def ClickOnShowDLG(self, evt):
"""
shows File, DirDialog depending on file extention
:param evt:
:return:
"""
try:
obj = evt.GetEventObject()
except:
obj = evt
# txt ctrl
p = jb.expandvars(obj.GetValue())
if os.path.isdir(p):
with wx.DirDialog(self,
message=obj.GetName(),
defaultPath=p,
style=wx.DD_DEFAULT_STYLE,
name=obj.GetName() + "_DLG") as DLG:
DLG.SetPath(p)
if DLG.ShowModal() == wx.ID_CANCEL:
return # the user changed their mind
obj.SetValue(DLG.GetPath())
else:
fext = p.rsplit(".", 1)[-1]
wc = "files (*." + fext + ",*.*)|*." + fext + ";*.all"
with wx.FileDialog(self,
"{} => Select File Name".format(obj.GetName()),
wildcard=wc,
style=wx.DD_DEFAULT_STYLE,
name=obj.GetName() + "_DLG") as DLG:
DLG.SetPath(p)
if DLG.ShowModal() == wx.ID_CANCEL:
return # the user changed their mind
obj.SetValue(DLG.GetPath())
def save_cfg(self, fname=None, data=None):
"""
"""
if data:
self._cfg = data
if fname:
self._fname = jb.expandvars(fname)
with open(self._fname, "w") as f:
self._yaml.dump(self._cfg, f)
def load_cfg(self, fname=None, key=None):
if fname:
self._fname = jb.expandvars(fname)
with open(self._fname) as f:
self._cfg = self._yaml.load(f)
if key:
self._cfg = self._cfg.get(key)
self._data = Struct(self._cfg)
return self._data
def main(argv):
opt, parser = get_args(argv, version=__version__)
if len(argv) < 2:
parser.print_help()
sys.exit(-1)
if opt.test:
os.environ["JUMEG_PATH_BTI_EXPORT"] = jb.expandvars(
"$JUMEG_PATH_LOCAL_DATA") + "/megdaw_data21"
#if opt.archive:
# opt.run = True
if opt.run: apply(name=argv[0], opt=opt)
def fname(self, v):
self._fname = jb.expandvars(v)
from jumeg.filter.jumeg_mne_filter import JuMEG_MNE_FILTER
from jumeg.base import jumeg_logger
logger = logging.getLogger("jumeg")
logger = jumeg_logger.setup_script_logging(logger=logger,
fname="quaters_epocher.log",
level="INFO",
logfile=True) #,mode="w" )
#---
DO_EVENTS = True
DO_FILTER = True
DO_EPOCHS = True
verbose = True
debug = False
stage = jb.expandvars("$JUMEG_PATH_LOCAL_DATA/exp/QUATERS/mne")
epocher_path = None
hdf_path = None
raw = None
jumeg_epocher.use_yaml = True
template_name = "QUATERS"
template_path = os.path.dirname(__file__)
condition_list = ["RCC_ST", "RCC_FB"
] #,"RCI_ST","RCI_FB","RII_ST","RII_FB","RIC_ST","RIC_FB",
# "PCC_ST","PCC_FB","PCI_ST","PCI_FB","PII_ST","PII_FB","PIC_ST","PIC_FB"]
fraws = [
#"207048/QUATERS01/191218_1447/2/207049_QUATERS01_191218_1447_2_c,rfDC,meeg-raw.fif",
def path(self,v):
if v:
self._path = jb.expandvars(v)
mkpath(self._path,mode=0o770)
else:
self._path=v
def run(self,**kwargs):
"""
:param kwargs:
:return:
stage=jpl.stage,subject_id=subject_id,fname=raw_fname,config=jpl.config.get("report")
jReport.run(path=report_path,report_config_file=report_config_file,
experiment="QUARTERS",subject_id=210857,config=config)
open/read cfg /reprt/fname-report.yaml
MNEreport.open
update NR
update ICa
save HDf5
save htlm
report config as dict
report_path=report_path,path=path,fname=raw_fname,subject_id=210857,config=config
report:
run: True
save: True
overwrite: False
noise_reducer:
run: True
ica:
run: True
"""
# logger.info(kwargs)
self._update_from_kwargs(**kwargs)
self.Report._update_from_kwargs(**kwargs)
#--- try from jumeg config <report> config=config.get("report")
if "config" in kwargs:
self._jumeg_cfg = kwargs.get("config")
#logger.info("jumeg config report: {}".format( self.jumeg_cfg))
#--- update from kwargs
self.stage = jb.expandvars(self.stage)
self.path = kwargs.get("path",self.path) #--- report image path / image yaml file
if self.stage.endswith("mne"):
rp = self.stage.replace("mne","report")
else:
rp = self.stage
#--- setup & open MNE report
if not self.Report.open(path=rp): return False
#--- report image config
self.update_report_cfg()
#--- noise reducer
if self.jumeg_cfg.get("noise_reducer",False):
cfg = self.report_cfg.GetDataDict("noise_reducer")
if cfg:
self.Report.update_report(data=cfg.get("files"), path=self.path,section="Noise Reducer",prefix="NR")
#--- ica
if self.jumeg_cfg.get("ica",False):
cfg = self.report_cfg.GetDataDict("ica")
if cfg:
self.Report.update_report(data=cfg,path=self.path,section="ICA",prefix="ICA")
#--- save
if self.jumeg_cfg.get("save",False):
self.Report.save(overwrite=True)
def path(self,v):
pext = self._jumeg_cfg.get("path","report")
if not v.endswith(pext):
self._path = jb.expandvars( os.path.join(v,pext) )
else:
self._path = jb.expandvars(v)
def fhdf(self,v):
self._fhdf = jb.expandvars(v)
mkpath(os.path.dirname(self._fhdf),mode=0o770)