def main(argv):
epocher_hdf_fname = None
#--- get args from parser
opt,parser = jpp_utils.get_args()
#--- set debug & test mode
if opt.debug :
opt.experiment = 'TEST01'
opt.stage = os.getenv('MY_LOCAL_DATA','.') + '/Chrono/mne'
opt.fifname = '201195_Chrono01_110516_1413_1_c,rfDC-raw.fif' #'201195_test.fif' #None
opt.pathfif = '201195/Chrono01/110516_1413/1' #None
opt.verbose = True
opt.run = True
#condition_list = ('LRst','LRrt')
#---
if opt.verbose :
print"\n---> ARGV parameter:"
print" --> experiment : " + str(opt.experiment)
print" --> condition : " + str(opt.conditions)
print" --> stage : " + str(opt.stage)
print" --> stage eeg : " + str(opt.stage_eeg)
print" --> path to fif : " + str(opt.pathfif)
print" --> fif name : " + str(opt.fifname)
print" --> path to list: " + str(opt.pathlist)
print" --> fname list : " + str(opt.fnamelist)
print" --> verbose : " + str(opt.verbose)
print" --> run : " + str(opt.run)
print" --> debug mode : " + str(opt.debug)
print"\n\n"
#--- update base
jumeg_base.verbose = opt.verbose
#--- init experiment template parameter
jtmp_exp.template_name = opt.experiment
jtmp_exp.verbose = opt.verbose
#- read template parameters into dict
tmp = jtmp_exp.template_update_file()
#--- make obj from dict
TMP = jtmp_exp.template_get_as_obj()
path_exp = TMP.experiment.path.experiment
if opt.stage is None:
opt.stage = TMP.experiment.path.mne
#---
if opt.verbose :
print"\n---> Experiment Template parameter:"
print" --> name : "+ jtmp_exp.template_name
print" --> template file: "+ jtmp_exp.template_full_file_name
print"\n"
#---
if not opt.run:
print "===> Done jumeg preprocessing , set run flag for real data processing\n"
print parser.print_help()
print"\n"
exit()
#--- get existing files from list e.g.
# 005/MEG94T/121219_1311/1/005_MEG94T_121219_1311_1_c,rfDC-raw.fif -bads=A1
# 007/MEG94T/121217_1239/1/007_MEG94T_121217_1239_1_c,rfDC-raw.fif -bads=A1,A2
fn_raw_list=[]
fn_raw_bad_channel_dict=[]
opt_dict = {}
if opt.fnamelist:
# fn_raw_list,fn_raw_bad_channel_dict = jumeg_base.get_filename_list_from_file(opt.pathlist + "/" + opt.fnamelist,start_path = opt.stage)
fn_raw_list,opt_dict = jumeg_base.get_filename_list_from_file(opt.pathlist + "/" + opt.fnamelist,start_path=opt.stage)
#--- check & add fif file to list update bad channel dict
if opt.fifname:
if opt.pathfif :
f = opt.pathfif +"/"+ opt.fifname
f = opt.fifname
if os.path.isfile(f):
fn_raw_list.append(f)
elif os.path.isfile(opt.stage + '/' + f):
f = opt.stage + '/' + f
fn_raw_list.append(f)
opt_dict[f] = {'bads': None, 'feeg': None}
if opt.bads:
opt_dict[f]['bads'] = opt.bads
if opt.eeg_fname: # --- bad channels
opt_dict[f]['feeg'] = opt.eeg_fname
#--- raw obj short-cut
tmp_pp_raw = TMP.experiment.data_preprocessing.raw
#--- loop preproc for each fif file
for fif_file in (fn_raw_list) :
raw = None
fif_file_raw = fif_file
#--- check opt / set bad channels / merge eeg
if ( fif_file in opt_dict ):
if opt_dict[fif_file]['bads']:
print "\n ===> Bad Channel -> " + fif_file
print" --> BADs: " + str(opt_dict[fif_file]['bads'])
if opt_dict[fif_file]['bads']:
raw, _ = jumeg_base.update_bad_channels(fif_file,raw=raw,bads=opt_dict[fif_file]['bads'])
#--- merge eeg save=True, append=False, interpolate=True)
if opt_dict[fif_file]['feeg']:
feeg = str(opt_dict[fif_file]['feeg'])
print "\n ===> Merge EEG data ->"
print" --> MEG: " + fif_file
if opt.stage_eeg:
if os.path.isfile(opt.stage_eeg + '/' + feeg):
feeg= opt.stage_eeg + '/' + feeg
if os.path.isfile(feeg):
print" --> EEG: " + feeg
raw,fif_file = jppd.apply_merge_meeg(fif_file,raw=raw,eeg_fname=feeg,save=True,do_run=opt.run,verbose=opt.verbose) #opt.run
else:
print"!!! ERROR: no eeg file to merge with fif:"
print " --> FIF : " + fif_file_raw
print " --> EEG : " + feeg
assert" No EEG file to merge"
#--- epocher search for events save to HDF
if hasattr(tmp_pp_raw.epocher,"do_run"):
if tmp_pp_raw.epocher.do_run :
tmp_pp_raw.epocher['verbose'] = opt.verbose
print"\n===> PP Info: start apply epocher => event code search"
print"File : " + fif_file
if opt.verbose:
print"Parameter:"
print tmp_pp_raw.epocher
print"\n\n"
(fname,raw,epocher_hdf_fname) = jppd.apply_epocher_events_data(fif_file,raw=raw,condition_list=opt.conditions, **tmp_pp_raw.epocher)
else:
jpp_utils.msg_on_attribute_error("raw epocher")
#--- noise_covariance
#--- will search and find empty room file if fif is no empty room file
if hasattr(tmp_pp_raw.noise_covariance,"do_run"):
if tmp_pp_raw.noise_covariance.do_run :
tmp_pp_raw.noise_covariance['verbose'] = opt.verbose
print"\n===> PP Info: start apply create noise_covariance"
print"File :" + fif_file
if opt.verbose:
print"Parameter:"
print tmp_pp_raw.noise_covariance
print"\n\n"
fname_noise_covariance = jppd.apply_create_noise_covariance_data(fif_file,raw=raw,**tmp_pp_raw.noise_covariance)
print"\n\n==> PP Info: done apply create noise_covariance :\n ---> "
try:
print fname_noise_covariance +"\n"
except:
print " !!! not found !!!\n\n"
else:
jpp_utils.msg_on_attribute_error("raw noise covariance")
#--- noise_reducer
#--- will apply magic ee noise reducer7
if hasattr(tmp_pp_raw.noise_reducer,"do_run"):
if tmp_pp_raw.noise_reducer.do_run :
tmp_pp_raw.noise_reducer['verbose'] = opt.verbose
print"\n===> PP Info: start apply ee noise_reducer"
print"File :" + fif_file
if opt.verbose:
print"Parameter:"
print tmp_pp_raw.noise_reducer
print"\n\n"
(fif_file, raw) = jppd.apply_noise_reducer_data(fif_file,raw=raw,**tmp_pp_raw.noise_reducer)
print"\n\n==> PP Info: done apply noise reducer raw\n ---> " + fif_file
print"RAW fname: "+raw.info['filename']
else:
fif_file = jumeg_base.get_fif_name(fname=fif_file,postfix=tmp_pp_raw.noise_reducer.fif_postfix,extention=tmp_pp_raw.noise_reducer.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("raw noise reducer")
# ToDo if ( raw.info.fname == fname ) check if has to be loaded reloaded
#--- filter raw data
if hasattr(tmp_pp_raw.filter,"do_run"):
if tmp_pp_raw.filter.do_run :
tmp_pp_raw.filter['verbose'] = opt.verbose
print"\n===> PP Info: start apply filter raw:"
print"File : " + fif_file
if opt.verbose:
print"Parameter :"
print tmp_pp_raw.filter
print"\n\n"
(fif_file, raw) = jppd.apply_filter_data(fif_file,raw=raw,**tmp_pp_raw.filter)
print"\n\n==> PP Info: done apply filter raw\n ---> " + fname
else:
fif_file = jumeg_base.get_fif_name(fname=fif_file,postfix=tmp_pp_raw.filter.fif_postfix,extention=tmp_pp_raw.filter.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("raw filter")
# ToDo if ( raw.info.fname == fname ) check if has to be reloaded
#--- ocarta
if hasattr(tmp_pp_raw.ocarta,"do_run"):
if tmp_pp_raw.ocarta.do_run :
tmp_pp_raw.ocarta['verbose'] = opt.verbose
print"\n===> PP Info: start apply ocarta fit"
print"File :" + fif_file
if opt.verbose :
print"Parameter :"
print tmp_pp_raw.ocarta
print"\n\n"
(fif_file,raw,fhdf) = jppd.apply_ocarta_data(fif_file,raw=raw,**tmp_pp_raw.ocarta)
print"\n\n==> PP Info: done apply ocarta\n ---> " + fif_file
else:
fif_file = jumeg_base.get_fif_name(fname=fif_file,postfix=tmp_pp_raw.ocarta.fif_postfix,extention=tmp_pp_raw.ocarta.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("raw ocarta")
# ToDo if ( raw.info.fname == fname ) check if has to be reloaded
#--- filter after ocarta
if hasattr(tmp_pp_raw.filter_after_ocarta,"do_run"):
if tmp_pp_raw.filter_after_ocarta.do_run :
tmp_pp_raw.filter_after_ocarta['verbose'] = opt.verbose
print"\n===> PP Info: start apply filter after ocarta:"
print"File : " + fif_file
if opt.verbose:
print"Parameter :"
print tmp_pp_raw.filter_after_ocarta
print"\n\n"
(fif_file, raw) = jppd.apply_filter_data(fif_file,raw=raw,**tmp_pp_raw.filter_after_ocarta)
print"\n\n==> PP Info: done apply filter after ocarta\n ---> " + fname
else:
fif_file = jumeg_base.get_fif_name(fname=fif_file,postfix=tmp_pp_raw.filter_after_ocarta.fif_postfix,extention=tmp_pp_raw.filter_after_ocarta.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("filter after ocarta")
# ToDo if ( raw.info.fname == fname ) check if has to be reloaded
#--- events
if hasattr(tmp_pp_raw.events,"do_run"):
if tmp_pp_raw.events.do_run :
tmp_pp_raw.events['verbose'] = opt.verbose
print"\n===> PP Info: start apply event export"
print"File :" + fif_file
if opt.verbose :
print"Parameter :"
print tmp_pp_raw.events
print"\n\n"
(fif_file,raw,event_ids) = jppd.apply_epocher_export_events_data(fif_file,raw=raw,condition_list=opt.conditions,**tmp_pp_raw.events)
print"\n\n==> PP Info: done apply events\n ---> " + fif_file
print event_ids
print"\n\n"
else:
jpp_utils.msg_on_attribute_error("raw events")
'''
# !!! under construction
#--- brainresponse obj short-cut
tmp_pp_brs = TMP.experiment.data_preprocessing.brainresponse
# ToDo if ( raw.info.fname == fname ) check if has to be reloaded
#--- brain response apply mne ica: fastica
if hasattr(tmp_pp_brs.ica,"do_run"):
if tmp_pp_brs.ica.do_run :
tmp_pp_brs.ica['verbose'] = opt.verbose
print "\n===> PP Info: start apply brain-response ica"
print"File : " + fif_file
if opt.verbose:
print"Parameter :"
print tmp_pp_brs.ica
print"\n\n"
(fif_file_ica,raw,ICAobj) = jppd.apply_ica_data(fif_file,raw=raw,**tmp_pp_brs.ica)
print"\n\n==> PP Info: done apply ica for brain responses\n ---> " + fif_file_ica
else:
fif_file_ica = jumeg_base.get_fif_name(fname=fif_file,postfix=tmp_pp_brs.ica.fif_postfix,extention=tmp_pp_brs.ica.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("brain response ica")
# 201195_Chrono01_110516_1413_1_c,rfDC,fihp1n,ocarta-ica.fif
#--- brain response ctps
#--- run for all condition combine and or exclude CTPs-ICs for different conditions
if hasattr(tmp_pp_brs.ctps,"do_run"):
if tmp_pp_brs.ctps.do_run :
tmp_pp_brs.ctps['verbose'] = opt.verbose
print"\n===> PP Info: start brainresponse ica"
print"File : " + fif_file_ica
if opt.verbose :
print"Parameters:"
print tmp_pp_brs.ctps
print"\n\n"
(fif_file,raw,fhdf)=jppd.apply_ctps_brain_responses_data(fif_file,raw=raw,fname_ica=fif_file_ica,ica_raw=None,
condition_list=opt.condition,**tmp_pp_brs.ctps)
print"\n\n==> PP Info: done apply ctp for brain responses\n ---> " + fif_file
else:
fhdf = raw = None
else:
jpp_utils.msg_on_attribute_error("brain response ctps")
#--- brain response ctps ica cleaning
#--- run for global ics, all ctp-ics-condition create raw,epochs,average
if hasattr(tmp_pp_brs.clean,"do_run"):
if tmp_pp_brs.clean.do_run :
tmp_pp_brs.clean['verbose'] = opt.verbose
print"\n===> PP Info: start brain-response cleaning"
print"File : " + fif_file
if opt.verbose :
print"Parameters:"
print tmp_pp_brs.clean
print"\n\n"
fhdf = jppd.apply_ctps_brain_responses_cleaning_data(fif_file,raw=raw,fname_ica=fif_file_ica,ica_raw=None,fhdf=fhdf,
condition_list=opt.condition,**tmp_pp_brs.clean)
else:
jpp_utils.msg_on_attribute_error("brain response clean")
'''
print"===> Done JuMEG Pre-Processing Data"
# print" --> FIF file input : " + fif_file_raw
# print" --> Information stored in HDF file: " + str(fhdf)
print"\n\n"
raw = None
#--- brainresponse obj short-cut
tmp_pp_brs = TMP.experiment.data_preprocessing.brainresponse
#--- loop preproc for each fif file
for fif_file in (fn_raw_list):
raw = None
#--- check / set bad channels
if (fif_file in fn_raw_bad_channel_dict):
print "BAD CH DICT -> " + fif_file
print "BADS: " + fn_raw_bad_channel_dict[fif_file]
if fn_raw_bad_channel_dict[fif_file]:
raw = jumeg_base.update_bad_channels(
fif_file,
raw=raw,
bads=fn_raw_bad_channel_dict[fif_file],
save=True)
#--- epocher search for events save to HDF
if tmp_pp_raw.epocher.do_run:
tmp_pp_raw.epocher['verbose'] = verbose
print "\n===> PP Info: start apply epocher => event code search"
print "File : " + fif_file
if verbose:
print "Parameter:"
print tmp_pp_raw.epocher
print "\n\n"
(fname, raw, epocher_hdf_fname) = jppd.apply_epocher_events_data(
fif_file,
raw=raw,
#--- raw obj short-cut
tmp_pp_raw = TMP.experiment.data_preprocessing.raw
#--- brainresponse obj short-cut
tmp_pp_brs = TMP.experiment.data_preprocessing.brainresponse
#--- loop preproc for each fif file
for fif_file in (fn_raw_list) :
raw = None
#--- check / set bad channels
if ( fif_file in fn_raw_bad_channel_dict ):
print "\n ===> BAD Channel -> " + fif_file
print" --> BADs: " + str(fn_raw_bad_channel_dict[fif_file])
if fn_raw_bad_channel_dict[fif_file]:
raw,bads_dict = jumeg_base.update_bad_channels(fif_file,raw=raw,bads=fn_raw_bad_channel_dict[fif_file],save=True)
#--- epocher search for events save to HDF
if tmp_pp_raw.epocher.do_run :
tmp_pp_raw.epocher['verbose'] = verbose
print"\n===> PP Info: start apply epocher => event code search"
print"File : " + fif_file
if verbose:
print"Parameter:"
print tmp_pp_raw.epocher
print"\n\n"
(fname,raw,epocher_hdf_fname) = jppd.apply_epocher_events_data(fif_file,raw=raw,condition_list=condition_list, **tmp_pp_raw.epocher)
#--- noise_covariance
#--- will search and find empty room file if fif is no empty room file
def main(argv):
#-- default argv
# experiment_name = None
# path_list = os.getcwd()
# fname_list = None
# # fif_name = None
# pfif = os.getcwd()
# path_mne_stage = None
# bad_channels = None
# verbose, do_run = False,False
# condition_list = None
epocher_hdf_fname = None
#--- get args from parser
opt,parser = jpp_utils.get_args()
#--- set debug & test mode
if opt.debug :
opt.experiment = 'TEST01'
opt.stage = '/localdata/frank/data/Chrono/mne'
#path_list = "/localdata/frank/data/Chrono/doc"
#fname_list = 'chrono_normal_inkomp.txt'
opt.fifname = '201195_Chrono01_110516_1413_1_c,rfDC-raw.fif' #'201195_test.fif' #None
opt.pathfif = '201195/Chrono01/110516_1413/1' #None
opt.verbose = True
opt.run = True
#condition_list = ('LRst','LRrt')
#---
if opt.verbose :
print"\n---> ARGV parameter:"
print"experiment : " + str(opt.experiment)
print"condition : " + str(opt.conditions)
print"stage : " + str(opt.stage)
print"path to fif : " + str(opt.pathfif)
print"fif name : " + str(opt.fifname)
print"path to list: " + str(opt.pathlist)
print"fname list : " + str(opt.fnamelist)
print"verbose : " + str(opt.verbose)
print"run : " + str(opt.run)
print"debug mode : " + str(opt.debug)
print"\n\n"
#--- update base
jumeg_base.verbose = opt.verbose
#--- init experiment template parameter
jtmp_exp.template_name = opt.experiment
jtmp_exp.verbose = opt.verbose
#- read template parameters into dict
tmp = jtmp_exp.template_update_file()
#--- make obj from dict
TMP = jtmp_exp.template_get_as_obj()
path_exp = TMP.experiment.path.experiment
if opt.stage is None:
opt.stage = TMP.experiment.path.mne
#---
if opt.verbose :
print"\n---> Experiment Template parameter:"
print" --> name : "+ jtmp_exp.template_name
print" --> template file: "+ jtmp_exp.template_full_file_name
print"\n"
#---
if not opt.run:
print "===> Done jumeg preprocessing , set run flag for real data processing\n"
print parser.print_help()
print"\n"
exit()
#--- get existing files from list
# 005/MEG94T/121219_1311/1/005_MEG94T_121219_1311_1_c,rfDC-raw.fif -nc=A1
# 007/MEG94T/121217_1239/1/007_MEG94T_121217_1239_1_c,rfDC-raw.fif -nc=A1,A2
fn_raw_list=[]
fn_raw_bad_channel_dict=[]
if opt.fnamelist:
fn_raw_list,fn_raw_bad_channel_dict = jumeg_base.get_filename_list_from_file(opt.pathlist + "/" + opt.fnamelist,start_path = opt.stage)
#--- check & add fif file to list update bad channel dict
if opt.fifname:
if opt.pathfif :
f = opt.pathfif +"/"+ opt.fifname
else:
f = opt.fifname
if os.path.isfile(f):
fn_raw_list.append(f)
if opt.bads: #--- bad channels
fn_raw_bad_channel_dict[f]= opt.bads
elif os.path.isfile(opt.stage + '/' + f):
fn_raw_list.append(opt.stage + '/' + f)
if opt.bads:
fn_raw_bad_channel_dict[f]= opt.bads
#--- raw obj short-cut
tmp_pp_raw = TMP.experiment.data_preprocessing.raw
#--- brainresponse obj short-cut
tmp_pp_brs = TMP.experiment.data_preprocessing.brainresponse
#--- loop preproc for each fif file
for fif_file in (fn_raw_list) :
raw = None
#--- check / set bad channels
if ( fif_file in fn_raw_bad_channel_dict ):
print "\n ===> BAD Channel -> " + fif_file
print" --> BADs: " + str(fn_raw_bad_channel_dict[fif_file])
if fn_raw_bad_channel_dict[fif_file]:
raw,bads_dict = jumeg_base.update_bad_channels(fif_file,raw=raw,bads=fn_raw_bad_channel_dict[fif_file],save=True)
#--- epocher search for events save to HDF
if tmp_pp_raw.epocher.do_run :
tmp_pp_raw.epocher['verbose'] = opt.verbose
print"\n===> PP Info: start apply epocher => event code search"
print"File : " + fif_file
if opt.verbose:
print"Parameter:"
print tmp_pp_raw.epocher
print"\n\n"
(fname,raw,epocher_hdf_fname) = jppd.apply_epocher_events_data(fif_file,raw=raw,condition_list=opt.conditions, **tmp_pp_raw.epocher)
#--- noise_covariance
#--- will search and find empty room file if fif is no empty room file
if tmp_pp_raw.noise_covariance.do_run :
tmp_pp_raw.noise_covariance['verbose'] = opt.verbose
print"\n===> PP Info: start apply create noise_covariance"
print"File :" + fif_file
if opt.verbose:
print"Parameter:"
print tmp_pp_raw.noise_covariance
print"\n\n"
fname_noise_covariance = jppd.apply_create_noise_covariance_data(fif_file,raw=raw,**tmp_pp_raw.noise_covariance)
print"\n\n==> PP Info: done apply create noise_covariance :\n ---> "
try:
print fname_noise_covariance +"\n"
except:
print " !!! not found !!!\n\n"
#--- noise_reducer
#--- will apply magic ee noise reducer
if tmp_pp_raw.noise_reducer.do_run :
tmp_pp_raw.noise_reducer['verbose'] = opt.verbose
print"\n===> PP Info: start apply ee noise_reducer"
print"File :" + fif_file
if opt.verbose:
print"Parameter:"
print tmp_pp_raw.noise_reducer
print"\n\n"
(fif_file, raw) = jppd.apply_noise_reducer_data(fif_file,raw=raw,**tmp_pp_raw.noise_reducer)
print"\n\n==> PP Info: done apply noise reducer raw\n ---> " + fname
else:
fif_file = jumeg_base.get_fif_name(fif_file,postfix=tmp_pp_raw.noise_reducer.fif_postfix,extention=tmp_pp_raw.noise_reducer.fif_extention)
raw = None
#--- filter raw data
if tmp_pp_raw.filter.do_run :
tmp_pp_raw.filter['verbose'] = opt.verbose
print"\n===> PP Info: start apply filter raw:"
print"File : " + fif_file
if opt.verbose:
print"Parameter :"
print tmp_pp_raw.filter
print"\n\n"
(fname, raw) = jppd.apply_filter_data(fif_file,raw=raw,**tmp_pp_raw.filter)
print"\n\n==> PP Info: done apply filter raw\n ---> " + fname
else:
fname = jumeg_base.get_fif_name(fif_file,postfix=tmp_pp_raw.filter.fif_postfix,extention=tmp_pp_raw.filter.fif_extention)
raw = None
#--- average raw filtered data
# if tmp_pp_raw.average.do_run :
# tmp_pp_raw.average.verbose = verbose
# print"\n===> PP Info: start apply averager raw"
# print"File :" + fname
# if verbose:
# print"Parameter :"
# print tmp_pp_raw.average
# print"\n\n"
# jppd.apply_averager(fn_raw_list,**tmp_pp_raw.averager)
# print"\n\n==> PP Info: done apply averager filterd raw data\n"
#--- ocarta
if tmp_pp_raw.ocarta.do_run :
tmp_pp_raw.ocarta['verbose'] = opt.verbose
print"\n===> PP Info: start apply ocarta fit"
print"File :" + fname
if opt.verbose :
print"Parameter :"
print tmp_pp_raw.ocarta
print"\n\n"
(fname_oca,raw,fhdf) = jppd.apply_ocarta_data(fname,raw=raw,**tmp_pp_raw.ocarta)
print"\n\n==> PP Info: done apply ocarta\n ---> " + fname_oca
else:
fname_oca = jumeg_base.get_fif_name(fname,postfix=tmp_pp_raw.ocarta.fif_postfix,extention=tmp_pp_raw.ocarta.fif_extention)
raw = None
#--- brain response apply mne ica: fastica
if tmp_pp_brs.ica.do_run :
tmp_pp_brs.ica['verbose'] = opt.verbose
print "\n===> PP Info: start apply brain-response ica"
print"File : " + fname_oca
if opt.verbose:
print"Parameter :"
print tmp_pp_brs.ica
print"\n\n"
(fname_oca_ica,raw,ICAobj) = jppd.apply_ica_data(fname_oca,raw=raw,**tmp_pp_brs.ica)
print"\n\n==> PP Info: done apply ica for brain responses\n ---> " + fname_oca_ica
else:
fname_oca_ica = jumeg_base.get_fif_name(fname_oca,postfix=tmp_pp_brs.ica.fif_postfix,extention=tmp_pp_brs.ica.fif_extention)
raw = None
# 201195_Chrono01_110516_1413_1_c,rfDC,fihp1n,ocarta-ica.fif
#--- brain response ctps
#--- run for all condition combine and or exclude CTPs-ICs for different conditions
if tmp_pp_brs.ctps.do_run :
tmp_pp_brs.ctps['verbose'] = opt.verbose
print"\n===> PP Info: start brainresponse ica"
print"File : " + fname_oca_ica
if opt.verbose :
print"Parameters:"
print tmp_pp_brs.ctps
print"\n\n"
(fname_oca,raw,fhdf)=jppd.apply_ctps_brain_responses_data(fname_oca,raw=raw,fname_ica=fname_oca_ica,ica_raw=None,
condition_list=condition_list,**tmp_pp_brs.ctps)
print"\n\n==> PP Info: done apply ctp for brain responses\n ---> " + fname_oca
else:
fhdf = None
raw = None
#--- brain response ctps ica cleaning
#--- run for global ics, all ctp-ics-condition create raw,epochs,average
if tmp_pp_brs.clean.do_run :
tmp_pp_brs.clean['verbose'] = opt.verbose
print"\n===> PP Info: start brain-response cleaning"
print"File : " + fname_oca
if opt.verbose :
print"Parameters:"
print tmp_pp_brs.clean
print"\n\n"
fhdf = jppd.apply_ctps_brain_responses_cleaning_data(fname_oca,raw=raw,fname_ica=fname_oca_ica,ica_raw=None,fhdf=fhdf,
condition_list=condition_list,**tmp_pp_brs.clean)
print"===> Done JuMEG Pre-Processing Data"
print" --> FIF file input : " + fif_file
print" --> Information stored in HDF file: " + str(fhdf)
print"\n\n"
raw = None
def main(argv):
epocher_hdf_fname = None
#--- get args from parser
opt, parser = jpp_utils.get_args()
#--- set debug & test mode
if opt.debug:
opt.experiment = 'TEST01'
opt.stage = '/localdata/frank/data/Chrono/mne'
#path_list = "/localdata/frank/data/Chrono/doc"
#fname_list = 'chrono_normal_inkomp.txt'
opt.fifname = '201195_Chrono01_110516_1413_1_c,rfDC-raw.fif' #'201195_test.fif' #None
opt.pathfif = '201195/Chrono01/110516_1413/1' #None
opt.verbose = True
opt.run = True
#condition_list = ('LRst','LRrt')
#---
if opt.verbose:
print "\n---> ARGV parameter:"
print "experiment : " + str(opt.experiment)
print "condition : " + str(opt.conditions)
print "stage : " + str(opt.stage)
print "path to fif : " + str(opt.pathfif)
print "fif name : " + str(opt.fifname)
print "path to list: " + str(opt.pathlist)
print "fname list : " + str(opt.fnamelist)
print "verbose : " + str(opt.verbose)
print "run : " + str(opt.run)
print "debug mode : " + str(opt.debug)
print "\n\n"
#--- update base
jumeg_base.verbose = opt.verbose
#--- init experiment template parameter
jtmp_exp.template_name = opt.experiment
jtmp_exp.verbose = opt.verbose
#- read template parameters into dict
tmp = jtmp_exp.template_update_file()
#--- make obj from dict
TMP = jtmp_exp.template_get_as_obj()
path_exp = TMP.experiment.path.experiment
if opt.stage is None:
opt.stage = TMP.experiment.path.mne
#---
if opt.verbose:
print "\n---> Experiment Template parameter:"
print " --> name : " + jtmp_exp.template_name
print " --> template file: " + jtmp_exp.template_full_file_name
print "\n"
#---
if not opt.run:
print "===> Done jumeg preprocessing , set run flag for real data processing\n"
print parser.print_help()
print "\n"
exit()
#--- get existing files from list e.g.
# 005/MEG94T/121219_1311/1/005_MEG94T_121219_1311_1_c,rfDC-raw.fif -nc=A1
# 007/MEG94T/121217_1239/1/007_MEG94T_121217_1239_1_c,rfDC-raw.fif -nc=A1,A2
fn_raw_list = []
fn_raw_bad_channel_dict = []
if opt.fnamelist:
fn_raw_list, fn_raw_bad_channel_dict = jumeg_base.get_filename_list_from_file(
opt.pathlist + "/" + opt.fnamelist, start_path=opt.stage)
#--- check & add fif file to list update bad channel dict
if opt.fifname:
if opt.pathfif:
f = opt.pathfif + "/" + opt.fifname
else:
f = opt.fifname
if os.path.isfile(f):
fn_raw_list.append(f)
if opt.bads: #--- bad channels
fn_raw_bad_channel_dict[f] = opt.bads
elif os.path.isfile(opt.stage + '/' + f):
fn_raw_list.append(opt.stage + '/' + f)
if opt.bads:
fn_raw_bad_channel_dict[f] = opt.bads
#--- raw obj short-cut
tmp_pp_raw = TMP.experiment.data_preprocessing.raw
#--- brainresponse obj short-cut
tmp_pp_brs = TMP.experiment.data_preprocessing.brainresponse
#--- loop preproc for each fif file
for fif_file in (fn_raw_list):
raw = None
fif_file_raw = fif_file
#--- check / set bad channels
if (fif_file in fn_raw_bad_channel_dict):
print "\n ===> BAD Channel -> " + fif_file
print " --> BADs: " + str(fn_raw_bad_channel_dict[fif_file])
if fn_raw_bad_channel_dict[fif_file]:
raw, bads_dict = jumeg_base.update_bad_channels(
fif_file,
raw=raw,
bads=fn_raw_bad_channel_dict[fif_file],
save=True)
#--- epocher search for events save to HDF
if hasattr(tmp_pp_raw.epocher, "do_run"):
if tmp_pp_raw.epocher.do_run:
tmp_pp_raw.epocher['verbose'] = opt.verbose
print "\n===> PP Info: start apply epocher => event code search"
print "File : " + fif_file
if opt.verbose:
print "Parameter:"
print tmp_pp_raw.epocher
print "\n\n"
(fname, raw,
epocher_hdf_fname) = jppd.apply_epocher_events_data(
fif_file,
raw=raw,
condition_list=opt.conditions,
**tmp_pp_raw.epocher)
else:
jpp_utils.msg_on_attribute_error("raw epocher")
#--- noise_covariance
#--- will search and find empty room file if fif is no empty room file
if hasattr(tmp_pp_raw.noise_covariance, "do_run"):
if tmp_pp_raw.noise_covariance.do_run:
tmp_pp_raw.noise_covariance['verbose'] = opt.verbose
print "\n===> PP Info: start apply create noise_covariance"
print "File :" + fif_file
if opt.verbose:
print "Parameter:"
print tmp_pp_raw.noise_covariance
print "\n\n"
fname_noise_covariance = jppd.apply_create_noise_covariance_data(
fif_file, raw=raw, **tmp_pp_raw.noise_covariance)
print "\n\n==> PP Info: done apply create noise_covariance :\n ---> "
try:
print fname_noise_covariance + "\n"
except:
print " !!! not found !!!\n\n"
else:
jpp_utils.msg_on_attribute_error("raw noise covariance")
#--- noise_reducer
#--- will apply magic ee noise reducer7
if hasattr(tmp_pp_raw.noise_reducer, "do_run"):
if tmp_pp_raw.noise_reducer.do_run:
tmp_pp_raw.noise_reducer['verbose'] = opt.verbose
print "\n===> PP Info: start apply ee noise_reducer"
print "File :" + fif_file
if opt.verbose:
print "Parameter:"
print tmp_pp_raw.noise_reducer
print "\n\n"
(fif_file, raw) = jppd.apply_noise_reducer_data(
fif_file, raw=raw, **tmp_pp_raw.noise_reducer)
print "\n\n==> PP Info: done apply noise reducer raw\n ---> " + fif_file
print "RAW fname: " + raw.info['filename']
else:
fif_file = jumeg_base.get_fif_name(
fname=fif_file,
postfix=tmp_pp_raw.noise_reducer.fif_postfix,
extention=tmp_pp_raw.noise_reducer.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("raw noise reducer")
#--- filter raw data
if hasattr(tmp_pp_raw.filter, "do_run"):
if tmp_pp_raw.filter.do_run:
tmp_pp_raw.filter['verbose'] = opt.verbose
print "\n===> PP Info: start apply filter raw:"
print "File : " + fif_file
if opt.verbose:
print "Parameter :"
print tmp_pp_raw.filter
print "\n\n"
(fif_file, raw) = jppd.apply_filter_data(fif_file,
raw=raw,
**tmp_pp_raw.filter)
print "\n\n==> PP Info: done apply filter raw\n ---> " + fname
else:
fif_file = jumeg_base.get_fif_name(
fname=fif_file,
postfix=tmp_pp_raw.filter.fif_postfix,
extention=tmp_pp_raw.filter.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("raw filter")
#--- average raw filtered data
# if tmp_pp_raw.average.do_run :
# tmp_pp_raw.average.verbose = verbose
# print"\n===> PP Info: start apply averager raw"
# print"File :" + fname
# if verbose:
# print"Parameter :"
# print tmp_pp_raw.average
# print"\n\n"
# jppd.apply_averager(fn_raw_list,**tmp_pp_raw.averager)
# print"\n\n==> PP Info: done apply averager filterd raw data\n"
#--- ocarta
if hasattr(tmp_pp_raw.ocarta, "do_run"):
if tmp_pp_raw.ocarta.do_run:
tmp_pp_raw.ocarta['verbose'] = opt.verbose
print "\n===> PP Info: start apply ocarta fit"
print "File :" + fif_file
if opt.verbose:
print "Parameter :"
print tmp_pp_raw.ocarta
print "\n\n"
(fif_file, raw,
fhdf) = jppd.apply_ocarta_data(fif_file,
raw=raw,
**tmp_pp_raw.ocarta)
print "\n\n==> PP Info: done apply ocarta\n ---> " + fif_file
else:
fif_file = jumeg_base.get_fif_name(
fname=fif_file,
postfix=tmp_pp_raw.ocarta.fif_postfix,
extention=tmp_pp_raw.ocarta.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("raw ocarta")
#--- events
if hasattr(tmp_pp_raw.events, "do_run"):
if tmp_pp_raw.events.do_run:
tmp_pp_raw.events['verbose'] = opt.verbose
print "\n===> PP Info: start apply event export"
print "File :" + fif_file
if opt.verbose:
print "Parameter :"
print tmp_pp_raw.events
print "\n\n"
(fif_file, raw,
event_ids) = jppd.apply_epocher_export_events_data(
fif_file,
raw=raw,
condition_list=opt.conditions,
**tmp_pp_raw.events)
print "\n\n==> PP Info: done apply events\n ---> " + fif_file
print event_ids
print "\n\n"
else:
jpp_utils.msg_on_attribute_error("raw events")
#--- brain response apply mne ica: fastica
if hasattr(tmp_pp_brs.ica, "do_run"):
if tmp_pp_brs.ica.do_run:
tmp_pp_brs.ica['verbose'] = opt.verbose
print "\n===> PP Info: start apply brain-response ica"
print "File : " + fif_file
if opt.verbose:
print "Parameter :"
print tmp_pp_brs.ica
print "\n\n"
(fif_file_ica, raw,
ICAobj) = jppd.apply_ica_data(fif_file,
raw=raw,
**tmp_pp_brs.ica)
print "\n\n==> PP Info: done apply ica for brain responses\n ---> " + fif_file_ica
else:
fif_file_ica = jumeg_base.get_fif_name(
fname=fif_file,
postfix=tmp_pp_brs.ica.fif_postfix,
extention=tmp_pp_brs.ica.fif_extention)
raw = None
else:
jpp_utils.msg_on_attribute_error("brain response ica")
# 201195_Chrono01_110516_1413_1_c,rfDC,fihp1n,ocarta-ica.fif
#--- brain response ctps
#--- run for all condition combine and or exclude CTPs-ICs for different conditions
if hasattr(tmp_pp_brs.ctps, "do_run"):
if tmp_pp_brs.ctps.do_run:
tmp_pp_brs.ctps['verbose'] = opt.verbose
print "\n===> PP Info: start brainresponse ica"
print "File : " + fif_file_ica
if opt.verbose:
print "Parameters:"
print tmp_pp_brs.ctps
print "\n\n"
(fif_file, raw, fhdf) = jppd.apply_ctps_brain_responses_data(
fif_file,
raw=raw,
fname_ica=fif_file_ica,
ica_raw=None,
condition_list=opt.condition,
**tmp_pp_brs.ctps)
print "\n\n==> PP Info: done apply ctp for brain responses\n ---> " + fif_file
else:
fhdf = raw = None
else:
jpp_utils.msg_on_attribute_error("brain response ctps")
#--- brain response ctps ica cleaning
#--- run for global ics, all ctp-ics-condition create raw,epochs,average
if hasattr(tmp_pp_brs.clean, "do_run"):
if tmp_pp_brs.clean.do_run:
tmp_pp_brs.clean['verbose'] = opt.verbose
print "\n===> PP Info: start brain-response cleaning"
print "File : " + fif_file
if opt.verbose:
print "Parameters:"
print tmp_pp_brs.clean
print "\n\n"
fhdf = jppd.apply_ctps_brain_responses_cleaning_data(
fif_file,
raw=raw,
fname_ica=fif_file_ica,
ica_raw=None,
fhdf=fhdf,
condition_list=opt.condition,
**tmp_pp_brs.clean)
else:
jpp_utils.msg_on_attribute_error("brain response clean")
print "===> Done JuMEG Pre-Processing Data"
print " --> FIF file input : " + fif_file_raw
print " --> Information stored in HDF file: " + str(fhdf)
print "\n\n"
raw = None