def click_estimate_parameters(self):
window = (15, 120)
idx = self.trace_idx
data = self.cf.get_trace_data(idx)
tattrs = self.cf.get_trace_attrs(idx)
data = process_data(data, tattrs, key="_log")
pre = decode(tattrs["samples_pre_event"])
shift = decode(tattrs["onset_shift"]) or 0
fs = decode(tattrs["samplingrate"])
onset = pre - shift
print(shift, fs)
minlat = int(window[0] * fs / 1000)
maxlat = int(window[1] * fs / 1000)
a = onset + minlat
b = onset + maxlat
mep = data[a:b]
nlat = mep.argmin()
plat = mep.argmax()
namp = float(mep[nlat])
pamp = float(mep[plat])
nlat = mep.argmin() * 1000 / fs
plat = mep.argmax() * 1000 / fs
print("Estimating latencies to be", nlat, plat)
print("Estimating amplitudes to be", namp, pamp)
tattrs["neg_peak_latency_ms"] = encode(float(nlat + window[0]))
tattrs["neg_peak_magnitude_uv"] = encode(namp)
tattrs["pos_peak_latency_ms"] = encode(float(plat + window[0]))
tattrs["pos_peak_magnitude_uv"] = encode(pamp)
self.cf.set_trace_attrs(idx, tattrs)
self.draw_hasmep_button()
self.callback()
def click_hasmep(self):
print(self.hasmep_button.text())
if self.hasmep_button.text() == "MEP positive":
tattrs = self.cf.get_trace_attrs(self.trace_idx)
tattrs["neg_peak_latency_ms"] = encode(0)
tattrs["pos_peak_latency_ms"] = encode(0)
tattrs["neg_peak_magnitude_uv"] = encode(0)
tattrs["pos_peak_magnitude_uv"] = encode(0)
self.cf.set_trace_attrs(self.trace_idx, tattrs)
self.draw_hasmep_button()
self.callback()
def rescale_coords(attrs: TraceAttributes,
scaling_factor: float = 1.0) -> TraceAttributes:
"""scale the coordinates of this trace by a scaling factor"""
coords = decode(attrs["xyz_coords"])
coords = [float * c for c in coords]
attrs["xyz_coords"] = encode(coords)
return attrs
def translate_coords(
attrs: TraceAttributes,
translation: List[float] = [0.0, 0.0, 0.0]) -> TraceAttributes:
"""move the coordinates of this trace by a translation"""
coords = decode(attrs["xyz_coords"])
coords = [c - t for c, t in zip(coords, translation)]
attrs["xyz_coords"] = encode(coords)
return attrs
def save(cf, idx: int, key: str, read: Callable):
tattr = cf.get_trace_attrs(idx)
text = read()
if tattr[key] == text:
return
else:
tattr[key] = encode(text)
cf.set_trace_attrs(idx, tattr)
print(f"CF: Wrote {idx}: {key} {text}")
def log(self, event: str, idx: int):
attrs = self.cf.get_trace_attrs(idx)
if "_log" in attrs.keys():
log = decode(attrs["_log"])
else:
log = []
happening = str(event) + " on " + datetime.now().strftime(
"%Y-%m-%d %H:%M:%S")
print("Logging", happening, "to", log)
log.append(happening)
attrs["_log"] = encode(log)
self.cf.set_trace_attrs(self.trace_idx, attrs)
def click_estimate_amplitudes(self):
idx = self.trace_idx
data = self.cf.get_trace_data(idx)
tattrs = self.cf.get_trace_attrs(idx)
data = process_data(data, tattrs, key="_log")
fs = decode(tattrs["samplingrate"])
nlat = int((decode(tattrs["neg_peak_latency_ms"]) or 0) * fs / 1000)
plat = int((decode(tattrs["pos_peak_latency_ms"]) or 0) * fs / 1000)
# MEP negative trials
if nlat == plat:
print("MEP negative or identical latencies", nlat, plat)
tattrs["neg_peak_latency_ms"] = encode(0)
tattrs["pos_peak_latency_ms"] = encode(0)
tattrs["neg_peak_magnitude_uv"] = encode(0)
tattrs["pos_peak_magnitude_uv"] = encode(0)
else:
pre = decode(tattrs["samples_pre_event"])
shift = decode(tattrs["onset_shift"]) or 0
namp = float(data[nlat + pre + shift])
pamp = float(data[plat + pre + shift])
print("Estimating amplitudes to be", namp, pamp)
tattrs["neg_peak_magnitude_uv"] = encode(namp)
tattrs["pos_peak_magnitude_uv"] = encode(pamp)
self.cf.set_trace_attrs(idx, tattrs)
self.draw_hasmep_button()
self.callback()
def save_global(cf, idx: int, key: str, read: Callable):
tattr = cf.get_trace_attrs(idx)
text = read()
if tattr[key] == text:
return
else:
origin = tattr["origin"]
for idx in range(len(cf)):
tattr = cf.get_trace_attrs(idx)
if tattr["origin"] == origin:
tattr[key] = encode(text)
cf.set_trace_attrs(idx, tattr)
print(f"CF: Wrote globaly {origin}: {key} {text}")
def undo(self, idx):
attrs = self.cf.get_trace_attrs(idx)
if "_log" in attrs.keys():
log = decode(attrs["_log"])
else:
log = []
if len(log) > 0:
event = log.pop()
step, when = event.split(" on ")
print("Undoing", step, "from", when)
else:
print("Nothing to undo")
attrs["_log"] = encode(log)
self.cf.set_trace_attrs(self.trace_idx, attrs)
def get_cleaned_tattrs(self, cf, idx):
tattrs = cf.get_trace_attrs(idx)
initialize_with_zero = [
"onset_shift",
"neg_peak_latency_ms",
"pos_peak_latency_ms",
"neg_peak_magnitude_uv",
"pos_peak_magnitude_uv",
]
for key in initialize_with_zero:
tattrs[key] = encode(decode(tattrs[key]) or 0)
cf.set_trace_attrs(idx, tattrs)
keys = get_valid_trace_keys(tattrs["readin"], tattrs["readout"]).copy()
keys.remove("reject")
keys.remove("onset_shift")
keys.remove("comment")
show_tattrs = dict()
for key in sorted(keys):
if key[0] != "_":
show_tattrs[key] = tattrs[key]
return show_tattrs