def run(self):
self.logger.info("START FDA...")
f_name = self.config.get_param("data_file_name")
f_dir = self.config.get_param("data_file_path")
in_file = acquisition_helper.get_file_path(f_dir, f_name)
filename = os.path.join(f_dir, f_name + ".obci")
data = sp.signalParser(filename)
fs = int(float(data.getSamplingFrequency()))
mgr = read_manager.ReadManager(
in_file+'.obci.xml',
in_file+'.obci.raw',
in_file+'.obci.tag')
if self.use_channels is None:
self.use_channels = data.getChannelList()
if self.ignore_channels is not None:
for i in self.ignore_channels:
try:
self.use_channels.remove(i)
except:
pass
self.montage = self.config.get_param("montage")
tmp = self.config.get_param("montage_channels")
if len(tmp) > 0:
self.montage_channels = tmp.split(';')
else:
self.montage_channels = []
self.logger.info("USE CHANNELS: "+str(self.use_channels))
self.logger.info("CHANNELS NAMES: "+str(mgr.get_param('channels_names')))
## Get data and tags
data.setMontage(self.montage_channels)
Signal = data.getData(self.use_channels)
trgTags = data.get_p300_tags(idx=[1,7])
ntrgTags = data.get_not_p300_tags(idx=[1,7])
trgTags = trgTags[trgTags<Signal.shape[1]-fs]
ntrgTags = ntrgTags[ntrgTags<Signal.shape[1]-fs]
trgTags = trgTags[trgTags>0]
ntrgTags = ntrgTags[ntrgTags>0]
target, nontarget = data.getTargetNontarget(Signal, trgTags, ntrgTags)
## Get params from file
pPer = float(self.config.get_param("p_per"))
nRepeat = int(self.config.get_param("n_repeat"))
nMin = int(self.config.get_param("n_min"))
nMax = int(self.config.get_param("n_max"))
avrM_l = map(lambda x: int(x), self.config.get_param("avr_m").split(';'))
conN_l = map(lambda x: int(x), self.config.get_param("con_n").split(';'))
csp_dt_l = map(lambda x: float(x), self.config.get_param("csp_dt").split(';'))
csp_time_l = map(lambda x: float(x), self.config.get_param("csp_time").split(';'))
plotFlag = int(self.config.get_param("plot_flag"))
debugFlag = int(self.config.get_param("debug_flag"))
## Define buffer
buffer = 1.1*fs
self.logger.info("Computer buffer len: "+str(buffer))
## Make montage matrix
conf = self.use_channels, self.montage, self.montage_channels
self.montage_matrix = self._get_montage_matrix(conf[0], conf[1], conf[2], mgr.get_param('channels_names'))
print "self.montage_matrix: ", self.montage_matrix
channels = ";".join(self.use_channels)
# Test all combination of parameters
N = 0
d = {}
for avrM in avrM_l:
for conN in conN_l:
for csp_time in csp_time_l:
for dt in csp_dt_l:
d[N] = {"avrM":avrM, "conN":conN, "csp_time":[csp_time, csp_time+dt]}
print "d[%i] = " %N, d[N]
N += 1
#################################
## CROSS CHECKING
P_dict, dVal_dict = {}, {}
l = np.zeros(N)
for idxN in range(N):
KEY = d[idxN].keys()
for k in KEY:
exec "{0}_tmp = {1}".format(k, d[idxN][k]) in globals(), locals()
self.logger.info("Zestaw: {0} / {1}".format(idxN, N))
self.logger.info(str(d[idxN]))
csp = csp_time_tmp[0]*fs, csp_time_tmp[1]*fs
# Crop signalas to csp_time : csp_time+csp_dt
_target = target[:,:,csp[0]:csp[1]]
_nontarget = nontarget[:,:,csp[0]:csp[1]]
p300 = P300_train(channels, fs, avrM_tmp, conN_tmp, csp_time_tmp, pPer)
l[idxN] = p300.valid_kGroups(Signal, _target, _nontarget, 2)
P_dict[idxN] = p300.getPWC()
dVal_dict[idxN] = p300.getDValDistribution()
if debugFlag:
p300.saveDist2File("target_%i"%idxN, "nontarget_%i"%idxN)
self.logger.info("Test score: " + str(l[idxN]))
self.logger.info("Calibration passed")
#################################
if debugFlag:
distributionDraw = P300_draw(fs)
# Plot all d distributions
for idx in range(N):
dTarget, dNontarget = dVal_dict[idx]
distributionDraw.plotDistribution(dTarget, dNontarget)
#################################
# Finding best
self.logger.info("\n"*5)
self.logger.info( "L: " + str(l) )
P, conN, avrM, csp_time = None, None, None, None
BEST = -1
arr = np.arange(len(l))
for i in range(5):
bestN = int(arr[l==l.min()][0])
print "best_{0}: {1}".format(i, bestN)
print "d[bestN]: ", d[bestN]
print "l[bestN]: ", l.min()
#~ if (l.min() > 100) and (BEST == -1): BEST = bestN
if (BEST == -1): BEST = bestN
l[bestN] = l.max()-1
P, w, c = P_dict[BEST]
dTarget, dNontarget = dVal_dict[BEST]
pVal = st.scoreatpercentile(dNontarget, pPer)
pdf = dNontarget
avrM = d[BEST]["avrM"]
conN = d[BEST]["conN"]
csp_time = d[BEST]["csp_time"]
cfg = {"csp_time":csp_time,
"use_channels": ';'.join(self.use_channels),
'avrM':avrM,
'conN':conN,
'pdf':pdf,
"P":P,
"w":w,
"c":c,
"montage":self.montage,
"montage_channels":';'.join(self.montage_channels),
"buffer":buffer
}
f_name = self.config.get_param("fda_file_name")
f_dir = self.config.get_param("fda_file_path")
csp_helper.set_csp_config(f_dir, f_name, cfg)
if plotFlag:
## Plotting best
p300_draw = P300_draw()
p300_draw.setCalibration(target, nontarget)
p300_draw.setCSP(P)
p300_draw.setTimeLine(conN, avrM, csp_time)
p300_draw.plotSignal()
#~ p300_draw.plotSignal_ds()
self.logger.info("FDA classifier -- DONE")
if not self.run_offline:
self._run_next_scenario()
def run(self):
self.logger.info("START FDA...")
f_name = self.config.get_param("data_file_name")
f_dir = self.config.get_param("data_file_path")
in_file = acquisition_helper.get_file_path(f_dir, f_name)
filename = os.path.join(f_dir, f_name + ".obci")
data = sp.signalParser(filename)
fs = int(float(data.getSamplingFrequency()))
mgr = read_manager.ReadManager(in_file + '.obci.xml',
in_file + '.obci.raw',
in_file + '.obci.tag')
if self.use_channels is None:
self.use_channels = data.getChannelList()
if self.ignore_channels is not None:
for i in self.ignore_channels:
try:
self.use_channels.remove(i)
except:
pass
self.montage = self.config.get_param("montage")
tmp = self.config.get_param("montage_channels")
if len(tmp) > 0:
self.montage_channels = tmp.split(';')
else:
self.montage_channels = []
self.logger.info("USE CHANNELS: " + str(self.use_channels))
self.logger.info("CHANNELS NAMES: " +
str(mgr.get_param('channels_names')))
## Get data and tags
data.setMontage(self.montage_channels)
Signal = data.getData(self.use_channels)
trgTags = data.get_p300_tags()
ntrgTags = data.get_not_p300_tags()
print "Signal.shape[1]: ", Signal.shape[1]
print "last trg: ", trgTags[-1]
print "last ntrg: ", ntrgTags[-1]
m = max([trgTags[-1], ntrgTags[-1]])
# ?!?!?!?!?!?!?!?! Why blinks are <0
trgTags = trgTags[trgTags > 0]
ntrgTags = ntrgTags[ntrgTags > 0]
trgTags = trgTags[trgTags < Signal.shape[1] - fs]
ntrgTags = ntrgTags[ntrgTags < Signal.shape[1] - fs]
print "last trg: ", trgTags[-1]
print "last ntrg: ", ntrgTags[-1]
target, nontarget = data.getTargetNontarget(Signal, trgTags, ntrgTags)
## Get params from file
pPer = float(self.config.get_param("p_per"))
nRepeat = int(self.config.get_param("n_repeat"))
nMin = int(self.config.get_param("n_min"))
nMax = int(self.config.get_param("n_max"))
avrM_l = map(lambda x: int(x),
self.config.get_param("avr_m").split(';'))
conN_l = map(lambda x: int(x),
self.config.get_param("con_n").split(';'))
csp_dt_l = map(lambda x: float(x),
self.config.get_param("csp_dt").split(';'))
csp_time_l = map(lambda x: float(x),
self.config.get_param("csp_time").split(';'))
plotFlag = int(self.config.get_param("plot_flag"))
debugFlag = int(self.config.get_param("debug_flag"))
## Define buffer
buffer = 1.1 * fs
self.logger.info("Computer buffer len: " + str(buffer))
## Make montage matrix
conf = self.use_channels, self.montage, self.montage_channels
self.montage_matrix = self._get_montage_matrix(
conf[0], conf[1], conf[2], mgr.get_param('channels_names'))
print "self.montage_matrix: ", self.montage_matrix
channels = ";".join(self.use_channels)
# Test all combination of parameters
N = 0
d = {}
for avrM in avrM_l:
for conN in conN_l:
for csp_time in csp_time_l:
for dt in csp_dt_l:
d[N] = {
"avrM": avrM,
"conN": conN,
"csp_time": [csp_time, csp_time + dt]
}
print "d[%i] = " % N, d[N]
N += 1
#################################
## CROSS CHECKING
P_dict, dVal_dict = {}, {}
l = np.zeros(N)
for idxN in range(N):
KEY = d[idxN].keys()
for k in KEY:
exec "{0}_tmp = {1}".format(k,
d[idxN][k]) in globals(), locals()
self.logger.info("Zestaw: {0} / {1}".format(idxN, N))
self.logger.info(str(d[idxN]))
csp = csp_time_tmp[0] * fs, csp_time_tmp[1] * fs
# Crop signalas to csp_time : csp_time+csp_dt
_target = target[:, :, csp[0]:csp[1]]
_nontarget = nontarget[:, :, csp[0]:csp[1]]
p300 = P300_train(channels, fs, avrM_tmp, conN_tmp, csp_time_tmp,
pPer)
l[idxN] = p300.valid_kGroups(Signal, _target, _nontarget, 2)
P_dict[idxN] = p300.getPWC()
dVal_dict[idxN] = p300.getDValDistribution()
if debugFlag:
p300.saveDist2File("target_%i" % idxN, "nontarget_%i" % idxN)
self.logger.info("Test score: " + str(l[idxN]))
self.logger.info("Calibration passed")
#################################
if debugFlag:
distributionDraw = P300_draw(fs)
# Plot all d distributions
for idx in range(N):
dTarget, dNontarget = dVal_dict[idx]
distributionDraw.plotDistribution(dTarget, dNontarget)
#################################
# Finding best
self.logger.info("\n" * 5)
self.logger.info("L: " + str(l))
P, conN, avrM, csp_time = None, None, None, None
BEST = -1
arr = np.arange(len(l))
for i in range(5):
bestN = int(arr[l == l.min()][0])
print "best_{0}: {1}".format(i, bestN)
print "d[bestN]: ", d[bestN]
print "l[bestN]: ", l.min()
if (l.min() > 100) and (BEST == -1): BEST = bestN
l[bestN] = l.max() - 1
P, w, c = P_dict[BEST]
dTarget, dNontarget = dVal_dict[BEST]
pVal = st.scoreatpercentile(dNontarget, pPer)
pdf = dNontarget
avrM = d[BEST]["avrM"]
conN = d[BEST]["conN"]
csp_time = d[BEST]["csp_time"]
cfg = {
"csp_time": csp_time,
"use_channels": ';'.join(self.use_channels),
'avrM': avrM,
'conN': conN,
'pdf': pdf,
"P": P,
"w": w,
"c": c,
"montage": self.montage,
"montage_channels": ';'.join(self.montage_channels),
"buffer": buffer
}
f_name = self.config.get_param("fda_file_name")
f_dir = self.config.get_param("fda_file_path")
csp_helper.set_csp_config(f_dir, f_name, cfg)
if plotFlag:
## Plotting best
p300_draw = P300_draw()
p300_draw.setCalibration(target, nontarget)
p300_draw.setCSP(P)
p300_draw.setTimeLine(conN, avrM, csp_time)
p300_draw.plotSignal()
#~ p300_draw.plotSignal_ds()
self.logger.info("FDA classifier -- DONE")
if not self.run_offline:
self._run_next_scenario()
dt = 1.0/Fs
t = np.arange(0,T,dt)
s = np.sin(2*np.pi*f*t + phi)
return s
if __name__ == "__main__":
fnCalibration = "dawid1.obci"
fnClasification = "dawid2.obci"
#~ CHANNELS = "PO7,O1,Oz,O2,PO8,PO3,PO4,Pz,Cz".split(',')
CHANNELS = "PO7,O1,O2,PO8,PO3,PO4,Pz,Cz".split(',')
REF_CHANNEL = ["Pz"]
chL = len(CHANNELS)
sigPars = signalParser(fnCalibration)
refSig = sigPars.extract_channel(REF_CHANNEL)
eegSig = sigPars.extract_channel(CHANNELS)
eegSigCalibration = eegSig - refSig
sigPars = signalParser(fnClasification)
refSig = sigPars.extract_channel(REF_CHANNEL)
eegSig = sigPars.extract_channel(CHANNELS)
eegSigClassification = eegSig - refSig
#~ eegSig = eegSig - np.mean(eegSig, axis=1)
Fs = 128.0
filtr = Filtr(Fs)
filtr.set_lowPass_filter()
filtr.set_highPass_filter()
def run(self):
LOGGER.info("START FDA...")
f_name = self.config.get_param("data_file_name")
f_dir = self.config.get_param("data_file_path")
in_file = acquisition_helper.get_file_path(f_dir, f_name)
filename = os.path.join(f_dir, f_name + ".obci")
data = sp.signalParser(filename)
fs = int(float(data.getSamplingFrequency()))
mgr = read_manager.ReadManager(
in_file+'.obci.xml',
in_file+'.obci.raw',
in_file+'.obci.tag')
if self.use_channels is None:
self.use_channels = data.getChannelList()
if self.ignore_channels is not None:
for i in self.ignore_channels:
try:
self.use_channels.remove(i)
except:
pass
self.montage = self.config.get_param("montage")
tmp = self.config.get_param("montage_channels")
if len(tmp) > 0:
self.montage_channels = tmp.split(';')
else:
self.montage_channels = []
LOGGER.info("USE CHANNELS: "+str(self.use_channels))
LOGGER.info("CHANNELS NAMES: "+str(mgr.get_param('channels_names')))
## Get data and tags
data.setMontage(self.montage_channels)
Signal = data.getData(self.use_channels)
trgTags = data.get_p300_tags()
ntrgTags = data.get_not_p300_tags()
target, nontarget = data.getTargetNontarget(Signal, trgTags, ntrgTags)
## Get params from file
pVal = float(self.config.get_param("p_val"))
nRepeat = int(self.config.get_param("n_repeat"))
nMin = int(self.config.get_param("n_min"))
nMax = int(self.config.get_param("n_max"))
avrM_l = map(lambda x: int(x), self.config.get_param("avr_m").split(';'))
conN_l = map(lambda x: int(x), self.config.get_param("con_n").split(';'))
csp_dt_l = map(lambda x: float(x), self.config.get_param("csp_dt").split(';'))
csp_time_l = map(lambda x: float(x), self.config.get_param("csp_time").split(';'))
## Define buffer
buffer = 1.1*fs
LOGGER.info("Computer buffer len: "+str(buffer))
## Make montage matrix
conf = self.use_channels, self.montage, self.montage_channels
self.montage_matrix = self._get_montage_matrix(conf[0], conf[1], conf[2], mgr.get_param('channels_names'))
print "self.montage_matrix: ", self.montage_matrix
channels = ";".join(self.use_channels)
# make sure that:
# channels -- is in format like "P07;O1;Oz;O2"
# fs -- is a number
# avrM -- are int
# conN -- are int
# csp_time -- is a list of two float 0 < x < 1
N = 0
d, P_dict = {}, {}
for avrM in avrM_l:
for conN in conN_l:
for csp_time in csp_time_l:
for dt in csp_dt_l:
d[N] = {"avrM":avrM, "conN":conN, "csp_time":[csp_time, csp_time+dt]}
print "d[%i] = " %N, d[N]
N += 1
#################################
## CROSS CHECKING
l = np.zeros(N)
for idxN in range(N):
KEY = d[idxN].keys()
for k in KEY:
#~ c = "{0} = {1}".format(k, d[idxN][k])
#~ print c
#~ exec(c)
exec "{0}_tmp = {1}".format(k, d[idxN][k]) in globals(), locals()
p300 = P300_train(channels, fs, avrM_tmp, conN_tmp, csp_time_tmp)
l[idxN] = p300.valid_kGroups(Signal, target, nontarget, 2)
P_dict[idxN] = p300.getPWC()
#################################
# Finding best
print "\n"*5
print "L: ", l
P, conN, avrM, csp_time = None, None, None, None
BEST = -1
arr = np.arange(len(l))
for i in range(5):
bestN = int(arr[l==l.max()])
print "best_{0}: {1}".format(i, bestN)
print "d[bestN]: ", d[bestN]
print "l[bestN]: ", l.max()
if (l.max() < 1000) and (BEST == -1): BEST = bestN
l[bestN] = l.min()-1
print "best: ", BEST
P, w, c = P_dict[BEST]
avrM = d[BEST]["avrM"]
conN = d[BEST]["conN"]
csp_time = d[BEST]["csp_time"]
cfg = {"csp_time":csp_time,
"use_channels": ';'.join(self.use_channels),
'pVal':pVal,
'avrM':avrM,
'conN':conN,
"nRepeat":nRepeat,
"P":P,
"w":w,
"c":c,
"montage":self.montage,
"montage_channels":';'.join(self.montage_channels),
"buffer":buffer
}
f_name = self.config.get_param("csp_file_name")
f_dir = self.config.get_param("csp_file_path")
ssvep_csp_helper.set_csp_config(f_dir, f_name, cfg)
## Plotting best
p300_draw = P300_draw()
p300_draw.setCalibration(target, nontarget, trgTags, ntrgTags)
p300_draw.setCSP(P)
p300_draw.setTimeLine(conN, avrM, csp_time)
p300_draw.plotSignal()
p300_draw.plotSignal_ds()
LOGGER.info("FDA Calibration complete")
if not self.run_offline:
self._run_next_scenario()
def run(self):
LOGGER.info("START FDA...")
f_name = self.config.get_param("data_file_name")
f_dir = self.config.get_param("data_file_path")
in_file = acquisition_helper.get_file_path(f_dir, f_name)
filename = os.path.join(f_dir, f_name + ".obci")
data = sp.signalParser(filename)
fs = int(float(data.getSamplingFrequency()))
mgr = read_manager.ReadManager(in_file + '.obci.xml',
in_file + '.obci.raw',
in_file + '.obci.tag')
if self.use_channels is None:
self.use_channels = data.getChannelList()
if self.ignore_channels is not None:
for i in self.ignore_channels:
try:
self.use_channels.remove(i)
except:
pass
self.montage = self.config.get_param("montage")
tmp = self.config.get_param("montage_channels")
if len(tmp) > 0:
self.montage_channels = tmp.split(';')
else:
self.montage_channels = []
LOGGER.info("USE CHANNELS: " + str(self.use_channels))
LOGGER.info("CHANNELS NAMES: " + str(mgr.get_param('channels_names')))
## Get data and tags
data.setMontage(self.montage_channels)
Signal = data.getData(self.use_channels)
trgTags = data.get_p300_tags()
ntrgTags = data.get_not_p300_tags()
target, nontarget = data.getTargetNontarget(Signal, trgTags, ntrgTags)
## Get params from file
pVal = float(self.config.get_param("p_val"))
nRepeat = int(self.config.get_param("n_repeat"))
nMin = int(self.config.get_param("n_min"))
nMax = int(self.config.get_param("n_max"))
avrM_l = map(lambda x: int(x),
self.config.get_param("avr_m").split(';'))
conN_l = map(lambda x: int(x),
self.config.get_param("con_n").split(';'))
csp_dt_l = map(lambda x: float(x),
self.config.get_param("csp_dt").split(';'))
csp_time_l = map(lambda x: float(x),
self.config.get_param("csp_time").split(';'))
## Define buffer
buffer = 1.1 * fs
LOGGER.info("Computer buffer len: " + str(buffer))
## Make montage matrix
conf = self.use_channels, self.montage, self.montage_channels
self.montage_matrix = self._get_montage_matrix(
conf[0], conf[1], conf[2], mgr.get_param('channels_names'))
print "self.montage_matrix: ", self.montage_matrix
channels = ";".join(self.use_channels)
# make sure that:
# channels -- is in format like "P07;O1;Oz;O2"
# fs -- is a number
# avrM -- are int
# conN -- are int
# csp_time -- is a list of two float 0 < x < 1
N = 0
d, P_dict = {}, {}
for avrM in avrM_l:
for conN in conN_l:
for csp_time in csp_time_l:
for dt in csp_dt_l:
d[N] = {
"avrM": avrM,
"conN": conN,
"csp_time": [csp_time, csp_time + dt]
}
print "d[%i] = " % N, d[N]
N += 1
#################################
## CROSS CHECKING
l = np.zeros(N)
for idxN in range(N):
KEY = d[idxN].keys()
for k in KEY:
#~ c = "{0} = {1}".format(k, d[idxN][k])
#~ print c
#~ exec(c)
exec "{0}_tmp = {1}".format(k,
d[idxN][k]) in globals(), locals()
p300 = P300_train(channels, fs, avrM_tmp, conN_tmp, csp_time_tmp)
l[idxN] = p300.valid_kGroups(Signal, target, nontarget, 2)
P_dict[idxN] = p300.getPWC()
#################################
# Finding best
print "\n" * 5
print "L: ", l
P, conN, avrM, csp_time = None, None, None, None
BEST = -1
arr = np.arange(len(l))
for i in range(5):
bestN = int(arr[l == l.max()])
print "best_{0}: {1}".format(i, bestN)
print "d[bestN]: ", d[bestN]
print "l[bestN]: ", l.max()
if (l.max() < 1000) and (BEST == -1): BEST = bestN
l[bestN] = l.min() - 1
print "best: ", BEST
P, w, c = P_dict[BEST]
avrM = d[BEST]["avrM"]
conN = d[BEST]["conN"]
csp_time = d[BEST]["csp_time"]
cfg = {
"csp_time": csp_time,
"use_channels": ';'.join(self.use_channels),
'pVal': pVal,
'avrM': avrM,
'conN': conN,
"nRepeat": nRepeat,
"P": P,
"w": w,
"c": c,
"montage": self.montage,
"montage_channels": ';'.join(self.montage_channels),
"buffer": buffer
}
f_name = self.config.get_param("csp_file_name")
f_dir = self.config.get_param("csp_file_path")
ssvep_csp_helper.set_csp_config(f_dir, f_name, cfg)
## Plotting best
p300_draw = P300_draw()
p300_draw.setCalibration(target, nontarget, trgTags, ntrgTags)
p300_draw.setCSP(P)
p300_draw.setTimeLine(conN, avrM, csp_time)
p300_draw.plotSignal()
p300_draw.plotSignal_ds()
LOGGER.info("FDA Calibration complete")
if not self.run_offline:
self._run_next_scenario()
dt = 1.0 / Fs
t = np.arange(0, T, dt)
s = np.sin(2 * np.pi * f * t + phi)
return s
if __name__ == "__main__":
fnCalibration = "dawid1.obci"
fnClasification = "dawid2.obci"
# ~ CHANNELS = "PO7,O1,Oz,O2,PO8,PO3,PO4,Pz,Cz".split(',')
CHANNELS = "PO7,O1,O2,PO8,PO3,PO4,Pz,Cz".split(",")
REF_CHANNEL = ["Pz"]
chL = len(CHANNELS)
sigPars = signalParser(fnCalibration)
refSig = sigPars.extract_channel(REF_CHANNEL)
eegSig = sigPars.extract_channel(CHANNELS)
eegSigCalibration = eegSig - refSig
sigPars = signalParser(fnClasification)
refSig = sigPars.extract_channel(REF_CHANNEL)
eegSig = sigPars.extract_channel(CHANNELS)
eegSigClassification = eegSig - refSig
# ~ eegSig = eegSig - np.mean(eegSig, axis=1)
Fs = 128.0
filtr = Filtr(Fs)
filtr.set_lowPass_filter()
filtr.set_highPass_filter()
