def get_TR_offset_stats(self, tr):
"""create a list of TR offsets (per-run and overall)
tr : must be positive
return: 8 values in a list:
min, mean, maxabs, stdev of absolute and fractional offsets
empty list on error
"""
if not self.ready:
print('** M Timing: nothing to compute ISI stats from')
return []
if self.nrows != len(self.data):
print('** bad MTiming, nrows=%d, datalen=%d, failing...' % \
(self.nrows, len(self.data)))
return []
if tr < 0.0:
print('** show_TR_offset_stats: invalid TR %s' % tr)
return []
tr = float(tr) # to be sure
# make a copy of format run x stim x [start,end], i.e. is 3-D
tdata = self.get_start_end_timing()
offsets = [] # stim offsets within given TRs
for rind in range(self.nrows):
run = tdata[rind]
if len(run) == 0: continue
roffsets = UTIL.interval_offsets([val[0] for val in run], tr)
offsets.extend(roffsets)
if len(offsets) < 1: return []
# get overall stats (absolute and fractional)
# absolute
m0, m1, m2, s = UTIL.min_mean_max_stdev(offsets)
offmn = m0
offm = m1
offs = s
mn = abs(min(offsets))
offmax = abs(max(offsets))
if mn > offmax: offmax = mn
# fractional
for ind, val in enumerate(offsets):
offsets[ind] = val / tr
m0, m1, m2, s = UTIL.min_mean_max_stdev(offsets)
del (offsets)
return [offmn, offm, offmax, offs, m0, m1, offmax / tr, s]
def get_TR_offset_stats(self, tr):
"""create a list of TR offsets (per-run and overall)
tr : must be positive
return: 8 values in a list:
min, mean, maxabs, stdev of absolute and fractional offsets
empty list on error
"""
if not self.ready:
print '** M Timing: nothing to compute ISI stats from'
return []
if self.nrows != len(self.data):
print '** bad MTiming, nrows=%d, datalen=%d, failing...' % \
(self.nrows, len(self.data))
return []
if tr < 0.0:
print '** show_TR_offset_stats: invalid TR %s' % tr
return []
# make a copy of format run x stim x [start,end], i.e. is 3-D
tdata = self.get_start_end_timing()
offsets = [] # stim offsets within given TRs
for rind in range(self.nrows):
run = tdata[rind]
if len(run) == 0: continue
roffsets = UTIL.interval_offsets([val[0] for val in run], tr)
offsets.extend(roffsets)
if len(offsets) < 1: return []
# get overall stats (absolute and fractional)
# absolute
m0, m1, m2, s = UTIL.min_mean_max_stdev(offsets)
offmn = m0; offm = m1; offs = s
mn = abs(min(offsets))
offmax = abs(max(offsets))
if mn > offmax: offmax = mn
# fractional
for ind, val in enumerate(offsets):
offsets[ind] = val/tr
m0, m1, m2, s = UTIL.min_mean_max_stdev(offsets)
del(offsets)
return [offmn, offm, offmax, offs, m0, m1, offmax/tr, s]
def get_TR_offset_stats_str(self, tr, mesg='', wlimit=0.4):
"""return a string to display statistics regarding within-TR
offsets of stimuli
tr : show mean/stdev for stimuli within TRs
(so 0 <= mean < tr)
mesg : display the user message in the output
return status, stats string
status > 0 : success, warnings were issued
= 0 : success, no warnings
< 0 : errors
"""
if not self.ready:
return 1, '** M Timing: nothing to compute ISI stats from'
if self.nrows != len(self.data):
return 1, '** bad MTiming, nrows=%d, datalen=%d, failing...' % \
(self.nrows, len(self.data))
if tr < 0.0:
return 1, '** show_TR_offset_stats: invalid TR %s' % tr
off_means = [] # ... means per run
off_stdev = [] # ... stdevs per run
for rind in range(self.nrows):
run = self.data[rind]
if len(run) == 0: continue
# start with list of time remainders (offsets) within each TR
roffsets = UTIL.interval_offsets([val for val in run], tr)
m0, m1, m2, s = UTIL.min_mean_max_stdev(roffsets)
off_means.append(m1)
off_stdev.append(s)
# if no events ere found, we're outta here
if len(off_means) == 0:
print 'file %s: no events?' % self.name
return 0, ''
# and get overall stats (absolute and fractional)
offs = self.get_TR_offset_stats(tr)
# print out offset info
if mesg: mstr = '(%s) ' % mesg
else: mstr = ''
rstr = '\nwithin-TR stimulus offset statistics %s:\n' % mstr
hdr1 = ' overall: '
hdr2 = ' fractional: '
shdr = ' '
rv = 0
if self.nrows > 1:
rstr += ' per run\n' \
' ------------------------------\n' \
' offset means %s\n' \
' offset stdevs %s\n' \
'\n' \
% (float_list_string(off_means,ndec=3),
float_list_string(off_stdev,ndec=3))
else: hdr1 = ' one run: '
rstr += '%smean = %.3f maxoff = %.3f stdev = %.4f\n' \
% (hdr1, offs[1], offs[2], offs[3])
rstr += '%smean = %.3f maxoff = %.3f stdev = %.4f\n' \
% (hdr2, offs[5], offs[6], offs[7])
# a warning may be issued if the min is positive and the max is small
if offs[6] == 0: rstr += '\n%s(stimuli are TR-locked)\n' % shdr
elif wlimit > 0.0 and offs[4] > 0 and offs[6] < wlimit:
rstr += '\n' \
'%s** WARNING: small maxoff suggests (almost) TR-locked stimuli\n'\
'%s consider: timing_tool.py -round_times (if basis = TENT)\n' \
%(shdr,shdr)
rv = 1
# clean up, just to be kind
del(off_means); del(off_stdev)
return rv, rstr
def get_TR_offset_stats_str(self, tr, mesg='', wlimit=0.4):
"""return a string to display statistics regarding within-TR
offsets of stimuli
tr : show mean/stdev for stimuli within TRs
(so 0 <= mean < tr)
mesg : display the user message in the output
return status, stats string
status > 0 : success, warnings were issued
= 0 : success, no warnings
< 0 : errors
"""
if not self.ready:
return 1, '** M Timing: nothing to compute ISI stats from'
if self.nrows != len(self.data):
return 1, '** bad MTiming, nrows=%d, datalen=%d, failing...' % \
(self.nrows, len(self.data))
if tr < 0.0:
return 1, '** show_TR_offset_stats: invalid TR %s' % tr
off_means = [] # ... means per run
off_stdev = [] # ... stdevs per run
for rind in range(self.nrows):
run = self.data[rind]
if len(run) == 0: continue
# start with list of time remainders (offsets) within each TR
roffsets = UTIL.interval_offsets([val for val in run], tr)
m0, m1, m2, s = UTIL.min_mean_max_stdev(roffsets)
off_means.append(m1)
off_stdev.append(s)
# if no events ere found, we're outta here
if len(off_means) == 0:
print 'file %s: no events?' % self.name
return 0, ''
# and get overall stats (absolute and fractional)
offs = self.get_TR_offset_stats(tr)
# print out offset info
if mesg: mstr = '(%s) ' % mesg
else: mstr = ''
rstr = '\nwithin-TR stimulus offset statistics %s:\n' % mstr
hdr1 = ' overall: '
hdr2 = ' fractional: '
shdr = ' '
rv = 0
if self.nrows > 1:
rstr += ' per run\n' \
' ------------------------------\n' \
' offset means %s\n' \
' offset stdevs %s\n' \
'\n' \
% (float_list_string(off_means,ndec=3),
float_list_string(off_stdev,ndec=3))
else:
hdr1 = ' one run: '
rstr += '%smean = %.3f maxoff = %.3f stdev = %.4f\n' \
% (hdr1, offs[1], offs[2], offs[3])
rstr += '%smean = %.3f maxoff = %.3f stdev = %.4f\n' \
% (hdr2, offs[5], offs[6], offs[7])
# a warning may be issued if the min is positive and the max is small
if offs[6] == 0: rstr += '\n%s(stimuli are TR-locked)\n' % shdr
elif wlimit > 0.0 and offs[4] > 0 and offs[6] < wlimit:
rstr += '\n' \
'%s** WARNING: small maxoff suggests (almost) TR-locked stimuli\n'\
'%s consider: timing_tool.py -round_times (if basis = TENT)\n' \
%(shdr,shdr)
rv = 1
# clean up, just to be kind
del (off_means)
del (off_stdev)
return rv, rstr