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 __init__(self, cf: CacheFile, idx: int, *args, **kwargs):
super(TattrWidget, self).__init__(*args, **kwargs)
tattrs = self.get_cleaned_tattrs(cf, idx)
layout = QtWidgets.QGridLayout()
row = 0
for key in tattrs.keys():
label = QtWidgets.QLabel(text=key.replace("_", " ").capitalize())
if type(decode(tattrs[key])) == float:
val = "{0:3.3f}".format(decode(tattrs[key]))
line = QtWidgets.QLineEdit(val)
else:
line = QtWidgets.QLineEdit(tattrs[key])
trig = partial(save, cf=cf, idx=idx, key=key, read=line.text)
line.textChanged.connect(trig)
layout.addWidget(label, row, 0)
layout.addWidget(line, row, 1)
row += 1
key = "comment"
tattrs = cf.get_trace_attrs(idx)
label = QtWidgets.QLabel(text=key)
line = VTextEdit(tattrs[key])
trig = partial(save, cf=cf, idx=idx, key=key, read=line.toPlainText)
line.editingFinished.connect(trig)
layout.addWidget(label, row, 0)
layout.addWidget(line, row, 1)
self.setLayout(layout)
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 draw_hasmep_button(self):
tattrs = self.cf.get_trace_attrs(self.trace_idx)
pamp = decode(tattrs["pos_peak_magnitude_uv"]) or 0
namp = decode(tattrs["neg_peak_magnitude_uv"]) or 0
ptp = pamp - namp
if ptp != 0:
self.hasmep_button.setStyleSheet("background-color: green")
self.hasmep_button.setText("MEP positive")
else:
self.hasmep_button.setStyleSheet("background-color: red")
self.hasmep_button.setText("MEP negative")
def plot_trace(self, cf, idx: int = 0):
data = cf.get_trace_data(idx)
attrs = cf.get_trace_attrs(idx)
pre = decode(attrs["samples_pre_event"])
post = decode(attrs["samples_post_event"])
fs = decode(attrs["samplingrate"])
shift = decode(attrs["onset_shift"])
shift = shift or 0
t0 = -float(pre) / float(fs)
t1 = float(post) / float(fs)
nlat = decode(attrs["neg_peak_latency_ms"]) or 0.0
plat = decode(attrs["pos_peak_latency_ms"]) or 1.0
namp = decode(attrs["neg_peak_magnitude_uv"]) or 0.0
pamp = decode(attrs["pos_peak_magnitude_uv"]) or 0.0
nlat = int(nlat * float(fs) / 1000)
plat = int(plat * float(fs) / 1000)
if nlat < plat:
amps = (namp, pamp)
lats = (nlat, plat)
else:
amps = (pamp, namp)
lats = (plat, nlat)
try:
# perform preprocessing steps
data = process_data(data, attrs, key="_log")
plot_trace_on(self.canvas.axes, data, t0, t1, pre, post, lats, amps, shift)
print(f"PLOT: Plotting trace number {idx+1} shifted by {shift} samples")
except Exception as e:
print(e)
def flip_reject_button(self):
tattrs = self.cf.get_trace_attrs(self.trace_idx)
reject = decode(tattrs["reject"])
reject = True if reject is None else not reject
tattrs["reject"] = reject
self.cf.set_trace_attrs(self.trace_idx, tattrs)
self.draw_reject_button()
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 draw_undo_button(self):
_log = decode(
self.cf.get_trace_attrs(self.trace_idx).get("_log", "[]"))
if _log != []:
log = "\n".join(_log)
self.undo_button.setToolTip(log)
self.undo_button.setStyleSheet("background-color: gray")
else:
self.undo_button.setToolTip("No processing steps in cache")
self.undo_button.setStyleSheet("background-color: None")
def _draw(self, cf: CacheFile, idx: int, tmpdir):
tattrs = cf.get_trace_attrs(idx)
coords = decode(tattrs["xyz_coords"])
print(f"COORDS: Stimulation target was at {coords}")
try:
plot_glass_on(axes=self.canvas.axes, coords=coords, tmpdir=tmpdir)
except Exception as e:
InvalidCoordsDialog(cf=cf, idx=idx, message=str(e))
self.canvas.axes.axis("off")
self.canvas.draw()
def draw_reject_button(self):
tattrs = self.cf.get_trace_attrs(self.trace_idx)
reject = decode(tattrs["reject"])
reject = False if reject is None else reject
self.cf.set_trace_attrs(self.trace_idx, tattrs)
if reject:
self.reject_button.setStyleSheet("background-color: red")
self.reject_button.setText("Rejected")
else:
self.reject_button.setStyleSheet("background-color: green")
self.reject_button.setText("Accepted")
def draw_int(self, idx: int = 0):
self.idx = idx
tattr = self.cf.get_trace_attrs(self.idx)
val = decode(tattr[self.key])
val = val or 0
if type(val) == str:
val = 0
elif type(val) == float:
val = int(val)
val = "{0:3.0f}".format(val)
print(f"TATTR: Loading {self.key}:{val} for {idx}")
self.line.setText(val)
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 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
def __init__(self, cf: CacheFile, idx: int, *args, **kwargs):
super(OattrWidget, self).__init__(*args, **kwargs)
tattr = cf.get_trace_attrs(idx)
layout = QtWidgets.QGridLayout()
keys = sorted(valid_origin_keys).copy()
keys.remove("global_comment")
keys.remove("channel_labels")
row = 0
for key in keys:
label = QtWidgets.QLabel(text=key)
line = QtWidgets.QLabel(tattr[key])
layout.addWidget(label, row, 0)
layout.addWidget(line, row, 1)
row += 1
key = "channel_labels"
label = QtWidgets.QLabel(text=key)
line = QtWidgets.QListWidget()
entries = decode(tattr[key])
line.addItems(entries)
line.setFlow(line.LeftToRight)
line.setMaximumHeight(50)
layout.addWidget(label, row, 0)
layout.addWidget(line, row, 1)
row += 1
key = "global_comment"
label = QtWidgets.QLabel(text=key)
line = VTextEdit(tattr[key])
trig = partial(save_global,
cf=cf,
idx=idx,
key=key,
read=line.toPlainText)
line.editingFinished.connect(trig)
layout.addWidget(label, row, 0)
layout.addWidget(line, row, 1)
self.setLayout(layout)