def apply_interpolate_bads(raw_fname, raw=None, **cfg):
"""
:param raw_fname:
:param raw:
:param cfg:
:return:
filename,raw-obj
"""
fname_out = None
logger.info(" -> apply_interpolate_bad file name: {}".format(raw_fname))
logger.debug(" -> config parameter:\n{}".format(cfg))
jb.verbose = cfg.get("verbose")
if not jb.check_file_extention(fname=raw_fname,
file_extention=cfg.get("file_extention")):
return
#--- return raw_fname,raw
if not cfg.get("run"):
return jb.update_and_save_raw(raw,
fin=raw_fname,
fout=None,
save=False,
update_raw_filenname=True,
postfix=cfg.get("postfix", "int"),
overwrite=cfg.get("overwrite", True))
raw, raw_fname = jb.get_raw_obj(raw_fname, raw=raw)
if raw:
logger.info("fname: {}".format(raw_fname))
#--- Interpolate bad channels using jumeg
with jumeg_logger.StreamLoggerSTD(label="interpolate_bads"):
raw = jumeg_interpolate_bads(
raw
) #,**cfg.get("parameter")) #,origin=cfg.get("origin",None),reset_bads=cfg.get("reset_bads",True) )
#-- check results
if cfg.get("plot_block"):
raw.plot(block=cfg.get("plot_block"))
#--- update filename in raw and save if save
fname_out, raw = jb.update_and_save_raw(raw,
fin=raw_fname,
fout=None,
save=cfg.get("save"),
postfix=cfg.get("postfix", "int"),
overwrite=cfg.get(
"overwrite", True))
if fname_out:
return fname_out, raw
else:
raise Exception("---> ERROR file name not defined !!!")
def apply_suggest_bads(raw_fname, raw=None, **cfg):
"""
:param raw_fname:
:param raw:
:param cfg:
:return:
filename,raw-obj
"""
fname_out = None
logger.info(" -> apply_suggest_bads file name: {}".format(raw_fname))
logger.debug(" -> config parameter:\n{}".format(cfg))
if not jb.check_file_extention(fname=raw_fname,
file_extention=cfg.get("file_extention")):
return
#--- return raw_fname,raw
if not cfg.get("run"):
return jb.update_and_save_raw(raw,
fin=raw_fname,
fout=None,
save=False,
postfix=cfg.get("postfix", "bcc"),
overwrite=cfg.get("overwrite", True))
raw_changed = True
jb.verbose = cfg.get("verbose")
raw, raw_fname = jb.get_raw_obj(raw_fname, raw=raw)
if raw:
with jumeg_logger.StreamLoggerSTD(label="suggest_bads"):
marked, raw = suggest_bads(
raw) #,**cfg["parameter"]) #show_raw=cfg.get("show_raw") )
fname_out, raw = jb.update_and_save_raw(raw,
fin=raw_fname,
fout=None,
save=cfg.get("save"),
update_raw_filenname=True,
postfix=cfg.get("postfix", "bcc"),
overwrite=cfg.get(
"overwrite", True))
if fname_out:
return fname_out, raw
else:
raise Exception("---> ERROR file name not defined !!!")
def apply_resample(raw_fname, raw=None, **cfg):
"""
:param raw_fname:
:param raw:
:param cfg:
:return:
filename,raw-obj
"""
return
logger.info(" -> apply_resample file name: {}".format(raw_fname))
logger.debug(" -> config parameter:\n{}".format(cfg))
if not jb.check_file_extention(fname=raw_fname,
file_extention=cfg.get("file_extention")):
return
#--- return raw_fname,raw
if not cfg.get("run"):
return jb.update_and_save_raw(raw,
fin=raw_fname,
fout=None,
save=False,
postfix=cfg.get("postfix", "res"),
overwrite=cfg.get("overwrite", True))
#--- catch stdout,stderr
#jumeg_logger.log_stdout(label="filter")
#jumeg_logger.log_stderr(label="filter")
jb.verbose = cfg.get("verbose")
raw, raw_fname = jb.get_raw_obj(raw_fname, raw=raw)
#--- ToDo setup resampling
#raw,raw_fname = jumeg_mne_fileter(raw)
raw_changed = True
#--- save and update filename in raw
#if raw_changed:
# fname_out,raw = jb.update_and_save_raw(raw,fin=raw_fname,fout=None,save=cfg.get("save"),update_raw_filenname=True,
# postfix=cfg.get("postfix","bcc"),overwrite=cfg.get("overwrite",True))
#--- return back stdout/stderr from logger
#jumeg_logger.log_stdout(reset=True)
#jumeg_logger.log_stderr(reset=True)
return fname_out, raw
def apply_noise_reducer(raw_fname, raw=None, **cfg):
'''
apply <magic ee noise reducer> thrice to reference channels with different freq parameters
save PSD plot in subfolder /plots
!!! overwrite raw-obj, works inplace !!!
0) reset bads and check for dead channels
1) apply nr low pass filter for freq below e.g.: 5Hz <reflp>
2) apply nr high pass filter if defined <reflp>
3) apply nr notch filter to remove power line noise <refnotch>
4) save PSD plot
Parameter:
-----------
<noise_reducer> parameter used in this function :
fname_raw : input raw filename
raw : <None>\n
cfg : dict, part of config file <None>
from config file <noise_reducer> part\n
reflp : <None>\n
refhp : <None>\n
refnotch : <None>\n
plot: True
plot_show : True
plot_dir : subdir to save plots
postfix : "nr"
file_extention: ["meeg-raw.fif","rfDC-empty.fif"]
run : True
save : True
overwrite: True
ToDo add parameter extended
<noise_reducer> parameter extended
signals=[], noiseref=[], detrending=None,
tmin=None, tmax=None,
exclude_artifacts=True, checkresults=True, return_raw=False,
complementary_signal=False, fnout=None, verbose=False
Return:
--------
filename,raw-obj
'''
#--- init plot
fname_out = None
logger.info(" -> apply_noise_reducer file name: {}".format(raw_fname))
logger.debug(" -> config parameter:\n{}".format(cfg))
if not jb.check_file_extention(fname=raw_fname,
file_extention=cfg.get("file_extention")):
return
if not cfg.get("run"):
#--- return raw_fname,raw
return jb.update_and_save_raw(raw,
fin=raw_fname,
fout=None,
save=False,
postfix=cfg.get("postfix", "nr"),
overwrite=cfg.get("overwrite", True))
logger.info(
" --> preproc noise_reducer for raw file: {}".format(raw_fname))
#--- noise reduction
# apply noise reducer thrice to reference channels with different freq parameters
# !!! overwrite raw-obj !!!
save = False
raw_changed = False
jb.verbose = cfg.get("verbose")
#--- load raw, reset bads
raw, raw_fname = jb.get_raw_obj(raw_fname, raw=raw, reset_bads=True)
#--- check dead channes and mark them as bad
jb.picks.check_dead_channels(raw=raw)
#--- start plot denoising orig raw psd, avoid reloading raw data
if cfg.get("plot"):
jplt = JuMEG_PLOT_PSD(n_plots=2, name="denoising", verbose=True)
jplt.plot(raw,
title="orig: " + os.path.basename(raw_fname),
check_dead_channels=False)
#--- with redirect stdout/err
with jumeg_logger.StreamLoggerSTD(label="noise_reducer"):
#--- 1 nr low pass filter for freq below 5 hz
if cfg.get("reflp"):
raw = noise_reducer(None,
raw=raw,
reflp=cfg.get("reflp"),
return_raw=True,
verbose=cfg.get("verbose"),
exclude_artifacts=False)
raw_changed = True
#--- 2 nr high pass filter
if cfg.get("refhp"):
raw = noise_reducer(None,
raw=raw,
reflp=cfg.get("refhp"),
return_raw=True,
verbose=cfg.get("verbose"),
exclude_artifacts=False)
raw_changed = True
#--- 3 nr notch filter to remove power line noise
if cfg.get("refnotch"):
raw = noise_reducer(None,
raw=raw,
refnotch=cfg.get("refnotch"),
fnout=None,
return_raw=True,
verbose=cfg.get("verbose"),
exclude_artifacts=False)
raw_changed = True
#--- save and update filename in raw
if cfg.get("save"):
save = raw_changed
#--- update filename in raw and save if save
fname_out, raw = jb.update_and_save_raw(raw,
fin=raw_fname,
fout=None,
save=save,
update_raw_filenname=True,
postfix=cfg.get("postfix", "nr"),
overwrite=cfg.get(
"overwrite", True))
#--- plot results, avoid reloading raw data
if cfg.get("plot"):
jplt.plot(raw,
title="denoised: " + os.path.basename(fname_out),
check_dead_channels=False)
if cfg.get("plot_show"):
jplt.show()
jplt.save(fname=fname_out, plot_dir=cfg.get("plor_dir", "plots"))
if fname_out:
return fname_out, raw
else:
raise Exception("---> ERROR file name not defined !!!")
def _on_enter(self, **kwargs):
"""
:return:
raw_fname, raw obj
"""
self._update_from_kwargs(**kwargs)
#print(Fore.GREEN)
logger.info("Start: < {} > file name: {}".format(
self.label, self._raw_fname))
#print(Style.RESET_ALL)
if self._debug:
logger.debug("config parameter:\n{}".format(self._cfg))
# self._raw = None
self._run = True
self._fname_out = None
#--- check file extention in list
if not jb.check_file_extention(
fname=self._raw_fname,
file_extention=self._cfg.get("file_extention")):
logger.info(
"preproc {}: SKIPPED : <file extention not in extention list>\n"
.format(self.label) + self.info())
self._run = False
self._raw = None
return None, None
self._fname_out, self._raw = jb.update_and_save_raw(
self._raw,
fin=self._raw_fname,
fout=None,
save=False,
postfix=self.postfix,
overwrite=False)
#--- return raw_fname,raw
if not self._cfg.get("run"):
logger.info(
"preproc {}: SKIPPED : <run> is False\n".format(self.label) +
self.info())
self._run = False
self._raw = None
return self._raw_fname, None
#--- if file exist and do not overwrite
if os.path.isfile(self._fname_out) and (self._cfg.get(
"overwrite", False) == False):
logger.info(
"preproc {}: SKIPPED : do not overwrite existing output file\n"
.format(self.label) + self.info())
self._run = False
self._raw = None
return self._fname_out, None
#--- OK load raw, reset bads
self._raw, self._raw_fname = jb.get_raw_obj(
self._raw_fname, raw=self._raw, reset_bads=self._reset_bads)
logger.info("preproc {}\n".format(self.label) + self.info())
return self._raw_fname, self._raw