Ensure train inputs are almost equal

batdetect2/compat/params.py

@@ -0,0 +1,148 @@
+from batdetect2.preprocess import (
+    AudioConfig,
+    FFTConfig,
+    FrequencyConfig,
+    PcenConfig,
+    PreprocessingConfig,
+    ResampleConfig,
+    SpecSizeConfig,
+    SpectrogramConfig,
+)
+from batdetect2.preprocess.spectrogram import get_spectrogram_resolution
+from batdetect2.terms import TagInfo
+from batdetect2.train.preprocess import (
+    HeatmapsConfig,
+    TargetConfig,
+    TrainPreprocessingConfig,
+)
+
+
+def get_spectrogram_scale(scale: str):
+    if scale == "pcen":
+        return PcenConfig()
+    if scale == "log":
+        return "log"
+    return None
+
+
+def get_preprocessing_config(params: dict) -> PreprocessingConfig:
+    return PreprocessingConfig(
+        audio=AudioConfig(
+            resample=ResampleConfig(
+                samplerate=params["target_samp_rate"],
+                mode="poly",
+            ),
+            scale=params["scale_raw_audio"],
+            center=params["scale_raw_audio"],
+            duration=None,
+        ),
+        spectrogram=SpectrogramConfig(
+            fft=FFTConfig(
+                window_duration=params["fft_win_length"],
+                window_overlap=params["fft_overlap"],
+                window_fn="hann",
+            ),
+            frequencies=FrequencyConfig(
+                min_freq=params["min_freq"],
+                max_freq=params["max_freq"],
+            ),
+            scale=get_spectrogram_scale(params["spec_scale"]),
+            denoise=params["denoise_spec_avg"],
+            size=SpecSizeConfig(
+                height=params["spec_height"],
+                resize_factor=params["resize_factor"],
+            ),
+            max_scale=params["max_scale_spec"],
+        ),
+    )
+
+
+def get_training_preprocessing_config(
+    params: dict,
+) -> TrainPreprocessingConfig:
+    generic = params["generic_class"][0]
+    preprocessing = get_preprocessing_config(params)
+
+    freq_bin_width, time_bin_width = get_spectrogram_resolution(
+        preprocessing.spectrogram
+    )
+
+    return TrainPreprocessingConfig(
+        preprocessing=preprocessing,
+        target=TargetConfig(
+            classes=[
+                TagInfo(key="class", value=class_name, label=class_name)
+                for class_name in params["class_names"]
+            ],
+            generic_class=TagInfo(
+                key="class",
+                value=generic,
+                label=generic,
+            ),
+            include=[
+                TagInfo(key="event", value=event)
+                for event in params["events_of_interest"]
+            ],
+            exclude=[
+                TagInfo(key="class", value=value)
+                for value in params["classes_to_ignore"]
+            ],
+        ),
+        heatmaps=HeatmapsConfig(
+            position="bottom-left",
+            time_scale=1 / time_bin_width,
+            frequency_scale=1 / freq_bin_width,
+            sigma=params["target_sigma"],
+        ),
+    )
+
+
+#  'standardize_classs_names_ip',
+#  'convert_to_genus',
+#  'genus_mapping',
+#  'standardize_classs_names',
+#  'genus_names',
+
+# ['data_dir',
+#  'ann_dir',
+#  'train_split',
+#  'model_name',
+#  'num_filters',
+#  'experiment',
+#  'model_file_name',
+#  'op_im_dir',
+#  'op_im_dir_test',
+#  'notes',
+#  'spec_divide_factor',
+#  'detection_overlap',
+#  'ignore_start_end',
+#  'detection_threshold',
+#  'nms_kernel_size',
+#  'nms_top_k_per_sec',
+#  'aug_prob',
+#  'augment_at_train',
+#  'augment_at_train_combine',
+#  'echo_max_delay',
+#  'stretch_squeeze_delta',
+#  'mask_max_time_perc',
+#  'mask_max_freq_perc',
+#  'spec_amp_scaling',
+#  'aug_sampling_rates',
+#  'train_loss',
+#  'det_loss_weight',
+#  'size_loss_weight',
+#  'class_loss_weight',
+#  'individual_loss_weight',
+#  'emb_dim',
+#  'lr',
+#  'batch_size',
+#  'num_workers',
+#  'num_epochs',
+#  'num_eval_epochs',
+#  'device',
+#  'save_test_image_during_train',
+#  'save_test_image_after_train',
+#  'train_sets',
+#  'test_sets',
+#  'class_inv_freq',
+#  'ip_height']

batdetect2/preprocess/audio.py

@@ -27,6 +27,28 @@ class AudioConfig(BaseConfig):
     duration: Optional[float] = DEFAULT_DURATION
 
 
+def load_file_audio(
+    path: data.PathLike,
+    config: Optional[AudioConfig] = None,
+    dtype: DTypeLike = np.float32,
+) -> xr.DataArray:
+    recording = data.Recording.from_file(path)
+    return load_recording_audio(recording, config=config, dtype=dtype)
+
+
+def load_recording_audio(
+    recording: data.Recording,
+    config: Optional[AudioConfig] = None,
+    dtype: DTypeLike = np.float32,
+) -> xr.DataArray:
+    clip = data.Clip(
+        recording=recording,
+        start_time=0,
+        end_time=recording.duration,
+    )
+    return load_clip_audio(clip, config=config, dtype=dtype)
+
+
 def load_clip_audio(
     clip: data.Clip,
     config: Optional[AudioConfig] = None,

batdetect2/preprocess/spectrogram.py

@@ -10,29 +10,17 @@ from soundevent import arrays, audio
 from soundevent.arrays import operations as ops
 
 from batdetect2.configs import BaseConfig
-from batdetect2.preprocess.audio import DEFAULT_DURATION
-
-FFT_WIN_LENGTH_S = 512 / 256000.0
-FFT_OVERLAP = 0.75
-MAX_FREQ_HZ = 120000
-MIN_FREQ_HZ = 10000
-SPEC_HEIGHT = 128
-SPEC_WIDTH = 256
-SPEC_SCALE = "pcen"
-SPEC_TIME_PERIOD = DEFAULT_DURATION / SPEC_WIDTH
-DENOISE_SPEC_AVG = True
-MAX_SCALE_SPEC = False
 
 
 class FFTConfig(BaseConfig):
-    window_duration: float = Field(default=FFT_WIN_LENGTH_S, gt=0)
+    window_duration: float = Field(default=0.002, gt=0)
-    window_overlap: float = Field(default=FFT_OVERLAP, ge=0, lt=1)
+    window_overlap: float = Field(default=0.75, ge=0, lt=1)
     window_fn: str = "hann"
 
 
 class FrequencyConfig(BaseConfig):
-    max_freq: int = Field(default=MAX_FREQ_HZ, gt=0)
+    max_freq: int = Field(default=120_000, gt=0)
-    min_freq: int = Field(default=MIN_FREQ_HZ, gt=0)
+    min_freq: int = Field(default=10_000, gt=0)
 
 
 class PcenConfig(BaseConfig):
@@ -44,17 +32,20 @@ class PcenConfig(BaseConfig):
 
 
 class SpecSizeConfig(BaseConfig):
-    height: int = SPEC_HEIGHT
+    height: int = 256
-    time_period: float = SPEC_TIME_PERIOD
+    resize_factor: Optional[float] = 0.5
+    divide_factor: Optional[int] = 32
 
 
 class SpectrogramConfig(BaseConfig):
     fft: FFTConfig = Field(default_factory=FFTConfig)
     frequencies: FrequencyConfig = Field(default_factory=FrequencyConfig)
-    scale: Union[Literal["log"], None, PcenConfig] = "log"
+    scale: Union[Literal["log"], None, PcenConfig] = Field(
+        default_factory=PcenConfig
+    )
+    size: Optional[SpecSizeConfig] = Field(default_factory=SpecSizeConfig)
     denoise: bool = True
-    resize: Optional[SpecSizeConfig] = Field(default_factory=SpecSizeConfig)
+    max_scale: bool = False
-    max_scale: bool = MAX_SCALE_SPEC
 
 
 def compute_spectrogram(
@@ -64,6 +55,16 @@ def compute_spectrogram(
 ) -> xr.DataArray:
     config = config or SpectrogramConfig()
 
+    if config.size and config.size.divide_factor:
+        # Need to pad the audio to make sure the spectrogram has a
+        # width compatible with the divide factor
+        wav = pad_audio(
+            wav,
+            window_duration=config.fft.window_duration,
+            window_overlap=config.fft.window_overlap,
+            divide_factor=config.size.divide_factor,
+        )
+
     spec = stft(
         wav,
         window_duration=config.fft.window_duration,
@@ -83,8 +84,12 @@ def compute_spectrogram(
     if config.denoise:
         spec = denoise_spectrogram(spec)
 
-    if config.resize:
+    if config.size:
-        spec = resize_spectrogram(spec, config=config.resize)
+        spec = resize_spectrogram(
+            spec,
+            height=config.size.height,
+            resize_factor=config.size.resize_factor,
+        )
 
     if config.max_scale:
         spec = ops.scale(spec, 1 / (10e-6 + np.max(spec)))
@@ -94,8 +99,8 @@ def compute_spectrogram(
 
 def crop_spectrogram_frequencies(
     spec: xr.DataArray,
-    min_freq: int = MIN_FREQ_HZ,
+    min_freq: int = 10_000,
-    max_freq: int = MAX_FREQ_HZ,
+    max_freq: int = 120_000,
 ) -> xr.DataArray:
     return arrays.crop_dim(
         spec,
@@ -116,9 +121,10 @@ def stft(
     step = arrays.get_dim_step(wave, dim="time")
     sampling_rate = 1 / step
 
-    hop_len = window_duration * (1 - window_overlap)
     nfft = int(window_duration * sampling_rate)
     noverlap = int(window_overlap * nfft)
+    hop_len = nfft - noverlap
+    hop_duration = hop_len / sampling_rate
 
     spec, _ = librosa.core.spectrum._spectrogram(
         y=wave.data.astype(dtype),
@@ -146,12 +152,12 @@ def stft(
             "time": arrays.create_time_dim_from_array(
                 np.linspace(
                     start_time,
-                    end_time - (window_duration - hop_len),
+                    end_time - (window_duration - hop_duration),
                     spec.shape[1],
                     endpoint=False,
                     dtype=dtype,
                 ),
-                step=hop_len,
+                step=hop_duration,
             ),
         },
         attrs={
@@ -202,7 +208,6 @@ def scale_pcen(
     power: float = 0.5,
 ) -> xr.DataArray:
     samplerate = spec.attrs["original_samplerate"]
-    # NOTE: Not sure why the 10 is there
     t_frames = time_constant * samplerate / (float(hop_length) * 10)
     smoothing_constant = (np.sqrt(1 + 4 * t_frames**2) - 1) / (2 * t_frames**2)
     return audio.pcen(
@@ -231,12 +236,114 @@ def scale_log(
 
 def resize_spectrogram(
     spec: xr.DataArray,
-    config: SpecSizeConfig,
+    height: int = 128,
+    resize_factor: Optional[float] = 0.5,
 ) -> xr.DataArray:
-    duration = arrays.get_dim_width(spec, dim="time")
+    resize_factor = resize_factor or 1
+    current_width = spec.sizes["time"]
     return ops.resize(
         spec,
-        time=int(np.ceil(duration / config.time_period)),
+        time=int(resize_factor * current_width),
-        frequency=config.height,
+        frequency=int(resize_factor * height),
         dtype=np.float32,
     )
+
+
+def adjust_spectrogram_width(
+    spec: xr.DataArray,
+    divide_factor: int = 32,
+    time_period: float = 0.001,
+) -> xr.DataArray:
+    time_width = spec.sizes["time"]
+
+    if time_width % divide_factor == 0:
+        return spec
+
+    target_size = int(
+        np.ceil(spec.sizes["time"] / divide_factor) * divide_factor
+    )
+    extra_duration = (target_size - time_width) * time_period
+    _, stop = arrays.get_dim_range(spec, dim="time")
+    resized = ops.extend_dim(
+        spec,
+        dim="time",
+        stop=stop + extra_duration,
+    )
+    return resized
+
+
+def pad_audio(
+    wave: xr.DataArray,
+    window_duration: float,
+    window_overlap: float,
+    divide_factor: int = 32,
+) -> xr.DataArray:
+    current_duration = arrays.get_dim_width(wave, dim="time")
+    step = arrays.get_dim_step(wave, dim="time")
+    samplerate = int(1 / step)
+
+    estimated_spec_width = duration_to_spec_width(
+        current_duration,
+        samplerate=samplerate,
+        window_duration=window_duration,
+        window_overlap=window_overlap,
+    )
+
+    if estimated_spec_width % divide_factor == 0:
+        return wave
+
+    target_spec_width = int(
+        np.ceil(estimated_spec_width / divide_factor) * divide_factor
+    )
+    target_samples = spec_width_to_samples(
+        target_spec_width,
+        samplerate=samplerate,
+        window_duration=window_duration,
+        window_overlap=window_overlap,
+    )
+    return ops.adjust_dim_width(
+        wave,
+        dim="time",
+        width=target_samples,
+        position="start",
+    )
+
+
+def duration_to_spec_width(
+    duration: float,
+    samplerate: int,
+    window_duration: float,
+    window_overlap: float,
+) -> int:
+    samples = int(duration * samplerate)
+    fft_len = int(window_duration * samplerate)
+    fft_overlap = int(window_overlap * fft_len)
+    hop_len = fft_len - fft_overlap
+    width = (samples - fft_len + hop_len) / hop_len
+    return int(np.floor(width))
+
+
+def spec_width_to_samples(
+    width: int,
+    samplerate: int,
+    window_duration: float,
+    window_overlap: float,
+) -> int:
+    fft_len = int(window_duration * samplerate)
+    fft_overlap = int(window_overlap * fft_len)
+    hop_len = fft_len - fft_overlap
+    return width * hop_len + fft_len - hop_len
+
+
+def get_spectrogram_resolution(
+    config: SpectrogramConfig,
+) -> tuple[float, float]:
+    max_freq = config.frequencies.max_freq
+    min_freq = config.frequencies.min_freq
+    assert config.size is not None
+
+    spec_height = config.size.height
+    resize_factor = config.size.resize_factor or 1
+    freq_bin_width = (max_freq - min_freq) / (spec_height * resize_factor)
+    hop_duration = config.fft.window_duration * (1 - config.fft.window_overlap)
+    return freq_bin_width, hop_duration / resize_factor

batdetect2/terms.py

@@ -22,9 +22,9 @@ class TermInfo(BaseModel):
 
 class TagInfo(BaseModel):
     value: str
-    label: Optional[str] = None
     term: Optional[TermInfo] = None
     key: Optional[str] = None
+    label: Optional[str] = None
 
 
 call_type = data.Term(

batdetect2/train/labels.py

@@ -7,23 +7,29 @@ from soundevent import arrays, data, geometry
 from soundevent.geometry.operations import Positions
 from soundevent.types import ClassMapper
 
+from batdetect2.configs import BaseConfig
+
 __all__ = [
     "ClassMapper",
     "generate_heatmaps",
 ]
 
 
-TARGET_SIGMA = 3.0
+class HeatmapsConfig(BaseConfig):
+    position: Positions = "bottom-left"
+    sigma: float = 3.0
+    time_scale: float = 1000.0
+    frequency_scale: float = 1 / 859.375
 
 
 def generate_heatmaps(
     sound_events: Sequence[data.SoundEventAnnotation],
     spec: xr.DataArray,
     class_mapper: ClassMapper,
-    target_sigma: float = TARGET_SIGMA,
+    target_sigma: float = 3.0,
     position: Positions = "bottom-left",
-    time_scale: float = 1.0,
+    time_scale: float = 1000.0,
-    frequency_scale: float = 1.0,
+    frequency_scale: float = 1 / 859.375,
     dtype=np.float32,
 ) -> Tuple[xr.DataArray, xr.DataArray, xr.DataArray]:
     shape = dict(zip(spec.dims, spec.shape))
@@ -39,7 +45,7 @@ def generate_heatmaps(
         data=np.zeros((class_mapper.num_classes, *spec.shape), dtype=dtype),
         dims=["category", *spec.dims],
         coords={
-            "category": class_mapper.class_labels,
+            "category": [*class_mapper.class_labels],
             **spec.coords,
         },
     )

batdetect2/train/preprocess.py

@@ -14,12 +14,10 @@ from tqdm.auto import tqdm
 from batdetect2.configs import BaseConfig
 from batdetect2.preprocess import (
     PreprocessingConfig,
-    preprocess_audio_clip,
+    compute_spectrogram,
-)
+    load_clip_audio,
-from batdetect2.train.labels import (
-    TARGET_SIGMA,
-    generate_heatmaps,
 )
+from batdetect2.train.labels import HeatmapsConfig, generate_heatmaps
 from batdetect2.train.targets import (
     TargetConfig,
     build_class_mapper,
@@ -34,16 +32,12 @@ __all__ = [
 ]
 
 
-class MasksConfig(BaseConfig):
-    sigma: float = TARGET_SIGMA
-
-
 class TrainPreprocessingConfig(BaseConfig):
     preprocessing: PreprocessingConfig = Field(
         default_factory=PreprocessingConfig
     )
     target: TargetConfig = Field(default_factory=TargetConfig)
-    masks: MasksConfig = Field(default_factory=MasksConfig)
+    heatmaps: HeatmapsConfig = Field(default_factory=HeatmapsConfig)
 
 
 def generate_train_example(
@@ -53,9 +47,14 @@ def generate_train_example(
     """Generate a training example."""
     config = config or TrainPreprocessingConfig()
 
-    spectrogram = preprocess_audio_clip(
+    wave = load_clip_audio(
         clip_annotation.clip,
-        config=config.preprocessing,
+        config=config.preprocessing.audio,
+    )
+
+    spectrogram = compute_spectrogram(
+        wave,
+        config=config.preprocessing.spectrogram,
     )
 
     filter_fn = build_sound_event_filter(
@@ -65,17 +64,24 @@ def generate_train_example(
     selected_events = [
         event for event in clip_annotation.sound_events if filter_fn(event)
     ]
-
     class_mapper = build_class_mapper(config.target.classes)
     detection_heatmap, class_heatmap, size_heatmap = generate_heatmaps(
         selected_events,
         spectrogram,
         class_mapper,
-        target_sigma=config.masks.sigma,
+        target_sigma=config.heatmaps.sigma,
+        position=config.heatmaps.position,
+        time_scale=config.heatmaps.time_scale,
+        frequency_scale=config.heatmaps.frequency_scale,
     )
 
     dataset = xr.Dataset(
         {
+            # NOTE: Need to rename the time dimension to avoid conflicts with
+            # the spectrogram time dimension, otherwise xarray will interpolate
+            # the spectrogram and the heatmaps to the same temporal resolution
+            # as the waveform.
+            "audio": wave.rename({"time": "audio_time"}),
             "spectrogram": spectrogram,
             "detection": detection_heatmap,
             "class": class_heatmap,

batdetect2/train/targets.py

@@ -13,9 +13,9 @@ class TargetConfig(BaseConfig):
     """Configuration for target generation."""
 
     classes: List[TagInfo] = Field(default_factory=list)
+    generic_class: Optional[TagInfo] = None
 
     include: Optional[List[TagInfo]] = None
-
     exclude: Optional[List[TagInfo]] = None
 
 
@@ -73,7 +73,7 @@ class GenericMapper(ClassMapper):
             raise ValueError("Number of targets and class labels must match.")
 
         self.targets = set(classes)
-        self.class_labels = labels
+        self.class_labels = list(dict.fromkeys(labels))
 
         self._mapping = {tag: label for tag, label in zip(classes, labels)}
         self._inverse_mapping = {

pyproject.toml

@@ -17,7 +17,7 @@ dependencies = [
   "torch>=1.13.1,<2.5.0",
   "torchaudio>=1.13.1,<2.5.0",
   "torchvision>=0.14.0",
-  "soundevent[audio,geometry,plot]>=2.2",
+  "soundevent[audio,geometry,plot]>=2.3",
   "click>=8.1.7",
   "netcdf4>=1.6.5",
   "tqdm>=4.66.2",

tests/conftest.py

@@ -1,7 +1,11 @@
+import uuid
 from pathlib import Path
-from typing import List
+from typing import Callable, List, Optional
 
+import numpy as np
 import pytest
+import soundfile as sf
+from soundevent import data
 
 
 @pytest.fixture
@@ -19,6 +23,13 @@ def example_audio_dir(example_data_dir: Path) -> Path:
     return example_audio_dir
 
 
+@pytest.fixture
+def example_anns_dir(example_data_dir: Path) -> Path:
+    example_anns_dir = example_data_dir / "anns"
+    assert example_anns_dir.exists()
+    return example_anns_dir
+
+
 @pytest.fixture
 def example_audio_files(example_audio_dir: Path) -> List[Path]:
     audio_files = list(example_audio_dir.glob("*.[wW][aA][vV]"))
@@ -38,3 +49,61 @@ def contrib_dir(data_dir) -> Path:
     dir = data_dir / "contrib"
     assert dir.exists()
     return dir
+
+
+@pytest.fixture
+def wav_factory(tmp_path: Path):
+    def _wav_factory(
+        path: Optional[Path] = None,
+        duration: float = 0.3,
+        channels: int = 1,
+        samplerate: int = 441_000,
+        bit_depth: int = 16,
+    ) -> Path:
+        path = path or tmp_path / f"{uuid.uuid4()}.wav"
+        frames = int(samplerate * duration)
+        shape = (frames, channels)
+        subtype = f"PCM_{bit_depth}"
+
+        if bit_depth == 16:
+            dtype = np.int16
+        elif bit_depth == 32:
+            dtype = np.int32
+        else:
+            raise ValueError(f"Unsupported bit depth: {bit_depth}")
+
+        wav = np.random.uniform(
+            low=np.iinfo(dtype).min,
+            high=np.iinfo(dtype).max,
+            size=shape,
+        ).astype(dtype)
+        sf.write(str(path), wav, samplerate, subtype=subtype)
+        return path
+
+    return _wav_factory
+
+
+@pytest.fixture
+def recording_factory(wav_factory: Callable[..., Path]):
+    def _recording_factory(
+        tags: Optional[list[data.Tag]] = None,
+        path: Optional[Path] = None,
+        recording_id: Optional[uuid.UUID] = None,
+        duration: float = 1,
+        channels: int = 1,
+        samplerate: int = 44100,
+        time_expansion: float = 1,
+    ) -> data.Recording:
+        path = path or wav_factory(
+            duration=duration,
+            channels=channels,
+            samplerate=samplerate,
+        )
+        return data.Recording.from_file(
+            path=path,
+            uuid=recording_id or uuid.uuid4(),
+            time_expansion=time_expansion,
+            tags=tags or [],
+        )
+
+    return _recording_factory

tests/test_migration/test_preprocessing.py

@@ -4,7 +4,7 @@ import numpy as np
 import pytest
 from soundevent import data
 
-from batdetect2.data import preprocessing
+from batdetect2 import preprocess
 from batdetect2.utils import audio_utils
 
 ROOT_DIR = Path(__file__).parent.parent.parent
@@ -44,10 +44,10 @@ def test_audio_loading_hasnt_changed(
         target_samp_rate=target_sampling_rate,
         scale=scale,
     )
-    audio_new = preprocessing.load_clip_audio(
+    audio_new = preprocess.load_clip_audio(
         clip,
-        config=preprocessing.AudioConfig(
+        config=preprocess.AudioConfig(
-            resample=preprocessing.ResampleConfig(
+            resample=preprocess.ResampleConfig(
                 samplerate=target_sampling_rate,
             ),
             center=scale,
@@ -84,20 +84,20 @@ def test_spectrogram_generation_hasnt_changed(
     if spec_scale == "log":
         scale = "log"
     elif spec_scale == "pcen":
-        scale = preprocessing.PcenConfig()
+        scale = preprocess.PcenConfig()
 
-    config = preprocessing.SpectrogramConfig(
+    config = preprocess.SpectrogramConfig(
-        fft=preprocessing.FFTConfig(
+        fft=preprocess.FFTConfig(
             window_overlap=fft_overlap,
             window_duration=fft_win_length,
         ),
-        frequencies=preprocessing.FrequencyConfig(
+        frequencies=preprocess.FrequencyConfig(
             min_freq=min_freq,
             max_freq=max_freq,
         ),
         scale=scale,
         denoise=denoise_spec_avg,
-        resize=None,
+        size=None,
         max_scale=max_scale_spec,
     )
 
@@ -112,10 +112,10 @@ def test_spectrogram_generation_hasnt_changed(
         end_time=recording.duration,
     )
 
-    audio = preprocessing.load_clip_audio(
+    audio = preprocess.load_clip_audio(
         clip,
-        config=preprocessing.AudioConfig(
+        config=preprocess.AudioConfig(
-            resample=preprocessing.ResampleConfig(
+            resample=preprocess.ResampleConfig(
                 samplerate=target_sampling_rate,
             )
         ),
@@ -135,7 +135,7 @@ def test_spectrogram_generation_hasnt_changed(
         ),
     )
 
-    new_spec = preprocessing.compute_spectrogram(
+    new_spec = preprocess.compute_spectrogram(
         audio,
         config=config,
         dtype=np.float32,

tests/test_migration/test_training.py

@@ -0,0 +1,75 @@
+import json
+from pathlib import Path
+from typing import List
+
+import numpy as np
+import pytest
+
+from batdetect2.compat.data import load_annotation_project
+from batdetect2.compat.params import get_training_preprocessing_config
+from batdetect2.train.preprocess import generate_train_example
+
+
+@pytest.fixture
+def regression_dir(data_dir: Path) -> Path:
+    dir = data_dir / "regression"
+    assert dir.exists()
+    return dir
+
+
+def test_can_generate_similar_training_inputs(
+    example_audio_dir: Path,
+    example_audio_files: List[Path],
+    example_anns_dir: Path,
+    regression_dir: Path,
+):
+    old_parameters = json.loads((regression_dir / "params.json").read_text())
+    config = get_training_preprocessing_config(old_parameters)
+
+    for audio_file in example_audio_files:
+        example_file = regression_dir / f"{audio_file.name}.npz"
+
+        dataset = np.load(example_file)
+
+        spec = dataset["spec"][0]
+        detection_mask = dataset["detection_mask"][0]
+        size_mask = dataset["size_mask"]
+        class_mask = dataset["class_mask"]
+
+        project = load_annotation_project(
+            example_anns_dir,
+            audio_dir=example_audio_dir,
+        )
+
+        clip_annotation = next(
+            ann
+            for ann in project.clip_annotations
+            if ann.clip.recording.path == audio_file
+        )
+
+        new_dataset = generate_train_example(clip_annotation, config)
+        new_spec = new_dataset["spectrogram"].values
+        new_detection_mask = new_dataset["detection"].values
+        new_size_mask = new_dataset["size"].values
+        new_class_mask = new_dataset["class"].values
+
+        assert spec.shape == new_spec.shape
+        assert detection_mask.shape == new_detection_mask.shape
+        assert size_mask.shape == new_size_mask.shape
+        assert class_mask.shape[1:] == new_class_mask.shape[1:]
+        assert class_mask.shape[0] == new_class_mask.shape[0] + 1
+
+        x_new, y_new = np.nonzero(new_size_mask.max(axis=0))
+        x_orig, y_orig = np.nonzero(np.flipud(size_mask.max(axis=0)))
+
+        assert (x_new == x_orig).all()
+
+        # NOTE: a difference of 1 pixel is due to discrepancies on how
+        # frequency bins are interpreted. Shouldn't be an issue
+        assert (y_new == y_orig + 1).all()
+
+        width_new, height_new = new_size_mask[:, x_new, y_new]
+        width_orig, height_orig = np.flip(size_mask, axis=1)[:, x_orig, y_orig]
+
+        assert (np.floor(width_new) == width_orig).all()
+        assert (np.ceil(height_new) == height_orig).all()

tests/test_preprocessing/test_spectrogram.py

@@ -0,0 +1,141 @@
+import math
+from pathlib import Path
+from typing import Callable
+
+from hypothesis import HealthCheck, given, settings
+from hypothesis import strategies as st
+from soundevent import arrays
+
+from batdetect2.preprocess.audio import AudioConfig, load_file_audio
+from batdetect2.preprocess.spectrogram import (
+    FFTConfig,
+    FrequencyConfig,
+    SpecSizeConfig,
+    SpectrogramConfig,
+    compute_spectrogram,
+    duration_to_spec_width,
+    get_spectrogram_resolution,
+    pad_audio,
+    spec_width_to_samples,
+    stft,
+)
+
+
+@settings(suppress_health_check=[HealthCheck.function_scoped_fixture])
+@given(
+    duration=st.floats(min_value=0.1, max_value=1.0),
+    window_duration=st.floats(min_value=0.001, max_value=0.01),
+    window_overlap=st.floats(min_value=0.2, max_value=0.9),
+    samplerate=st.integers(min_value=256_000, max_value=512_000),
+)
+def test_can_estimate_correctly_spectrogram_width_from_duration(
+    duration: float,
+    window_duration: float,
+    window_overlap: float,
+    samplerate: int,
+    wav_factory: Callable[..., Path],
+):
+    path = wav_factory(duration=duration, samplerate=samplerate)
+    audio = load_file_audio(
+        path,
+        # NOTE: Dont resample nor adjust duration to test if the width
+        # estimation works on all scenarios
+        config=AudioConfig(resample=None, duration=None),
+    )
+    spectrogram = stft(audio, window_duration, window_overlap)
+
+    spec_width = duration_to_spec_width(
+        duration,
+        samplerate=samplerate,
+        window_duration=window_duration,
+        window_overlap=window_overlap,
+    )
+    assert spectrogram.sizes["time"] == spec_width
+
+    rebuilt_duration = (
+        spec_width_to_samples(
+            spec_width,
+            samplerate=samplerate,
+            window_duration=window_duration,
+            window_overlap=window_overlap,
+        )
+        / samplerate
+    )
+
+    assert (
+        abs(duration - rebuilt_duration)
+        < (1 - window_overlap) * window_duration
+    )
+
+
+@settings(
+    suppress_health_check=[HealthCheck.function_scoped_fixture],
+    deadline=400,
+)
+@given(
+    duration=st.floats(min_value=0.1, max_value=1.0),
+    window_duration=st.floats(min_value=0.001, max_value=0.01),
+    window_overlap=st.floats(min_value=0.2, max_value=0.9),
+    samplerate=st.integers(min_value=256_000, max_value=512_000),
+    divide_factor=st.integers(min_value=16, max_value=64),
+)
+def test_can_pad_audio_to_adjust_spectrogram_width(
+    duration: float,
+    window_duration: float,
+    window_overlap: float,
+    samplerate: int,
+    divide_factor: int,
+    wav_factory: Callable[..., Path],
+):
+    path = wav_factory(duration=duration, samplerate=samplerate)
+
+    audio = load_file_audio(
+        path,
+        # NOTE: Dont resample nor adjust duration to test if the width
+        # estimation works on all scenarios
+        config=AudioConfig(resample=None, duration=None),
+    )
+
+    audio = pad_audio(
+        audio,
+        window_duration=window_duration,
+        window_overlap=window_overlap,
+        divide_factor=divide_factor,
+    )
+
+    spectrogram = stft(audio, window_duration, window_overlap)
+    assert spectrogram.sizes["time"] % divide_factor == 0
+
+
+def test_can_estimate_spectrogram_resolution(
+    wav_factory: Callable[..., Path],
+):
+    path = wav_factory(duration=0.2, samplerate=256_000)
+
+    audio = load_file_audio(
+        path,
+        # NOTE: Dont resample nor adjust duration to test if the width
+        # estimation works on all scenarios
+        config=AudioConfig(resample=None, duration=None),
+    )
+
+    config = SpectrogramConfig(
+        fft=FFTConfig(),
+        size=SpecSizeConfig(height=256, resize_factor=0.5),
+        frequencies=FrequencyConfig(min_freq=10_000, max_freq=120_000),
+    )
+
+    spec = compute_spectrogram(audio, config=config)
+
+    freq_res, time_res = get_spectrogram_resolution(config)
+
+    assert math.isclose(
+        arrays.get_dim_step(spec, dim="frequency"),
+        freq_res,
+        rel_tol=0.1,
+    )
+    assert math.isclose(
+        arrays.get_dim_step(spec, dim="time"),
+        time_res,
+        rel_tol=0.1,
+    )

uv.lock

@@ -236,7 +236,7 @@ requires-dist = [
     { name = "pytorch-lightning", specifier = ">=2.2.2" },
     { name = "scikit-learn", specifier = ">=1.2.2" },
     { name = "scipy", specifier = ">=1.10.1" },
-    { name = "soundevent", extras = ["audio", "geometry", "plot"], specifier = ">=2.2" },
+    { name = "soundevent", extras = ["audio", "geometry", "plot"], specifier = ">=2.3" },
     { name = "tensorboard", specifier = ">=2.16.2" },
     { name = "torch", specifier = ">=1.13.1,<2.5.0" },
     { name = "torchaudio", specifier = ">=1.13.1,<2.5.0" },
@@ -2679,15 +2679,15 @@ wheels = [
 
 [[package]]
 name = "soundevent"
-version = "2.2.0"
+version = "2.3.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "email-validator" },
     { name = "pydantic" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/5a/f9/77d723df4d8d3a390d32c07325a08bfc669d5fb55e88b98181b5793e7333/soundevent-2.2.0.tar.gz", hash = "sha256:a87a97c8e4bfdadec4b6edc128470919ef9240a344cf924d2ac21f8c6b50acf1", size = 8715229 }
+sdist = { url = "https://files.pythonhosted.org/packages/ff/51/83093cabe9ada781a0f7a78f82cc04162d005755b2f0ca3fdcb4ecd47a01/soundevent-2.3.0.tar.gz", hash = "sha256:b75d7674578a52bf196619f8b4b3d9170f2ca321d165ceb45916579a549c3e76", size = 8716539 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/09/d8/ce6e2830d47fc3d24db264b94384fa7cdcb8069fd7547d55b7a83857e730/soundevent-2.2.0-py3-none-any.whl", hash = "sha256:c40913c15fc697a82a02df5f62d18ad3b77bfae80a9a5d54c47bc1377d3b4d7c", size = 144188 },
+    { url = "https://files.pythonhosted.org/packages/ee/67/4c2d881f9b4a0b453dbee91e119e1e48df0fc92de2cc3062fcd8ad0a7e6b/soundevent-2.3.0-py3-none-any.whl", hash = "sha256:f7c74b1d73a347ebe843187c93130dc8af3214add95e6bc485f64944bea0d690", size = 145513 },
 ]
 
 [package.optional-dependencies]