def parse_infile_names(self):
"""try to get subject and possibly group names from infiles
fill self.snames and self.gnames, if possible
1. get SID
- if files look like out.ss_review.SID.txt, that is a good start
- else, look for varying part of filename
2. get GID
- replace SID in infile names and for varying group name
"""
rv, slist = UTIL.list_minus_pref_suf(self.infiles,'out.ss_review.','.txt')
if rv < 0: return
if rv > 0:
if self.verb > 1: print '++ trying to get SID from glob form'
slist = UTIL.list_minus_glob_form(self.infiles, strip='dir')
else:
if self.verb > 1: print "++ have SIDs from 'out.ss_reiview' form"
if len(slist) == 0:
if self.verb > 1: print "-- empty SID list"
return
# make sure names are unique and not empty
if not UTIL.vals_are_unique(slist):
if self.verb > 1: print '-- SIDs not detected: not unique'
return
minlen = min([len(ss) for ss in slist])
if minlen < 1:
if self.verb > 1: print '-- SIDs not detected: some would be empty'
return
# we have a subject list
self.snames = slist
# now go for GID, start by replacing SIDs in infiles
newfiles = [fname.replace(slist[ind], 'SUBJ') for ind, fname in
enumerate(self.infiles)]
if UTIL.vals_are_constant(newfiles):
print '-- no groups detected from filenames'
return
# okay, try to make a group list
glist = UTIL.list_minus_glob_form(newfiles)
# cannot have dirs in result
for gid in glist:
if gid.find('/') >= 0:
if self.verb>1: print '-- no GIDs, dirs vary in multiple places'
return
minlen = min([len(ss) for ss in glist])
if minlen < 1:
if self.verb > 1: print '-- GIDs not detected: some would be empty'
return
if self.verb > 1: print "++ have GIDs from infiles"
self.gnames = glist
def parse_infile_names(self):
"""try to get subject and possibly group names from infiles
fill self.snames and self.gnames, if possible
1. get SID
- if files look like out.ss_review.SID.txt, that is a good start
- else, look for varying part of filename
2. get GID
- replace SID in infile names and for varying group name
"""
rv, slist = UTIL.list_minus_pref_suf(self.infiles,'out.ss_review.','.txt')
if rv < 0: return
if rv > 0:
if self.verb > 1: print '++ trying to get SID from glob form'
slist = UTIL.list_minus_glob_form(self.infiles, strip='dir')
else:
if self.verb > 1: print "++ have SIDs from 'out.ss_reiview' form"
if len(slist) == 0:
if self.verb > 1: print "-- empty SID list"
return
# make sure names are unique and not empty
if not UTIL.vals_are_unique(slist):
if self.verb > 1: print '-- SIDs not detected: not unique'
return
minlen = min([len(ss) for ss in slist])
if minlen < 1:
if self.verb > 1: print '-- SIDs not detected: some would be empty'
return
# we have a subject list
self.snames = slist
# now go for GID, start by replacing SIDs in infiles
newfiles = [fname.replace(slist[ind], 'SUBJ') for ind, fname in
enumerate(self.infiles)]
if UTIL.vals_are_constant(newfiles):
print '-- no groups detected from filenames'
return
# okay, try to make a group list
glist = UTIL.list_minus_glob_form(newfiles)
# cannot have dirs in result
for gid in glist:
if gid.find('/') >= 0:
if self.verb>1: print '-- no GIDs, dirs vary in multiple places'
return
minlen = min([len(ss) for ss in glist])
if minlen < 1:
if self.verb > 1: print '-- GIDs not detected: some would be empty'
return
if self.verb > 1: print "++ have GIDs from infiles"
self.gnames = glist
def set_ids_from_dsets(self, prefix='', suffix='', hpad=0, tpad=0, dpre=0):
"""use the varying part of the dataset names for subject IDs
If hpad > 0 or tpad > 0, expand into the head or tail of the dsets.
If prefix or suffix is passed, apply them.
return 0 on success, 1 on error
"""
if hpad < 0 or tpad < 0:
print('** set_ids_from_dsets: will not apply negative padding')
return 1
# try filenames without paths, first
dlist = [s.dset.split('/')[-1] for s in self.subjects]
if UTIL.vals_are_constant(dlist):
print('** constant dataset names (%s)' % dlist[0])
print(' trying directories...')
dlist = [s.dset for s in self.subjects]
slist = UTIL.list_minus_glob_form(dlist,
hpad,
tpad,
keep_dent_pre=dpre)
# in the case of diretories, check for success
# (maybe we can try to skip past them, that might be okay)
for index in range(len(slist)):
if '/' in slist[index]:
posn = slist[index].rfind('/')
slist[index] = slist[index][posn + 1:]
if len(slist[index]) < 1:
print(
'** failed to extract subject IDs from directory list')
print(' (directories do not vary at single level)')
return 1
if len(slist) != len(self.subjects):
print('** failed to set SIDs from dset names\n' \
' dsets = %s\n' \
' slist = %s' % (dlist, slist))
return 1
if not UTIL.vals_are_unique(slist):
print('** cannot set IDs from dsets, labels not unique: %s' %
slist)
print('-- labels come from dsets: %s' % dlist)
return 1
for ind, subj in enumerate(self.subjects):
subj.sid = '%s%s%s' % (prefix, slist[ind], suffix)
return 0
def set_ids_from_dsets(self, prefix='', suffix='', hpad=0, tpad=0, dpre=0):
"""use the varying part of the dataset names for subject IDs
If hpad > 0 or tpad > 0, expand into the head or tail of the dsets.
If prefix or suffix is passed, apply them.
return 0 on success, 1 on error
"""
if hpad < 0 or tpad < 0:
print '** set_ids_from_dsets: will not apply negative padding'
return 1
# try filenames without paths, first
dlist = [s.dset.split('/')[-1] for s in self.subjects]
if UTIL.vals_are_constant(dlist):
print '** constant dataset names (%s)' % dlist[0]
print ' trying directories...'
dlist = [s.dset for s in self.subjects]
slist = UTIL.list_minus_glob_form(dlist, hpad, tpad, keep_dent_pre=dpre)
# in the case of diretories, check for success
# (maybe we can try to skip past them, that might be okay)
for index in range(len(slist)):
if '/' in slist[index]:
posn = slist[index].rfind('/')
slist[index] = slist[index][posn+1:]
if len(slist[index]) < 1:
print '** failed to extract subject IDs from directory list'
print ' (directories do not vary at single level)'
return 1
if len(slist) != len(self.subjects):
print '** failed to set SIDs from dset names\n' \
' dsets = %s\n' \
' slist = %s' % (dlist, slist)
return 1
if not UTIL.vals_are_unique(slist):
print '** cannot set IDs from dsets, labels not unique: %s' % slist
print '-- labels come from dsets: %s' % dlist
return 1
for ind, subj in enumerate(self.subjects):
subj.sid = '%s%s%s' % (prefix, slist[ind], suffix)
return 0
def make_decon_script(self):
"""create the deconvolution (3dTfitter) script"""
nups = '%02d' % self.tr_nup
trup = self.tr / self.tr_nup
penalty = '012'
kernel = self.kernel
kfile = self.kfile
# todo: include run lengths
# maybe call the 3D version
if self.aname.type != '1D': return self.make_decon_script_3d()
cmd = '# ------------------------------------------------------\n' \
'# perform neuro deconvolution via 3dTfitter\n\n'
cmd += '# make and copy files into output directory\n' \
'set outdir = %s\n' \
'if ( ! -d $outdir ) mkdir $outdir\n\n' % self.outdir
# get a list of (hopefully shortened) file labels
llist = UTIL.list_minus_glob_form(self.infiles)
llen = len(self.infiles)
fix = 0
if len(llist) != llen: fix = 1
else:
if llist[0] == self.infiles[0]: fix = 1
if fix: llist = ['%02d.ts'%(ind+1) for ind in range(llen)]
else : llist = ['%02d.%s'%(ind+1,llist[ind]) for ind in range(llen)]
# when copying file in, use 1dtranspose if they are horizontal
adata = LD.AfniData(self.infiles[0], verb=self.verb)
if not adata: return 1
if adata.nrows == 1:
nt = adata.ncols/self.tr_nup
trstr = '(no transpose on read)'
trchr = ''
else:
nt = adata.nrows/self.tr_nup
transp = 1
trstr = '(transpose on read)'
trchr = '\\\''
cmd += 'set files = ( %s )\n' \
'set labels = ( %s )\n\n' \
'cp -pv $files $outdir\n' \
'cd $outdir\n\n' \
% (' '.join(self.infiles), ' '.join(llist))
if self.kfile_in: kfile = self.kfile_in
else:
# generate a response kernel using 3dDeconvolve
if kernel == 'GAM': ntk = 12/trup
elif kernel == 'BLOCK': ntk = 15/trup
else:
print '** only GAM/BLOCK basis functions are allowed now'
return 1
if kernel == 'BLOCK': kernel = 'BLOCK(0.1,1)'
tmpc = '# create response kernel\n' \
'3dDeconvolve -nodata %d %g -polort -1 \\\n' \
' -num_stimts 1 -stim_times 1 "1D:0" "%s" \\\n' \
' -x1D %s -x1D_stop\n\n' % (ntk, trup, kernel, kfile)
cmd += UTIL.add_line_wrappers(tmpc)
pind = 0
cmd += '# process each input file\n' \
'foreach findex ( `count -digits 2 1 $#files` )\n' \
' # no zero-padding in shell index\n' \
' set ival = `ccalc -i $findex`\n' \
' set infile = $files[$ival]:t\n' \
' set label = $labels[$ival]\n\n' \
polort = UTIL.get_default_polort(self.tr, self.reps)
olab = 'p%02d.det.$label.1D' % pind
cmd += ' # detrend the input %s\n' \
' 3dDetrend -polort %d -prefix %s $infile%s\n\n' \
% (trstr, polort, olab, trchr)
pind += 1
ilab = olab
olab = 'p%02d.det.tr.$label.1D' % pind
cmd += ' # transpose the detrended dataset\n' \
' 1dtranspose %s > %s\n\n' % (ilab, olab)
pind += 1
ilab = olab
olab = 'p%02d.up%s.$label.1D' % (pind, nups)
cmd += ' # upsample by factor of %d\n' \
' 1dUpsample %d %s > %s\n\n' \
% (self.tr_nup, self.tr_nup, ilab, olab)
sfile_up = olab # save original detrended upsample label
pind += 1
ilab = olab
olab = 'p%02d.neuro.up%s.$label.1D' % (pind, nups)
tmpc = ' 3dTfitter -RHS %s \\\n' \
' -FALTUNG %s %s \\\n' \
' 012 -2 -l2lasso -6\n\n' % (ilab,kfile,olab)
cmd += UTIL.add_line_wrappers(tmpc)
pind += 1
ilab = olab
olab = 'p%02d.neuro.up%s.tr.$label.1D' % (pind, nups)
cmd += ' # transpose the neuro signal\n' \
' 1dtranspose %s > %s\n\n' % (ilab, olab)
pind += 1
ilab = olab
olab = 'p%02d.reconv.up%s.tr.$label.1D' % (pind, nups)
cmd += ' # reconvolve the neuro signal to compare with orig\n'\
' set nt = `cat %s | wc -l`\n' \
' waver -FILE %g %s -input %s \\\n' \
' -numout $nt > %s\n\n' \
% (ilab, trup, kfile, ilab, olab)
rfile_up = olab # save reconvolved label
cmd += 'end\n\n\n'
cmd += 'echo "compare upsample input to reconvolved result via:"\n' \
'echo "set label = %s"\n' \
'echo "1dplot -one %s %s"\n\n' \
% (llist[0], sfile_up, rfile_up)
return UTIL.write_text_to_file(self.script, cmd, exe=1)
def make_decon_script(self):
"""create the deconvolution (3dTfitter) script"""
nups = '%02d' % self.tr_nup
trup = self.tr / self.tr_nup
penalty = '012'
kernel = self.kernel
kfile = self.kfile
# todo: include run lengths
# maybe call the 3D version
if self.aname.type != '1D': return self.make_decon_script_3d()
cmd = '# ------------------------------------------------------\n' \
'# perform neuro deconvolution via 3dTfitter\n\n'
cmd += '# make and copy files into output directory\n' \
'set outdir = %s\n' \
'if ( ! -d $outdir ) mkdir $outdir\n\n' % self.outdir
# get a list of (hopefully shortened) file labels
llist = UTIL.list_minus_glob_form(self.infiles)
llen = len(self.infiles)
fix = 0
if len(llist) != llen: fix = 1
else:
if llist[0] == self.infiles[0]: fix = 1
if fix: llist = ['%02d.ts' % (ind + 1) for ind in range(llen)]
else:
llist = ['%02d.%s' % (ind + 1, llist[ind]) for ind in range(llen)]
# when copying file in, use 1dtranspose if they are horizontal
adata = LD.AfniData(self.infiles[0], verb=self.verb)
if not adata: return 1
if adata.nrows == 1:
nt = adata.ncols / self.tr_nup
trstr = '(no transpose on read)'
trchr = ''
else:
nt = adata.nrows / self.tr_nup
transp = 1
trstr = '(transpose on read)'
trchr = '\\\''
cmd += 'set files = ( %s )\n' \
'set labels = ( %s )\n\n' \
'cp -pv $files $outdir\n' \
'cd $outdir\n\n' \
% (' '.join(self.infiles), ' '.join(llist))
if self.kfile_in: kfile = self.kfile_in
else:
# generate a response kernel using 3dDeconvolve
if kernel == 'GAM': ntk = 12 / trup
elif kernel == 'BLOCK': ntk = 15 / trup
else:
print '** only GAM/BLOCK basis functions are allowed now'
return 1
if kernel == 'BLOCK': kernel = 'BLOCK(0.1,1)'
tmpc = '# create response kernel\n' \
'3dDeconvolve -nodata %d %g -polort -1 \\\n' \
' -num_stimts 1 -stim_times 1 "1D:0" "%s" \\\n' \
' -x1D %s -x1D_stop\n\n' % (ntk, trup, kernel, kfile)
cmd += UTIL.add_line_wrappers(tmpc)
pind = 0
cmd += '# process each input file\n' \
'foreach findex ( `count -digits 2 1 $#files` )\n' \
' # no zero-padding in shell index\n' \
' set ival = `ccalc -i $findex`\n' \
' set infile = $files[$ival]:t\n' \
' set label = $labels[$ival]\n\n' \
polort = UTIL.get_default_polort(self.tr, self.reps)
olab = 'p%02d.det.$label.1D' % pind
cmd += ' # detrend the input %s\n' \
' 3dDetrend -polort %d -prefix %s $infile%s\n\n' \
% (trstr, polort, olab, trchr)
pind += 1
ilab = olab
olab = 'p%02d.det.tr.$label.1D' % pind
cmd += ' # transpose the detrended dataset\n' \
' 1dtranspose %s > %s\n\n' % (ilab, olab)
pind += 1
ilab = olab
olab = 'p%02d.up%s.$label.1D' % (pind, nups)
cmd += ' # upsample by factor of %d\n' \
' 1dUpsample %d %s > %s\n\n' \
% (self.tr_nup, self.tr_nup, ilab, olab)
sfile_up = olab # save original detrended upsample label
pind += 1
ilab = olab
olab = 'p%02d.neuro.up%s.$label.1D' % (pind, nups)
tmpc = ' 3dTfitter -RHS %s \\\n' \
' -FALTUNG %s %s \\\n' \
' 012 -2 -l2lasso -6\n\n' % (ilab,kfile,olab)
cmd += UTIL.add_line_wrappers(tmpc)
pind += 1
ilab = olab
olab = 'p%02d.neuro.up%s.tr.$label.1D' % (pind, nups)
cmd += ' # transpose the neuro signal\n' \
' 1dtranspose %s > %s\n\n' % (ilab, olab)
pind += 1
ilab = olab
olab = 'p%02d.reconv.up%s.tr.$label.1D' % (pind, nups)
cmd += ' # reconvolve the neuro signal to compare with orig\n'\
' set nt = `cat %s | wc -l`\n' \
' waver -FILE %g %s -input %s \\\n' \
' -numout $nt > %s\n\n' \
% (ilab, trup, kfile, ilab, olab)
rfile_up = olab # save reconvolved label
cmd += 'end\n\n\n'
cmd += 'echo "compare upsample input to reconvolved result via:"\n' \
'echo "set label = %s"\n' \
'echo "1dplot -one %s %s"\n\n' \
% (llist[0], sfile_up, rfile_up)
return UTIL.write_text_to_file(self.script, cmd, exe=1)
