def show_isi_stats(self, mesg='', run_len=[], tr=0, rest_file=''):
"""display ISI timing statistics
mesg : display the user message first
run_len : can be empty, length 1 or length nrows
tr : if > 0: show mean/stdev for stimuli within TRs
(so 0 <= mean < tr)
rest_file : if set, save all rest durations
display these statistics:
- total time, total stim time, total rest time
- total time per run
- total stim time per run
- total rest time per run
- pre-stim rest per run
- post-stim response rest per run (if run_len is given)
- total ISI rest per run
- min/mean/max (stdev) of stim duration
- min/mean/max (stdev) of ISI rest
"""
if not self.ready:
print '** M Timing: nothing to compute ISI stats from'
return 1
if not (self.mtype & LD.MTYPE_DUR):
print '** warning: computing stats without duration'
if self.nrows != len(self.data):
print '** bad MTiming, nrows=%d, datalen=%d, failing...' % \
(self.nrows, len(self.data))
return 1
# make a sorted copy
scopy = self.copy()
scopy.sort()
# make a copy of format run x stim x [start,end], i.e. is 3-D
tdata = scopy.get_start_end_timing()
# make an updated run lengths list
if len(run_len) == 0:
rlens = [0 for rind in range(self.nrows)]
elif len(run_len) == 1:
rlens = [run_len[0] for rind in range(self.nrows)]
elif len(run_len) == self.nrows:
rlens = run_len
else: # failure
print '** invalid len(run_len)=%d, must be one of 0,1,%d' % \
(len(run_len), self.nrows)
return 1
if self.verb > 1:
print '-- show_isi_stats, run_len = %s, tr = %s, rest_file = %s' \
% (run_len, tr, rest_file)
if self.verb > 3:
print scopy.make_data_string(nplaces=1, flag_empty=0, check_simple=0,
mesg='scopy data')
all_stim = [] # all stimulus durations (one row per run)
all_isi = [] # all isi times (one row per run)
pre_time = [] # pre-stim, per run
post_time = [] # pose-stim, per run
run_time = [] # total run time, per run
errs = 0 # allow a few errors before failing
max_errs = 10
for rind in range(self.nrows):
run = tdata[rind]
rlen = rlens[rind]
if len(run) == 0: # empty run
all_stim.append([])
all_isi.append([])
pre_time.append(rlen)
post_time.append(0.0)
run_time.append(rlen)
continue
# if no run len specified, use end of last stimulus
if rlen == 0.0: rlen = run[-1][1]
elif rlen < run[-1][1]:
print '** run %d: given length = %s, last stim ends at %s' % \
(rind+1, rlen, run[-1][1])
errs += 1
if errs > max_errs:
print '** bailing...'
return 1
# pre- and post-stim times are set
pre = run[0][0]
post = rlen - run[-1][1]
if pre < 0:
print '** ISI error: first stimulus of run %d at negative time %s'%\
(rind+1, run[0][0])
errs += 1
if errs > max_errs:
print '** bailing...'
return 1
# init accumulation vars
stimes = [run[0][1] - run[0][0]]
itimes = []
# for each following index, update stim and isi times
# (check for bad overlap)
for sind in range(1, len(run)):
if run[sind][0] < run[sind-1][1]:
print '** ISI error: stimuli overlap at run %d, time %s' % \
(rind+1, run[sind][0])
errs += 1
if errs > max_errs:
print '** bailing...'
return 1
stimes.append(run[sind][1]-run[sind][0])
itimes.append(run[sind][0]-run[sind-1][1])
# store results
all_stim.append(stimes)
all_isi.append(itimes)
pre_time.append(pre)
post_time.append(post)
run_time.append(rlen)
if errs > 0: return 1
# tally the results
rtot_stim = [] ; rtot_isi = [] ; rtot_rest = []
stim_list = [] ; isi_list = [] ; nstim_list = []
for rind in range(self.nrows):
rtot_stim.append(UTIL.loc_sum(all_stim[rind]))
rtot_rest.append(pre_time[rind] + UTIL.loc_sum(all_isi[rind]) +
post_time[rind])
rtot_isi.append(UTIL.loc_sum(all_isi[rind]))
stim_list.extend(all_stim[rind])
isi_list.extend(all_isi[rind])
nstim_list.append(len(all_stim[rind]))
if mesg: mstr = '(%s) ' % mesg
else: mstr = ''
print '\nISI statistics %s:\n' % mstr
print ' total per run'
print ' ------ ------------------------------'
print ' total time %6.1f %s' % \
(UTIL.loc_sum(run_time), float_list_string(run_time, ndec=1))
print ' total time: stim %6.1f %s' % \
(UTIL.loc_sum(rtot_stim),float_list_string(rtot_stim,7,ndec=1))
print ' total time: rest %6.1f %s' % \
(UTIL.loc_sum(rtot_rest),float_list_string(rtot_rest,7,ndec=1))
print ''
print ' rest: total isi %6.1f %s' % \
(UTIL.loc_sum(rtot_isi), float_list_string(rtot_isi,7,ndec=1))
print ' rest: pre stim %6.1f %s' % \
(UTIL.loc_sum(pre_time), float_list_string(pre_time,7,ndec=1))
print ' rest: post stim %6.1f %s' % \
(UTIL.loc_sum(post_time),float_list_string(post_time,7,ndec=1))
print ''
print ' num stimuli %6d %s' % \
(UTIL.loc_sum(nstim_list), float_list_string(nstim_list,7,ndec=0))
print '\n'
print ' min mean max stdev'
print ' ------- ------- ------- -------'
print ' rest: pre-stim %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(pre_time))
print ' rest: post-stim %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(post_time))
print ''
for ind in range(self.nrows):
m0, m1, m2, s = UTIL.min_mean_max_stdev(all_isi[ind])
print ' rest: run #%d ISI %7.3f %7.3f %7.3f %7.3f' % \
(ind, m0, m1, m2, s)
print ''
print ' all runs: ISI %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(isi_list))
print ' all runs: stimuli %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(stim_list))
print ''
# and possibly print out offset info
if tr > 0: self.show_TR_offset_stats(tr, '')
# maybe write all rest durations
if rest_file:
all_rest = copy.deepcopy(all_isi)
for run, rest in enumerate(all_rest):
rest[:0] = [pre_time[run]]
rest.append(post_time[run])
UTIL.write_to_timing_file(all_rest, rest_file)
# clean up, just to be kind
del(all_stim); del(all_isi); del(pre_time); del(post_time); del(run_time)
del(rtot_stim); del(rtot_isi); del(rtot_rest); del(stim_list)
del(isi_list); del(nstim_list)
del(scopy)
del(tdata)
def proc_mats(uopts):
offset = 0.0 # offset for output times
if uopts == None: return
opt = uopts.find_opt('-verb')
if opt:
try:
verb = int(opt.parlist[0])
except:
print("** error: verb must be int, have '%s'" % opt.parlist[0])
return
else:
verb = 0
opt = uopts.find_opt('-files')
files = opt.parlist
consec_ok = (uopts.find_opt('-no_consec') == None)
# set run_trs nruns from either -run_trs or -nruns and -nt
opt = uopts.find_opt('-run_trs')
if opt:
val, err = uopts.get_type_list(int, '', opt=opt)
if err: return 1
run_trs = val
nruns = len(run_trs)
if uopts.find_opt('-nruns') or uopts.find_opt('-nt'):
print('** please use either -run_trs or -nt/-nruns')
return 1
else:
if not uopts.find_opt('-nruns') or not uopts.find_opt('-nt'):
print('** please use either -run_trs or both -nt and -nruns')
return 1
opt = uopts.find_opt('-nruns')
nruns = int(opt.parlist[0])
opt = uopts.find_opt('-nt')
try:
nt = int(opt.parlist[0])
except:
print("** error: -nt must be int, have '%s'" % opt.parlist[0])
return
run_trs = [nt] * nruns
# note the total number of TRs, regardless
ntotal = afni_util.loc_sum(run_trs)
opt = uopts.find_opt('-offset')
if opt:
try:
offset = float(opt.parlist[0])
except:
print("** error: offset must be float, have '%s'" % opt.parlist[0])
return
opt = uopts.find_opt('-prefix')
prefix = opt.parlist[0]
opt = uopts.find_opt('-tr')
try:
tr = float(opt.parlist[0])
except:
print("** error: TR must be float, have '%s'" % opt.parlist[0])
return
opt = uopts.find_opt('-labels')
if opt: labels = opt.parlist
else: labels = []
nlab = len(labels)
# print some info
if verb: print("-- run_trs = %s, TR = %s, %d labels" \
% (run_trs, str(tr), nlab))
# new option, -amplitudes (columns of amplitudes to Marry, not just 1s)
use_amp = 0
opt = uopts.find_opt('-amplitudes')
if opt:
use_amp = 1
if verb: print('-- using amplitudes to Marry with times...')
newfile_index = 1 # index over output files
for fname in files:
tmat = TD.read_1D_file(fname, verb=verb)
if not tmat:
print("read_1D_file failed for file: %s" % fname)
return
mat = afni_util.transpose(tmat)
del (tmat)
if len(mat[0]) < ntotal:
print('** error: file %s has only %d entries (%d required)' % \
(fname, len(mat[0]), ntotal))
return
elif len(mat[0]) > ntotal:
print('** warning: file %s has %d entries (expected only %d)' % \
(fname, len(mat[0]), ntotal))
for row in mat:
# maybe add a label to the file name
if newfile_index <= nlab: label = ".%s" % labels[newfile_index - 1]
elif nlab == 0: label = ""
else:
print("** %d labels given, but we are on column %d..." % \
(nlab, newfile_index))
label = ".label%d" % (newfile_index)
newp = "%s.%02d%s" % (prefix, newfile_index, label)
newfile = afni_util.change_path_basename(fname, newp + ".1D")
if newfile == None: return
if prefix == '-' or prefix == 'stdout': fp = sys.stdout
elif prefix == 'stderr': fp = sys.stderr
else: fp = open(newfile, 'w')
blocked_consec = 0 # note whether we block consecutive events
runend = -1
for run in range(nruns):
runstart = runend + 1
runend = runstart + run_trs[run] - 1
# old: rindex = run * nt # point to start of run
rindex = runstart
# if empty run, use placeholders
if not stim_in_run(row[runstart:runend + 1], use_amp):
if run == 0: fp.write('* *\n') # first run gets 2
else: fp.write('*\n')
continue
# print '=== have stim in run, row = %s' % row[rindex:rindex+nt]
time = 0 # in this run
nstim = 0 # be sure we have more than 1 somewhere
first = 1 # first occurance if no consec
for lcol in range(run_trs[run]):
if row[rindex + lcol]:
# note whether anything has been blocked
if not first and not consec_ok:
if verb > 2:
print('-- blocked consec: file %s, run %d, ind %d'\
% (newp, run, lcol))
blocked_consec = 1
# if consec is bad, only write on first occurance
if first or consec_ok:
nstim += 1
tstr = '%s' % str(time + offset)
# if -amplitudes write as time*amplitude
if use_amp: astr = '*%s' % str(row[rindex + lcol])
else: astr = ''
fp.write('%s%s ' % (tstr, astr))
first = 0 # not first occurance
else:
first = 1
time += tr
if run == 0 and nstim == 1:
fp.write('*') # if first time has 1 stim, add '*'
fp.write('\n')
if fp != sys.stdout and fp != sys.stderr: fp.close()
newfile_index += 1
if verb and blocked_consec:
print('-- blocked consecutive events file %s, output %s' \
% (fname, newp))
def show_isi_stats(self, mesg='', run_len=[], tr=0, rest_file=''):
"""display ISI timing statistics
mesg : display the user message first
run_len : can be empty, length 1 or length nrows
tr : if > 0: show mean/stdev for stimuli within TRs
(so 0 <= mean < tr)
rest_file : if set, save all rest durations
display these statistics:
- total time, total stim time, total rest time
- total time per run
- total stim time per run
- total rest time per run
- pre-stim rest per run
- post-stim response rest per run (if run_len is given)
- total ISI rest per run
- min/mean/max (stdev) of stim duration
- min/mean/max (stdev) of ISI rest
"""
if not self.ready:
print '** M Timing: nothing to compute ISI stats from'
return 1
if not (self.mtype & LD.MTYPE_DUR):
print '** warning: computing stats without duration'
if self.nrows != len(self.data):
print '** bad MTiming, nrows=%d, datalen=%d, failing...' % \
(self.nrows, len(self.data))
return 1
# make a sorted copy
scopy = self.copy()
scopy.sort()
# make a copy of format run x stim x [start,end], i.e. is 3-D
tdata = scopy.get_start_end_timing()
# make an updated run lengths list
if len(run_len) == 0:
rlens = [0 for rind in range(self.nrows)]
elif len(run_len) == 1:
rlens = [run_len[0] for rind in range(self.nrows)]
elif len(run_len) == self.nrows:
rlens = run_len
else: # failure
print '** invalid len(run_len)=%d, must be one of 0,1,%d' % \
(len(run_len), self.nrows)
return 1
if self.verb > 1:
print '-- show_isi_stats, run_len = %s, tr = %s, rest_file = %s' \
% (run_len, tr, rest_file)
if self.verb > 3:
print scopy.make_data_string(nplaces=1,
flag_empty=0,
check_simple=0,
mesg='scopy data')
all_stim = [] # all stimulus durations (one row per run)
all_isi = [] # all isi times (one row per run)
pre_time = [] # pre-stim, per run
post_time = [] # pose-stim, per run
run_time = [] # total run time, per run
errs = 0 # allow a few errors before failing
max_errs = 10
for rind in range(self.nrows):
run = tdata[rind]
rlen = rlens[rind]
if len(run) == 0: # empty run
all_stim.append([])
all_isi.append([])
pre_time.append(rlen)
post_time.append(0.0)
run_time.append(rlen)
continue
# if no run len specified, use end of last stimulus
if rlen == 0.0: rlen = run[-1][1]
elif rlen < run[-1][1]:
print '** run %d: given length = %s, last stim ends at %s' % \
(rind+1, rlen, run[-1][1])
errs += 1
if errs > max_errs:
print '** bailing...'
return 1
# pre- and post-stim times are set
pre = run[0][0]
post = rlen - run[-1][1]
if pre < 0:
print '** ISI error: first stimulus of run %d at negative time %s'%\
(rind+1, run[0][0])
errs += 1
if errs > max_errs:
print '** bailing...'
return 1
# init accumulation vars
stimes = [run[0][1] - run[0][0]]
itimes = []
# for each following index, update stim and isi times
# (check for bad overlap)
for sind in range(1, len(run)):
if run[sind][0] < run[sind - 1][1]:
print '** ISI error: stimuli overlap at run %d, time %s' % \
(rind+1, run[sind][0])
errs += 1
if errs > max_errs:
print '** bailing...'
return 1
stimes.append(run[sind][1] - run[sind][0])
itimes.append(run[sind][0] - run[sind - 1][1])
# store results
all_stim.append(stimes)
all_isi.append(itimes)
pre_time.append(pre)
post_time.append(post)
run_time.append(rlen)
if errs > 0: return 1
# tally the results
rtot_stim = []
rtot_isi = []
rtot_rest = []
stim_list = []
isi_list = []
nstim_list = []
for rind in range(self.nrows):
rtot_stim.append(UTIL.loc_sum(all_stim[rind]))
rtot_rest.append(pre_time[rind] + UTIL.loc_sum(all_isi[rind]) +
post_time[rind])
rtot_isi.append(UTIL.loc_sum(all_isi[rind]))
stim_list.extend(all_stim[rind])
isi_list.extend(all_isi[rind])
nstim_list.append(len(all_stim[rind]))
if mesg: mstr = '(%s) ' % mesg
else: mstr = ''
print '\nISI statistics %s:\n' % mstr
print ' total per run'
print ' ------ ------------------------------'
print ' total time %6.1f %s' % \
(UTIL.loc_sum(run_time), float_list_string(run_time, ndec=1))
print ' total time: stim %6.1f %s' % \
(UTIL.loc_sum(rtot_stim),float_list_string(rtot_stim,7,ndec=1))
print ' total time: rest %6.1f %s' % \
(UTIL.loc_sum(rtot_rest),float_list_string(rtot_rest,7,ndec=1))
print ''
print ' rest: total isi %6.1f %s' % \
(UTIL.loc_sum(rtot_isi), float_list_string(rtot_isi,7,ndec=1))
print ' rest: pre stim %6.1f %s' % \
(UTIL.loc_sum(pre_time), float_list_string(pre_time,7,ndec=1))
print ' rest: post stim %6.1f %s' % \
(UTIL.loc_sum(post_time),float_list_string(post_time,7,ndec=1))
print ''
print ' num stimuli %6d %s' % \
(UTIL.loc_sum(nstim_list), float_list_string(nstim_list,7,ndec=0))
print '\n'
print ' min mean max stdev'
print ' ------- ------- ------- -------'
print ' rest: pre-stim %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(pre_time))
print ' rest: post-stim %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(post_time))
print ''
for ind in range(self.nrows):
m0, m1, m2, s = UTIL.min_mean_max_stdev(all_isi[ind])
print ' rest: run #%d ISI %7.3f %7.3f %7.3f %7.3f' % \
(ind, m0, m1, m2, s)
print ''
print ' all runs: ISI %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(isi_list))
print ' all runs: stimuli %7.3f %7.3f %7.3f %7.3f' % \
(UTIL.min_mean_max_stdev(stim_list))
print ''
# and possibly print out offset info
if tr > 0: self.show_TR_offset_stats(tr, '')
# maybe write all rest durations
if rest_file:
all_rest = copy.deepcopy(all_isi)
for run, rest in enumerate(all_rest):
rest[:0] = [pre_time[run]]
rest.append(post_time[run])
UTIL.write_to_timing_file(all_rest, rest_file)
# clean up, just to be kind
del (all_stim)
del (all_isi)
del (pre_time)
del (post_time)
del (run_time)
del (rtot_stim)
del (rtot_isi)
del (rtot_rest)
del (stim_list)
del (isi_list)
del (nstim_list)
del (scopy)
del (tdata)
def proc_mats(uopts):
offset = 0.0 # offset for output times
if uopts == None: return
opt = uopts.find_opt('-verb')
if opt:
try:
verb = int(opt.parlist[0])
except:
print "** error: verb must be int, have '%s'" % opt.parlist[0]
return
else:
verb = 0
opt = uopts.find_opt('-files')
files = opt.parlist
# set run_trs nruns from either -run_trs or -nruns and -nt
opt = uopts.find_opt('-run_trs')
if opt:
val, err = uopts.get_type_list(int, '', opt=opt)
if err: return 1
run_trs = val
nruns = len(run_trs)
if uopts.find_opt('-nruns') or uopts.find_opt('-nt'):
print '** please use either -run_trs or -nt/-nruns'
return 1
else:
if not uopts.find_opt('-nruns') and not uopts.find_opt('-nt'):
print '** please use either -run_trs or -nt/-nruns (missing one)'
return 1
opt = uopts.find_opt('-nruns')
nruns = int(opt.parlist[0])
opt = uopts.find_opt('-nt')
try:
nt = int(opt.parlist[0])
except:
print "** error: -nt must be int, have '%s'" % opt.parlist[0]
return
run_trs = [nt] * nruns
# not the total number of TRs, regardless
ntotal = afni_util.loc_sum(run_trs)
opt = uopts.find_opt('-offset')
if opt:
try:
offset = float(opt.parlist[0])
except:
print "** error: offset must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-prefix')
prefix = opt.parlist[0]
opt = uopts.find_opt('-tr')
try:
tr = float(opt.parlist[0])
except:
print "** error: TR must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-labels')
if opt: labels = opt.parlist
else: labels = []
nlab = len(labels)
# print some info
if verb: print "-- run_trs = %s, TR = %s, %d labels" \
% (run_trs, str(tr), nlab)
# new option, -amplitudes (columns of amplitudes to Marry, not just 1s)
use_amp = 0
opt = uopts.find_opt('-amplitudes')
if opt:
use_amp = 1
if verb: print '-- using amplitudes to Marry with times...'
newfile_index = 1 # index over output files
for file in files:
tmat = TD.read_1D_file(file, verb=verb)
if not tmat:
print "read_1D_file failed for file: %s" % file
return
mat = afni_util.transpose(tmat)
del (tmat)
if len(mat[0]) < ntotal:
print '** error: file %s has only %d entries (%d required)' % \
(file, len(mat[0]), ntotal)
return
elif len(mat[0]) > ntotal:
print '** warning: file %s has %d entries (expected only %d)' % \
(file, len(mat[0]), ntotal)
for row in mat:
# maybe add a label to the file name
if newfile_index <= nlab: label = ".%s" % labels[newfile_index - 1]
elif nlab == 0: label = ""
else:
print "** %d labels given, but we are on column %d..." % \
(nlab, newfile_index)
label = ".label%d" % (newfile_index)
newp = "%s.%02d%s" % (prefix, newfile_index, label)
newfile = afni_util.change_path_basename(file, newp, ".1D")
if newfile == None: return
fp = open(newfile, 'w')
runend = -1
for run in range(nruns):
runstart = runend + 1
runend = runstart + run_trs[run] - 1
# old: rindex = run * nt # point to start of run
rindex = runstart
# if empty run, use placeholders
if not stim_in_run(row[runstart:runend + 1], use_amp):
if run == 0: fp.write('* *\n') # first run gets 2
else: fp.write('*\n')
continue
# print '=== have stim in run, row = %s' % row[rindex:rindex+nt]
time = 0 # in this run
nstim = 0 # be sure we have more than 1 somewhere
for lcol in range(run_trs[run]):
if row[rindex + lcol]:
nstim += 1
# if -amplitudes write as time:amplitude
if use_amp:
fp.write('%s*%s ' % \
(str(time+offset),str(row[rindex+lcol])))
else:
fp.write('%s ' % str(time + offset))
time += tr
if run == 0 and nstim == 1:
fp.write('*') # if first time has 1 stim, add '*'
fp.write('\n')
fp.close()
newfile_index += 1
def proc_mats(uopts):
offset = 0.0 # offset for output times
if uopts == None: return
opt = uopts.find_opt('-verb')
if opt:
try: verb = int(opt.parlist[0])
except:
print "** error: verb must be int, have '%s'" % opt.parlist[0]
return
else: verb = 0
opt = uopts.find_opt('-files')
files = opt.parlist
consec_ok = (uopts.find_opt('-no_consec') == None)
# set run_trs nruns from either -run_trs or -nruns and -nt
opt = uopts.find_opt('-run_trs')
if opt:
val, err = uopts.get_type_list(int, '', opt=opt)
if err: return 1
run_trs = val
nruns = len(run_trs)
if uopts.find_opt('-nruns') or uopts.find_opt('-nt'):
print '** please use either -run_trs or -nt/-nruns'
return 1
else:
if not uopts.find_opt('-nruns') or not uopts.find_opt('-nt'):
print '** please use either -run_trs or both -nt and -nruns'
return 1
opt = uopts.find_opt('-nruns')
nruns = int(opt.parlist[0])
opt = uopts.find_opt('-nt')
try: nt = int(opt.parlist[0])
except:
print "** error: -nt must be int, have '%s'" % opt.parlist[0]
return
run_trs = [nt]*nruns
# note the total number of TRs, regardless
ntotal = afni_util.loc_sum(run_trs)
opt = uopts.find_opt('-offset')
if opt:
try: offset = float(opt.parlist[0])
except:
print "** error: offset must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-prefix')
prefix = opt.parlist[0]
opt = uopts.find_opt('-tr')
try: tr = float(opt.parlist[0])
except:
print "** error: TR must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-labels')
if opt: labels = opt.parlist
else: labels = []
nlab = len(labels)
# print some info
if verb: print "-- run_trs = %s, TR = %s, %d labels" \
% (run_trs, str(tr), nlab)
# new option, -amplitudes (columns of amplitudes to Marry, not just 1s)
use_amp = 0
opt = uopts.find_opt('-amplitudes')
if opt:
use_amp = 1
if verb: print '-- using amplitudes to Marry with times...'
newfile_index = 1 # index over output files
for fname in files:
tmat = TD.read_1D_file(fname, verb=verb)
if not tmat:
print "read_1D_file failed for file: %s" % fname
return
mat = afni_util.transpose(tmat)
del(tmat)
if len(mat[0]) < ntotal:
print '** error: file %s has only %d entries (%d required)' % \
(fname, len(mat[0]), ntotal)
return
elif len(mat[0]) > ntotal:
print '** warning: file %s has %d entries (expected only %d)' % \
(fname, len(mat[0]), ntotal)
for row in mat:
# maybe add a label to the file name
if newfile_index <= nlab: label = ".%s" % labels[newfile_index-1]
elif nlab == 0: label = ""
else:
print "** %d labels given, but we are on column %d..." % \
(nlab, newfile_index)
label = ".label%d" % (newfile_index)
newp = "%s.%02d%s" % (prefix,newfile_index,label)
newfile = afni_util.change_path_basename(fname, newp, ".1D")
if newfile == None: return
if prefix == '-' or prefix == 'stdout': fp = sys.stdout
elif prefix == 'stderr': fp = sys.stderr
else: fp = open(newfile, 'w')
blocked_consec = 0 # note whether we block consecutive events
runend = -1
for run in range(nruns):
runstart = runend + 1
runend = runstart + run_trs[run] - 1
# old: rindex = run * nt # point to start of run
rindex = runstart
# if empty run, use placeholders
if not stim_in_run(row[runstart:runend+1], use_amp):
if run == 0: fp.write('* *\n') # first run gets 2
else: fp.write('*\n')
continue
# print '=== have stim in run, row = %s' % row[rindex:rindex+nt]
time = 0 # in this run
nstim = 0 # be sure we have more than 1 somewhere
first = 1 # first occurance if no consec
for lcol in range(run_trs[run]):
if row[rindex+lcol]:
# note whether anything has been blocked
if not first and not consec_ok:
if verb > 2:
print '-- blocked consec: file %s, run %d, ind %d'\
% (newp, run, lcol)
blocked_consec = 1
# if consec is bad, only write on first occurance
if first or consec_ok:
nstim += 1
tstr = '%s' % str(time+offset)
# if -amplitudes write as time*amplitude
if use_amp: astr = '*%s' % str(row[rindex+lcol])
else: astr = ''
fp.write('%s%s ' % (tstr, astr))
first = 0 # not first occurance
else: first = 1
time += tr
if run == 0 and nstim == 1:
fp.write('*') # if first time has 1 stim, add '*'
fp.write('\n')
if fp != sys.stdout and fp != sys.stderr: fp.close()
newfile_index += 1
if verb and blocked_consec:
print '-- blocked consecutive events file %s, output %s' \
% (fname, newp)