstop = time.clock()
if GENERATE:
if not VERBOSE:
print
dirname = self.breakfast_dir + \
'%s/%s/prob_%dmin_tbin%ds_%s/' %(
act, text, num_mins, tbin_size, cycle)
print "binary output saved to: %s" % dirname
print "..took %1.2f minutes" % ((cstop - cstart) / 60.)
E = self
data, labels = my_utils.get_1d_averages_errors(E, md_data, md_labels,
level, err_type,
group_avg_type)
return data, labels
def generate_time_budgets(self,
cycle='24H',
level='mouseday',
err_type='sd',
AS=False,
days=None,
group_avg_type='over_mds',
GENERATE=False,
VERBOSE=False):
cstart = time.clock()
if days is None:
days_to_use = self.daysToUse
num_md = self.num_mousedays
else:
days_to_use = days
num_md, _ = self.count_mousedays(days=days_to_use)
print "Exp: %s, %s, %s" % (self.short_name,
self.generate_time_budgets.__name__, cycle)
num_act = 5 if not AS else 4 #move, feed, drink, other_AS, inactive
md_data = np.zeros((num_md, num_act))
md_labels = np.zeros((num_md, 3), dtype=int)
cnt = 0
for group in self.groups:
for mouse in group.individuals:
for MD in mouse.mouse_days:
if MD.dayNumber in days_to_use:
if MD.ignored:
md_data[cnt] = np.nan
else:
md_data[cnt] = MD.generate_time_budgets(
cycle, num_act, GENERATE)
md_labels[
cnt] = MD.groupNumber, MD.mouseNumber, MD.dayNumber
if not VERBOSE:
my_utils.print_progress(cnt, self.num_md_ok)
else:
print MD
cnt += 1
cstop = time.clock()
if GENERATE:
if not VERBOSE:
print
dirname = self.time_budgets_dir + '%s/' % cycle
print "binary output saved to: %s" % dirname
print "..took %1.2f minutes" % ((cstop - cstart) / 60.)
E = self
data, labels = my_utils.get_1d_averages_errors(E, md_data, md_labels,
level, err_type)
return data, labels
def generate_feature_vectors(self,
feature='ASP',
level='mouseday',
bin_type='12bins',
err_type='sd',
days=None,
group_avg_type='over_mds',
GENERATE=False,
VERBOSE=False):
"""
"""
cstart = time.clock()
num_bins = int(bin_type.strip('bins').strip('AS').strip('cycles'))
# days_to_use = self.daysToUse if days is None else days
if days is None:
days_to_use = self.daysToUse
num_md = self.num_mousedays
else:
days_to_use = days
num_md, _ = self.count_mousedays(days=days_to_use)
print "--Exp: %s, %s\n%s, %s, bin_type: %s, err_type: %s,\ndays: %s, BIN_SHIFT: %s" % (
self.short_name, self.generate_feature_vectors.__name__, feature,
level, bin_type, err_type, days_to_use, self.BIN_SHIFT)
md_data = np.zeros((num_md, num_bins))
md_labels = np.zeros((num_md, 3), dtype=int)
cnt = 0
for group in self.groups:
for mouse in group.individuals:
for MD in mouse.mouse_days:
if MD.dayNumber in days_to_use:
if MD.ignored:
# md_data.append(np.nan)
md_data[cnt] = np.nan
else:
# md_data.append(MD.generate_feature_vector(feature, bin_type, GENERATE, VERBOSE))
md_data[cnt] = MD.generate_feature_vector(
feature, bin_type, GENERATE, VERBOSE)
# md_labels.append((MD.groupNumber, MD.mouseNumber, MD.dayNumber))
md_labels[
cnt] = MD.groupNumber, MD.mouseNumber, MD.dayNumber
if GENERATE and not VERBOSE:
my_utils.print_progress(cnt, self.num_md_ok)
cnt += 1
cstop = time.clock()
if GENERATE:
if not VERBOSE:
print
string = '_shifted%+02dm' % (self.binTimeShift /
60) if self.BIN_SHIFT else ''
dirname = self.features_dir + 'vectors_CT/%s/%s%s/' % (
feature, bin_type, string)
print "binary output saved to: %s" % dirname
print "..took %1.2f minutes" % ((cstop - cstart) / 60.)
E = self
data, labels = my_utils.get_1d_averages_errors(E, md_data, md_labels,
level, err_type,
group_avg_type)
return data, labels
