tests: added tests for feature computation

batdetect2/detector/compute_features.py

@@ -88,19 +88,28 @@ def compute_max_power_bb(
         return np.nan
 
     x_start = max(0, prediction["x_pos"])
-    x_end = min(spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"])
+    x_end = min(
-
+        spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"]
-    y_low = max(0, prediction["y_pos"])
-    y_high = min(
-        spec.shape[0] - 1, prediction["y_pos"] + prediction["bb_height"]
     )
 
-    spec_bb = spec[y_low:y_high, x_start:x_end]
+    # y low is the lowest freq but it will have a higher value due to array
+    # starting at 0 at top
+    y_low = min(spec.shape[0] - 1, prediction["y_pos"])
+    y_high = max(0, prediction["y_pos"] - prediction["bb_height"])
+
+    spec_bb = spec[y_high:y_low, x_start:x_end]
     power_per_freq_band = np.sum(spec_bb, axis=1)
-    max_power_ind = np.argmax(power_per_freq_band)
+
+    try:
+        max_power_ind = np.argmax(power_per_freq_band)
+    except ValueError:
+        # If the call is too short, the bounding box might be empty.
+        # In this case, return NaN.
+        return np.nan
+
     return int(
         convert_int_to_freq(
-            y_low - max_power_ind,
+            y_high + max_power_ind,
             spec.shape[0],
             min_freq,
             max_freq,
@@ -120,7 +129,9 @@ def compute_max_power(
         return np.nan
 
     x_start = max(0, prediction["x_pos"])
-    x_end = min(spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"])
+    x_end = min(
+        spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"]
+    )
     spec_call = spec[:, x_start:x_end]
     power_per_freq_band = np.sum(spec_call, axis=1)
     max_power_ind = np.argmax(power_per_freq_band)
@@ -146,7 +157,9 @@ def compute_max_power_first(
         return np.nan
 
     x_start = max(0, prediction["x_pos"])
-    x_end = min(spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"])
+    x_end = min(
+        spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"]
+    )
     spec_call = spec[:, x_start:x_end]
     first_half = spec_call[:, : int(spec_call.shape[1] / 2)]
     power_per_freq_band = np.sum(first_half, axis=1)
@@ -173,7 +186,9 @@ def compute_max_power_second(
         return np.nan
 
     x_start = max(0, prediction["x_pos"])
-    x_end = min(spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"])
+    x_end = min(
+        spec.shape[1] - 1, prediction["x_pos"] + prediction["bb_width"]
+    )
     spec_call = spec[:, x_start:x_end]
     second_half = spec_call[:, int(spec_call.shape[1] / 2) :]
     power_per_freq_band = np.sum(second_half, axis=1)

tests/test_features.py

@@ -1,9 +1,17 @@
 """Test suite for feature extraction functions."""
 
+import logging
+
+import librosa
 import numpy as np
+import pytest
 
 import batdetect2.detector.compute_features as feats
-from batdetect2 import types
+from batdetect2 import api, types
+from batdetect2.utils import audio_utils as au
+
+numba_logger = logging.getLogger("numba")
+numba_logger.setLevel(logging.WARNING)
 
 
 def index_to_freq(
@@ -29,6 +37,11 @@ def index_to_time(
 
 
 def test_get_feats_function_with_empty_spectrogram():
+    """Test get_feats function with empty spectrogram.
+
+    This tests that the overall flow of the function works, even if the
+    spectrogram is empty.
+    """
     spec_duration = 3
     spec_width = 100
     spec_height = 100
@@ -43,12 +56,14 @@ def test_get_feats_function_with_empty_spectrogram():
 
     start_time = index_to_time(x_pos, spec_width, spec_duration)
     end_time = index_to_time(x_pos + bb_width, spec_width, spec_duration)
-    high_freq = index_to_freq(y_pos, spec_height, min_freq, max_freq)
+    low_freq = index_to_freq(y_pos, spec_height, min_freq, max_freq)
-    low_freq = index_to_freq(y_pos + bb_height, spec_height, min_freq, max_freq)
+    high_freq = index_to_freq(
+        y_pos - bb_height, spec_height, min_freq, max_freq
+    )
 
     pred_nms: types.PredictionResults = {
         "det_probs": np.array([1]),
-        "class_probs": np.array([1]),
+        "class_probs": np.array([[1]]),
         "x_pos": np.array([x_pos]),
         "y_pos": np.array([y_pos]),
         "bb_width": np.array([bb_width]),
@@ -76,7 +91,7 @@ def test_get_feats_function_with_empty_spectrogram():
                 low_freq,
                 high_freq,
                 high_freq - low_freq,
-                max_freq,
+                high_freq,
                 max_freq,
                 max_freq,
                 max_freq,
@@ -85,3 +100,192 @@ def test_get_feats_function_with_empty_spectrogram():
         ),
         equal_nan=True,
     ).all()
+
+
+@pytest.mark.parametrize(
+    "max_power",
+    [
+        30_000,
+        31_000,
+        32_000,
+        33_000,
+        34_000,
+        35_000,
+        36_000,
+        37_000,
+        38_000,
+        39_000,
+        40_000,
+    ],
+)
+def test_compute_max_power_bb(max_power: int):
+    """Test compute_max_power_bb function."""
+    duration = 1
+    samplerate = 256_000
+    min_freq = 0
+    max_freq = 128_000
+
+    start_time = 0.3
+    end_time = 0.6
+    low_freq = 30_000
+    high_freq = 40_000
+
+    audio = np.zeros((int(duration * samplerate),))
+
+    # Add a signal during the time and frequency range of interest
+    audio[
+        int(start_time * samplerate) : int(end_time * samplerate)
+    ] = 0.5 * librosa.tone(
+        max_power, sr=samplerate, duration=end_time - start_time
+    )
+
+    # Add a more powerful signal outside frequency range of interest
+    audio[
+        int(start_time * samplerate) : int(end_time * samplerate)
+    ] += 2 * librosa.tone(
+        80_000, sr=samplerate, duration=end_time - start_time
+    )
+
+    params = api.get_config(
+        min_freq=min_freq,
+        max_freq=max_freq,
+        target_samp_rate=samplerate,
+    )
+
+    spec, _ = au.generate_spectrogram(
+        audio,
+        samplerate,
+        params,
+    )
+
+    x_start = int(
+        au.time_to_x_coords(
+            start_time,
+            samplerate,
+            params["fft_win_length"],
+            params["fft_overlap"],
+        )
+    )
+
+    x_end = int(
+        au.time_to_x_coords(
+            end_time,
+            samplerate,
+            params["fft_win_length"],
+            params["fft_overlap"],
+        )
+    )
+
+    num_freq_bins = spec.shape[0]
+    y_low = num_freq_bins - int(num_freq_bins * low_freq / max_freq)
+    y_high = num_freq_bins - int(num_freq_bins * high_freq / max_freq)
+
+    prediction: types.Prediction = {
+        "det_prob": 1,
+        "class_prob": np.ones((1,)),
+        "x_pos": x_start,
+        "y_pos": int(y_low),
+        "bb_width": int(x_end - x_start),
+        "bb_height": int(y_low - y_high),
+        "start_time": start_time,
+        "end_time": end_time,
+        "low_freq": low_freq,
+        "high_freq": high_freq,
+    }
+
+    print(prediction)
+
+    max_power_bb = feats.compute_max_power_bb(
+        prediction,
+        spec,
+        min_freq=min_freq,
+        max_freq=max_freq,
+    )
+
+    assert abs(max_power_bb - max_power) <= 500
+
+
+def test_compute_max_power():
+    """Test compute_max_power_bb function."""
+    duration = 3
+    samplerate = 16_000
+    min_freq = 0
+    max_freq = 8_000
+
+    start_time = 1
+    end_time = 2
+    low_freq = 3_000
+    high_freq = 4_000
+    max_power = 5_000
+
+    audio = np.zeros((int(duration * samplerate),))
+
+    # Add a signal during the time and frequency range of interest
+    audio[
+        int(start_time * samplerate) : int(end_time * samplerate)
+    ] = 0.5 * librosa.tone(
+        3_500, sr=samplerate, duration=end_time - start_time
+    )
+
+    # Add a more powerful signal outside frequency range of interest
+    audio[
+        int(start_time * samplerate) : int(end_time * samplerate)
+    ] += 2 * librosa.tone(
+        max_power, sr=samplerate, duration=end_time - start_time
+    )
+
+    params = api.get_config(
+        min_freq=min_freq,
+        max_freq=max_freq,
+        target_samp_rate=samplerate,
+    )
+
+    spec, _ = au.generate_spectrogram(
+        audio,
+        samplerate,
+        params,
+    )
+
+    x_start = int(
+        au.time_to_x_coords(
+            start_time,
+            samplerate,
+            params["fft_win_length"],
+            params["fft_overlap"],
+        )
+    )
+
+    x_end = int(
+        au.time_to_x_coords(
+            end_time,
+            samplerate,
+            params["fft_win_length"],
+            params["fft_overlap"],
+        )
+    )
+
+    num_freq_bins = spec.shape[0]
+    y_low = int(num_freq_bins * low_freq / max_freq)
+    y_high = int(num_freq_bins * high_freq / max_freq)
+
+    prediction: types.Prediction = {
+        "det_prob": 1,
+        "class_prob": np.ones((1,)),
+        "x_pos": x_start,
+        "y_pos": int(y_high),
+        "bb_width": int(x_end - x_start),
+        "bb_height": int(y_high - y_low),
+        "start_time": start_time,
+        "end_time": end_time,
+        "low_freq": low_freq,
+        "high_freq": high_freq,
+    }
+
+    computed_max_power = feats.compute_max_power(
+        prediction,
+        spec,
+        min_freq=min_freq,
+        max_freq=max_freq,
+    )
+
+    assert abs(computed_max_power - max_power) < 100