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)