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Depth error handling #27

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Merged
micahjohnson150 merged 3 commits into from
Jan 28, 2026
+62 −23
Merged

Depth error handling #27

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74d9516
Working towards a better depth interpretation and a calibration
micahjohnson150 Jan 24, 2026
b0b6202
Merged in main
micahjohnson150 Jan 28, 2026
624a5f4
Added back in original fused data in the event things fully blow up
micahjohnson150 Jan 28, 2026
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5 changes: 4 additions & 1 deletion study_lyte/adjustments.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,12 +175,15 @@ def remove_ambient(active, ambient, min_ambient_range=100, direction='forward'):
return clean


def apply_calibration(series, coefficients, minimum=None, maximum=None):
def apply_calibration(series, coefficients, minimum=None, maximum=None, tare=False):
"""
Apply any calibration using poly1d
"""
poly = np.poly1d(coefficients)
result = poly(series)
if tare:
result = result - np.nanmedian(result[0:50])

if maximum is not None:
result[result > maximum] = maximum
if minimum is not None:
Expand Down
80 changes: 58 additions & 22 deletions study_lyte/profile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,11 +81,12 @@ def __init__(self, filename, surface_detection_offset=4.5, calibration=None,
self._error = None
self._ground = None

def assign_event_depths(self):
def assign_event_depths(self, depth:pd.Series):
"""" Enable depth assignment post depth realization """
self.events
for event in [self._start, self._stop, self._surface.nir, self._surface.force]:
event.depth = self.depth.iloc[event.index]
for event in [self._start, self._stop]:
event.depth = depth.iloc[event.index]
self._surface = self.assign_surface_depths(depth)

@property
def serial_number(self):
Expand Down Expand Up @@ -182,8 +183,7 @@ def force(self):
force = self.raw['Sensor1'].values
if self.calibration is not None:
if 'Sensor1' in self.calibration.keys():
force = apply_calibration(self.raw['Sensor1'].values, self.calibration['Sensor1'], minimum=0, maximum=15000)
force = force - np.nanmean(force[0:20])
force = apply_calibration(self.raw['Sensor1'].values, self.calibration['Sensor1'], minimum=None, maximum=15000, tare=True)

self._force = pd.DataFrame({'force': force, 'depth': self.depth.values})
self._force = self._force.iloc[self.surface.force.index:self.end].reset_index()
Expand Down Expand Up @@ -424,14 +424,26 @@ def depth(self):
self.barometer.depth.values.copy(),
error=self.error.index)

if depth.min() < -230 and self.accelerometer.depth.min() > -230:
LOG.warning('Fused depth result produced a profile > 230 cm. Defaulting to accelerometer')
self._depth = self.accelerometer.depth

elif depth.min() < -230 and self.barometer.depth.min() > -230:
LOG.warning('Fused and accelerometer depth resulted in a profile > 230 cm. Defaulting to barometer')
self._depth = self.barometer.depth

# Failed fusion
unrealistic_depth = 230
travel = abs(depth.max() - depth.min())

# Unrealistic depth
if travel > unrealistic_depth:
warn_msg = f'Fused depth result produced a profile > {unrealistic_depth} cm.'

# Check if acceleration alone is reasonable
if self.accelerometer.distance_traveled < unrealistic_depth:
LOG.warning(warn_msg + ' Defaulting to accelerometer')
self._depth = self.accelerometer.depth

# Check if barometer alone is reasonable
elif self.barometer.distance_traveled < unrealistic_depth:
LOG.warning(warn_msg + ' Defaulting to barometer')
self._depth = self.barometer.depth
else:
LOG.error(warn_msg + ' Alternate sensors also unrealistic, using data as is.')
self._depth = pd.Series(data=depth, index=self.raw['time'])
else:
self._depth = pd.Series(data=depth, index=self.raw['time'])

Expand All @@ -444,7 +456,7 @@ def depth(self):
self._depth = self.barometer.depth

# Assign positions of each event detected
self.assign_event_depths()
self.assign_event_depths(self._depth)

return self._depth

Expand Down Expand Up @@ -481,6 +493,38 @@ def stop(self):

return self._stop

def assign_surface_depths(self, depth:pd.Series):
# Event according the NIR sensors
idx = self.surface.nir.index
self._surface.nir.depth = depth.iloc[idx]

# Event according to the force sensor
force_surface_depth = self._surface.nir.depth + self.surface_detection_offset
f_idx = abs(depth - force_surface_depth).argmin()
# Retrieve force estimated start
f_start = get_sensor_start(self.raw['Sensor1'], max_threshold=0.02, threshold=-0.02)
f_start = f_start or f_idx

# If the force start is before the NIR start then adjust
if f_start < self.start.index:
LOG.info(f'Choosing motion start ({self.start.index}) over force start ({f_start})...')
f_idx = self.start.index
force_surface_depth = depth.iloc[f_idx]

elif f_start < f_idx:
LOG.info(f'Choosing force start ({f_start}) over nir derived ({f_idx})...')
f_idx = f_start
force_surface_depth = depth.iloc[f_idx]

self._surface.force.index = f_idx
self._surface.force.depth = depth.iloc[f_idx]
self._surface.force.time = self.raw['time'].iloc[f_idx]

# Adjust surface detection to modify the start if there is conflict.
if self._surface.nir.time < self.start.time:
self._start = self._surface.nir
self._start.name = 'start'

@property
def surface(self):
"""
Expand Down Expand Up @@ -517,11 +561,6 @@ def surface(self):
force = Event(name='surface', index=f_idx, depth=force_surface_depth, time=self.raw['time'].iloc[f_idx])
self._surface = SimpleNamespace(name='surface', nir=nir, force=force)

# Allow surface detection to modify the start if there is conflict.
if nir.time < self.start.time:
self._start = nir
self._start.name = 'start'

return self._surface

@property
Expand Down Expand Up @@ -651,10 +690,7 @@ def fuse_depths(cls, acc_depth, baro_depth, error=None):
# Scale total
sensor_diff = abs(acc_bottom) - abs(baro_bottom)
delta = 0.572 * abs(acc_bottom) + 0.308 * abs(baro_bottom) + 0.264 * sensor_diff + 8.916
# delta = (acc_bottom * (5 - scale) + baro_bottom * scale) / 5
avg = (avg / avg_bottom) * -1 * delta
# from study_lyte.plotting import plot_ts
# ax = plot_ts(avg, show=True)

return avg

Expand Down