birdnet-analyzer 2.0.1__py3-none-any.whl → 2.1.1__py3-none-any.whl

birdnet_analyzer/segments/utils.py

@@ -1,383 +1,383 @@
-"""Extract segments from audio files based on BirdNET detections.
-
-Can be used to save the segments of the audio files for each detection.
-"""
-
-import os
-
-import numpy as np
-
-import birdnet_analyzer.config as cfg
-from birdnet_analyzer import audio, utils
-
-# Set numpy random seed
-RNG = np.random.default_rng(cfg.RANDOM_SEED)
-SCRIPT_DIR = os.path.abspath(os.path.dirname(__file__))
-
-
-def detect_rtype(line: str):
-    """Detects the type of result file.
-
-    Args:
-        line: First line of text.
-
-    Returns:
-        Either "table", "kaleidoscope", "csv" or "audacity".
-    """
-    if line.lower().startswith("selection"):
-        return "table"
-
-    if line.lower().startswith("indir"):
-        return "kaleidoscope"
-
-    if line.lower().startswith("start (s)"):
-        return "csv"
-
-    return "audacity"
-
-
-def get_header_mapping(line: str) -> dict:
-    """
-    Parses a header line and returns a mapping of column names to their indices.
-
-    Args:
-        line (str): A string representing the header line of a file.
-
-    Returns:
-        dict: A dictionary where the keys are column names and the values are their respective indices.
-    """
-    rtype = detect_rtype(line)
-
-    sep = "\t" if rtype in ("table", "audacity") else ","
-
-    cols = line.split(sep)
-
-    return {col: i for i, col in enumerate(cols)}
-
-
-def parse_folders(apath: str, rpath: str, allowed_result_filetypes: tuple[str] = ("txt", "csv")) -> list[dict]:
-    """Read audio and result files.
-
-    Reads all audio files and BirdNET output inside directory recursively.
-
-    Args:
-        apath (str): Path to search for audio files.
-        rpath (str): Path to search for result files.
-        allowed_result_filetypes (tuple[str]): List of extensions for the result files.
-
-    Returns:
-        list[dict]: A list of {"audio": path_to_audio, "result": path_to_result }.
-    """
-    data = {}
-    apath = apath.replace("/", os.sep).replace("\\", os.sep)
-    rpath = rpath.replace("/", os.sep).replace("\\", os.sep)
-
-    # Check if combined selection table is present and read that.
-    if os.path.exists(os.path.join(rpath, cfg.OUTPUT_RAVEN_FILENAME)):
-        # Read combined Raven selection table
-        rfile = os.path.join(rpath, cfg.OUTPUT_RAVEN_FILENAME)
-        data["combined"] = {"isCombinedFile": True, "result": rfile}
-    elif os.path.exists(os.path.join(rpath, cfg.OUTPUT_CSV_FILENAME)):
-        rfile = os.path.join(rpath, cfg.OUTPUT_CSV_FILENAME)
-        data["combined"] = {"isCombinedFile": True, "result": rfile}
-    elif os.path.exists(os.path.join(rpath, cfg.OUTPUT_KALEIDOSCOPE_FILENAME)):
-        rfile = os.path.join(rpath, cfg.OUTPUT_KALEIDOSCOPE_FILENAME)
-        data["combined"] = {"isCombinedFile": True, "result": rfile}
-    else:
-        # Get all audio files
-        for root, _, files in os.walk(apath):
-            for f in files:
-                if f.rsplit(".", 1)[-1].lower() in cfg.ALLOWED_FILETYPES and not f.startswith("."):
-                    table_key = os.path.join(root.strip(apath), f.rsplit(".", 1)[0])
-                    data[table_key] = {"audio": os.path.join(root, f), "result": ""}
-
-        # Get all result files
-        for root, _, files in os.walk(rpath):
-            for f in files:
-                if f.rsplit(".", 1)[-1] in allowed_result_filetypes and ".BirdNET." in f:
-                    table_key = os.path.join(root.strip(rpath), f.split(".BirdNET.", 1)[0])
-                    if table_key in data:
-                        data[table_key]["result"] = os.path.join(root, f)
-
-    # Convert to list
-    flist = [f for f in data.values() if f["result"]]
-
-    print(f"Found {len(flist)} audio files with valid result file.")
-
-    return flist
-
-
-def parse_files(flist: list[dict], max_segments=100):
-    """
-    Parses a list of files to extract and organize bird call segments by species.
-
-    Args:
-        flist (list[dict]): A list of dictionaries, each containing 'audio' and 'result' file paths.
-                            Optionally, a dictionary can have 'isCombinedFile' set to True to indicate
-                            that it is a combined result file.
-        max_segments (int, optional): The maximum number of segments to retain per species. Defaults to 100.
-    Returns:
-        list[tuple]: A list of tuples where each tuple contains an audio file path and a list of segments
-                     associated with that audio file.
-    Raises:
-        KeyError: If the dictionaries in flist do not contain the required keys ('audio' and 'result').
-    Example:
-        flist = [
-            {"audio": "path/to/audio1.wav", "result": "path/to/result1.csv"},
-            {"audio": "path/to/audio2.wav", "result": "path/to/result2.csv"}
-        ]
-        segments = parseFiles(flist, max_segments=50)
-    """
-    species_segments: dict[str, list] = {}
-
-    is_combined_rfile = len(flist) == 1 and flist[0].get("isCombinedFile", False)
-
-    if is_combined_rfile:
-        rfile = flist[0]["result"]
-        segments = find_segments_from_combined(rfile)
-
-        # Parse segments by species
-        for s in segments:
-            if s["species"] not in species_segments:
-                species_segments[s["species"]] = []
-
-            species_segments[s["species"]].append(s)
-    else:
-        for f in flist:
-            # Paths
-            afile = f["audio"]
-            rfile = f["result"]
-
-            # Get all segments for result file
-            segments = find_segments(afile, rfile)
-
-            # Parse segments by species
-            for s in segments:
-                if s["species"] not in species_segments:
-                    species_segments[s["species"]] = []
-
-                species_segments[s["species"]].append(s)
-
-    # Shuffle segments for each species and limit to max_segments
-    for s in species_segments:
-        RNG.shuffle(species_segments[s])
-        species_segments[s] = species_segments[s][:max_segments]
-
-    # Make dict of segments per audio file
-    segments: dict[str, list] = {}
-    seg_cnt = 0
-
-    for s in species_segments:
-        for seg in species_segments[s]:
-            if seg["audio"] not in segments:
-                segments[seg["audio"]] = []
-
-            segments[seg["audio"]].append(seg)
-            seg_cnt += 1
-
-    print(f"Found {seg_cnt} segments in {len(segments)} audio files.")
-
-    # Convert to list
-    return [tuple(e) for e in segments.items()]
-
-
-def find_segments_from_combined(rfile: str) -> list[dict]:
-    """Extracts the segments from a combined results file
-
-    Args:
-        rfile (str): Path to the result file.
-
-    Returns:
-        list[dict]: A list of dicts in the form of
-        {"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence}
-    """
-    segments: list[dict] = []
-
-    # Open and parse result file
-    lines = utils.read_lines(rfile)
-
-    # Auto-detect result type
-    rtype = detect_rtype(lines[0])
-
-    if rtype == "audacity":
-        raise Exception("Audacity files are not supported for combined results.")
-
-    # Get mapping from the header column
-    header_mapping = get_header_mapping(lines[0])
-
-    # Get start and end times based on rtype
-    confidence = 0
-    start = end = 0.0
-    species = ""
-    afile = ""
-
-    for i, line in enumerate(lines):
-        if rtype == "table" and i > 0:
-            d = line.split("\t")
-            file_offset = float(d[header_mapping["File Offset (s)"]])
-            start = file_offset
-            end = file_offset + (float(d[header_mapping["End Time (s)"]]) - float(d[header_mapping["Begin Time (s)"]]))
-            species = d[header_mapping["Common Name"]]
-            confidence = float(d[header_mapping["Confidence"]])
-            afile = d[header_mapping["Begin Path"]].replace("/", os.sep).replace("\\", os.sep)
-
-        elif rtype == "kaleidoscope" and i > 0:
-            d = line.split(",")
-            start = float(d[header_mapping["OFFSET"]])
-            end = float(d[header_mapping["DURATION"]]) + start
-            species = d[header_mapping["scientific_name"]]
-            confidence = float(d[header_mapping["confidence"]])
-            in_dir = d[header_mapping["INDIR"]]
-            folder = d[header_mapping["FOLDER"]]
-            in_file = d[header_mapping["IN FILE"]]
-            afile = os.path.join(in_dir, folder, in_file).replace("/", os.sep).replace("\\", os.sep)
-
-        elif rtype == "csv" and i > 0:
-            d = line.split(",")
-            start = float(d[header_mapping["Start (s)"]])
-            end = float(d[header_mapping["End (s)"]])
-            species = d[header_mapping["Common name"]]
-            confidence = float(d[header_mapping["Confidence"]])
-            afile = d[header_mapping["File"]].replace("/", os.sep).replace("\\", os.sep)
-
-        # Check if confidence is high enough and label is not "nocall"
-        if confidence >= cfg.MIN_CONFIDENCE and species.lower() != "nocall" and afile:
-            segments.append({"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence})
-
-    return segments
-
-
-def find_segments(afile: str, rfile: str):
-    """Extracts the segments for an audio file from the results file
-
-    Args:
-        afile: Path to the audio file.
-        rfile: Path to the result file.
-
-    Returns:
-        A list of dicts in the form of
-        {"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence}
-    """
-    segments: list[dict] = []
-
-    # Open and parse result file
-    lines = utils.read_lines(rfile)
-
-    # Auto-detect result type
-    rtype = detect_rtype(lines[0])
-
-    # Get mapping from the header column
-    header_mapping = get_header_mapping(lines[0])
-
-    # Get start and end times based on rtype
-    confidence = 0
-    start = end = 0.0
-    species = ""
-
-    for i, line in enumerate(lines):
-        if rtype == "table" and i > 0:
-            d = line.split("\t")
-            start = float(d[header_mapping["Begin Time (s)"]])
-            end = float(d[header_mapping["End Time (s)"]])
-            species = d[header_mapping["Common Name"]]
-            confidence = float(d[header_mapping["Confidence"]])
-
-        elif rtype == "audacity":
-            d = line.split("\t")
-            start = float(d[0])
-            end = float(d[1])
-            species = d[2].split(", ")[1]
-            confidence = float(d[-1])
-
-        elif rtype == "kaleidoscope" and i > 0:
-            d = line.split(",")
-            start = float(d[header_mapping["OFFSET"]])
-            end = float(d[header_mapping["DURATION"]]) + start
-            species = d[header_mapping["scientific_name"]]
-            confidence = float(d[header_mapping["confidence"]])
-
-        elif rtype == "csv" and i > 0:
-            d = line.split(",")
-            start = float(d[header_mapping["Start (s)"]])
-            end = float(d[header_mapping["End (s)"]])
-            species = d[header_mapping["Common name"]]
-            confidence = float(d[header_mapping["Confidence"]])
-
-        # Check if confidence is high enough and label is not "nocall"
-        if confidence >= cfg.MIN_CONFIDENCE and species.lower() != "nocall":
-            segments.append({"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence})
-
-    return segments
-
-
-def extract_segments(item: tuple[tuple[str, list[dict]], float, dict[str]]):
-    """
-    Extracts audio segments from a given audio file based on provided segment information.
-    Args:
-        item (tuple): A tuple containing:
-            - A tuple with:
-                - A string representing the path to the audio file.
-                - A list of dictionaries, each containing segment information with keys "start", "end", "species", "confidence", and "audio".
-            - A float representing the segment length.
-            - A dictionary containing configuration settings.
-    Returns:
-        bool: True if segments were successfully extracted, False otherwise.
-    Raises:
-        Exception: If there is an error opening the audio file or extracting segments.
-    """
-    # Paths and config
-    afile = item[0][0]
-    segments = item[0][1]
-    seg_length = item[1]
-    cfg.set_config(item[2])
-
-    # Status
-    print(f"Extracting segments from {afile}")
-
-    try:
-        # Open audio file
-        sig, rate = audio.open_audio_file(afile, cfg.SAMPLE_RATE, speed=cfg.AUDIO_SPEED)
-    except Exception as ex:
-        print(f"Error: Cannot open audio file {afile}", flush=True)
-        utils.write_error_log(ex)
-
-        return None
-
-    # Extract segments
-    for seg_cnt, seg in enumerate(segments, 1):
-        try:
-            # Get start and end times
-            start = int((seg["start"] * rate) / cfg.AUDIO_SPEED)
-            end = int((seg["end"] * rate) / cfg.AUDIO_SPEED)
-
-            offset = max(0, ((seg_length * rate) - (end - start)) // 2)
-            start = max(0, start - offset)
-            end = min(len(sig), end + offset)
-
-            # Make sure segment is long enough
-            if end > start:
-                # Get segment raw audio from signal
-                seg_sig = sig[int(start) : int(end)]
-
-                # Make output path
-                outpath = os.path.join(cfg.OUTPUT_PATH, seg["species"])
-                os.makedirs(outpath, exist_ok=True)
-
-                # Save segment
-                seg_name = "{:.3f}_{}_{}_{:.1f}s_{:.1f}s.wav".format(
-                    seg["confidence"],
-                    seg_cnt,
-                    seg["audio"].rsplit(os.sep, 1)[-1].rsplit(".", 1)[0],
-                    seg["start"],
-                    seg["end"],
-                )
-                seg_path = os.path.join(outpath, seg_name)
-                audio.save_signal(seg_sig, seg_path, rate)
-
-        except Exception as ex:
-            # Write error log
-            print(f"Error: Cannot extract segments from {afile}.", flush=True)
-            utils.write_error_log(ex)
-            return False
-
-    return True
+"""Extract segments from audio files based on BirdNET detections.
+
+Can be used to save the segments of the audio files for each detection.
+"""
+
+import os
+
+import numpy as np
+
+import birdnet_analyzer.config as cfg
+from birdnet_analyzer import audio, utils
+
+# Set numpy random seed
+RNG = np.random.default_rng(cfg.RANDOM_SEED)
+SCRIPT_DIR = os.path.abspath(os.path.dirname(__file__))
+
+
+def detect_rtype(line: str):
+    """Detects the type of result file.
+
+    Args:
+        line: First line of text.
+
+    Returns:
+        Either "table", "kaleidoscope", "csv" or "audacity".
+    """
+    if line.lower().startswith("selection"):
+        return "table"
+
+    if line.lower().startswith("indir"):
+        return "kaleidoscope"
+
+    if line.lower().startswith("start (s)"):
+        return "csv"
+
+    return "audacity"
+
+
+def get_header_mapping(line: str) -> dict:
+    """
+    Parses a header line and returns a mapping of column names to their indices.
+
+    Args:
+        line (str): A string representing the header line of a file.
+
+    Returns:
+        dict: A dictionary where the keys are column names and the values are their respective indices.
+    """
+    rtype = detect_rtype(line)
+
+    sep = "\t" if rtype in ("table", "audacity") else ","
+
+    cols = line.split(sep)
+
+    return {col: i for i, col in enumerate(cols)}
+
+
+def parse_folders(apath: str, rpath: str, allowed_result_filetypes: tuple[str] = ("txt", "csv")) -> list[dict]:
+    """Read audio and result files.
+
+    Reads all audio files and BirdNET output inside directory recursively.
+
+    Args:
+        apath (str): Path to search for audio files.
+        rpath (str): Path to search for result files.
+        allowed_result_filetypes (tuple[str]): List of extensions for the result files.
+
+    Returns:
+        list[dict]: A list of {"audio": path_to_audio, "result": path_to_result }.
+    """
+    data = {}
+    apath = apath.replace("/", os.sep).replace("\\", os.sep)
+    rpath = rpath.replace("/", os.sep).replace("\\", os.sep)
+
+    # Check if combined selection table is present and read that.
+    if os.path.exists(os.path.join(rpath, cfg.OUTPUT_RAVEN_FILENAME)):
+        # Read combined Raven selection table
+        rfile = os.path.join(rpath, cfg.OUTPUT_RAVEN_FILENAME)
+        data["combined"] = {"isCombinedFile": True, "result": rfile}
+    elif os.path.exists(os.path.join(rpath, cfg.OUTPUT_CSV_FILENAME)):
+        rfile = os.path.join(rpath, cfg.OUTPUT_CSV_FILENAME)
+        data["combined"] = {"isCombinedFile": True, "result": rfile}
+    elif os.path.exists(os.path.join(rpath, cfg.OUTPUT_KALEIDOSCOPE_FILENAME)):
+        rfile = os.path.join(rpath, cfg.OUTPUT_KALEIDOSCOPE_FILENAME)
+        data["combined"] = {"isCombinedFile": True, "result": rfile}
+    else:
+        # Get all audio files
+        for root, _, files in os.walk(apath):
+            for f in files:
+                if f.rsplit(".", 1)[-1].lower() in cfg.ALLOWED_FILETYPES and not f.startswith("."):
+                    table_key = os.path.join(root.strip(apath), f.rsplit(".", 1)[0])
+                    data[table_key] = {"audio": os.path.join(root, f), "result": ""}
+
+        # Get all result files
+        for root, _, files in os.walk(rpath):
+            for f in files:
+                if f.rsplit(".", 1)[-1] in allowed_result_filetypes and ".BirdNET." in f:
+                    table_key = os.path.join(root.strip(rpath), f.split(".BirdNET.", 1)[0])
+                    if table_key in data:
+                        data[table_key]["result"] = os.path.join(root, f)
+
+    # Convert to list
+    flist = [f for f in data.values() if f["result"]]
+
+    print(f"Found {len(flist)} audio files with valid result file.")
+
+    return flist
+
+
+def parse_files(flist: list[dict], max_segments=100):
+    """
+    Parses a list of files to extract and organize bird call segments by species.
+
+    Args:
+        flist (list[dict]): A list of dictionaries, each containing 'audio' and 'result' file paths.
+                            Optionally, a dictionary can have 'isCombinedFile' set to True to indicate
+                            that it is a combined result file.
+        max_segments (int, optional): The maximum number of segments to retain per species. Defaults to 100.
+    Returns:
+        list[tuple]: A list of tuples where each tuple contains an audio file path and a list of segments
+                     associated with that audio file.
+    Raises:
+        KeyError: If the dictionaries in flist do not contain the required keys ('audio' and 'result').
+    Example:
+        flist = [
+            {"audio": "path/to/audio1.wav", "result": "path/to/result1.csv"},
+            {"audio": "path/to/audio2.wav", "result": "path/to/result2.csv"}
+        ]
+        segments = parseFiles(flist, max_segments=50)
+    """
+    species_segments: dict[str, list] = {}
+
+    is_combined_rfile = len(flist) == 1 and flist[0].get("isCombinedFile", False)
+
+    if is_combined_rfile:
+        rfile = flist[0]["result"]
+        segments = find_segments_from_combined(rfile)
+
+        # Parse segments by species
+        for s in segments:
+            if s["species"] not in species_segments:
+                species_segments[s["species"]] = []
+
+            species_segments[s["species"]].append(s)
+    else:
+        for f in flist:
+            # Paths
+            afile = f["audio"]
+            rfile = f["result"]
+
+            # Get all segments for result file
+            segments = find_segments(afile, rfile)
+
+            # Parse segments by species
+            for s in segments:
+                if s["species"] not in species_segments:
+                    species_segments[s["species"]] = []
+
+                species_segments[s["species"]].append(s)
+
+    # Shuffle segments for each species and limit to max_segments
+    for s in species_segments:
+        RNG.shuffle(species_segments[s])
+        species_segments[s] = species_segments[s][:max_segments]
+
+    # Make dict of segments per audio file
+    segments: dict[str, list] = {}
+    seg_cnt = 0
+
+    for s in species_segments:
+        for seg in species_segments[s]:
+            if seg["audio"] not in segments:
+                segments[seg["audio"]] = []
+
+            segments[seg["audio"]].append(seg)
+            seg_cnt += 1
+
+    print(f"Found {seg_cnt} segments in {len(segments)} audio files.")
+
+    # Convert to list
+    return [tuple(e) for e in segments.items()]
+
+
+def find_segments_from_combined(rfile: str) -> list[dict]:
+    """Extracts the segments from a combined results file
+
+    Args:
+        rfile (str): Path to the result file.
+
+    Returns:
+        list[dict]: A list of dicts in the form of
+        {"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence}
+    """
+    segments: list[dict] = []
+
+    # Open and parse result file
+    lines = utils.read_lines(rfile)
+
+    # Auto-detect result type
+    rtype = detect_rtype(lines[0])
+
+    if rtype == "audacity":
+        raise Exception("Audacity files are not supported for combined results.")
+
+    # Get mapping from the header column
+    header_mapping = get_header_mapping(lines[0])
+
+    # Get start and end times based on rtype
+    confidence = 0
+    start = end = 0.0
+    species = ""
+    afile = ""
+
+    for i, line in enumerate(lines):
+        if rtype == "table" and i > 0:
+            d = line.split("\t")
+            file_offset = float(d[header_mapping["File Offset (s)"]])
+            start = file_offset
+            end = file_offset + (float(d[header_mapping["End Time (s)"]]) - float(d[header_mapping["Begin Time (s)"]]))
+            species = d[header_mapping["Common Name"]]
+            confidence = float(d[header_mapping["Confidence"]])
+            afile = d[header_mapping["Begin Path"]].replace("/", os.sep).replace("\\", os.sep)
+
+        elif rtype == "kaleidoscope" and i > 0:
+            d = line.split(",")
+            start = float(d[header_mapping["OFFSET"]])
+            end = float(d[header_mapping["DURATION"]]) + start
+            species = d[header_mapping["scientific_name"]]
+            confidence = float(d[header_mapping["confidence"]])
+            in_dir = d[header_mapping["INDIR"]]
+            folder = d[header_mapping["FOLDER"]]
+            in_file = d[header_mapping["IN FILE"]]
+            afile = os.path.join(in_dir, folder, in_file).replace("/", os.sep).replace("\\", os.sep)
+
+        elif rtype == "csv" and i > 0:
+            d = line.split(",")
+            start = float(d[header_mapping["Start (s)"]])
+            end = float(d[header_mapping["End (s)"]])
+            species = d[header_mapping["Common name"]]
+            confidence = float(d[header_mapping["Confidence"]])
+            afile = d[header_mapping["File"]].replace("/", os.sep).replace("\\", os.sep)
+
+        # Check if confidence is high enough and label is not "nocall"
+        if confidence >= cfg.MIN_CONFIDENCE and species.lower() != "nocall" and afile:
+            segments.append({"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence})
+
+    return segments
+
+
+def find_segments(afile: str, rfile: str):
+    """Extracts the segments for an audio file from the results file
+
+    Args:
+        afile: Path to the audio file.
+        rfile: Path to the result file.
+
+    Returns:
+        A list of dicts in the form of
+        {"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence}
+    """
+    segments: list[dict] = []
+
+    # Open and parse result file
+    lines = utils.read_lines(rfile)
+
+    # Auto-detect result type
+    rtype = detect_rtype(lines[0])
+
+    # Get mapping from the header column
+    header_mapping = get_header_mapping(lines[0])
+
+    # Get start and end times based on rtype
+    confidence = 0
+    start = end = 0.0
+    species = ""
+
+    for i, line in enumerate(lines):
+        if rtype == "table" and i > 0:
+            d = line.split("\t")
+            start = float(d[header_mapping["Begin Time (s)"]])
+            end = float(d[header_mapping["End Time (s)"]])
+            species = d[header_mapping["Common Name"]]
+            confidence = float(d[header_mapping["Confidence"]])
+
+        elif rtype == "audacity":
+            d = line.split("\t")
+            start = float(d[0])
+            end = float(d[1])
+            species = d[2].split(", ")[1]
+            confidence = float(d[-1])
+
+        elif rtype == "kaleidoscope" and i > 0:
+            d = line.split(",")
+            start = float(d[header_mapping["OFFSET"]])
+            end = float(d[header_mapping["DURATION"]]) + start
+            species = d[header_mapping["scientific_name"]]
+            confidence = float(d[header_mapping["confidence"]])
+
+        elif rtype == "csv" and i > 0:
+            d = line.split(",")
+            start = float(d[header_mapping["Start (s)"]])
+            end = float(d[header_mapping["End (s)"]])
+            species = d[header_mapping["Common name"]]
+            confidence = float(d[header_mapping["Confidence"]])
+
+        # Check if confidence is high enough and label is not "nocall"
+        if confidence >= cfg.MIN_CONFIDENCE and species.lower() != "nocall":
+            segments.append({"audio": afile, "start": start, "end": end, "species": species, "confidence": confidence})
+
+    return segments
+
+
+def extract_segments(item: tuple[tuple[str, list[dict]], float, dict[str]]):
+    """
+    Extracts audio segments from a given audio file based on provided segment information.
+    Args:
+        item (tuple): A tuple containing:
+            - A tuple with:
+                - A string representing the path to the audio file.
+                - A list of dictionaries, each containing segment information with keys "start", "end", "species", "confidence", and "audio".
+            - A float representing the segment length.
+            - A dictionary containing configuration settings.
+    Returns:
+        bool: True if segments were successfully extracted, False otherwise.
+    Raises:
+        Exception: If there is an error opening the audio file or extracting segments.
+    """
+    # Paths and config
+    afile = item[0][0]
+    segments = item[0][1]
+    seg_length = item[1]
+    cfg.set_config(item[2])
+
+    # Status
+    print(f"Extracting segments from {afile}")
+
+    try:
+        # Open audio file
+        sig, rate = audio.open_audio_file(afile, cfg.SAMPLE_RATE, speed=cfg.AUDIO_SPEED)
+    except Exception as ex:
+        print(f"Error: Cannot open audio file {afile}", flush=True)
+        utils.write_error_log(ex)
+
+        return None
+
+    # Extract segments
+    for seg_cnt, seg in enumerate(segments, 1):
+        try:
+            # Get start and end times
+            start = int((seg["start"] * rate) / cfg.AUDIO_SPEED)
+            end = int((seg["end"] * rate) / cfg.AUDIO_SPEED)
+
+            offset = max(0, ((seg_length * rate) - (end - start)) // 2)
+            start = max(0, start - offset)
+            end = min(len(sig), end + offset)
+
+            # Make sure segment is long enough
+            if end > start:
+                # Get segment raw audio from signal
+                seg_sig = sig[int(start) : int(end)]
+
+                # Make output path
+                outpath = os.path.join(cfg.OUTPUT_PATH, seg["species"])
+                os.makedirs(outpath, exist_ok=True)
+
+                # Save segment
+                seg_name = "{:.3f}_{}_{}_{:.1f}s_{:.1f}s.wav".format(
+                    seg["confidence"],
+                    seg_cnt,
+                    seg["audio"].rsplit(os.sep, 1)[-1].rsplit(".", 1)[0],
+                    seg["start"],
+                    seg["end"],
+                )
+                seg_path = os.path.join(outpath, seg_name)
+                audio.save_signal(seg_sig, seg_path, rate)
+
+        except Exception as ex:
+            # Write error log
+            print(f"Error: Cannot extract segments from {afile}.", flush=True)
+            utils.write_error_log(ex)
+            return False
+
+    return True