Force start error (#14)

* Added in function for general change detection

* Added test data set

* Added some safeguards around detecting the surface before other intuitive events

study_lyte/depth.py

@@ -96,7 +96,7 @@ def get_constrained_baro_depth(baro_depth, start, stop, method='nanmedian'):
         soft_stop = len(baro_depth.index) - 1
 
     valley_search = baro_depth.iloc[mid:].values
-    v_min = valley_search.min()
+    v_min = np.nanmin(valley_search)
     vmin_idx = np.where(valley_search == v_min)[0][0]
     bottom = nearest_peak(-1 * valley_search, stop - mid, default_index=vmin_idx, height=-10, distance=100)
     bottom += mid

study_lyte/detect.py

@@ -145,12 +145,22 @@ def get_acceleration_stop(acceleration, threshold=-0.05, max_threshold=0.05):
     if n > 40:
         n = 20
 
-    max_ind = np.argwhere(acceleration == acceleration.min())[0][0]
-    acceleration_stop = get_signal_event(acceleration[max_ind:], threshold=threshold,
+    min_idx = np.argwhere(acceleration == acceleration.min())[0][0]
+    max_idx = np.argwhere(acceleration == acceleration.max())[0][0]
+    # Large impact early in during the accelerating down
+    if min_idx < max_idx:
+        # Find the deceleration later than the maximum deceleration
+        search_start = np.argwhere(acceleration[max_idx:] == acceleration[max_idx:].min())[0][0]
+        search_start += max_idx
+    else:
+        # Use the farthest deceleration
+        search_start = min_idx
+
+    acceleration_stop = get_signal_event(acceleration[search_start:], threshold=threshold,
                                          max_threshold=max_threshold,
                                          n_points=n,
                                          search_direction='backward')
-    acceleration_stop = acceleration_stop + max_ind
+    acceleration_stop = acceleration_stop + search_start
     return acceleration_stop
 
 
@@ -203,3 +213,15 @@ def get_nir_stop(active, fractional_basis=0.05, max_threshold=0.008, threshold=-
 
     return stop
 
+
+def get_sensor_start(signal, fractional_basis=0.05, max_threshold=0.05, threshold=-0.05):
+    """
+    Before entering the snow we don't see much dynamic signal. This detects the first change in the signal
+    """
+    ind = np.where(signal == signal.max())[0][0]
+    n_points = get_points_from_fraction(len(signal), 0.01)
+    data = signal[:ind]
+    norm_signal = get_normalized_at_border(data, fractional_basis=fractional_basis, direction='forward') - 1
+    first_change = get_signal_event(norm_signal, search_direction='forward', threshold=threshold,
+                            max_threshold=max_threshold, n_points=n_points)
+    return first_change

study_lyte/profile.py

@@ -7,7 +7,7 @@
 
 from . io import read_csv
 from .adjustments import get_neutral_bias_at_border, remove_ambient, apply_calibration, get_points_from_fraction, zfilter
-from .detect import get_acceleration_start, get_acceleration_stop, get_nir_surface, get_nir_stop
+from .detect import get_acceleration_start, get_acceleration_stop, get_nir_surface, get_nir_stop, get_sensor_start
 from .depth import AccelerometerDepth, BarometerDepth
 from .logging import setup_log
 import logging
@@ -306,11 +306,23 @@ def surface(self):
                 # Event according to the force sensor
                 force_surface_depth = depth + self.surface_detection_offset
                 f_idx = abs(self.depth - force_surface_depth).argmin()
+                # Retrieve force estimated start
+                f_start = get_sensor_start(self.raw['Sensor1'], max_threshold=0.3, threshold=-0.3)
+                # If the force start is before the NIR start then adjust
+                if f_start < self.start.index:
+                    LOG.info('Choosing motion start over force start...')
+                    f_idx = self.start.index
+                    force_surface_depth = self.depth.iloc[f_idx]
+
+                elif f_start < f_idx:
+                    LOG.info('Choosing force start point over nir...')
+                    f_idx = f_start
+                    force_surface_depth = self.depth.iloc[f_idx]
 
                 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 we have conflict.
+                # Allow surface detection to modify the start if there is conflict.
                 if nir.time < self.start.time:
                     self._start = nir
                     self._start.name = 'start'

tests/conftest.py

@@ -1,6 +1,7 @@
 import pytest
 from os.path import dirname, join
 from study_lyte.io import read_csv
+from study_lyte.profile import LyteProfileV6
 
 
 @pytest.fixture(scope='session')
@@ -13,6 +14,10 @@ def raw_df(data_dir, fname):
     df, meta = read_csv(join(data_dir, fname))
     return df
 
+@pytest.fixture(scope='function')
+def lyte_profile(data_dir, fname):
+    return LyteProfileV6(join(data_dir, fname), calibration={'Sensor1': [1, 0]})
+
 
 @pytest.fixture(scope='session')
 def peripherals(data_dir):