def count_onsets_in_bin_joint(I, tbin):
"""for non-disjoint time bin, returns
- AS/Bout(I) time in bin, strict sense (intersected with bin)
- counts, onset-based
- I effective times in bin, onset-based
- I effective endpoints in bin, onset-based
"""
# time in AS/Bout, strictly inside bin
_I = Intervals(I).intersect(Intervals(tbin)).intervals
I_times = np.diff(_I).T[0] if len(_I) > 0 else np.array([])
# effective time in AS/Bout, onset-sensitive
I_times_eff = []
bin_start, bin_end = tbin
cnt = 0 # onsets
for start, end in I:
if (start > bin_start and start < bin_end):
I_times_eff.append(end - start)
if cnt < 1:
I_start = start
I_end = end
cnt +=1
if cnt == 0:
np.testing.assert_allclose(np.array(I_times_eff).sum(), 0, rtol=1e-5)
return I_times, 0, np.array([]), np.array([])
tbin_eff = np.array([[I_start, I_end]]) # I endpoints in bin
return I_times, cnt, np.array(I_times_eff), tbin_eff
def count_onsets_in_bin_disjoint(I, tbins):
"""same for disjoint bin, e.g. LC
"""
# time in AS/Bout, strictly
_I = Intervals(I).intersect(Intervals(tbins)).intervals
I_times = np.diff(_I).T[0] if len(_I) > 0 else np.array([])
# time in AS/Bout, onset-based
I_times_eff = []
cnt = 0 # counts, onset-based
I_endpoints = [] # I endpoints in bin, onset-based
for tbin in tbins:
_, _cnt, _I_times_eff, _tbin_eff = count_onsets_in_bin_joint(I, tbin)
cnt += _cnt
if _cnt > 0:
I_times_eff.extend(list(_I_times_eff))
I_endpoints.append(_tbin_eff)
if cnt == 0:
np.testing.assert_allclose(I_times, 0, rtol=1e-5)
np.testing.assert_allclose(I_times_eff, 0, rtol=1e-5)
return np.array([]), 0, np.array([]), np.array([])
if len(I_endpoints) == 1:
tbin_eff = I_endpoints[0] # np.array
elif len(I_endpoints) == 2:
tbin_eff = np.vstack([I_endpoints[0], I_endpoints[1]])
return I_times, cnt, np.array(I_times_eff), tbin_eff
def check_ingestion_bouts_overlap(fbouts, dbouts):
overlap = Intervals(fbouts).intersect(Intervals(dbouts))
# fdur, ddur = np.diff(f_bouts).T[0], np.diff(d_bouts).T[0]
if not overlap.is_empty():
overlap_diff = np.diff(overlap.intervals).T[0]
for n in xrange(len(overlap_diff)):
logger.error("feeding and drinking bouts: found overlap at CT{} for {:02.3f}sec".format(
hcm_time_to_ct_string_float(overlap.intervals[n, 0]), overlap_diff[n]))
def build_boxes(self):
intervals = Intervals()
intervals.interval_type = self.interval_type
intervals.x = self.x
intervals.start = self.start
intervals.finish = self.finish
intervals.resolution = self.resolution
intervals.week_start = self.week_start
box = Rectangle()
box.y = self.y
box.height = self.height
box.border_rounding = self.box_rounding
box.border_color = self.box_border_color
box.border_width = self.box_border_width
boxes = str()
for i in intervals.get_intervals():
box.x = i[0]
box.width = i[1]
if i[4] is False:
box.fill_color = self.ends
else:
box.fill_color = self.box_fill
boxes += box.svg
return boxes
def build_grid(self):
intervals = Intervals()
intervals.interval_type = self.interval_type
intervals.x = self.x
intervals.start = self.start
intervals.finish = self.finish
intervals.resolution = self.resolution
intervals.week_start = self.week_start
line = Line()
line.y = self.y
line.dy = self.y + self.height
line.stroke_color = self.line_color
line.stroke_width = self.line_width
line.stroke_dasharray = self.line_dashing
lines = str()
for i in intervals.get_intervals():
line.x = i[0]
line.dx = line.x
lines += line.svg
last_line = self.x + ((self.finish - self.start) * self.resolution)
line.x = last_line
line.dx = last_line
lines += line.svg
return lines
def get_timebin_in_recording_time(timebin, rec, ass):
arr = None
if timebin == '24H':
arr = rec
elif timebin in ['DC', 'LC']:
arr = Intervals(get_timebins(timebin)[0]).intersect(Intervals(rec)).intervals
elif timebin == 'AS24H':
arr = ass
elif timebin in ['ASDC', 'ASLC']:
arr = Intervals(ass).intersect(Intervals(get_timebins(timebin[-2:])[0])).intervals
return arr, np.diff(arr).sum()
def index_ingestion_bout_and_homebase_timestamps(t, idx, fbouts, dbouts):
"""returns a mask which excludes timestamps indexes corresponding to ingestion bouts
and position at homebase
"""
i_fdb = Intervals(fbouts).union(Intervals(dbouts))
mask = np.ones(t.shape[0], dtype=bool)
for timestamp in xrange(t.shape[0]):
if i_fdb.contains(t[timestamp]):
mask[timestamp] = False
mask = mask & idx
log_text = "locomotion: flagged {} events occurring at homebase and/or during ingestion bouts".format(
mask.shape[0] - mask.sum())
return mask, log_text
def make_mode(self, n, mode):
'''Re-arranges the intervals of this scale into a new scale'''
# get the key distance to adjust all others by
key_dist = self.intervals[mode - 1].distance
adj_dist = []
# build a list of distances
for i in range(len(self.intervals)):
# find the interval index for this iteration with
# respect to the requested mode
step_idx = (i + (mode - 1)) % len(self.intervals)
# pull out the distance for the interval and adjust
# it by the distance of the mother-key's step
step_dist = self.intervals[step_idx].distance - key_dist
# constrain the distance to within the chromatic scale
if step_dist < 0:
step_dist += 12
# get the interval and add it to the list
adj_dist.append(Intervals.by_distance(step_dist))
# create the scale and send it out
return Scale(n, adj_dist)
def build_labels(self):
intervals = Intervals()
intervals.interval_type = self.interval_type
intervals.x = self.x
intervals.start = self.start
intervals.finish = self.finish
intervals.resolution = self.resolution
intervals.week_start = self.week_start
date = Date()
date.week_start = self.week_start
date.separator = self.separator
date.date_format = self.date_format
label = Text()
label.text_y = self.y
label.text_translate_y = self.text_y
label.text_translate_x = self.text_x
label.font_fill_color = self.font_fill
label.font_size = self.font_size
label.font_weight = self.font_weight
label.font_family = self.font_family
label.font_style = self.font_style
labels = str()
if self.label_type == 'hidden':
label.text_visibility = 'hidden'
for i in intervals.get_intervals():
label.text_x = i[0]
if i[1] < self.min_label_width:
label.text = str(
) # you could set visibility to hidden but more verbose
elif self.label_type == 'count' and i[3] == 0:
label.text = str(
) # you could set visibility to hidden but more verbose
elif self.label_type == 'date':
date.ordinal_date = i[2]
label.text = date.get_date()
else:
label.text = i[3] # references count in intervals entry
labels += label.svg
return labels
def get_timebin_category(tbins, bin_type):
""" assigns timebin to a category based on start and end times
each time of day is coded with a number:
- cat_code1, primary
- 1 : LC, CT06-12 union CT24-06
- 2 : DC, CT12-18
- cat_code2, secondary
- 1 : CT06-12, or last part of LC, or LC2
- 2 : CT12-18, or first part of DC, or DC1
- 3 : CT18-24, or second part of DC, or DC2
- 4 : CT24-06, or first part of LC, or LC1
categories are formed by pairing numbers for start and end.
categories '13' (primary) and '14' (secondary) ought to be rare
returns cateogry code, descriptions and proportion of time spent in DC and LC
"""
# seconds after midnight
dc_start = 19 * 3600. # CT12
dc_mid = 25 * 3600. # CT18
dc_end = 31 * 3600. # CT24
starts, ends = np.array(tbins).T
# primary, DC and LC
bins = [0, dc_start, dc_end, 1000000]
inds1 = np.array([np.digitize(x, bins) for x in [starts, ends]]).T
inds1 = recode_indices1(inds1, bin_type)
cat_code1 = [''.join(str(i) for i in ind) for ind in inds1]
# secondary, day divided in 4 bins
bins = [0, dc_start, dc_mid, dc_end, 1000000]
inds2 = np.array([np.digitize(x, bins) for x in [starts, ends]]).T
if not bin_type.startswith('AS'):
inds2 = recode_inds2(inds2, bin_type)
cat_code2 = [''.join(str(i) for i in ind) for ind in inds2]
# proportions in LC and DC
dc, lc = [Intervals(get_timebins('3cycles')[x]) for x in [1, 2]]
return cat_code1, [AS_code_lookup['1'][x] for x in cat_code1], cat_code2, [AS_code_lookup['2'][x] for x in
cat_code2], [
Intervals(x).intersect(dc).measure() / Intervals(x).measure() for x in tbins], [
Intervals(x).intersect(lc).measure() / Intervals(x).measure() for x in tbins]
def plus(self, element):
if element.key == "!%s" % self.key or self.key == "!%s" % element.key:
return Element([(Intervals({}), Formula(sympy.S(1.0)))], "t")
if (self.key == "f"):
key = element.key
elif element.key == "f":
key = self.key
else:
key = "(%s + %s)" % (self.key, element.key)
combined = Element(self.list + element.list, key)
# print self, " + ", element, " = ", sum
return combined
def check_ingestion_position_concurrency(tset_raw, tset_at_loc, loc='F'):
""" check device events and position at device concurrency
returns array with corrected events and errors removed
this function is not used starting May 8th, 2018
"""
i_raw = Intervals(tset_raw)
i_at_device = Intervals(tset_at_loc)
i_true = i_raw.intersect(i_at_device)
tset_errors = (i_raw - i_true).intervals # photobeam firing when mouse not at device
np.testing.assert_almost_equal(np.diff(tset_raw).sum(),
np.diff(tset_errors).sum() + np.diff(i_true.intervals).sum(), decimal=2)
num_errors = len(tset_errors)
tot = i_raw.intervals.shape[0]
err_time = np.diff(tset_errors).sum() / 60.
error_msg = ""
if num_errors:
# todo: check this is working. plot on rasters
tset = i_true.intervals
error_msg = "{}: {}/{} events removed, device firing while mouse not at device " \
"(total time involved={:.2f} min)".format(act_to_actlabel[loc], num_errors, tot, err_time)
else:
tset = tset_raw
return tset, tset_errors, error_msg
# Tecott Lab HCM Data
# working with AS/IS, IS Duration Thresholds (ISDT)
# using class intervals objects
# C. Hillar, Jan 2016
from __future__ import print_function, absolute_import, division
import numpy as np
from intervals import Intervals
Events = Intervals([[-2, -1], [0, 1], [3, 5], [8, 11]])
ISDT = 2 # IST Threshold
ECG = Events.copy().connect_gaps(ISDT) # connect gaps <= ISDT
ETm = Events.copy().trim(ISDT) # trim inteversl <= ISDT
print("Events (%d intervals):" % Events.num(), Events)
# print ("Events connected gaps <= %1.3f:" % ISDT,
# Events.copy().connect_gaps(ISDT))
print("Events trim intervals <= %1.3f:" % ISDT, Events.copy().trim(ISDT))
print("IS/AS computation version 1")
IS1 = Events.complement().trim(ISDT) # complement is new object
AS1 = IS1.complement()
print("IS (%d):" % IS1.num(), IS1)
print("AS (%d):" % AS1.num(), AS1)
print("IS/AS computation version 2 (mathematically equivalent)")
AS2 = Events.copy().connect_gaps(ISDT) # trim alters object
IS2 = AS2.complement()
print("AS2 (%d):" % AS2.num(), AS2)
print("IS2 (%d):" % IS2.num(), IS2)
from intervals import Intervals
from notes import Notes
# read intervals out for reference
peru = Intervals.by_distance(0)
min2 = Intervals.by_distance(1)
maj2 = Intervals.by_distance(2)
min3 = Intervals.by_distance(3)
maj3 = Intervals.by_distance(4)
per4 = Intervals.by_distance(5)
trit = Intervals.by_distance(6)
per5 = Intervals.by_distance(7)
min6 = Intervals.by_distance(8)
maj6 = Intervals.by_distance(9)
min7 = Intervals.by_distance(10)
maj7 = Intervals.by_distance(11)
class Scale(object):
'''Defines a collection of intervals'''
def __init__(self, n, inters):
'''Creates a scale instance'''
self.name = n
self.intervals = inters
def voice(self, key):
'''Voices this scale in a particular key'''
# get a chromatic list of notes
chromatic = Scales.make_chromatic(key)
steps = []
# Tecott Lab HCM Data
# working with AS/IS, IS Duration Thresholds (ISDT)
# using class intervals objects
# C. Hillar, Jan 2016
from __future__ import print_function, absolute_import, division
import numpy as np
from intervals import Intervals
Events = Intervals([[-2, -1], [0, 1], [3, 5], [8, 11]])
ISDT = 2 # IST Threshold
ECG = Events.copy().connect_gaps(ISDT) # connect gaps <= ISDT
ETm = Events.copy().trim(ISDT) # trim inteversl <= ISDT
print("Events (%d intervals):" % Events.num(), Events)
# print ("Events connected gaps <= %1.3f:" % ISDT,
# Events.copy().connect_gaps(ISDT))
print("Events trim intervals <= %1.3f:" % ISDT, Events.copy().trim(ISDT))
print("IS/AS computation version 1")
IS1 = Events.complement().trim(ISDT) # complement is new object
AS1 = IS1.complement()
print("IS (%d):" % IS1.num(), IS1)
print("AS (%d):" % AS1.num(), AS1)
print("IS/AS computation version 2 (mathematically equivalent)")
AS2 = Events.copy().connect_gaps(ISDT) # trim alters object
IS2 = AS2.complement()
print("AS2 (%d):" % AS2.num(), AS2)
def intersect_arrays(arr1, arr2):
return Intervals(arr1).intersect(Intervals(arr2)).intervals
def wipe_data_outside_CT6_30(I):
bin_24h = get_CT_bins(bin_type='24H')
stop
return Intervals(I).intersect(Intervals(bin_24h)).intervals
def zero(self):
return Element([(Intervals({}), Formula(self.neutral))],
"f") # TODO empty intervals?
def one(self):
return Element([(Intervals({}), Formula(sympy.S(1.0)))], "t")
def pos_value(self, a, key=None):
m = re.search(r"w\((.*),.*,(.*)\)", str(a))
return Element(
[(Intervals.create(m.group(2)), Formula.create(m.group(1)))], key)
def intersect_timeset_with_timebin(tset, tbin):
return Intervals(tset).intersect(
Intervals(tbin)).intervals # todo: try: Intervals(tset).intersect_with_interval(tbin[0], tbin[1] # faster
def neg_value(self, a, key=None):
m = re.search(r"w\(.*,(.*),(.*)\)", str(a)) # TODO: aanpassing
return Element([(Intervals({}), Formula.create(m.group(1)))],
"!" + str(key))
for day in range(mice[mouse]):
arr = np.load('data/intervals/%s/%s_strain%d_mouse%d_day%d.npy' %
(event, event, i, mouse, day))
mices[mouse][day] = arr
strain_intervals[i] = mices
fmfs = first_mouse_first_strain = strain_intervals[0][0]
nd = nday_this_mouse = len(fmfs)
# number of AS (& time) are there on avg for this mouse per day
cnts = np.zeros(nd)
ttimesec = np.zeros(nd)
for c, md in enumerate(fmfs):
cnts[c] = md.shape[0]
ttimesec[c] = Intervals(md).measure() # some Intervals functionality
# print "%1.3f Active States (AS) (%1.3f sec on avg) per its %d days " %
# (cnts.mean(), ttimesec.mean(), nd)
# Turn this set of ASs into binary sequence
bin_AS = binary_from_intervals(Intervals(fmfs[0]))
plt.figure()
plt.plot(bin_AS)
plt.ylim([-.1, 1.1])
plt.xlabel('Time step from first AS [sec]')
plt.ylabel('Active State (1) / Inactive State (0)')
plt.title('Active States as binary sequence')
##################################
# (3) Make position density first mouse first day
##################################