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