def test1():
#--- init/update logger
jumeg_logger.setup_script_logging(logger=logger)
stage = "$JUMEG_PATH_LOCAL_DATA/exp/MEG94T/mne"
fcfg = os.path.join(stage, "meg94t_config01.yaml")
fpath = "206720/MEG94T0T2/130820_1335/2/"
path = os.path.join(stage, fpath)
raw_fname = "206720_MEG94T0T2_130820_1335_2_c,rfDC,meeg,nr,bcc,int-raw.fif"
stage = "$JUMEG_PATH_LOCAL_DATA/exp/QUATERS/mne"
fcfg = os.path.join(stage, "jumeg_config.yaml") #""quaters_config01.yaml")
fpath = "210857/QUATERS01/191210_1325/1"
path = os.path.join(stage, fpath)
raw_fname = "210857_QUATERS01_191210_1325_1_c,rfDC,meeg,nr,bcc,int-raw.fif"
#stage = "${JUMEG_TEST_DATA}/mne"
#fcfg = "intext_config01.yaml"
raw = None
#fpath = "211855/INTEXT01/190329_1004/6"
#path = os.path.join(stage,fpath)
# raw_fname = "211855_INTEXT01_190329_1004_6_c,rfDC,meeg,nr,bcc-raw.fif"
#raw_fname = "211855_INTEXT01_190329_1004_6_c,rfDC,meeg,nr,bcc,int-raw.fif"
logger.info("JuMEG Apply ICA mne-version: {}".format(mne.__version__))
#--
jICA = JuMEG_PIPELINES_ICA()
raw_unfiltered_clean, raw_filtered_clean = jICA.run(path=path,
raw_fname=raw_fname,
config=fcfg,
key="ica")
def test():
#--- init/update logger
from jumeg.base import jumeg_logger
jumeg_logger.setup_script_logging(logger=logger,level="DEBUG")
jplt = JuMEG_PLOT_PSD(n_plots=2,fmax=300.0,name="denoising",verbose=True)
#--- logfile prefix
p = "$JUMEG_LOCAL_DATA/exp/JUMEGTest/FV/211747"
fraw1 = "211747_FREEVIEW01_180109_1049_1_c,rfDC,meeg-raw.fif"
fraw2 = "211747_FREEVIEW01_180109_1049_1_c,rfDC,meeg,nr-raw.fif"
bads=['MEG 007', 'MEG 010', 'MEG 142', 'MEG 156', 'RFM 011']
raw,fnraw1 = jb.get_raw_obj( os.path.join(p,fraw1) )
jb.verbose = True
jb.update_bad_channels(fnraw1,raw=raw,bads=bads,save=True)
jplt.plot(raw,title=fraw1)
raw,fnraw2 = jb.get_raw_obj( os.path.join(p,fraw2) )
jb.update_bad_channels(fnraw2,raw=raw,bads=bads,save=True)
jplt.plot(raw,title=fraw2)
jplt.show()
plot_name = fraw2.rsplit('-raw.fif')[0] + '-plot'
jplt.save(fname=os.path.join(p,plot_name))
def apply(name=None, opt=None, defaults=None, logprefix="preproc"):
#--- init/update logger
if opt.debug:
level = "DEBUG"
else:
level = "INFO"
jumeg_logger.setup_script_logging(name=name,
opt=opt,
logger=logger,
level=level)
if opt.meg:
JDS_MEG = JuMEG_DSMArchive(config=opt.config,
verbose=opt.verbose,
debug=opt.debug,
archive=opt.archive,
overwrite=opt.overwrite)
JDS_MEG.archive(ids=opt.ids, scans=opt.scans, data_type="MEG")
if opt.eeg:
JDS_EEG = JuMEG_DSMArchiveEEG(data_type="EEG",
ids=opt.ids,
scans=opt.scans,
experiments=opt.experiments,
archive=opt.archive,
config=opt.config,
verbose=opt.verbose,
debug=opt.debug)
JDS_EEG.archive(ids=opt.ids, scans=opt.scans, data_type="EEG")
def apply(name=None, opt=None, defaults=None, logprefix="preproc"):
"""
jumeg preprocessing step 1
noise reducer
interpolate bads (bad channels & suggested_bads)
filter
resample
:param opt: arparser option obj
:param defaults: default dict
:param logprefix: prefix for logfile e.g. name of script
:return:
"""
#---
raw = None
#--- init/update logger
jumeg_logger.setup_script_logging(name=name, opt=opt, logger=logger)
jpl = JuMEG_PipelineLooper(options=opt, defaults=defaults)
jpl.ExitOnError = True
for fname, subject_id, raw_dir in jpl.file_list():
if not opt.run: continue
raw = None # !!! important !!!
#--- call noise reduction
raw_fname, raw = utils.apply_noise_reducer(
raw_fname=fname, raw=None, config=jpl.config.get("noise_reducer"))
#--- call suggest_bads
raw_fname, raw = utils.apply_suggest_bads(
raw_fname=raw_fname,
raw=raw,
config=jpl.config.get("suggest_bads"))
#--- call interploate_bads
raw_fname, raw = utils.apply_interpolate_bads(
raw_fname=raw_fname,
raw=raw,
config=jpl.config.get("interpolate_bads"))
#--- call filter
# raw_fname,raw = utils.apply_filter(raw_fname,raw=raw,config=jpl.config.get("filtering") )
#--- call resample
# raw_fname,raw = utils.apply_resample(raw_fname,raw=raw,config=jpl.config.get("resampling"))
#--- call interploate_bads
raw_fname, raw = utils.apply_ica(raw_fname=raw_fname,
raw=raw,
config=jpl.config.get("ica"))
logger.info(" --> DONE preproc subject id: {}\n".format(subject_id) +
" -> input file: {}\n".format(fname) +
" -> output file: {}\n".format(raw_fname))
def main(argv):
opt, parser = get_args(argv)
if (len(argv) < 2):
parser.print_help()
sys.exit()
jumeg_logger.setup_script_logging(name=argv[0], opt=opt, logger=logger)
if opt.run:
apply_jumeg_merge_meeg(opt)
def main(argv):
opt, parser = get_args(argv)
if len(argv) < 2:
parser.print_help()
sys.exit(-1)
#--- init/update logger
jumeg_logger.setup_script_logging(name=argv[0], opt=opt, logger=logger)
if opt.run: apply_import_to_fif(opt)
def test1():
#--- init/update logger
jumeg_logger.setup_script_logging(logger=logger)
raw = None
stage = "$JUMEG_PATH_LOCAL_DATA/exp/MEG94T/mne"
fcfg = os.path.join(stage, "meg94t_config01.yaml")
fpath = "206720/MEG94T0T2/130820_1335/1/"
path = os.path.join(stage, fpath)
raw_fname = "206720_MEG94T0T2_130820_1335_1_c,rfDC,meeg,nr,bcc,int-raw.fif"
logger.info("JuMEG Pipeline ICA Performance ICA mne-version: {}".format(
mne.__version__))
f = os.path.join(path, raw_fname)
raw, raw_fname = jb.get_raw_obj(f, raw=None)
raw_path = os.path.dirname(raw_fname)
#--- get picks from raw
picks = jb.picks.meg_nobads(raw)
#---
CFG = jCFG()
CFG.update(config=fcfg)
config = CFG.GetDataDict("ica")
#--
ICAPerformance = JuMEG_ICA_PERFORMANCE(
raw=raw,
path=path,
fname=raw_fname,
)
#--- find ECG
ICAPerformance.ECG.find_events(raw=raw, **config.get("ecg"))
ICAPerformance.ECG.GetInfo(debug=True)
#--- find EOG
ICAPerformance.EOG.find_events(raw=raw, **config.get("eog"))
ICAPerformance.EOG.GetInfo(debug=True)
def test2():
#--- init/update logger
jumeg_logger.setup_script_logging(logger=logger)
raw = None
stage = "$JUMEG_PATH_LOCAL_DATA/exp/MEG94T/mne"
fcfg = os.path.join(stage, "meg94t_config01.yaml")
fpath = "206720/MEG94T0T2/130820_1335/1/"
path = os.path.join(stage, fpath)
#fraw = "206720_MEG94T0T2_130820_1335_1_c,rfDC,meeg,nr,bcc,int,000516-000645-raw.fif"
#fraw_ar = "206720_MEG94T0T2_130820_1335_1_c,rfDC,meeg,nr,bcc,int,000516-000645,ar-raw.fif"
fraw = "206720_MEG94T0T2_130820_1335_1_c,rfDC,meeg,nr,bcc,int,fibp0.10-45.0-raw.fif"
fraw_ar = "206720_MEG94T0T2_130820_1335_1_c,rfDC,meeg,nr,bcc,int,fibp0.10-45.0,ar-raw.fif"
logger.info("JuMEG Pipeline ICA Performance ICA mne-version: {}".format(
mne.__version__))
#---
f = os.path.join(path, fraw)
raw, raw_fname = jb.get_raw_obj(f, raw=None)
raw_path = os.path.dirname(raw_fname)
picks = jb.picks.meg_nobads(raw)
#---
f = os.path.join(path, fraw_ar)
raw_ar, raw_ar_fname = jb.get_raw_obj(f, raw=None)
#--- read config
CFG = jCFG()
CFG.update(config=fcfg)
config = CFG.GetDataDict("ica")
#
jIP = JuMEG_ICA_PERFORMANCE(raw=raw, raw_clean=raw_ar, picks=picks)
#jIP.report()
fout = raw_fname.rsplit("-", 1)[0] + "-ar"
jIP.plot(verbose=True, fout=fout)
def run(opt):
jumeg_logger.setup_script_logging(logger=logger)
logger.info("JuMEG SVM ICA mne-version: {}".format(mne.__version__))
from jumeg.base.pipelines.jumeg_pipelines_ica_perfromance import JuMEG_ICA_PERFORMANCE
jIP = JuMEG_ICA_PERFORMANCE()
#--- init raw
raw = None
if opt.stage:
path = opt.stage
if opt.path:
path = os.path.join(path,opt.path)
#--- init SVM class & run : load raw obj & apply SVM for ICs
jSVM = JuMEG_ICA_SVM()
fname= os.path.join(path,opt.fraw)
ica, predict_proba = jSVM.run( fname= fname )
raw = jSVM.raw
#--- raw cleaned
raw_clean = ica.apply(raw.copy() )
#raw.plot(block=True)
#--- prepare performance plot
#--- find ECG
jIP.ECG.find_events(raw=raw)
#--- find EOG in raw
annotations = jIP.EOG.find_events(raw=raw)
raw.set_annotations(annotations)
#---
fout = fname.rsplit("-",1)[0] + "-ar"
jIP.plot(raw=raw,raw_clean=raw_clean,verbose=opt.verbose,plot_path=path,fout=fout)
jIP.Plot.figure.show()
logger.info("DONE JuMEG SVM ICA")
"log2file": True,
"logprefix": "preproc0",
"overwrite": False,
"verbose": False,
"debug": False,
"recursive": True
}
opt = None
jpl = JuMEG_PipelineLooper(defaults=defaults)
print("---> TEST4: config file")
print(jpl.config_file)
print("---> TEST4: config")
print(jpl.config)
print("\n\n")
for raw_fname, subject_id, dir in jpl.file_list():
print(" -> Test4 in loop PDF: {}".format(raw_fname))
if __name__ == "__main__":
#--- init/update logger
from jumeg.base import jumeg_logger
logger = jumeg_logger.setup_script_logging(logger=logger)
logger.setLevel(logging.DEBUG)
#test1()
#test2()
#test3()
test4()
:param data: the data which will be written into the file
:type data: dict
'''
if data:
self._cfg = data
self._update_struct()
if fname:
self.fname = fname
with open(self.fname, "w") as FH:
if fname.endswith(".yaml"):
if yaml_type == "ruamel":
yaml.dump(self._cfg, FH, Dumper=yaml.RoundTripDumper)
else:
yaml.dump(self._cfg, FH)
elif fname.endswith(".json"):
json.dump(self._cfg, FH)
else:
logger.exception(
"ERROR config file name must end with [.yaml | .json]: {}".
format(self.fname))
if self.verbose:
logger.info("done saving config file: {}".format(self.fname))
if __name__ == '__main__':
from jumeg.base.jumeg_logger import setup_script_logging
logger = setup_script_logging(logger=logger, name="jumeg", opt=None)
info = JuMEG_CONFIG_Info(version=__version__)
info.printInfo()
if __name__ == "__main__":
opt = None
#--- Testing DEBUG
from tsv.utils.jumeg_tsv_utils_io_data import JuMEG_TSV_Utils_IO_Data
from tsv.plot.jumeg_tsv_plot2d_data_options import JuMEG_TSV_PLOT2D_DATA_OPTIONS, GroupOptions
# from tsv.wxutils.jumeg_tsv_wxutils_dlg_settings import GroupDLG,ChannelDLG
verbose = True
path = "data"
path = "~/MEGBoers/programs/JuMEG/jumeg-py/jumeg-py-git-fboers-2019-08-21/projects/JuMEGTSV/data"
fname = '200098_leda_test_10_raw.fif'
raw = None
jumeg_logger.setup_script_logging(name="JuMEG", opt=opt, logger=logger)
IO = JuMEG_TSV_Utils_IO_Data()
raw, bads = IO.load_data(raw, fname, path)
#--- ToDo use only groups from raw
GRP = GroupOptions()
DOpt = JuMEG_TSV_PLOT2D_DATA_OPTIONS(raw=raw)
DOpt.update(verbose=True, debug=True)
app = wx.App()
MainFrame(None, 'JuMEG demo', grp=GRP)
app.MainLoop()
from jumeg.gui.wxlib.jumeg_gui_wxlib_main_frame import JuMEG_wxMainFrame
from jumeg.gui.wxlib.jumeg_gui_wxlib_main_panel import JuMEG_wxMainPanel
from jumeg.gui.wxlib.utils.jumeg_gui_wxlib_utils_controls import JuMEG_wxControlGrid
#--- Merger CTRLs
from jumeg.gui.wxlib.jumeg_gui_wxlib_experiment_template import JuMEG_wxExpTemplate
from jumeg.gui.wxlib.jumeg_gui_wxlib_psel_bti import JuMEG_wxPselBTi
#---
from jumeg.gui.wxlib.jumeg_gui_wxlib_pbshost import JuMEG_wxPBSHosts
from jumeg.gui.jumeg_gui_wx_argparser import JuMEG_GUI_wxArgvParser
#---
from jumeg.base.jumeg_base import jumeg_base as jb
from jumeg.base.ioutils.jumeg_ioutils_subprocess import JuMEG_IoUtils_SubProcess
import logging
from jumeg.base import jumeg_logger
jumeg_logger.setup_script_logging()
logger = logging.getLogger('jumeg') # init a logger
__version__ = "2019.09.27-001"
class JuMEG_wxImport_BTiCtrlGrid(wx.Panel):
def __init__(self, parent, *kargs, **kwargs):
super().__init__(parent, *kargs)
self._names = {
"stage_ck": "CK_STAGE",
"stage_txt": "TXT_STAGE",
"emptyroom_ck": "CK_EMPTYROOM",
"emptyroom_txt": "TXT_EMPTYROOM",
"path_flbt": "FLBT_PATH",
"path_combo": "COMBO_PATH"
Created 2020.01.08
@author: fboers
"""
import os, sys, logging
import os.path as op
from jumeg.base.jumeg_base import jumeg_base as jb
from jumeg.epocher.jumeg_epocher import jumeg_epocher
from jumeg.filter.jumeg_mne_filter import JuMEG_MNE_FILTER
from jumeg.base import jumeg_logger
logger = logging.getLogger("jumeg")
logger = jumeg_logger.setup_script_logging(logger=logger,
fname="quaters_epocher.log",
level="INFO",
logfile=True) #,mode="w" )
#---
DO_EVENTS = True
DO_FILTER = True
DO_EPOCHS = True
verbose = True
debug = False
stage = jb.expandvars("$JUMEG_PATH_LOCAL_DATA/exp/QUATERS/mne")
epocher_path = None
hdf_path = None
raw = None
jumeg_epocher.use_yaml = True
path = "$JUMEG_TEST_DATA/mne"
fname = "FREEVIEW01"
BCT = JuMEG_BadChannelTable(verbose=True)
BCT.open(path=path,fname=fname,overwrite=True)
id = "123456"
scan = "FREEVIEW01"
fname = "$JUMEG_TEST_DATA/mne/211747/FREEVIEW01/180109_0955/1/211747_FREEVIEW01_180109_0955_1_c,rfDC,meeg-raw.fif"
bads = "MEG 007,MEG 142,MEG 156,RFM 011"
BCT.set_bads(id=id,scan=scan,fname=fname,bads=bads)
BCT.show()
fname = "$JUMEG_TEST_DATA/mne/211747/FREEVIEW01/180109_0955/1/211747_FREEVIEW01_180109_0955_2_c,rfDC,meeg-raw.fif"
BCT.set_bads(id=id,scan=scan,fname=fname,bads=bads)
BCT.show()
BCT.set_bads(id=id,scan=scan,fname=fname,bads="NIX")
BCT.show()
print("bads: {}".format( BCT.get_badslist(fname=fname) ))
BCT.close()
if __name__ == "__main__":
#--- init/update logger
logger=jumeg_logger.setup_script_logging(logger=logger,level=logging.DEBUG)
_test()
#--- init flags
# ck if flag is set in argv as True
# problem can not switch on/off flag via cmd call
opt = parser.parse_args()
for g in parser._action_groups:
for obj in g._group_actions:
if str(type(obj)).endswith('_StoreTrueAction\'>'):
if vars(opt).get(obj.dest):
opt.__dict__[obj.dest] = False
for flg in argv:
if flg in obj.option_strings:
opt.__dict__[obj.dest] = True
break
return opt, parser
#=========================================================================================
#==== MAIN
#=========================================================================================
if __name__ == "__main__":
opt, parser = get_args(sys.argv)
if len(sys.argv) < 2:
parser.print_help()
sys.exit(-1)
jumeg_logger.setup_script_logging(name=sys.argv[0], opt=opt, logger=logger)
run(opt)
def apply(name=None, opt=None, defaults=None, logprefix="preproc"):
"""
jumeg preprocessing step 1
noise reducer
interpolate bads (bad channels & suggested_bads)
filter
resample
:param opt: arparser option obj
:param defaults: default dict
:param logprefix: prefix for logfile e.g. name of script
:return:
"""
#---
raw = None
jpl = JuMEG_PipelineLooper(options=opt, defaults=defaults)
jpl.ExitOnError = True
#--- init/update logger
#--- logfile
opt.log2file = jpl.log2file
opt.logprefix = jpl.logprefix
opt.logoverwrite = jpl.logoverwrite
if opt.debug:
level = "DEBUG"
else:
level = "INFO"
jumeg_logger.setup_script_logging(name=name,
opt=opt,
logger=logger,
version=__version__,
level=level)
for fname, subject_id, raw_dir in jpl.file_list():
if not opt.run: continue
raw = None # !!!
#--- call noise reduction
raw_fname, raw = utils.apply_noise_reducer(
raw_fname=fname, raw=None, config=jpl.config.get("noise_reducer"))
#--- call suggest_bads
raw_fname, raw = utils.apply_suggest_bads(
raw_fname=raw_fname,
raw=raw,
config=jpl.config.get("suggest_bads"))
#--- call bads to HDF
raw_fnamee, raw = utils.apply_bads_to_hdf(
raw_fname=raw_fname, raw=raw, config=jpl.config.get("bads_to_hdf"))
#--- call interploate_bads
raw_fname, raw = utils.apply_interpolate_bads(
raw_fname=raw_fname,
raw=raw,
config=jpl.config.get("interpolate_bads"))
#--- call ica
raw_fname, raw = utils.apply_ica(raw_fname=raw_fname,
path=raw_dir,
raw=raw,
config=jpl.config.get("ica"))
#--- call filter 1
raw_fname, raw = utils.apply_filter(raw_fname=raw_fname,
raw=raw,
config=jpl.config.get("filter_1"))
#--- call epocher
utils.apply_epocher(stage=jpl.stage,
subject_id=subject_id,
experiment=jpl.experiment,
path=raw_dir,
fname=raw_fname,
config=jpl.config.get("epocher"))
#--- call resample
utils.apply_report(stage=jpl.stage,
subject_id=subject_id,
experiment=jpl.experiment,
path=raw_dir,
fname=raw_fname,
config=jpl.config.get("report"))
logger.info("DONE preproc subject id: {}\n".format(subject_id) +
" -> input file: {}\n".format(fname) +
" -> output file: {}\n".format(raw_fname))
