def __init__(self, **kwargs):
self._init(**kwargs)
self._JuMEG_EPOCHER = JuMEG_Epocher()
self._CFG = jCFG(**kwargs)
self._plot_dir = "report"
self.report_key = "epocher"
def __init__(self,**kwargs):
super().__init__()
self.init()
self._jumeg_cfg = {"run":True,"save":True,"overwrite":False,"path":"report",
"noise_reducer":{"run":True,"extention":"nr-raw.png"},
"ica":{"run":True,"extention":"ar.png"}}
self._path = "."
self.report_cfg_extention = "-report.yaml"
self._REPORT = MNE_REPORT(**kwargs)
self._REPORT_CFG = jCFG()
def _update_report(self, data):
"""
:param fimages:
:return:
"""
#--- update report config
CFG = jCFG()
report_config = os.path.join(
self.plot_dir,
os.path.basename(self.raw_fname).rsplit("_", 1)[0] +
"-report.yaml")
d = None
if not CFG.load_cfg(fname=report_config):
d = {"ica": data}
else:
CFG.config["ica"] = data
CFG.save_cfg(fname=report_config, data=d)
def __init__(self, **kwargs):
super().__init__()
self.PreFilter = JuMEG_MNE_FILTER()
self.Chopper = JuMEG_PIPELINES_CHOPPER()
self.ICAPerformance = JuMEG_ICA_PERFORMANCE()
self.SVM = JuMEG_ICA_SVM()
self.useSVM = False
self.verbose = False
self.debug = False
self.report_key = "ica"
self._CFG = jCFG(**kwargs)
self._plot_dir = None
self._ics_found_svm = None
self._clear()
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 apply_noise_reducer(raw_fname=None,
raw=None,
config=None,
label='noise reducer',
fname_out=None):
'''
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
IN config
noise_reducer:
file_extention:
- meeg-raw.fif
- rfDC-empty.fif
fmax: 300
noiseref_hp:
- RFG ...
overwrite: false
plot: true
plot_dir: report
plot_show: false
postfix: nr
refhp: 0.1
reflp: 5.0
refnotch:
- 50.0
- 100.0
- 150.0
- 200.0
- 250.0
- 300.0
- 350.0
- 400.0
run: true
save: true
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
'''
#with JuMEG_PipelineFrame(raw_fname=raw_fname,raw=raw,name="noise reducer",config=cfg) as JPF:
RawIsChanged = False
#--- 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 config.get("plot"):
jplt = JuMEG_PLOT_PSD(n_plots=3, name="denoising",
verbose=True) #,pick_types=["meg","ref"])
jplt.plot(raw,
color="green",
title="REF: " + os.path.basename(raw_fname),
check_dead_channels=False,
fmax=config.get("fmax"),
picks=jb.picks.ref_nobads(raw))
jplt.plot(raw,
color="blue",
title="MEG orig: " + os.path.basename(raw_fname),
check_dead_channels=False,
fmax=config.get("fmax"),
picks=jb.picks.meg_nobads(raw))
#self.picks = jb.picks.meg_nobads(raw))
#--- with redirect stdout/err
with jumeg_logger.StreamLoggerSTD(label=label):
#--- 1 nr low pass filter for freq below 5 hz
if config.get("reflp"):
raw = noise_reducer(None,
raw=raw,
reflp=config.get("reflp"),
return_raw=True,
verbose=config.get("verbose"),
exclude_artifacts=False)
RawIsChanged = True
#--- 2 nr high pass filter
if config.get("refhp"):
raw = noise_reducer(None,
raw=raw,
reflp=config.get("refhp"),
return_raw=True,
verbose=config.get("verbose"),
exclude_artifacts=False)
RawIsChanged = True
#--- 3 nr notch filter to remove power line noise
if config.get("refnotch"):
raw = noise_reducer(None,
raw=raw,
refnotch=config.get("refnotch"),
fnout=None,
return_raw=True,
verbose=config.get("verbose"),
exclude_artifacts=False)
RawIsChanged = True
#--- plot results, avoid reloading raw data
if config.get("plot"):
jplt.plot(raw,
title="MEG denoised: " + os.path.basename(fname_out),
check_dead_channels=False,
fmax=config.get("fmax"),
picks=jb.picks.meg_nobads(raw))
if config.get("plot_show"):
jplt.show()
fout = jplt.save(fname=fname_out,
plot_dir=config.get("plot_dir", "report"))
#--- update image list in report-config for later update MNE Report
CFG = jCFG()
data = None
report_path = os.path.dirname(fout)
report_config = os.path.join(
report_path,
raw_fname.rsplit("_", 1)[0] + "-report.yaml")
if not CFG.load_cfg(fname=report_config):
data = {"noise_reducer": {"files": os.path.basename(fout)}}
else:
CFG.config["noise_reducer"] = {"files": os.path.basename(fout)}
CFG.save_cfg(fname=report_config, data=data)
return fname_out, raw, RawIsChanged, None
def test():
'''
from jumeg.base.jumeg_base import jumeg_base as jb
from jumeg.base.pipelines.jumeg_pipelines_ica_perfromance import ICAPerformance
from jumeg.base.pipelines.jumeg_base_pipelines_chopper import JuMEG_PIPELINES_CHOPPER,copy_crop_and_chop,concat_and_save
'''
#---
from jumeg.base.jumeg_base_config import JuMEG_CONFIG as jCFG
verbose = True
debug = False
stage = "$JUMEG_TEST_DATA/mne/201772/INTEXT01/190212_1334/2"
fn = "201772_INTEXT01_190212_1334_2_c,rfDC,meeg,nr,bcc,int-raw.fif"
fn = "201772_INTEXT01_190212_1334_2_c,rfDC,meeg,nr,bcc,int,fibp0.10-45.0,ar-raw.fif"
stage = '$JUMEG_TEST_DATA/mne/212842/INTEXT01/190430_1001/4'
fn = '212842_INTEXT01_190430_1001_4_c,rfDC,meeg,nr,bcc,int,fibp0.10-45.0,ar-raw.fif'
fin = os.path.join(stage, fn)
raw, fname = jb.get_raw_obj(fname=fin)
#--- ck for annotations in raw
try:
annota = raw.annotations
except:
from jumeg.base.pipelines.jumeg_pipelines_ica_perfromance import ICAPerformance
IP = ICAPerformance()
#--- find ECG
IP.ECG.find_events(raw=raw)
IP.ECG.GetInfo(debug=True)
#--- find EOG
IP.EOG.find_events(raw=raw)
IP.EOG.GetInfo(debug=True)
#--- read epocher config
#--- define template
template_path = "$JUMEG_PATH_TEMPLATE_EPOCHER"
template_name = "INTEXT"
template_extention = "jumeg_epocher_template.yaml"
#--- CFG
CFG = jCFG()
fcfg = os.path.join(template_path,
template_name + "_" + template_extention)
CFG.update(config=fcfg)
condition_list = []
for k, itm in CFG.config.items():
if itm.get("run"):
condition_list.append(k)
if not condition_list: return
epocher_path = os.path.join(os.path.dirname(fname), "epocher")
hdf_path = epocher_path
evt_param = {
"condition_list": condition_list,
"template_path": template_path,
"template_name": template_name,
"use_yaml": True,
"hdf_path": hdf_path,
"verbose": verbose,
"debug": debug
}
ep_param = {
"condition_list": condition_list,
"template_path": template_path,
"template_name": template_name,
"hdf_path": hdf_path,
"save_raw": True,
"verbose": verbose,
"debug": debug,
"event_extention": ".eve",
"output_mode": {
"events": True,
"epochs": True,
"evoked": True,
"annotations": True,
"stage": epocher_path,
"use_condition_in_path": True
}
# "weights" :{"mode":"equal","method":"median","skip_first":null}
# "exclude_events":{"eog_events":{"tmin":-0.4,"tmax":0.6} } },
}
jEP = JuMEG_PIPELIENS_EPOCHER()
jEP.run(raw=raw,
fname=fname,
ep_param=ep_param,
evt_param=evt_param,
verbose=True,
debug=False,
show=True)
#---ToDo
# use mne plots
'''