def make_decon_script_old(self):
"""OLD METHOD: create the deconvolution (3dTfitter) script"""
cmd = '# ------------------------------------------------------\n' \
'# perform neuro deconvolution via 3dTfitter\n\n'
cmd += "# create response kernel\n" \
"waver -%s -peak 1 -dt %s -inline 1@1 > %s\n\n" % \
(self.kernel, self.tr, self.kfile)
if self.aname.type == '1D': prefix = 'detrend.1D'
else: prefix = 'detrend%s' % self.aname.view
polort = UTIL.get_default_polort(self.tr, self.reps)
cmd += '# detrend the input\n' \
'3dDetrend -polort %d -prefix %s %s\n\n' % \
(polort,prefix,self.infiles[0])
if self.maskset: mask = ' -mask %s \\\n' % self.maskset
else: mask = ''
if self.aname.type == '1D':
cmd += '# transpose the detrended dataset\n' \
'1dtranspose detrend.1D > detrend_tr.1D\n\n'
dname = 'detrend_tr.1D'
else:
dname = 'detrend%s' % self.aname.view
c2 = '3dTfitter -lsqfit -RHS %s \\\n' \
'%s' \
' -FALTUNG %s %s \\\n' \
' 01 0.0\n\n' % (dname,mask,self.kfile,self.prefix)
cmd += UTIL.add_line_wrappers(c2)
return UTIL.write_text_to_file(self.script, cmd, exe=1)
def make_align_opts_str(self):
"""any align options, one per line"""
# keep comment separate to get indent length
cmnt = '# all other align_epi_anat.py options\n' \
cstr = 'set align_opts = ( '
clen = len(cstr)
istr = ' ' * clen
# put one option on first line
cstr += '%s \\\n' % '-tshift off'
# ---------- here is the main option application ---------
# then add each option offset by initial indentation
cstr += '%s%s \\\n' % (istr, '-volreg off')
if self.uvars.giant_move == 'yes':
cstr += '%s%s \\\n' % (istr, '-giant_move')
if self.uvars.add_edge == 'yes':
if len(self.uvars.cost_list) > 1:
self.errors.append(
'** -AddEdge does not currently work with -multi_cost')
else:
cstr += '%s%s \\\n' % (istr, '-AddEdge')
if len(self.uvars.aea_opts) > 0:
cstr += '%s%s \\\n' % (istr, ' '.join(self.uvars.aea_opts))
# does the anatomy have a skull?
if self.uvars.anat_has_skull != 'yes':
cstr += '%s%s \\\n' % (istr, '-anat_has_skull no')
# -epi_strip method
if self.uvars.epi_strip_meth != '3dSkullStrip':
cstr += '%s%s \\\n' % (istr,
'-epi_strip %s' % self.uvars.epi_strip_meth)
# want -save_all, -prep_off?
# last indent is left by 2 to align ()
cstr += '%*s)\n\n' % (clen - 2, '')
# finally, align the line wrappers
cstr = UTIL.add_line_wrappers(cstr)
return cmnt + cstr
def script_main(self):
"""write command with prefix, datasets and extra options
"""
cmd = SUBJ.comment_section_string('process the data') + '\n'
if self.uvars.program == '3dttest++':
cmd += self.script_ttest()
elif self.uvars.program == '3dMEMA':
cmd += self.script_MEMA()
else:
self.errors.append('** bad program name: %s' % self.uvars.program)
return ''
return UTIL.add_line_wrappers(cmd)
def make_uber_command(self):
"""generate a script that would invoke the uber_ttest.py interface
with control and user vars set (and so fields filled)
Put any key elements in quotes:
basis functions
gltsym
"""
if show_func_seq: print('=== xO ===')
# first apply subject variables
self.update_uvars_from_gui()
cmd = 'uber_ttest.py'
# apply each uvar with -uvar option
prefix = ' \\\n -uvar ' # append before next command
for atr in self.uvars.attributes():
if atr == 'name': continue # skip
if self.uvars.vals_are_equal(atr, LTT.g_udef_strs): continue
# show this one
val = self.uvars.val(atr)
# special cases first: stim_basis, gltsym
#if atr == 'gltsym': # special case
# val = ["'%s'" % v for v in val]
#elif atr == 'stim_basis': # special case
# val = ["'%s'" % v for v in val]
# cmd += (prefix + '%s %s' % (atr, ' '.join(val)))
# some options might need quotes
if self.uvars.has_simple_type(atr):
val = UTIL.quotize_list([val], quote_chars='#%<>')[0]
cmd += (prefix + '%s %s' % (atr, val))
elif type(val) == list:
val = UTIL.quotize_list(val, quote_chars='#%<>')
cmd += (prefix + '%s %s' % (atr, ' '.join(val)))
else:
print('** make_uber_command: bad attr %s' % atr)
return UTIL.add_line_wrappers(cmd + '\n')
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
# rcr - in progress? unused: adata, nt, transp
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 = int(12 / trup + 0.5)
elif kernel == 'BLOCK': ntk = int(15 / trup + 0.5)
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_script(self):
"""create the review EPI (plugout_drive) script"""
c2 = "#!/bin/tcsh\n\n"
c2 += "# ------------------------------------------------------\n" \
"# review EPI data via 'afni' and 'plugout_drive'\n\n" \
"# note that when running this script, prompts to change\n" \
"# datasets will appear in the terminal window\n\n"
c2 += "# ------------------------------------------------------\n" \
"# set the list of datasets\n" \
"set dsets = ( %s )\n\n" % \
' '.join([dset.prefix for dset in self.adsets])
c2 += '# ------------------------------------------------------\n' \
'# verify that the input data exists\n' \
'if ( ! -f $dsets[1]+orig.HEAD ) then\n' \
' echo "** missing data to review (e.g. $dsets[1])"\n' \
' exit\n' \
'endif\n\n'
c2 += '# ------------------------------------------------------\n' \
'# start afni is listening mode, and take a brief nap\n\n' \
'afni -yesplugouts &\n\n' \
'sleep 5\n\n'
cmd = UTIL.add_line_wrappers(c2)
c2 = '# ------------------------------------------------------\n' \
'# tell afni to load the first dataset and open windows\n\n' \
'plugout_drive \\\n' \
' -com "SWITCH_UNDERLAY %s" \\\n' \
% self.adsets[0].prefix
# open windows in the list
if self.verb > 1:
print('++ opening windows: %s' % ', '.join(self.windows))
for ind in range(len(self.windows)):
c2 += ' -com "OPEN_WINDOW %simage \\\n' \
' geom=%dx%d+%d+%d" \\\n' % \
(self.windows[ind], self.im_size[0], self.im_size[1],
self.im_xoff+ind*self.im_size[0], self.im_yoff)
c2 += ' -com "OPEN_WINDOW sagittalgraph \\\n' \
' geom=%dx%d+%d+%d" \\\n' % \
(self.gr_size[0], self.gr_size[1], self.gr_xoff, self.gr_yoff)
# terminate the initial plugout_drive command
c2 += ' -quit\n\n'
c2 = UTIL.add_line_wrappers(c2) # do it early, for verb
if self.verb > 2: print('initial drive command:\n%s' % c2)
cmd += c2
cmd += 'sleep 2 # give afni time to open the windows\n\n\n'
c2 = '# ------------------------------------------------------\n' \
'# process each dataset using video mode\n\n' \
'foreach dset ( $dsets )\n' \
' plugout_drive \\\n' \
' -com "SWITCH_UNDERLAY $dset" \\\n' \
' -com "OPEN_WINDOW sagittalgraph \\\n' \
' keypress=a\\\n' \
' keypress=v"\\\n' \
' -quit\n\n' \
' sleep 2 # wait for plugout_drive output\n\n' \
' echo ""\n' \
' echo "++ now viewing $dset, hit enter to continue"\n' \
' set ret = $< # wait for user to hit enter\n' \
'end\n\n\n'
cmd += UTIL.add_line_wrappers(c2)
c2 = '# ------------------------------------------------------\n' \
'# stop video mode when the user is done\n\n' \
'plugout_drive -com "OPEN_WINDOW sagittalgraph keypress=s"' \
' -quit\n\n\n' \
'sleep 2 # wait for plugout_drive output\n\n' \
'echo ""\n' \
'echo "data review complete"\n\n\n'
cmd += UTIL.add_line_wrappers(c2)
c2 = '# ----------------------------------------------------------'\
"------\n# auto-generated by gen_epi_review.py, %s\n" % g_version
c2 += "#\n# %s %s\n" % (os.path.basename(sys.argv[0]), ' '.join(
UTIL.quotize_list(sys.argv[1:], '')))
cmd += UTIL.add_line_wrappers(c2)
fp = open(self.script, "w")
if not fp:
print('** failed to open %s for writing decon script' %
self.script)
return 1
fp.write(cmd)
fp.close()
try:
os.chmod(self.script, 0o755)
except OSError as e:
print(e)
return
